2008-04-15 16:58:36 +00:00
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< a href = "obitools-module.html" > Package obitools< / a > ::
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Module parser
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< h1 class = "epydoc" > Source Code for < a href = "obitools.obo.parser-module.html" > Module obitools.obo.parser< / a > < / h1 >
< pre class = "py-src" >
< a name = "L1" > < / a > < tt class = "py-lineno" > 1< / tt > < tt class = "py-line" > < tt class = "py-keyword" > from< / tt > < tt id = "link-0" class = "py-name" targets = "Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html" > < a title = "obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-1" class = "py-name" targets = "Package obitools.utils=obitools.utils-module.html" > < a title = "obitools.utils" class = "py-name" href = "#" onclick = "return doclink('link-1', 'utils', 'link-1');" > utils< / a > < / tt > < tt class = "py-keyword" > import< / tt > < tt id = "link-2" class = "py-name" targets = "Function obitools.utils.skipWhiteLineIterator()=obitools.utils-module.html#skipWhiteLineIterator" > < a title = "obitools.utils.skipWhiteLineIterator" class = "py-name" href = "#" onclick = "return doclink('link-2', 'skipWhiteLineIterator', 'link-2');" > skipWhiteLineIterator< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt id = "link-3" class = "py-name" targets = "Function obitools.utils.multiLineWrapper()=obitools.utils-module.html#multiLineWrapper" > < a title = "obitools.utils.multiLineWrapper" class = "py-name" href = "#" onclick = "return doclink('link-3', 'multiLineWrapper', 'link-3');" > multiLineWrapper< / a > < / tt > < / tt >
< a name = "L2" > < / a > < tt class = "py-lineno" > 2< / tt > < tt class = "py-line" > < tt class = "py-keyword" > from< / tt > < tt id = "link-4" class = "py-name" > < a title = "obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-5" class = "py-name" > < a title = "obitools.utils" class = "py-name" href = "#" onclick = "return doclink('link-5', 'utils', 'link-1');" > utils< / a > < / tt > < tt class = "py-keyword" > import< / tt > < tt id = "link-6" class = "py-name" targets = "Function obitools.utils.universalOpen()=obitools.utils-module.html#universalOpen" > < a title = "obitools.utils.universalOpen" class = "py-name" href = "#" onclick = "return doclink('link-6', 'universalOpen', 'link-6');" > universalOpen< / a > < / tt > < / tt >
< a name = "L3" > < / a > < tt class = "py-lineno" > 3< / tt > < tt class = "py-line" > < tt class = "py-keyword" > from< / tt > < tt id = "link-7" class = "py-name" > < a title = "obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-7', 'obitools', 'link-0');">obitools< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-8" class = "py-name" targets = "Package obitools.format=obitools.format-module.html" > < a title = "obitools.format" class = "py-name" href = "#" onclick = "return doclink('link-8', 'format', 'link-8');" > format< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-9" class = "py-name" targets = "Package obitools.format.genericparser=obitools.format.genericparser-module.html" > < a title = "obitools.format.genericparser" class = "py-name" href = "#" onclick = "return doclink('link-9', 'genericparser', 'link-9');" > genericparser< / a > < / tt > < tt class = "py-keyword" > import< / tt > < tt id = "link-10" class = "py-name" targets = "Function obitools.format.genericparser.genericEntryIteratorGenerator()=obitools.format.genericparser-module.html#genericEntryIteratorGenerator" > < a title = "obitools.format.genericparser.genericEntryIteratorGenerator" class = "py-name" href = "#" onclick = "return doclink('link-10', 'genericEntryIteratorGenerator', 'link-10');" > genericEntryIteratorGenerator< / a > < / tt > < / tt >
< a name = "L4" > < / a > < tt class = "py-lineno" > 4< / tt > < tt class = "py-line" > < tt class = "py-keyword" > from< / tt > < tt class = "py-name" > logging< / tt > < tt class = "py-keyword" > import< / tt > < tt class = "py-name" > debug< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > warning< / tt > < / tt >
< a name = "L5" > < / a > < tt class = "py-lineno" > 5< / tt > < tt class = "py-line" > < / tt >
< a name = "L6" > < / a > < tt class = "py-lineno" > 6< / tt > < tt class = "py-line" > < tt class = "py-keyword" > import< / tt > < tt class = "py-name" > re< / tt > < / tt >
< a name = "L7" > < / a > < tt class = "py-lineno" > 7< / tt > < tt class = "py-line" > < / tt >
< a name = "L8" > < / a > < tt class = "py-lineno" > 8< / tt > < tt class = "py-line" > < / tt >
< a name = "L9" > < / a > < tt class = "py-lineno" > 9< / tt > < tt class = "py-line" > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L10" > < / a > < tt class = "py-lineno" > 10< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## Stanza preparation area ##< / tt > < / tt >
< a name = "L11" > < / a > < tt class = "py-lineno" > 11< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L12" > < / a > < tt class = "py-lineno" > 12< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < / tt >
< a name = "L13" > < / a > < tt class = "py-lineno" > 13< / tt > < tt class = "py-line" > < / tt >
< a name = "FileFormatError" > < / a > < div id = "FileFormatError-def" > < a name = "L14" > < / a > < tt class = "py-lineno" > 14< / tt > < a class = "py-toggle" href = "#" id = "FileFormatError-toggle" onclick = "return toggle('FileFormatError');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.FileFormatError-class.html" > FileFormatError< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > Exception< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "FileFormatError-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "FileFormatError-expanded" > < a name = "L15" > < / a > < tt class = "py-lineno" > 15< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L16" > < / a > < tt class = "py-lineno" > 16< / tt > < tt class = "py-line" > < tt class = "py-docstring" > An error derived from the class Exception.< / tt > < / tt >
< a name = "L17" > < / a > < tt class = "py-lineno" > 17< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L18" > < / a > < tt class = "py-lineno" > 18< / tt > < tt class = "py-line" > < tt class = "py-keyword" > pass< / tt > < / tt >
< / div > < a name = "L19" > < / a > < tt class = "py-lineno" > 19< / tt > < tt class = "py-line" > < / tt >
< a name = "L20" > < / a > < tt class = "py-lineno" > 20< / tt > < tt class = "py-line" > < tt class = "py-name" > _oboEntryIterator< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-11" class = "py-name" > < a title = "obitools.format.genericparser.genericEntryIteratorGenerator" class = "py-name" href = "#" onclick = "return doclink('link-11', 'genericEntryIteratorGenerator', 'link-10');" > genericEntryIteratorGenerator< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > endEntry< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > '^ *$'< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L21" > < / a > < tt class = "py-lineno" > 21< / tt > < tt class = "py-line" > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > True< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L22" > < / a > < tt class = "py-lineno" > 22< / tt > < tt class = "py-line" > < / tt >
< a name = "stanzaIterator" > < / a > < div id = "stanzaIterator-def" > < a name = "L23" > < / a > < tt class = "py-lineno" > 23< / tt > < a class = "py-toggle" href = "#" id = "stanzaIterator-toggle" onclick = "return toggle('stanzaIterator');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#stanzaIterator" > stanzaIterator< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > inputfile< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "stanzaIterator-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "stanzaIterator-expanded" > < a name = "L24" > < / a > < tt class = "py-lineno" > 24< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L25" > < / a > < tt class = "py-lineno" > 25< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Iterator of stanza. The stanza are the basic units of OBO files.< / tt > < / tt >
< a name = "L26" > < / a > < tt class = "py-lineno" > 26< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L27" > < / a > < tt class = "py-lineno" > 27< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param inputfile: a stream of strings from an opened OBO file.< / tt > < / tt >
< a name = "L28" > < / a > < tt class = "py-lineno" > 28< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type inputfile: a stream of strings< / tt > < / tt >
< a name = "L29" > < / a > < tt class = "py-lineno" > 29< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L30" > < / a > < tt class = "py-lineno" > 30< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @return: a stream of stanza< / tt > < / tt >
< a name = "L31" > < / a > < tt class = "py-lineno" > 31< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @rtype: a stream of aggregated strings< / tt > < / tt >
< a name = "L32" > < / a > < tt class = "py-lineno" > 32< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L33" > < / a > < tt class = "py-lineno" > 33< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The iterator constructs stanza by aggregate strings from the< / tt > < / tt >
< a name = "L34" > < / a > < tt class = "py-lineno" > 34< / tt > < tt class = "py-line" > < tt class = "py-docstring" > OBO file.< / tt > < / tt >
< a name = "L35" > < / a > < tt class = "py-lineno" > 35< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L36" > < / a > < tt class = "py-lineno" > 36< / tt > < tt class = "py-line" > < tt class = "py-name" > inputfile< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-12" class = "py-name" > < a title = "obitools.utils.universalOpen" class = "py-name" href = "#" onclick = "return doclink('link-12', 'universalOpen', 'link-6');" > universalOpen< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > inputfile< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L37" > < / a > < tt class = "py-lineno" > 37< / tt > < tt class = "py-line" > < tt class = "py-name" > inputfile< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-13" class = "py-name" > < a title = "obitools.utils.multiLineWrapper" class = "py-name" href = "#" onclick = "return doclink('link-13', 'multiLineWrapper', 'link-3');" > multiLineWrapper< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > inputfile< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L38" > < / a > < tt class = "py-lineno" > 38< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > _oboEntryIterator< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > inputfile< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < a name = "L39" > < / a > < tt class = "py-lineno" > 39< / tt > < tt class = "py-line" > < / tt >
< a name = "L40" > < / a > < tt class = "py-lineno" > 40< / tt > < tt class = "py-line" > < / tt >
< a name = "L41" > < / a > < tt class = "py-lineno" > 41< / tt > < tt class = "py-line" > < / tt >
< a name = "L42" > < / a > < tt class = "py-lineno" > 42< / tt > < tt class = "py-line" > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L43" > < / a > < tt class = "py-lineno" > 43< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## Trailing Modifiers treatment area ##< / tt > < / tt >
< a name = "L44" > < / a > < tt class = "py-lineno" > 44< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L45" > < / a > < tt class = "py-lineno" > 45< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < / tt >
< a name = "L46" > < / a > < tt class = "py-lineno" > 46< / tt > < tt class = "py-line" > < / tt >
< a name = "TrailingModifier" > < / a > < div id = "TrailingModifier-def" > < a name = "L47" > < / a > < tt class = "py-lineno" > 47< / tt > < a class = "py-toggle" href = "#" id = "TrailingModifier-toggle" onclick = "return toggle('TrailingModifier');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TrailingModifier-class.html" > TrailingModifier< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > dict< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TrailingModifier-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "TrailingModifier-expanded" > < a name = "L48" > < / a > < tt class = "py-lineno" > 48< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L49" > < / a > < tt class = "py-lineno" > 49< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A class object which inherits from the class dict. Trailing modifiers can be found< / tt > < / tt >
< a name = "L50" > < / a > < tt class = "py-lineno" > 50< / tt > < tt class = "py-line" > < tt class = "py-docstring" > at the end of TaggedValue objects when they exist.< / tt > < / tt >
< a name = "L51" > < / a > < tt class = "py-lineno" > 51< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L52" > < / a > < tt class = "py-lineno" > 52< / tt > < tt class = "py-line" > < / tt >
< a name = "L53" > < / a > < tt class = "py-lineno" > 53< / tt > < tt class = "py-line" > < tt id = "link-14" class = "py-name" targets = "Variable obitools.obo.parser.TrailingModifier._match_brace=obitools.obo.parser.TrailingModifier-class.html#_match_brace" > < a title = "obitools.obo.parser.TrailingModifier._match_brace" class = "py-name" href = "#" onclick = "return doclink('link-14', '_match_brace', 'link-14');" > _match_brace< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '(?< =\ {)[^\]]*(\}) *( !|$)'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L54" > < / a > < tt class = "py-lineno" > 54< / tt > < tt class = "py-line" > < / tt >
< a name = "TrailingModifier.__init__" > < / a > < div id = "TrailingModifier.__init__-def" > < a name = "L55" > < / a > < tt class = "py-lineno" > 55< / tt > < a class = "py-toggle" href = "#" id = "TrailingModifier.__init__-toggle" onclick = "return toggle('TrailingModifier.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TrailingModifier-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > string< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TrailingModifier.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "TrailingModifier.__init__-expanded" > < a name = "L56" > < / a > < tt class = "py-lineno" > 56< / tt > < tt class = "py-line" > < / tt >
< a name = "L57" > < / a > < tt class = "py-lineno" > 57< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## search for trailing modifiers signals< / tt > < / tt >
< a name = "L58" > < / a > < tt class = "py-lineno" > 58< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-15" class = "py-name" targets = "Class obitools.obo.parser.TrailingModifier=obitools.obo.parser.TrailingModifier-class.html" > < a title = "obitools.obo.parser.TrailingModifier" class = "py-name" href = "#" onclick = "return doclink('link-15', 'TrailingModifier', 'link-15');" > TrailingModifier< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-16" class = "py-name" > < a title = "obitools.obo.parser.TrailingModifier._match_brace" class = "py-name" href = "#" onclick = "return doclink('link-16', '_match_brace', 'link-14');" > _match_brace< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L59" > < / a > < tt class = "py-lineno" > 59< / tt > < tt class = "py-line" > < / tt >
< a name = "L60" > < / a > < tt class = "py-lineno" > 60< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the trailing modifiers exist< / tt > < / tt >
< a name = "L61" > < / a > < tt class = "py-lineno" > 61< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L62" > < / a > < tt class = "py-lineno" > 62< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L63" > < / a > < tt class = "py-lineno" > 63< / tt > < tt class = "py-line" > < tt class = "py-keyword" > print< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < / tt >
< a name = "L64" > < / a > < tt class = "py-lineno" > 64< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## creates and feeds the dictionary of trailing modifiers< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L65" > < / a > < tt class = "py-lineno" > 65< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > dict< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-17" class = "py-name" targets = "Method obitools . BioSequence . __init__ ( ) = obitools . BioSequence-class . html # __init__ , Method obitools . WrappedBioSequence . __init__ ( ) = obitools . WrappedBioSequence-class . html # __init__ , Method obitools . WrapperSetIterator . __init__ ( ) = obitools . WrapperSetIterator-class . html # __init__ , Method obitools . align . ssearch . SsearchParser . __init__ ( ) = obitools . align . ssearch . SsearchParser-class . html # __init__ , Method obitools . blast . Blast . __init__ ( ) = obitools . blast . Blast-class . html # __init__ , Method obitools . blast . BlastCovMinFilter . __init__ ( ) = obitools . blast . BlastCovMinFilter-class . html # __init__ , Method obitools . blast . BlastResultIterator . __init__ ( ) = obitools . blast . BlastResultIterator-class . html # __init__ , Method obitools . blast . NetBlast . __init__ ( ) = obitools . blast . NetBlast-class . html # __init__ , Method obitools . cns . quality . QualitySequence . __init__ ( ) = obitools . cns . quality . QualitySequence-class . html # __init__ , Method obitools . distances . DistanceMatrix . __init__ ( ) = obitools . distances . DistanceMatrix-class . html # __init__ , Method obitools . ecopcr . EcoPCRFile . __init__ ( ) = obitools . ecopcr . EcoPCRFile-class . html # __init__ , Method obitools . ecopcr . sequence . ecoPCRDBSequenceIterator . __init__ ( ) = obitools . ecopcr . sequence . ecoPCRDBSequenceIterator-class . html # __init__ , Method obitools . ecopcr . taxonomy . Taxonomy . __init__ ( ) = obitools . ecopcr . taxonomy . Taxonomy-class . html # __init__ , Method obitools . eutils . EFetch . __init__ ( ) = obitools . eutils . EFetch-class . html # __init__ , Method obitools . eutils . EUtils . __init__ ( ) = obitools . eutils . EUtils-class . html # __init__ , Method obitools . fast . Fast . __init__ ( ) = obitools . fast . Fast-class . html # __init__ , Method obitools . format . genericparser . GenericParser . __init__ ( ) = obitools . format . genericparser . GenericParser-class . html # __init__ , Method obitools . graph . DiGraph . __init__ ( ) = obitools . graph . DiGraph-class . html # __init__ , Method obitools . graph . Edge . __init__ ( ) = obitools . graph . Edge-class . html # __init__ , Method obitools . graph . Graph . __init__ ( ) = obitools . graph . Graph-class . html # __init__ , Method obitools . graph . Indexer . __init__ ( ) = obitools . graph . Indexer-class . html # __init__ , Method obitools . graph . Node . __init__ ( ) = obitools . graph . Node-class . html # __init__ , Method obitools . graph . UndirectedGraph . __init__ ( ) = obitools . graph . UndirectedGraph-class . html # __init__ , Method obitools . graph . dag . DAG . __init__ ( ) = obitools . graph . dag . DAG-class . html # __init__ , Method obitools . gzip . GzipFile . __init__ ( ) = obitools . gzip . GzipFile-class . html # __init__ , Method obitools . location . ComplementLocation . __init__ ( ) = obitools . location . ComplementLocation-class . html # __init__ , Method obitools . location . CompositeLocation . __init__ ( ) = obitools . location . CompositeLocation-class . html # __init__ , Method obitools . location . PointLocation . __init__ ( ) = obitools . location . PointLocation-class . html # __init__ , Method obitools . location . SimpleLocation . __init__ ( ) = obitools . location . SimpleLocation-class . html # __init__ , Method obitools . location . feature . Feature . __init__ ( ) = obitools . location . feature . Feature-class . html # __init__ , Method obitools . obo . parser . DefValue . __init__ ( ) = obitools . obo . parser . DefValue-class . html # __init__ , Method obitools . obo . parser . NameValue . __init__ ( ) = obitools . obo . parser . NameValue-class . html # __init__ , Method obitools . obo . parser . NamespaceValue . __init__ ( ) = obitools . obo . parser . NamespaceValue-class . html # __init__ , Method obitools . obo . parser . OBOEntry . __init__ ( ) = obitools . obo . parser . OBOEntry-class . html # __init__ , Method obitools . obo . parser . OBOTerm . __init__ ( ) = obitools . obo . parser . OBOTerm-class . html # __init__ , Method obitools . obo . parser . RelationshipValue . __init__ ( ) = obitools . obo . parser . RelationshipValue-class . html # __init__ , Method obitools . obo . parser . RemarkValue . __init__ ( ) = obitools . obo . parser . RemarkValue-class . html # __init__ , Method obitools . obo . parser . SynonymValue . __init__ ( ) = obitools . obo . parser . SynonymValue-class . html # __init__ , Method obitools . obo . parser . TaggedValue . __init__ ( ) = obitools . obo . parser . TaggedValue-class . html # __init__ , Method obitools . obo . parser . TrailingModifier . __init__ ( ) = obitools . obo . parser . TrailingModif
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
2008-04-29 11:07:08 +00:00
obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
2008-04-29 11:07:08 +00:00
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-17', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '='< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ','< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < / div > < a name = "L66" > < / a > < tt class = "py-lineno" > 66< / tt > < tt class = "py-line" > < / tt >
< a name = "L67" > < / a > < tt class = "py-lineno" > 67< / tt > < tt class = "py-line" > < / tt >
< a name = "trailingModifierFactory" > < / a > < div id = "trailingModifierFactory-def" > < a name = "L68" > < / a > < tt class = "py-lineno" > 68< / tt > < a class = "py-toggle" href = "#" id = "trailingModifierFactory-toggle" onclick = "return toggle('trailingModifierFactory');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#trailingModifierFactory" > trailingModifierFactory< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > string< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "trailingModifierFactory-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "trailingModifierFactory-expanded" > < a name = "L69" > < / a > < tt class = "py-lineno" > 69< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L70" > < / a > < tt class = "py-lineno" > 70< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Dispatcher of trailing modifiers.< / tt > < / tt >
< a name = "L71" > < / a > < tt class = "py-lineno" > 71< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L72" > < / a > < tt class = "py-lineno" > 72< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param string: a string from a TaggedValue object with a trailing modifiers signal.< / tt > < / tt >
< a name = "L73" > < / a > < tt class = "py-lineno" > 73< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type string: string< / tt > < / tt >
< a name = "L74" > < / a > < tt class = "py-lineno" > 74< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L75" > < / a > < tt class = "py-lineno" > 75< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @return: a class object< / tt > < / tt >
< a name = "L76" > < / a > < tt class = "py-lineno" > 76< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L77" > < / a > < tt class = "py-lineno" > 77< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The dispatcher is currently very simple. Only one case is treated by the function.< / tt > < / tt >
< a name = "L78" > < / a > < tt class = "py-lineno" > 78< / tt > < tt class = "py-line" > < tt class = "py-docstring" > `the function returns a class object inherited from the class dict if the trailing modifiers< / tt > < / tt >
< a name = "L79" > < / a > < tt class = "py-lineno" > 79< / tt > < tt class = "py-line" > < tt class = "py-docstring" > exist, None if they don't.< / tt > < / tt >
< a name = "L80" > < / a > < tt class = "py-lineno" > 80< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L81" > < / a > < tt class = "py-lineno" > 81< / tt > < tt class = "py-line" > < / tt >
< a name = "L82" > < / a > < tt class = "py-lineno" > 82< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-18" class = "py-name" > < a title = "obitools.obo.parser.TrailingModifier" class = "py-name" href = "#" onclick = "return doclink('link-18', 'TrailingModifier', 'link-15');" > TrailingModifier< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L83" > < / a > < tt class = "py-lineno" > 83< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L84" > < / a > < tt class = "py-lineno" > 84< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
< a name = "L85" > < / a > < tt class = "py-lineno" > 85< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < / tt >
< / div > < a name = "L86" > < / a > < tt class = "py-lineno" > 86< / tt > < tt class = "py-line" > < / tt >
< a name = "L87" > < / a > < tt class = "py-lineno" > 87< / tt > < tt class = "py-line" > < / tt >
< a name = "L88" > < / a > < tt class = "py-lineno" > 88< / tt > < tt class = "py-line" > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L89" > < / a > < tt class = "py-lineno" > 89< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## TaggedValue treatment area ##< / tt > < / tt >
< a name = "L90" > < / a > < tt class = "py-lineno" > 90< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L91" > < / a > < tt class = "py-lineno" > 91< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < / tt >
< a name = "L92" > < / a > < tt class = "py-lineno" > 92< / tt > < tt class = "py-line" > < / tt >
< a name = "TaggedValue" > < / a > < div id = "TaggedValue-def" > < a name = "L93" > < / a > < tt class = "py-lineno" > 93< / tt > < a class = "py-toggle" href = "#" id = "TaggedValue-toggle" onclick = "return toggle('TaggedValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TaggedValue-class.html" > TaggedValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > object< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TaggedValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "TaggedValue-expanded" > < a name = "L94" > < / a > < tt class = "py-lineno" > 94< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L95" > < / a > < tt class = "py-lineno" > 95< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'tag:value' of an OBOEntry.< / tt > < / tt >
< a name = "L96" > < / a > < tt class = "py-lineno" > 96< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L97" > < / a > < tt class = "py-lineno" > 97< / tt > < tt class = "py-line" > < / tt >
< a name = "L98" > < / a > < tt class = "py-lineno" > 98< / tt > < tt class = "py-line" > < tt id = "link-19" class = "py-name" targets = "Variable obitools.obo.parser.TaggedValue._match_value=obitools.obo.parser.TaggedValue-class.html#_match_value" > < a title = "obitools.obo.parser.TaggedValue._match_value" class = "py-name" href = "#" onclick = "return doclink('link-19', '_match_value', 'link-19');" > _match_value< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '(("(\\\\"|[^\"])*")|(\\\\"|[^\"]))*?( !| {|$)'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L99" > < / a > < tt class = "py-lineno" > 99< / tt > < tt class = "py-line" > < tt id = "link-20" class = "py-name" targets = "Variable obitools.obo.parser.TaggedValue._split_comment=obitools.obo.parser.TaggedValue-class.html#_split_comment" > < a title = "obitools.obo.parser.TaggedValue._split_comment" class = "py-name" href = "#" onclick = "return doclink('link-20', '_split_comment', 'link-20');" > _split_comment< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '^!| !'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L100" > < / a > < tt class = "py-lineno" > 100< / tt > < tt class = "py-line" > < tt id = "link-21" class = "py-name" targets = "Variable obitools.obo.parser.TaggedValue._match_quotedString=obitools.obo.parser.TaggedValue-class.html#_match_quotedString" > < a title = "obitools.obo.parser.TaggedValue._match_quotedString" class = "py-name" href = "#" onclick = "return doclink('link-21', '_match_quotedString', 'link-21');" > _match_quotedString< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '(?< =")(\\\\"|[^\"])*(?=")'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L101" > < / a > < tt class = "py-lineno" > 101< / tt > < tt class = "py-line" > < tt id = "link-22" class = "py-name" targets = "Variable obitools.obo.parser.TaggedValue._match_bracket=obitools.obo.parser.TaggedValue-class.html#_match_bracket" > < a title = "obitools.obo.parser.TaggedValue._match_bracket" class = "py-name" href = "#" onclick = "return doclink('link-22', '_match_bracket', 'link-22');" > _match_bracket< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '\[[^\]]*\]'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L102" > < / a > < tt class = "py-lineno" > 102< / tt > < tt class = "py-line" > < / tt >
< a name = "TaggedValue.__init__" > < / a > < div id = "TaggedValue.__init__-def" > < a name = "L103" > < / a > < tt class = "py-lineno" > 103< / tt > < a class = "py-toggle" href = "#" id = "TaggedValue.__init__-toggle" onclick = "return toggle('TaggedValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TaggedValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TaggedValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "TaggedValue.__init__-expanded" > < a name = "L104" > < / a > < tt class = "py-lineno" > 104< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L105" > < / a > < tt class = "py-lineno" > 105< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Constructor of the class TaggedValue.< / tt > < / tt >
< a name = "L106" > < / a > < tt class = "py-lineno" > 106< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L107" > < / a > < tt class = "py-lineno" > 107< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param line: a line of an OBOEntry composed of a tag and a value.< / tt > < / tt >
< a name = "L108" > < / a > < tt class = "py-lineno" > 108< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type line: string< / tt > < / tt >
< a name = "L109" > < / a > < tt class = "py-lineno" > 109< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L110" > < / a > < tt class = "py-lineno" > 110< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The constructor separates tags from right terms. 'value' is extracted < / tt > < / tt >
< a name = "L111" > < / a > < tt class = "py-lineno" > 111< / tt > < tt class = "py-line" > < tt class = "py-docstring" > from right terms using a regular expression (value is at the beginning of the< / tt > < / tt >
< a name = "L112" > < / a > < tt class = "py-lineno" > 112< / tt > < tt class = "py-line" > < tt class = "py-docstring" > string, between quotes or not). Then, 'comment' is extracted from the rest of the < / tt > < / tt >
< a name = "L113" > < / a > < tt class = "py-lineno" > 113< / tt > < tt class = "py-line" > < tt class = "py-docstring" > string using another regular expression ('comment' is at the end of the string < / tt > < / tt >
< a name = "L114" > < / a > < tt class = "py-lineno" > 114< / tt > < tt class = "py-line" > < tt class = "py-docstring" > after a '!'. By default, 'comment' is set to None). Finally, 'trailing_modifiers'< / tt > < / tt >
< a name = "L115" > < / a > < tt class = "py-lineno" > 115< / tt > < tt class = "py-line" > < tt class = "py-docstring" > are extracted from the last string using another regular expression.< / tt > < / tt >
< a name = "L116" > < / a > < tt class = "py-lineno" > 116< / tt > < tt class = "py-line" > < tt class = "py-docstring" > The tag, the value, the comment and the trailing_modifiers are saved.< / tt > < / tt >
< a name = "L117" > < / a > < tt class = "py-lineno" > 117< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L118" > < / a > < tt class = "py-lineno" > 118< / tt > < tt class = "py-line" > < / tt >
< a name = "L119" > < / a > < tt class = "py-lineno" > 119< / tt > < tt class = "py-line" > < tt class = "py-name" > debug< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > "tagValueParser : %s"< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L120" > < / a > < tt class = "py-lineno" > 120< / tt > < tt class = "py-line" > < / tt >
< a name = "L121" > < / a > < tt class = "py-lineno" > 121< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## by default :< / tt > < / tt >
< a name = "L122" > < / a > < tt class = "py-lineno" > 122< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
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< a name = "L123" > < / a > < tt class = "py-lineno" > 123< / tt > < tt class = "py-line" > < tt id = "link-23" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.comment=obitools.obo.parser.OBOTerm-class.html#comment,Variable obitools.zipfile.ZipInfo.comment=obitools.zipfile.ZipInfo-class.html#comment" > < a title = "obitools.obo.parser.OBOTerm.comment
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-23', 'comment', 'link-23');">comment< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
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< a name = "L124" > < / a > < tt class = "py-lineno" > 124< / tt > < tt class = "py-line" > < / tt >
< a name = "L125" > < / a > < tt class = "py-lineno" > 125< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the tag is saved. 'right' is composed of the value, the comment and the trailing modifiers< / tt > < / tt >
< a name = "L126" > < / a > < tt class = "py-lineno" > 126< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > rigth< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ':'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L127" > < / a > < tt class = "py-lineno" > 127< / tt > < tt class = "py-line" > < / tt >
< a name = "L128" > < / a > < tt class = "py-lineno" > 128< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the value is saved< / tt > < / tt >
< a name = "L129" > < / a > < tt class = "py-lineno" > 129< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-24" class = "py-name" targets = "Class obitools.obo.parser.TaggedValue=obitools.obo.parser.TaggedValue-class.html" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-24', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-25" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_value" class = "py-name" href = "#" onclick = "return doclink('link-25', '_match_value', 'link-19');" > _match_value< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > rigth< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L130" > < / a > < tt class = "py-lineno" > 130< / tt > < tt class = "py-line" > < tt class = "py-name" > debug< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > "Extracted value : %s"< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L131" > < / a > < tt class = "py-lineno" > 131< / tt > < tt class = "py-line" > < / tt >
< a name = "L132" > < / a > < tt class = "py-lineno" > 132< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## if there is a value AND a sign of a comment or trailing modifiers< / tt > < / tt >
< a name = "L133" > < / a > < tt class = "py-lineno" > 133< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-string" > '!{'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L134" > < / a > < tt class = "py-lineno" > 134< / tt > < tt class = "py-line" > < tt class = "py-name" > lvalue< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L135" > < / a > < tt class = "py-lineno" > 135< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## whatever it is a comment or trailing modifiers, it is saved into 'extra'< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L136" > < / a > < tt class = "py-lineno" > 136< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-26" class = "py-name" targets = "Variable obitools.zipfile.ZipInfo.extra=obitools.zipfile.ZipInfo-class.html#extra" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-26', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > rigth< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > lvalue< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L137" > < / a > < tt class = "py-lineno" > 137< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## a comment is extracted< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L138" > < / a > < tt class = "py-lineno" > 138< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-27" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-27', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-28" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-28', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-29" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._split_comment" class = "py-name" href = "#" onclick = "return doclink('link-29', '_split_comment', 'link-20');" > _split_comment< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-30" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-30', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L139" > < / a > < tt class = "py-lineno" > 139< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## and saved if it exists< / tt > < / tt >
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< a name = "L140" > < / a > < tt class = "py-lineno" > 140< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-31" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-31', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L141" > < / a > < tt class = "py-lineno" > 141< / tt > < tt class = "py-line" > < tt id = "link-32" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm.comment
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-32', 'comment', 'link-23');">comment< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-33" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-33', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L142" > < / a > < tt class = "py-lineno" > 142< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## trailing modifiers are extracted< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L143" > < / a > < tt class = "py-lineno" > 143< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-34" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-34', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-35" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-35', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L144" > < / a > < tt class = "py-lineno" > 144< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-36" class = "py-name" targets = "Function obitools.obo.parser.trailingModifierFactory()=obitools.obo.parser-module.html#trailingModifierFactory" > < a title = "obitools.obo.parser.trailingModifierFactory" class = "py-name" href = "#" onclick = "return doclink('link-36', 'trailingModifierFactory', 'link-36');" > trailingModifierFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt id = "link-37" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-37', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L145" > < / a > < tt class = "py-lineno" > 145< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the value is cleaned of any comment or trailing modifiers signals< / tt > < / tt >
< a name = "L146" > < / a > < tt class = "py-lineno" > 146< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L147" > < / a > < tt class = "py-lineno" > 147< / tt > < tt class = "py-line" > < / tt >
< a name = "L148" > < / a > < tt class = "py-lineno" > 148< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'use_term'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L149" > < / a > < tt class = "py-lineno" > 149< / tt > < tt class = "py-line" > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'consider'< / tt > < / tt >
< a name = "L150" > < / a > < tt class = "py-lineno" > 150< / tt > < tt class = "py-line" > < tt class = "py-keyword" > raise< / tt > < tt class = "py-name" > DeprecationWarning< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "user_term is a deprecated tag, you should instead use consider"< / tt > < / tt >
< a name = "L151" > < / a > < tt class = "py-lineno" > 151< / tt > < tt class = "py-line" > < / tt >
< a name = "L152" > < / a > < tt class = "py-lineno" > 152< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## recording zone< / tt > < / tt >
< a name = "L153" > < / a > < tt class = "py-lineno" > 153< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L154" > < / a > < tt class = "py-lineno" > 154< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > tag< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L155" > < / a > < tt class = "py-lineno" > 155< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > __doc__< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-38" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm.comment
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-38', 'comment', 'link-23');">comment< / a > < / tt > < / tt >
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< a name = "L156" > < / a > < tt class = "py-lineno" > 156< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < / tt >
< / div > < a name = "L157" > < / a > < tt class = "py-lineno" > 157< / tt > < tt class = "py-line" > < / tt >
< a name = "TaggedValue.__str__" > < / a > < div id = "TaggedValue.__str__-def" > < a name = "L158" > < / a > < tt class = "py-lineno" > 158< / tt > < a class = "py-toggle" href = "#" id = "TaggedValue.__str__-toggle" onclick = "return toggle('TaggedValue.__str__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TaggedValue-class.html#__str__" > __str__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TaggedValue.__str__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "TaggedValue.__str__-expanded" > < a name = "L159" > < / a > < tt class = "py-lineno" > 159< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > str< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < a name = "L160" > < / a > < tt class = "py-lineno" > 160< / tt > < tt class = "py-line" > < / tt >
< a name = "TaggedValue.__repr__" > < / a > < div id = "TaggedValue.__repr__-def" > < a name = "L161" > < / a > < tt class = "py-lineno" > 161< / tt > < a class = "py-toggle" href = "#" id = "TaggedValue.__repr__-toggle" onclick = "return toggle('TaggedValue.__repr__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.TaggedValue-class.html#__repr__" > __repr__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "TaggedValue.__repr__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "TaggedValue.__repr__-expanded" > < a name = "L162" > < / a > < tt class = "py-lineno" > 162< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-string" > '''"""%s"""'''< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-name" > str< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < / div > < a name = "L163" > < / a > < tt class = "py-lineno" > 163< / tt > < tt class = "py-line" > < / tt >
< a name = "L164" > < / a > < tt class = "py-lineno" > 164< / tt > < tt class = "py-line" > < / tt >
< a name = "NameValue" > < / a > < div id = "NameValue-def" > < a name = "L165" > < / a > < tt class = "py-lineno" > 165< / tt > < a class = "py-toggle" href = "#" id = "NameValue-toggle" onclick = "return toggle('NameValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.NameValue-class.html" > NameValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "NameValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "NameValue-expanded" > < a name = "L166" > < / a > < tt class = "py-lineno" > 166< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L167" > < / a > < tt class = "py-lineno" > 167< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'name:value' inherited from the class TaggedValue. Used to manage name tags.< / tt > < / tt >
< a name = "L168" > < / a > < tt class = "py-lineno" > 168< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L169" > < / a > < tt class = "py-lineno" > 169< / tt > < tt class = "py-line" > < / tt >
< a name = "NameValue.__init__" > < / a > < div id = "NameValue.__init__-def" > < a name = "L170" > < / a > < tt class = "py-lineno" > 170< / tt > < a class = "py-toggle" href = "#" id = "NameValue.__init__-toggle" onclick = "return toggle('NameValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.NameValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "NameValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "NameValue.__init__-expanded" > < a name = "L171" > < / a > < tt class = "py-lineno" > 171< / tt > < tt class = "py-line" > < / tt >
< a name = "L172" > < / a > < tt class = "py-lineno" > 172< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## no use of the TaggedValue constructor. The NameValue is very simple.< / tt > < / tt >
< a name = "L173" > < / a > < tt class = "py-lineno" > 173< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > rigth< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ':'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L174" > < / a > < tt class = "py-lineno" > 174< / tt > < tt class = "py-line" > < / tt >
< a name = "L175" > < / a > < tt class = "py-lineno" > 175< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## recording zone< / tt > < / tt >
< a name = "L176" > < / a > < tt class = "py-lineno" > 176< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > rigth< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L177" > < / a > < tt class = "py-lineno" > 177< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'name'< / tt > < / tt >
< a name = "L178" > < / a > < tt class = "py-lineno" > 178< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > __doc__< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
< a name = "L179" > < / a > < tt class = "py-lineno" > 179< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < / div > < a name = "L180" > < / a > < tt class = "py-lineno" > 180< / tt > < tt class = "py-line" > < / tt >
< a name = "L181" > < / a > < tt class = "py-lineno" > 181< / tt > < tt class = "py-line" > < / tt >
< a name = "L182" > < / a > < tt class = "py-lineno" > 182< / tt > < tt class = "py-line" > < / tt >
< a name = "DefValue" > < / a > < div id = "DefValue-def" > < a name = "L183" > < / a > < tt class = "py-lineno" > 183< / tt > < a class = "py-toggle" href = "#" id = "DefValue-toggle" onclick = "return toggle('DefValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.DefValue-class.html" > DefValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "DefValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "DefValue-expanded" > < a name = "L184" > < / a > < tt class = "py-lineno" > 184< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L185" > < / a > < tt class = "py-lineno" > 185< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'def:value' inherited from the class TaggedValue. Used to manage def tags.< / tt > < / tt >
< a name = "L186" > < / a > < tt class = "py-lineno" > 186< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L187" > < / a > < tt class = "py-lineno" > 187< / tt > < tt class = "py-line" > < / tt >
< a name = "DefValue.__init__" > < / a > < div id = "DefValue.__init__-def" > < a name = "L188" > < / a > < tt class = "py-lineno" > 188< / tt > < a class = "py-toggle" href = "#" id = "DefValue.__init__-toggle" onclick = "return toggle('DefValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.DefValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "DefValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "DefValue.__init__-expanded" > < a name = "L189" > < / a > < tt class = "py-lineno" > 189< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L190" > < / a > < tt class = "py-lineno" > 190< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Constructor of the class DefValue.< / tt > < / tt >
< a name = "L191" > < / a > < tt class = "py-lineno" > 191< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L192" > < / a > < tt class = "py-lineno" > 192< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param line: a line of an OBOEntry composed of a tag named 'def' and a value.< / tt > < / tt >
< a name = "L193" > < / a > < tt class = "py-lineno" > 193< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type line: string< / tt > < / tt >
< a name = "L194" > < / a > < tt class = "py-lineno" > 194< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L195" > < / a > < tt class = "py-lineno" > 195< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The constructor calls the TaggedValue constructor. A regular expression < / tt > < / tt >
< a name = "L196" > < / a > < tt class = "py-lineno" > 196< / tt > < tt class = "py-line" > < tt class = "py-docstring" > is used to extract the 'definition' from TaggedValue.value (definition is a not < / tt > < / tt >
< a name = "L197" > < / a > < tt class = "py-lineno" > 197< / tt > < tt class = "py-line" > < tt class = "py-docstring" > quoted TaggedValue.value). A regular expression is used to extract 'dbxrefs' < / tt > < / tt >
< a name = "L198" > < / a > < tt class = "py-lineno" > 198< / tt > < tt class = "py-line" > < tt class = "py-docstring" > from the aggedValue.value without the definition (dbxrefs are between brackets< / tt > < / tt >
< a name = "L199" > < / a > < tt class = "py-lineno" > 199< / tt > < tt class = "py-line" > < tt class = "py-docstring" > and definition can be so). Definition is saved as the new value of the DefValue.< / tt > < / tt >
< a name = "L200" > < / a > < tt class = "py-lineno" > 200< / tt > < tt class = "py-line" > < tt class = "py-docstring" > dbxrefs are saved.< / tt > < / tt >
< a name = "L201" > < / a > < tt class = "py-lineno" > 201< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L202" > < / a > < tt class = "py-lineno" > 202< / tt > < tt class = "py-line" > < / tt >
< a name = "L203" > < / a > < tt class = "py-lineno" > 203< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use of the TaggedValue constructor< / tt > < / tt >
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< a name = "L204" > < / a > < tt class = "py-lineno" > 204< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-39" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-39', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-40" class = "py-name" > < a title = "obitools.BioSequence.__init__
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obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
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obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
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obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
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obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-40', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L205" > < / a > < tt class = "py-lineno" > 205< / tt > < tt class = "py-line" > < / tt >
< a name = "L206" > < / a > < tt class = "py-lineno" > 206< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## definition, which is quoted, is extracted from the standard value of a TaggedValue.< / tt > < / tt >
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< a name = "L207" > < / a > < tt class = "py-lineno" > 207< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-41" class = "py-name" targets = "Variable obitools.BioSequence.definition=obitools.BioSequence-class.html#definition,Variable obitools.WrappedBioSequence.definition=obitools.WrappedBioSequence-class.html#definition,Variable obitools.cns.quality.QualitySequence.definition=obitools.cns.quality.QualitySequence-class.html#definition,Variable obitools.obo.parser.OBOTerm.definition=obitools.obo.parser.OBOTerm-class.html#definition" > < a title = "obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
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obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-41', 'definition', 'link-41');">definition< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-42" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-42', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-43" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_quotedString" class = "py-name" href = "#" onclick = "return doclink('link-43', '_match_quotedString', 'link-21');" > _match_quotedString< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L208" > < / a > < tt class = "py-lineno" > 208< / tt > < tt class = "py-line" > < / tt >
< a name = "L209" > < / a > < tt class = "py-lineno" > 209< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the standard value is cleaned of the definition.< / tt > < / tt >
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< a name = "L210" > < / a > < tt class = "py-lineno" > 210< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > replace< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-44" class = "py-name" > < a title = "obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
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obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-44', 'definition', 'link-41');">definition< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > ''< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L211" > < / a > < tt class = "py-lineno" > 211< / tt > < tt class = "py-line" > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > replace< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ' '< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > ' '< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L212" > < / a > < tt class = "py-lineno" > 212< / tt > < tt class = "py-line" > < / tt >
< a name = "L213" > < / a > < tt class = "py-lineno" > 213< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## dbxrefs are searched into the rest of the standard value.< / tt > < / tt >
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< a name = "L214" > < / a > < tt class = "py-lineno" > 214< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-45" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-45', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-46" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_bracket" class = "py-name" href = "#" onclick = "return doclink('link-46', '_match_bracket', 'link-22');" > _match_bracket< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L215" > < / a > < tt class = "py-lineno" > 215< / tt > < tt class = "py-line" > < / tt >
< a name = "L216" > < / a > < tt class = "py-lineno" > 216< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## recording zone< / tt > < / tt >
< a name = "L217" > < / a > < tt class = "py-lineno" > 217< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## the value of a DefValue is not the standard value but the definition.< / tt > < / tt >
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< a name = "L218" > < / a > < tt class = "py-lineno" > 218< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-47" class = "py-name" > < a title = "obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
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obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-47', 'definition', 'link-41');">definition< / a > < / tt > < / tt >
< a name = "L219" > < / a > < tt class = "py-lineno" > 219< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-48" class = "py-name" targets = "Function obitools.obo.parser.xrefFactory()=obitools.obo.parser-module.html#xrefFactory" > < a title = "obitools.obo.parser.xrefFactory" class = "py-name" href = "#" onclick = "return doclink('link-48', 'xrefFactory', 'link-48');" > xrefFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< / div > < / div > < a name = "L220" > < / a > < tt class = "py-lineno" > 220< / tt > < tt class = "py-line" > < / tt >
< a name = "L221" > < / a > < tt class = "py-lineno" > 221< / tt > < tt class = "py-line" > < / tt >
< a name = "SynonymValue" > < / a > < div id = "SynonymValue-def" > < a name = "L222" > < / a > < tt class = "py-lineno" > 222< / tt > < a class = "py-toggle" href = "#" id = "SynonymValue-toggle" onclick = "return toggle('SynonymValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.SynonymValue-class.html" > SynonymValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "SynonymValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "SynonymValue-expanded" > < a name = "L223" > < / a > < tt class = "py-lineno" > 223< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L224" > < / a > < tt class = "py-lineno" > 224< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'synonym:value' inherited from the class TaggedValue. Used to manage < / tt > < / tt >
< a name = "L225" > < / a > < tt class = "py-lineno" > 225< / tt > < tt class = "py-line" > < tt class = "py-docstring" > synonym tags, exact_synonym tags, broad_synonym tags and narrow_synonym tags.< / tt > < / tt >
< a name = "L226" > < / a > < tt class = "py-lineno" > 226< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L227" > < / a > < tt class = "py-lineno" > 227< / tt > < tt class = "py-line" > < / tt >
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< a name = "L228" > < / a > < tt class = "py-lineno" > 228< / tt > < tt class = "py-line" > < tt id = "link-49" class = "py-name" targets = "Variable obitools.obo.parser.SynonymValue._match_scope=obitools.obo.parser.SynonymValue-class.html#_match_scope" > < a title = "obitools.obo.parser.SynonymValue._match_scope" class = "py-name" href = "#" onclick = "return doclink('link-49', '_match_scope', 'link-49');" > _match_scope< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '(?< ="")[^\[]*(?=\[|$)'< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L229" > < / a > < tt class = "py-lineno" > 229< / tt > < tt class = "py-line" > < / tt >
< a name = "SynonymValue.__init__" > < / a > < div id = "SynonymValue.__init__-def" > < a name = "L230" > < / a > < tt class = "py-lineno" > 230< / tt > < a class = "py-toggle" href = "#" id = "SynonymValue.__init__-toggle" onclick = "return toggle('SynonymValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.SynonymValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "SynonymValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "SynonymValue.__init__-expanded" > < a name = "L231" > < / a > < tt class = "py-lineno" > 231< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L232" > < / a > < tt class = "py-lineno" > 232< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Constructor of the class SynonymValue.< / tt > < / tt >
< a name = "L233" > < / a > < tt class = "py-lineno" > 233< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L234" > < / a > < tt class = "py-lineno" > 234< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param line: a line of an OBOEntry composed of a tag named 'synonym' or< / tt > < / tt >
< a name = "L235" > < / a > < tt class = "py-lineno" > 235< / tt > < tt class = "py-line" > < tt class = "py-docstring" > 'exact_synonym' or 'broad_synonym' or 'narrow_synonym' and a value.< / tt > < / tt >
< a name = "L236" > < / a > < tt class = "py-lineno" > 236< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type line: string< / tt > < / tt >
< a name = "L237" > < / a > < tt class = "py-lineno" > 237< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L238" > < / a > < tt class = "py-lineno" > 238< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: SynonymValue is composed of a tag, a value, a scope, a list of types and < / tt > < / tt >
< a name = "L239" > < / a > < tt class = "py-lineno" > 239< / tt > < tt class = "py-line" > < tt class = "py-docstring" > dbxrefs.< / tt > < / tt >
< a name = "L240" > < / a > < tt class = "py-lineno" > 240< / tt > < tt class = "py-line" > < tt class = "py-docstring" > The constructor calls the TaggedValue constructor. A regular expression < / tt > < / tt >
< a name = "L241" > < / a > < tt class = "py-lineno" > 241< / tt > < tt class = "py-line" > < tt class = "py-docstring" > is used to extract 'definition' from TaggedValue.value (definition is a not < / tt > < / tt >
< a name = "L242" > < / a > < tt class = "py-lineno" > 242< / tt > < tt class = "py-line" > < tt class = "py-docstring" > quoted TaggedValue.value). Definition is saved as the new value of the class< / tt > < / tt >
< a name = "L243" > < / a > < tt class = "py-lineno" > 243< / tt > < tt class = "py-line" > < tt class = "py-docstring" > SynonymValue.< / tt > < / tt >
< a name = "L244" > < / a > < tt class = "py-lineno" > 244< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A regular expression is used to extract 'attributes' from the rest of the< / tt > < / tt >
< a name = "L245" > < / a > < tt class = "py-lineno" > 245< / tt > < tt class = "py-line" > < tt class = "py-docstring" > string. Attributes may contain an optional synonym scope and an optional list < / tt > < / tt >
< a name = "L246" > < / a > < tt class = "py-lineno" > 246< / tt > < tt class = "py-line" > < tt class = "py-docstring" > of synonym types. The scope is extracted from attributes or set by default to< / tt > < / tt >
< a name = "L247" > < / a > < tt class = "py-lineno" > 247< / tt > < tt class = "py-line" > < tt class = "py-docstring" > 'RELATED'. It is saved as the scope of the class. The types are the rest of the < / tt > < / tt >
< a name = "L248" > < / a > < tt class = "py-lineno" > 248< / tt > < tt class = "py-line" > < tt class = "py-docstring" > attributes and are saved as the list of types of the class.< / tt > < / tt >
< a name = "L249" > < / a > < tt class = "py-lineno" > 249< / tt > < tt class = "py-line" > < tt class = "py-docstring" > For deprecated tags 'exact_synonym', 'broad_synonym' and 'narrow_synonym', tag< / tt > < / tt >
< a name = "L250" > < / a > < tt class = "py-lineno" > 250< / tt > < tt class = "py-line" > < tt class = "py-docstring" > is set to 'synonym' and scope is set respectively to 'EXACT', 'BROAD' and 'NARROW'.< / tt > < / tt >
< a name = "L251" > < / a > < tt class = "py-lineno" > 251< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A regular expression is used to extract 'dbxrefs' from the TaggedValue.value < / tt > < / tt >
< a name = "L252" > < / a > < tt class = "py-lineno" > 252< / tt > < tt class = "py-line" > < tt class = "py-docstring" > without the definition (dbxrefs are between brackets and definition can be so).< / tt > < / tt >
< a name = "L253" > < / a > < tt class = "py-lineno" > 253< / tt > < tt class = "py-line" > < tt class = "py-docstring" > dbxrefs are saved.< / tt > < / tt >
< a name = "L254" > < / a > < tt class = "py-lineno" > 254< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L255" > < / a > < tt class = "py-lineno" > 255< / tt > < tt class = "py-line" > < / tt >
< a name = "L256" > < / a > < tt class = "py-lineno" > 256< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use of the TaggedValue constructor< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L257" > < / a > < tt class = "py-lineno" > 257< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-50" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-50', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-51" class = "py-name" > < a title = "obitools.BioSequence.__init__
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obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
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obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
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obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
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obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-51', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L258" > < / a > < tt class = "py-lineno" > 258< / tt > < tt class = "py-line" > < / tt >
< a name = "L259" > < / a > < tt class = "py-lineno" > 259< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## definition, which is quoted, is extracted from the standard value of a TaggedValue.< / tt > < / tt >
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< a name = "L260" > < / a > < tt class = "py-lineno" > 260< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-52" class = "py-name" > < a title = "obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
2008-04-29 11:07:08 +00:00
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-52', 'definition', 'link-41');">definition< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-53" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-53', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-54" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_quotedString" class = "py-name" href = "#" onclick = "return doclink('link-54', '_match_quotedString', 'link-21');" > _match_quotedString< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L261" > < / a > < tt class = "py-lineno" > 261< / tt > < tt class = "py-line" > < / tt >
< a name = "L262" > < / a > < tt class = "py-lineno" > 262< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the standard value is cleaned of the definition.< / tt > < / tt >
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< a name = "L263" > < / a > < tt class = "py-lineno" > 263< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > replace< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-55" class = "py-name" > < a title = "obitools.BioSequence.definition
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
2008-04-29 11:07:08 +00:00
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-55', 'definition', 'link-41');">definition< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > ''< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L264" > < / a > < tt class = "py-lineno" > 264< / tt > < tt class = "py-line" > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > replace< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ' '< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > ' '< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L265" > < / a > < tt class = "py-lineno" > 265< / tt > < tt class = "py-line" > < / tt >
< a name = "L266" > < / a > < tt class = "py-lineno" > 266< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## 1) attributes are searched into the rest of the standard value.< / tt > < / tt >
< a name = "L267" > < / a > < tt class = "py-lineno" > 267< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## 2) then they are stripped.< / tt > < / tt >
< a name = "L268" > < / a > < tt class = "py-lineno" > 268< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## 3) then they are split on every ' '.< / tt > < / tt >
< a name = "L269" > < / a > < tt class = "py-lineno" > 269< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## 4) finally they are ordered into a set.< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L270" > < / a > < tt class = "py-lineno" > 270< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > attributes< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-56" class = "py-name" targets = "Class obitools.obo.parser.SynonymValue=obitools.obo.parser.SynonymValue-class.html" > < a title = "obitools.obo.parser.SynonymValue" class = "py-name" href = "#" onclick = "return doclink('link-56', 'SynonymValue', 'link-56');" > SynonymValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-57" class = "py-name" > < a title = "obitools.obo.parser.SynonymValue._match_scope" class = "py-name" href = "#" onclick = "return doclink('link-57', '_match_scope', 'link-49');" > _match_scope< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L271" > < / a > < tt class = "py-lineno" > 271< / tt > < tt class = "py-line" > < / tt >
< a name = "L272" > < / a > < tt class = "py-lineno" > 272< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the scopes are the junction between the attributes and a set of specific terms. < / tt > < / tt >
< a name = "L273" > < / a > < tt class = "py-lineno" > 273< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > scopes< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > attributes< / tt > < tt class = "py-op" > & < / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'RELATED'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'EXACT'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'BROAD'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'NARROW'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L274" > < / a > < tt class = "py-lineno" > 274< / tt > < tt class = "py-line" > < / tt >
< a name = "L275" > < / a > < tt class = "py-lineno" > 275< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the types are the rest of the attributes.< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L276" > < / a > < tt class = "py-lineno" > 276< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-58" class = "py-name" targets = "Variable obitools.blast.BlastResultIterator.types=obitools.blast.BlastResultIterator-class.html#types,Variable obitools.table.ProjectionIterator.types=obitools.table.ProjectionIterator-class.html#types,Variable obitools.table.SelectionIterator.types=obitools.table.SelectionIterator-class.html#types,Variable obitools.table.Table.types=obitools.table.Table-class.html#types,Variable obitools.table.TableIterator.types=obitools.table.TableIterator-class.html#types,Variable obitools.table.TableIteratorAsDict.types=obitools.table.TableIteratorAsDict-class.html#types,Variable obitools.table.TableRow.types=obitools.table.TableRow-class.html#types,Variable obitools.table.UnionIterator.types=obitools.table.UnionIterator-class.html#types,Variable obitools.table.iTableIterator.types=obitools.table.iTableIterator-class.html#types" > < a title = "obitools.blast.BlastResultIterator.types
2008-04-15 16:58:36 +00:00
obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-58', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > attributes< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-name" > scopes< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L277" > < / a > < tt class = "py-lineno" > 277< / tt > < tt class = "py-line" > < / tt >
< a name = "L278" > < / a > < tt class = "py-lineno" > 278< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## this is a constraint of the OBO format< / tt > < / tt >
< a name = "L279" > < / a > < tt class = "py-lineno" > 279< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > assert< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > scopes< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > < < / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "Only one synonym scope allowed"< / tt > < / tt >
< a name = "L280" > < / a > < tt class = "py-lineno" > 280< / tt > < tt class = "py-line" > < / tt >
< a name = "L281" > < / a > < tt class = "py-lineno" > 281< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the scope of the SynonymValue is into scopes or set by default to RELATED< / tt > < / tt >
< a name = "L282" > < / a > < tt class = "py-lineno" > 282< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > scopes< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L283" > < / a > < tt class = "py-lineno" > 283< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > scopes< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-59" class = "py-name" targets = "Method obitools.table.TableRow.pop()=obitools.table.TableRow-class.html#pop,Method obitools.table._Row.pop()=obitools.table._Row-class.html#pop" > < a title = "obitools.table.TableRow.pop
obitools.table._Row.pop" class="py-name" href="#" onclick="return doclink('link-59', 'pop', 'link-59');">pop< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L284" > < / a > < tt class = "py-lineno" > 284< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L285" > < / a > < tt class = "py-lineno" > 285< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'RELATED'< / tt > < / tt >
< a name = "L286" > < / a > < tt class = "py-lineno" > 286< / tt > < tt class = "py-line" > < / tt >
< a name = "L287" > < / a > < tt class = "py-lineno" > 287< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## Specific rules are defined for the following tags : < / tt > < / tt >
< a name = "L288" > < / a > < tt class = "py-lineno" > 288< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'exact_synonym'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L289" > < / a > < tt class = "py-lineno" > 289< / tt > < tt class = "py-line" > < tt class = "py-keyword" > raise< / tt > < tt class = "py-name" > DeprecationWarning< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'exact_synonym is a deprecated tag use instead synonym tag'< / tt > < / tt >
< a name = "L290" > < / a > < tt class = "py-lineno" > 290< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'synonym'< / tt > < / tt >
< a name = "L291" > < / a > < tt class = "py-lineno" > 291< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'EXACT'< / tt > < / tt >
< a name = "L292" > < / a > < tt class = "py-lineno" > 292< / tt > < tt class = "py-line" > < / tt >
< a name = "L293" > < / a > < tt class = "py-lineno" > 293< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'broad_synonym'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L294" > < / a > < tt class = "py-lineno" > 294< / tt > < tt class = "py-line" > < tt class = "py-keyword" > raise< / tt > < tt class = "py-name" > DeprecationWarning< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'broad_synonym is a deprecated tag use instead synonym tag'< / tt > < / tt >
< a name = "L295" > < / a > < tt class = "py-lineno" > 295< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'synonym'< / tt > < / tt >
< a name = "L296" > < / a > < tt class = "py-lineno" > 296< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'BROAD'< / tt > < / tt >
< a name = "L297" > < / a > < tt class = "py-lineno" > 297< / tt > < tt class = "py-line" > < / tt >
< a name = "L298" > < / a > < tt class = "py-lineno" > 298< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'narrow_synonym'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L299" > < / a > < tt class = "py-lineno" > 299< / tt > < tt class = "py-line" > < tt class = "py-keyword" > raise< / tt > < tt class = "py-name" > DeprecationWarning< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'narrow_synonym is a deprecated tag use instead synonym tag'< / tt > < / tt >
< a name = "L300" > < / a > < tt class = "py-lineno" > 300< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'synonym'< / tt > < / tt >
< a name = "L301" > < / a > < tt class = "py-lineno" > 301< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'NARROW'< / tt > < / tt >
< a name = "L302" > < / a > < tt class = "py-lineno" > 302< / tt > < tt class = "py-line" > < / tt >
< a name = "L303" > < / a > < tt class = "py-lineno" > 303< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'systematic_synonym'< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L304" > < / a > < tt class = "py-lineno" > 304< / tt > < tt class = "py-line" > < tt class = "py-comment" > #raise DeprecationWarning,'narrow_synonym is a deprecated tag use instead sysnonym tag'< / tt > < / tt >
< a name = "L305" > < / a > < tt class = "py-lineno" > 305< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'synonym'< / tt > < / tt >
< a name = "L306" > < / a > < tt class = "py-lineno" > 306< / tt > < tt class = "py-line" > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'SYSTEMATIC'< / tt > < / tt >
< a name = "L307" > < / a > < tt class = "py-lineno" > 307< / tt > < tt class = "py-line" > < / tt >
< a name = "L308" > < / a > < tt class = "py-lineno" > 308< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## this is our own constraint. deprecated tags are not saved by this parser. < / tt > < / tt >
< a name = "L309" > < / a > < tt class = "py-lineno" > 309< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > assert< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'synonym'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "%s synonym type is not managed"< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < / tt >
< a name = "L310" > < / a > < tt class = "py-lineno" > 310< / tt > < tt class = "py-line" > < / tt >
< a name = "L311" > < / a > < tt class = "py-lineno" > 311< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## dbxrefs are searched into the rest of the standard value.< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L312" > < / a > < tt class = "py-lineno" > 312< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-60" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-60', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-61" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_bracket" class = "py-name" href = "#" onclick = "return doclink('link-61', '_match_bracket', 'link-22');" > _match_bracket< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > cleanvalue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L313" > < / a > < tt class = "py-lineno" > 313< / tt > < tt class = "py-line" > < / tt >
< a name = "L314" > < / a > < tt class = "py-lineno" > 314< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## recording zone< / tt > < / tt >
< a name = "L315" > < / a > < tt class = "py-lineno" > 315< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## the value of a SynonymValue is not the standard value but the definition.< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L316" > < / a > < tt class = "py-lineno" > 316< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-62" class = "py-name" > < a title = "obitools.BioSequence.definition
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
2008-04-29 11:07:08 +00:00
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-62', 'definition', 'link-41');">definition< / a > < / tt > < / tt >
< a name = "L317" > < / a > < tt class = "py-lineno" > 317< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-63" class = "py-name" > < a title = "obitools.obo.parser.xrefFactory" class = "py-name" href = "#" onclick = "return doclink('link-63', 'xrefFactory', 'link-48');" > xrefFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L318" > < / a > < tt class = "py-lineno" > 318< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > scope< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L319" > < / a > < tt class = "py-lineno" > 319< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-64" class = "py-name" > < a title = "obitools.blast.BlastResultIterator.types
2008-04-15 16:58:36 +00:00
obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-64', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-65" class = "py-name" > < a title = "obitools.blast.BlastResultIterator.types
2008-04-15 16:58:36 +00:00
obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-65', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L320" > < / a > < tt class = "py-lineno" > 320< / tt > < tt class = "py-line" > < / tt >
< a name = "SynonymValue.__eq__" > < / a > < div id = "SynonymValue.__eq__-def" > < a name = "L321" > < / a > < tt class = "py-lineno" > 321< / tt > < a class = "py-toggle" href = "#" id = "SynonymValue.__eq__-toggle" onclick = "return toggle('SynonymValue.__eq__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.SynonymValue-class.html#__eq__" > __eq__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > b< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "SynonymValue.__eq__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "SynonymValue.__eq__-expanded" > < a name = "L322" > < / a > < tt class = "py-lineno" > 322< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L323" > < / a > < tt class = "py-lineno" > 323< / tt > < tt class = "py-line" > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-66" class = "py-name" > < a title = "obitools.blast.BlastResultIterator.types
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obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-66', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-67" class = "py-name" > < a title = "obitools.blast.BlastResultIterator.types
2008-04-15 16:58:36 +00:00
obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-67', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L324" > < / a > < tt class = "py-lineno" > 324< / tt > < tt class = "py-line" > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > __doc__< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > __doc__< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L325" > < / a > < tt class = "py-lineno" > 325< / tt > < tt class = "py-line" > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < a name = "L326" > < / a > < tt class = "py-lineno" > 326< / tt > < tt class = "py-line" > < / tt >
< a name = "SynonymValue.__hash__" > < / a > < div id = "SynonymValue.__hash__-def" > < a name = "L327" > < / a > < tt class = "py-lineno" > 327< / tt > < a class = "py-toggle" href = "#" id = "SynonymValue.__hash__-toggle" onclick = "return toggle('SynonymValue.__hash__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.SynonymValue-class.html#__hash__" > __hash__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "SynonymValue.__hash__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "SynonymValue.__hash__-expanded" > < a name = "L328" > < / a > < tt class = "py-lineno" > 328< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > reduce< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-keyword" > lambda< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > y< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > +< / tt > < tt class = "py-name" > y< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > hash< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > z< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > z< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > __doc__< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L329" > < / a > < tt class = "py-lineno" > 329< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L330" > < / a > < tt class = "py-lineno" > 330< / tt > < tt class = "py-line" > < tt class = "py-name" > frozenset< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > dbxrefs< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L331" > < / a > < tt class = "py-lineno" > 331< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > scope< / tt > < tt class = "py-op" > ,< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L332" > < / a > < tt class = "py-lineno" > 332< / tt > < tt class = "py-line" > < tt class = "py-name" > frozenset< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-68" class = "py-name" > < a title = "obitools.blast.BlastResultIterator.types
2008-04-15 16:58:36 +00:00
obitools.table.ProjectionIterator.types
obitools.table.SelectionIterator.types
obitools.table.Table.types
obitools.table.TableIterator.types
obitools.table.TableIteratorAsDict.types
obitools.table.TableRow.types
obitools.table.UnionIterator.types
2008-04-29 11:07:08 +00:00
obitools.table.iTableIterator.types" class="py-name" href="#" onclick="return doclink('link-68', 'types', 'link-58');">types< / a > < / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ,< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L333" > < / a > < tt class = "py-lineno" > 333< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L334" > < / a > < tt class = "py-lineno" > 334< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > **< / tt > < tt class = "py-number" > 31< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < / div > < a name = "L335" > < / a > < tt class = "py-lineno" > 335< / tt > < tt class = "py-line" > < / tt >
< a name = "L336" > < / a > < tt class = "py-lineno" > 336< / tt > < tt class = "py-line" > < / tt >
< a name = "XrefValue" > < / a > < div id = "XrefValue-def" > < a name = "L337" > < / a > < tt class = "py-lineno" > 337< / tt > < a class = "py-toggle" href = "#" id = "XrefValue-toggle" onclick = "return toggle('XrefValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.XrefValue-class.html" > XrefValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "XrefValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "XrefValue-expanded" > < a name = "L338" > < / a > < tt class = "py-lineno" > 338< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L339" > < / a > < tt class = "py-lineno" > 339< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'xref:value' inherited from the class TaggedValue. Used to manage < / tt > < / tt >
< a name = "L340" > < / a > < tt class = "py-lineno" > 340< / tt > < tt class = "py-line" > < tt class = "py-docstring" > xref tags.< / tt > < / tt >
< a name = "L341" > < / a > < tt class = "py-lineno" > 341< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L342" > < / a > < tt class = "py-lineno" > 342< / tt > < tt class = "py-line" > < / tt >
< a name = "XrefValue.__init__" > < / a > < div id = "XrefValue.__init__-def" > < a name = "L343" > < / a > < tt class = "py-lineno" > 343< / tt > < a class = "py-toggle" href = "#" id = "XrefValue.__init__-toggle" onclick = "return toggle('XrefValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.XrefValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "XrefValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "XrefValue.__init__-expanded" > < a name = "L344" > < / a > < tt class = "py-lineno" > 344< / tt > < tt class = "py-line" > < / tt >
< a name = "L345" > < / a > < tt class = "py-lineno" > 345< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use of the TaggedValue constructor< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L346" > < / a > < tt class = "py-lineno" > 346< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-69" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-69', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-70" class = "py-name" > < a title = "obitools.BioSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
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obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
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obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
2008-04-29 11:07:08 +00:00
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-70', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L347" > < / a > < tt class = "py-lineno" > 347< / tt > < tt class = "py-line" > < / tt >
< a name = "L348" > < / a > < tt class = "py-lineno" > 348< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use the same function as the dbxrefs< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L349" > < / a > < tt class = "py-lineno" > 349< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-71" class = "py-name" > < a title = "obitools.obo.parser.xrefFactory" class = "py-name" href = "#" onclick = "return doclink('link-71', 'xrefFactory', 'link-48');" > xrefFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L350" > < / a > < tt class = "py-lineno" > 350< / tt > < tt class = "py-line" > < / tt >
< a name = "L351" > < / a > < tt class = "py-lineno" > 351< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'xref_analog'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > 'xref_unk'< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L352" > < / a > < tt class = "py-lineno" > 352< / tt > < tt class = "py-line" > < tt class = "py-keyword" > raise< / tt > < tt class = "py-name" > DeprecationWarning< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > '%s is a deprecated tag use instead sysnonym tag'< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < / tt >
< a name = "L353" > < / a > < tt class = "py-lineno" > 353< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'xref'< / tt > < / tt >
< a name = "L354" > < / a > < tt class = "py-lineno" > 354< / tt > < tt class = "py-line" > < / tt >
< a name = "L355" > < / a > < tt class = "py-lineno" > 355< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## this is our own constraint. deprecated tags are not saved by this parser. < / tt > < / tt >
< a name = "L356" > < / a > < tt class = "py-lineno" > 356< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > assert< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'xref'< / tt > < / tt >
< / div > < / div > < a name = "L357" > < / a > < tt class = "py-lineno" > 357< / tt > < tt class = "py-line" > < / tt >
< a name = "L358" > < / a > < tt class = "py-lineno" > 358< / tt > < tt class = "py-line" > < / tt >
< a name = "RelationshipValue" > < / a > < div id = "RelationshipValue-def" > < a name = "L359" > < / a > < tt class = "py-lineno" > 359< / tt > < a class = "py-toggle" href = "#" id = "RelationshipValue-toggle" onclick = "return toggle('RelationshipValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.RelationshipValue-class.html" > RelationshipValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "RelationshipValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "RelationshipValue-expanded" > < a name = "L360" > < / a > < tt class = "py-lineno" > 360< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L361" > < / a > < tt class = "py-lineno" > 361< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A couple 'xref:value' inherited from the class TaggedValue. Used to manage < / tt > < / tt >
< a name = "L362" > < / a > < tt class = "py-lineno" > 362< / tt > < tt class = "py-line" > < tt class = "py-docstring" > xref tags.< / tt > < / tt >
< a name = "L363" > < / a > < tt class = "py-lineno" > 363< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L364" > < / a > < tt class = "py-lineno" > 364< / tt > < tt class = "py-line" > < / tt >
< a name = "RelationshipValue.__init__" > < / a > < div id = "RelationshipValue.__init__-def" > < a name = "L365" > < / a > < tt class = "py-lineno" > 365< / tt > < a class = "py-toggle" href = "#" id = "RelationshipValue.__init__-toggle" onclick = "return toggle('RelationshipValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.RelationshipValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "RelationshipValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "RelationshipValue.__init__-expanded" > < a name = "L366" > < / a > < tt class = "py-lineno" > 366< / tt > < tt class = "py-line" > < / tt >
< a name = "L367" > < / a > < tt class = "py-lineno" > 367< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use of the TaggedValue constructor< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L368" > < / a > < tt class = "py-lineno" > 368< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-72" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-72', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-73" class = "py-name" > < a title = "obitools.BioSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
2008-04-29 11:07:08 +00:00
obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
2008-04-29 11:07:08 +00:00
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-73', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L369" > < / a > < tt class = "py-lineno" > 369< / tt > < tt class = "py-line" > < / tt >
< a name = "L370" > < / a > < tt class = "py-lineno" > 370< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## the value is split on the first ' '.< / tt > < / tt >
< a name = "L371" > < / a > < tt class = "py-lineno" > 371< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L372" > < / a > < tt class = "py-lineno" > 372< / tt > < tt class = "py-line" > < / tt >
< a name = "L373" > < / a > < tt class = "py-lineno" > 373< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## succesful split !< / tt > < / tt >
< a name = "L374" > < / a > < tt class = "py-lineno" > 374< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L375" > < / a > < tt class = "py-lineno" > 375< / tt > < tt class = "py-line" > < tt class = "py-name" > relationship< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L376" > < / a > < tt class = "py-lineno" > 376< / tt > < tt class = "py-line" > < tt class = "py-name" > term< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L377" > < / a > < tt class = "py-lineno" > 377< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## unsuccesful split. The relationship is set by default to IS_A< / tt > < / tt >
< a name = "L378" > < / a > < tt class = "py-lineno" > 378< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L379" > < / a > < tt class = "py-lineno" > 379< / tt > < tt class = "py-line" > < tt class = "py-name" > relationship< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > 'is_a'< / tt > < / tt >
< a name = "L380" > < / a > < tt class = "py-lineno" > 380< / tt > < tt class = "py-line" > < tt class = "py-name" > term< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L381" > < / a > < tt class = "py-lineno" > 381< / tt > < tt class = "py-line" > < / tt >
< a name = "L382" > < / a > < tt class = "py-lineno" > 382< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## recording zone < / tt > < / tt >
< a name = "L383" > < / a > < tt class = "py-lineno" > 383< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > term< / tt > < / tt >
< a name = "L384" > < / a > < tt class = "py-lineno" > 384< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > relationship< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > relationship< / tt > < / tt >
< / div > < / div > < a name = "L385" > < / a > < tt class = "py-lineno" > 385< / tt > < tt class = "py-line" > < / tt >
< a name = "L386" > < / a > < tt class = "py-lineno" > 386< / tt > < tt class = "py-line" > < / tt >
< a name = "NamespaceValue" > < / a > < div id = "NamespaceValue-def" > < a name = "L387" > < / a > < tt class = "py-lineno" > 387< / tt > < a class = "py-toggle" href = "#" id = "NamespaceValue-toggle" onclick = "return toggle('NamespaceValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.NamespaceValue-class.html" > NamespaceValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "NamespaceValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "NamespaceValue-expanded" > < a name = "NamespaceValue.__init__" > < / a > < div id = "NamespaceValue.__init__-def" > < a name = "L388" > < / a > < tt class = "py-lineno" > 388< / tt > < a class = "py-toggle" href = "#" id = "NamespaceValue.__init__-toggle" onclick = "return toggle('NamespaceValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.NamespaceValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "NamespaceValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "NamespaceValue.__init__-expanded" > < a name = "L389" > < / a > < tt class = "py-lineno" > 389< / tt > < tt class = "py-line" > < tt id = "link-74" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-74', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-75" class = "py-name" > < a title = "obitools.BioSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
2008-04-29 11:07:08 +00:00
obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
2008-04-29 11:07:08 +00:00
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-75', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < / div > < a name = "L390" > < / a > < tt class = "py-lineno" > 390< / tt > < tt class = "py-line" > < / tt >
< a name = "RemarkValue" > < / a > < div id = "RemarkValue-def" > < a name = "L391" > < / a > < tt class = "py-lineno" > 391< / tt > < a class = "py-toggle" href = "#" id = "RemarkValue-toggle" onclick = "return toggle('RemarkValue');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.RemarkValue-class.html" > RemarkValue< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > TaggedValue< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "RemarkValue-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "RemarkValue-expanded" > < a name = "RemarkValue.__init__" > < / a > < div id = "RemarkValue.__init__-def" > < a name = "L392" > < / a > < tt class = "py-lineno" > 392< / tt > < a class = "py-toggle" href = "#" id = "RemarkValue.__init__-toggle" onclick = "return toggle('RemarkValue.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.RemarkValue-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "RemarkValue.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "RemarkValue.__init__-expanded" > < a name = "L393" > < / a > < tt class = "py-lineno" > 393< / tt > < tt class = "py-line" > < tt id = "link-76" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-76', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-77" class = "py-name" > < a title = "obitools.BioSequence.__init__
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
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obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
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obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
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obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-77', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L394" > < / a > < tt class = "py-lineno" > 394< / tt > < tt class = "py-line" > < tt id = "link-78" class = "py-name" targets = "Variable obitools.graph.Node.label=obitools.graph.Node-class.html#label,Variable obitools.phylogeny.PhylogenicNode.label=obitools.phylogeny.PhylogenicNode-class.html#label,Variable obitools.seqdb.genbank.graph.Node.label=obitools.seqdb.genbank.graph.Node-class.html#label" > < a title = "obitools.graph.Node.label
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obitools.phylogeny.PhylogenicNode.label
2008-04-29 11:07:08 +00:00
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-78', 'label', 'link-78');">label< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ':'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L395" > < / a > < tt class = "py-lineno" > 395< / tt > < tt class = "py-line" > < tt id = "link-79" class = "py-name" > < a title = "obitools.graph.Node.label
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obitools.phylogeny.PhylogenicNode.label
2008-04-29 11:07:08 +00:00
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-79', 'label', 'link-78');">label< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-80" class = "py-name" > < a title = "obitools.graph.Node.label
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obitools.phylogeny.PhylogenicNode.label
2008-04-29 11:07:08 +00:00
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-80', 'label', 'link-78');">label< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L396" > < / a > < tt class = "py-lineno" > 396< / tt > < tt class = "py-line" > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L397" > < / a > < tt class = "py-lineno" > 397< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > value< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > value< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L398" > < / a > < tt class = "py-lineno" > 398< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-81" class = "py-name" > < a title = "obitools.graph.Node.label
2008-04-15 16:58:36 +00:00
obitools.phylogeny.PhylogenicNode.label
2008-04-29 11:07:08 +00:00
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-81', 'label', 'link-78');">label< / a > < / tt > < tt class = "py-op" > =< / tt > < tt id = "link-82" class = "py-name" > < a title = "obitools.graph.Node.label
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obitools.phylogeny.PhylogenicNode.label
2008-04-29 11:07:08 +00:00
obitools.seqdb.genbank.graph.Node.label" class="py-name" href="#" onclick="return doclink('link-82', 'label', 'link-78');">label< / a > < / tt > < / tt >
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< / div > < / div > < a name = "L399" > < / a > < tt class = "py-lineno" > 399< / tt > < tt class = "py-line" > < / tt >
< a name = "L400" > < / a > < tt class = "py-lineno" > 400< / tt > < tt class = "py-line" > < / tt >
< a name = "taggedValueFactory" > < / a > < div id = "taggedValueFactory-def" > < a name = "L401" > < / a > < tt class = "py-lineno" > 401< / tt > < a class = "py-toggle" href = "#" id = "taggedValueFactory-toggle" onclick = "return toggle('taggedValueFactory');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#taggedValueFactory" > taggedValueFactory< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > line< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "taggedValueFactory-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "taggedValueFactory-expanded" > < a name = "L402" > < / a > < tt class = "py-lineno" > 402< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L403" > < / a > < tt class = "py-lineno" > 403< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A function used to dispatch lines of an OBOEntry between the class TaggedValue< / tt > < / tt >
< a name = "L404" > < / a > < tt class = "py-lineno" > 404< / tt > < tt class = "py-line" > < tt class = "py-docstring" > and its inherited classes.< / tt > < / tt >
< a name = "L405" > < / a > < tt class = "py-lineno" > 405< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L406" > < / a > < tt class = "py-lineno" > 406< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param line: a line of an OBOEntry composed of a tag and a value.< / tt > < / tt >
< a name = "L407" > < / a > < tt class = "py-lineno" > 407< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type line: string< / tt > < / tt >
< a name = "L408" > < / a > < tt class = "py-lineno" > 408< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L409" > < / a > < tt class = "py-lineno" > 409< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @return: a class object< / tt > < / tt >
< a name = "L410" > < / a > < tt class = "py-lineno" > 410< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L411" > < / a > < tt class = "py-lineno" > 411< / tt > < tt class = "py-line" > < / tt >
< a name = "L412" > < / a > < tt class = "py-lineno" > 412< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 9< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'namespace'< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L413" > < / a > < tt class = "py-lineno" > 413< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 17< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'default-namespace'< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L414" > < / a > < tt class = "py-lineno" > 414< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-83" class = "py-name" targets = "Class obitools.obo.parser.NamespaceValue=obitools.obo.parser.NamespaceValue-class.html" > < a title = "obitools.obo.parser.NamespaceValue" class = "py-name" href = "#" onclick = "return doclink('link-83', 'NamespaceValue', 'link-83');" > NamespaceValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L415" > < / a > < tt class = "py-lineno" > 415< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## DefValue is an inherited class of TaggedValue< / tt > < / tt >
< a name = "L416" > < / a > < tt class = "py-lineno" > 416< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > elif< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 3< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'def'< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L417" > < / a > < tt class = "py-lineno" > 417< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-84" class = "py-name" targets = "Class obitools.obo.parser.DefValue=obitools.obo.parser.DefValue-class.html" > < a title = "obitools.obo.parser.DefValue" class = "py-name" href = "#" onclick = "return doclink('link-84', 'DefValue', 'link-84');" > DefValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L418" > < / a > < tt class = "py-lineno" > 418< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## SynonymValue is an inherited class of TaggedValue< / tt > < / tt >
< a name = "L419" > < / a > < tt class = "py-lineno" > 419< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > elif< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 7< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > "synonym"< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 14< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > !=< / tt > < tt class = "py-string" > "synonymtypedef"< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L420" > < / a > < tt class = "py-lineno" > 420< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 13< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > "exact_synonym"< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L421" > < / a > < tt class = "py-lineno" > 421< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 13< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > "broad_synonym"< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L422" > < / a > < tt class = "py-lineno" > 422< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 14< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > "narrow_synonym"< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L423" > < / a > < tt class = "py-lineno" > 423< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-85" class = "py-name" > < a title = "obitools.obo.parser.SynonymValue" class = "py-name" href = "#" onclick = "return doclink('link-85', 'SynonymValue', 'link-56');" > SynonymValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L424" > < / a > < tt class = "py-lineno" > 424< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## XrefValue is an inherited class of TaggedValue< / tt > < / tt >
< a name = "L425" > < / a > < tt class = "py-lineno" > 425< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > elif< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 4< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'xref'< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L426" > < / a > < tt class = "py-lineno" > 426< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-86" class = "py-name" targets = "Class obitools.obo.parser.XrefValue=obitools.obo.parser.XrefValue-class.html" > < a title = "obitools.obo.parser.XrefValue" class = "py-name" href = "#" onclick = "return doclink('link-86', 'XrefValue', 'link-86');" > XrefValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L427" > < / a > < tt class = "py-lineno" > 427< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## NameValue is an inherited class of TaggedValue< / tt > < / tt >
< a name = "L428" > < / a > < tt class = "py-lineno" > 428< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > elif< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 4< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'name'< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L429" > < / a > < tt class = "py-lineno" > 429< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-87" class = "py-name" targets = "Class obitools.obo.parser.NameValue=obitools.obo.parser.NameValue-class.html" > < a title = "obitools.obo.parser.NameValue" class = "py-name" href = "#" onclick = "return doclink('link-87', 'NameValue', 'link-87');" > NameValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L430" > < / a > < tt class = "py-lineno" > 430< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## RelationshipValue is an inherited class of TaggedValue< / tt > < / tt >
< a name = "L431" > < / a > < tt class = "py-lineno" > 431< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > elif< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 15< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'intersection_of'< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L432" > < / a > < tt class = "py-lineno" > 432< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 8< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'union_of'< / tt > < tt class = "py-keyword" > or< / tt > < / tt >
< a name = "L433" > < / a > < tt class = "py-lineno" > 433< / tt > < tt class = "py-line" > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 12< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'relationship'< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L434" > < / a > < tt class = "py-lineno" > 434< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-88" class = "py-name" targets = "Class obitools.obo.parser.RelationshipValue=obitools.obo.parser.RelationshipValue-class.html" > < a title = "obitools.obo.parser.RelationshipValue" class = "py-name" href = "#" onclick = "return doclink('link-88', 'RelationshipValue', 'link-88');" > RelationshipValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L435" > < / a > < tt class = "py-lineno" > 435< / tt > < tt class = "py-line" > < tt class = "py-keyword" > elif< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-number" > 6< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'remark'< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L436" > < / a > < tt class = "py-lineno" > 436< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-89" class = "py-name" targets = "Class obitools.obo.parser.RemarkValue=obitools.obo.parser.RemarkValue-class.html" > < a title = "obitools.obo.parser.RemarkValue" class = "py-name" href = "#" onclick = "return doclink('link-89', 'RemarkValue', 'link-89');" > RemarkValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L437" > < / a > < tt class = "py-lineno" > 437< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## each line is a couple : tag / value (and some more features)< / tt > < / tt >
< a name = "L438" > < / a > < tt class = "py-lineno" > 438< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L439" > < / a > < tt class = "py-lineno" > 439< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-90" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-90', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L440" > < / a > < tt class = "py-lineno" > 440< / tt > < tt class = "py-line" > < / tt >
< a name = "L441" > < / a > < tt class = "py-lineno" > 441< / tt > < tt class = "py-line" > < / tt >
< a name = "L442" > < / a > < tt class = "py-lineno" > 442< / tt > < tt class = "py-line" > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L443" > < / a > < tt class = "py-lineno" > 443< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## Xref treatment area ##< / tt > < / tt >
< a name = "L444" > < / a > < tt class = "py-lineno" > 444< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L445" > < / a > < tt class = "py-lineno" > 445< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < / tt >
< a name = "L446" > < / a > < tt class = "py-lineno" > 446< / tt > < tt class = "py-line" > < / tt >
< a name = "L447" > < / a > < tt class = "py-lineno" > 447< / tt > < tt class = "py-line" > < / tt >
< a name = "Xref" > < / a > < div id = "Xref-def" > < a name = "L448" > < / a > < tt class = "py-lineno" > 448< / tt > < a class = "py-toggle" href = "#" id = "Xref-toggle" onclick = "return toggle('Xref');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.Xref-class.html" > Xref< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > object< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "Xref-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "Xref-expanded" > < a name = "L449" > < / a > < tt class = "py-lineno" > 449< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L450" > < / a > < tt class = "py-lineno" > 450< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A xref object of an OBOentry. It may be the 'dbxrefs' of SynonymValue and < / tt > < / tt >
< a name = "L451" > < / a > < tt class = "py-lineno" > 451< / tt > < tt class = "py-line" > < tt class = "py-docstring" > DefValue objects or the 'value' of XrefValue objects.< / tt > < / tt >
< a name = "L452" > < / a > < tt class = "py-lineno" > 452< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L453" > < / a > < tt class = "py-lineno" > 453< / tt > < tt class = "py-line" > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L454" > < / a > < tt class = "py-lineno" > 454< / tt > < tt class = "py-line" > < tt id = "link-91" class = "py-name" targets = "Variable obitools.obo.parser.Xref.__splitdata__=obitools.obo.parser.Xref-class.html#__splitdata__" > < a title = "obitools.obo.parser.Xref.__splitdata__" class = "py-name" href = "#" onclick = "return doclink('link-91', '__splitdata__', 'link-91');" > __splitdata__< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ' +(?=["{])'< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L455" > < / a > < tt class = "py-lineno" > 455< / tt > < tt class = "py-line" > < / tt >
< a name = "Xref.__init__" > < / a > < div id = "Xref.__init__-def" > < a name = "L456" > < / a > < tt class = "py-lineno" > 456< / tt > < a class = "py-toggle" href = "#" id = "Xref.__init__-toggle" onclick = "return toggle('Xref.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.Xref-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > ref< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "Xref.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "Xref.__init__-expanded" > < a name = "L457" > < / a > < tt class = "py-lineno" > 457< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > ref< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > ''< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-comment" > #< / tt > < / tt >
< a name = "L458" > < / a > < tt class = "py-lineno" > 458< / tt > < tt class = "py-line" > < tt class = "py-name" > ref< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-comment" > #< / tt > < / tt >
< a name = "L459" > < / a > < tt class = "py-lineno" > 459< / tt > < tt class = "py-line" > < tt class = "py-name" > data< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-string" > ''< / tt > < tt class = "py-comment" > #< / tt > < / tt >
< a name = "L460" > < / a > < tt class = "py-lineno" > 460< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-comment" > # Modifs JJ sinon erreur : list index out of range< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L461" > < / a > < tt class = "py-lineno" > 461< / tt > < tt class = "py-line" > < tt class = "py-name" > data< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-92" class = "py-name" targets = "Class obitools.obo.parser.Xref=obitools.obo.parser.Xref-class.html" > < a title = "obitools.obo.parser.Xref" class = "py-name" href = "#" onclick = "return doclink('link-92', 'Xref', 'link-92');" > Xref< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-93" class = "py-name" > < a title = "obitools.obo.parser.Xref.__splitdata__" class = "py-name" href = "#" onclick = "return doclink('link-93', '__splitdata__', 'link-91');" > __splitdata__< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > ref< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-comment" > #< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L462" > < / a > < tt class = "py-lineno" > 462< / tt > < tt class = "py-line" > < tt class = "py-name" > ref< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > data< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-comment" > #< / tt > < / tt >
< a name = "L463" > < / a > < tt class = "py-lineno" > 463< / tt > < tt class = "py-line" > < tt class = "py-name" > description< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
< a name = "L464" > < / a > < tt class = "py-lineno" > 464< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > None< / tt > < / tt >
< a name = "L465" > < / a > < tt class = "py-lineno" > 465< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > data< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > > < / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L466" > < / a > < tt class = "py-lineno" > 466< / tt > < tt class = "py-line" > < tt id = "link-94" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-94', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > data< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L467" > < / a > < tt class = "py-lineno" > 467< / tt > < tt class = "py-line" > < tt class = "py-name" > description< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-95" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue" class = "py-name" href = "#" onclick = "return doclink('link-95', 'TaggedValue', 'link-24');" > TaggedValue< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-96" class = "py-name" > < a title = "obitools.obo.parser.TaggedValue._match_quotedString" class = "py-name" href = "#" onclick = "return doclink('link-96', '_match_quotedString', 'link-21');" > _match_quotedString< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-97" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-97', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L468" > < / a > < tt class = "py-lineno" > 468< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-keyword" > is< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L469" > < / a > < tt class = "py-lineno" > 469< / tt > < tt class = "py-line" > < tt class = "py-name" > description< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L470" > < / a > < tt class = "py-lineno" > 470< / tt > < tt class = "py-line" > < tt id = "link-98" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-98', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > replace< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > ''< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L471" > < / a > < tt class = "py-lineno" > 471< / tt > < tt class = "py-line" > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-99" class = "py-name" > < a title = "obitools.obo.parser.trailingModifierFactory" class = "py-name" href = "#" onclick = "return doclink('link-99', 'trailingModifierFactory', 'link-36');" > trailingModifierFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt id = "link-100" class = "py-name" > < a title = "obitools.zipfile.ZipInfo.extra" class = "py-name" href = "#" onclick = "return doclink('link-100', 'extra', 'link-26');" > extra< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L472" > < / a > < tt class = "py-lineno" > 472< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > reference< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > ref< / tt > < / tt >
< a name = "L473" > < / a > < tt class = "py-lineno" > 473< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > description< / tt > < / tt >
< a name = "L474" > < / a > < tt class = "py-lineno" > 474< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < / tt >
< / div > < a name = "L475" > < / a > < tt class = "py-lineno" > 475< / tt > < tt class = "py-line" > < / tt >
< a name = "Xref.__eq__" > < / a > < div id = "Xref.__eq__-def" > < a name = "L476" > < / a > < tt class = "py-lineno" > 476< / tt > < a class = "py-toggle" href = "#" id = "Xref.__eq__-toggle" onclick = "return toggle('Xref.__eq__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.Xref-class.html#__eq__" > __eq__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > b< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "Xref.__eq__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "Xref.__eq__-expanded" > < a name = "L477" > < / a > < tt class = "py-lineno" > 477< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > reference< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > reference< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L478" > < / a > < tt class = "py-lineno" > 478< / tt > < tt class = "py-line" > < tt class = "py-keyword" > and< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-name" > b< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < a name = "L479" > < / a > < tt class = "py-lineno" > 479< / tt > < tt class = "py-line" > < / tt >
< a name = "Xref.__hash__" > < / a > < div id = "Xref.__hash__-def" > < a name = "L480" > < / a > < tt class = "py-lineno" > 480< / tt > < a class = "py-toggle" href = "#" id = "Xref.__hash__-toggle" onclick = "return toggle('Xref.__hash__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.Xref-class.html#__hash__" > __hash__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "Xref.__hash__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "Xref.__hash__-expanded" > < a name = "L481" > < / a > < tt class = "py-lineno" > 481< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > reduce< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-keyword" > lambda< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > y< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > +< / tt > < tt class = "py-name" > y< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > hash< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > z< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > z< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > reference< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L482" > < / a > < tt class = "py-lineno" > 482< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > description< / tt > < tt class = "py-op" > ,< / tt > < / tt >
< a name = "L483" > < / a > < tt class = "py-lineno" > 483< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > trailing_modifiers< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > %< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > **< / tt > < tt class = "py-number" > 31< / tt > < tt class = "py-op" > )< / tt > < / tt >
< / div > < / div > < a name = "L484" > < / a > < tt class = "py-lineno" > 484< / tt > < tt class = "py-line" > < / tt >
< a name = "L485" > < / a > < tt class = "py-lineno" > 485< / tt > < tt class = "py-line" > < / tt >
< a name = "xrefFactory" > < / a > < div id = "xrefFactory-def" > < a name = "L486" > < / a > < tt class = "py-lineno" > 486< / tt > < a class = "py-toggle" href = "#" id = "xrefFactory-toggle" onclick = "return toggle('xrefFactory');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#xrefFactory" > xrefFactory< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > string< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "xrefFactory-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "xrefFactory-expanded" > < a name = "L487" > < / a > < tt class = "py-lineno" > 487< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L488" > < / a > < tt class = "py-lineno" > 488< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Dispatcher of xrefs.< / tt > < / tt >
< a name = "L489" > < / a > < tt class = "py-lineno" > 489< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L490" > < / a > < tt class = "py-lineno" > 490< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param string: a string (between brackets) from an inherited TaggedValue object with a dbxrefs < / tt > < / tt >
< a name = "L491" > < / a > < tt class = "py-lineno" > 491< / tt > < tt class = "py-line" > < tt class = "py-docstring" > signal (actually, the signal can only be found into SynonymValue and DefValue < / tt > < / tt >
< a name = "L492" > < / a > < tt class = "py-lineno" > 492< / tt > < tt class = "py-line" > < tt class = "py-docstring" > objects) or a string (without brackets) from a XrefValue object.< / tt > < / tt >
< a name = "L493" > < / a > < tt class = "py-lineno" > 493< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type string: string< / tt > < / tt >
< a name = "L494" > < / a > < tt class = "py-lineno" > 494< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L495" > < / a > < tt class = "py-lineno" > 495< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @return: a class object< / tt > < / tt >
< a name = "L496" > < / a > < tt class = "py-lineno" > 496< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L497" > < / a > < tt class = "py-lineno" > 497< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The dispatcher treats differently the strings between brackets (from SynonymValue and < / tt > < / tt >
< a name = "L498" > < / a > < tt class = "py-lineno" > 498< / tt > < tt class = "py-line" > < tt class = "py-docstring" > DefValue objects) and without brackets (from XrefValue objects).< / tt > < / tt >
< a name = "L499" > < / a > < tt class = "py-lineno" > 499< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L500" > < / a > < tt class = "py-lineno" > 500< / tt > < tt class = "py-line" > < / tt >
< a name = "L501" > < / a > < tt class = "py-lineno" > 501< / tt > < tt class = "py-line" > < tt class = "py-name" > string< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L502" > < / a > < tt class = "py-lineno" > 502< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > '['< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< a name = "L503" > < / a > < tt class = "py-lineno" > 503< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-op" > [< / tt > < tt id = "link-101" class = "py-name" > < a title = "obitools.obo.parser.Xref" class = "py-name" href = "#" onclick = "return doclink('link-101', 'Xref', 'link-92');" > Xref< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > x< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > ','< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ]< / tt > < / tt >
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< a name = "L504" > < / a > < tt class = "py-lineno" > 504< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< a name = "L505" > < / a > < tt class = "py-lineno" > 505< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-102" class = "py-name" > < a title = "obitools.obo.parser.Xref" class = "py-name" href = "#" onclick = "return doclink('link-102', 'Xref', 'link-92');" > Xref< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > string< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< / div > < a name = "L506" > < / a > < tt class = "py-lineno" > 506< / tt > < tt class = "py-line" > < / tt >
< a name = "L507" > < / a > < tt class = "py-lineno" > 507< / tt > < tt class = "py-line" > < / tt >
< a name = "L508" > < / a > < tt class = "py-lineno" > 508< / tt > < tt class = "py-line" > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L509" > < / a > < tt class = "py-lineno" > 509< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > ## Stanza treatment area ##< / tt > < / tt >
< a name = "L510" > < / a > < tt class = "py-lineno" > 510< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-comment" > #################################################################################< / tt > < / tt >
< a name = "L511" > < / a > < tt class = "py-lineno" > 511< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < / tt >
< a name = "L512" > < / a > < tt class = "py-lineno" > 512< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOEntry" > < / a > < div id = "OBOEntry-def" > < a name = "L513" > < / a > < tt class = "py-lineno" > 513< / tt > < a class = "py-toggle" href = "#" id = "OBOEntry-toggle" onclick = "return toggle('OBOEntry');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOEntry-class.html" > OBOEntry< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > dict< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOEntry-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "OBOEntry-expanded" > < a name = "L514" > < / a > < tt class = "py-lineno" > 514< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L515" > < / a > < tt class = "py-lineno" > 515< / tt > < tt class = "py-line" > < tt class = "py-docstring" > An entry of an OBOFile. It can be a header (without a stanza name) or< / tt > < / tt >
< a name = "L516" > < / a > < tt class = "py-lineno" > 516< / tt > < tt class = "py-line" > < tt class = "py-docstring" > a stanza (with a stanza name between brackets). It inherits from the class dict.< / tt > < / tt >
< a name = "L517" > < / a > < tt class = "py-lineno" > 517< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
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< a name = "L518" > < / a > < tt class = "py-lineno" > 518< / tt > < tt class = "py-line" > < tt id = "link-103" class = "py-name" targets = "Variable obitools.obo.parser.OBOEntry._match_stanza_name=obitools.obo.parser.OBOEntry-class.html#_match_stanza_name" > < a title = "obitools.obo.parser.OBOEntry._match_stanza_name" class = "py-name" href = "#" onclick = "return doclink('link-103', '_match_stanza_name', 'link-103');" > _match_stanza_name< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > re< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > compile< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '(?< =^\[)[^\]]*(?=\])'< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L519" > < / a > < tt class = "py-lineno" > 519< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOEntry.__init__" > < / a > < div id = "OBOEntry.__init__-def" > < a name = "L520" > < / a > < tt class = "py-lineno" > 520< / tt > < a class = "py-toggle" href = "#" id = "OBOEntry.__init__-toggle" onclick = "return toggle('OBOEntry.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOEntry-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > stanza< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOEntry.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOEntry.__init__-expanded" > < a name = "L521" > < / a > < tt class = "py-lineno" > 521< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## tests if it is the header of the OBO file (returns TRUE) or not (returns FALSE)< / tt > < / tt >
< a name = "L522" > < / a > < tt class = "py-lineno" > 522< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > isHeader< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > !=< / tt > < tt class = "py-string" > '['< / tt > < / tt >
< a name = "L523" > < / a > < tt class = "py-lineno" > 523< / tt > < tt class = "py-line" > < tt class = "py-name" > lines< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > split< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > '\n'< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L524" > < / a > < tt class = "py-lineno" > 524< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## not the header : there is a [stanzaName]< / tt > < / tt >
< a name = "L525" > < / a > < tt class = "py-lineno" > 525< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > if< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > isHeader< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L526" > < / a > < tt class = "py-lineno" > 526< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > stanzaName< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > lines< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > strip< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-op" > -< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L527" > < / a > < tt class = "py-lineno" > 527< / tt > < tt class = "py-line" > < tt class = "py-name" > lines< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > lines< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > :< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L528" > < / a > < tt class = "py-lineno" > 528< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## whatever the stanza is. < / tt > < / tt >
< a name = "L529" > < / a > < tt class = "py-lineno" > 529< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > lines< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L530" > < / a > < tt class = "py-lineno" > 530< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## each line is a couple : tag / value< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L531" > < / a > < tt class = "py-lineno" > 531< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-104" class = "py-name" targets = "Function obitools.obo.parser.taggedValueFactory()=obitools.obo.parser-module.html#taggedValueFactory" > < a title = "obitools.obo.parser.taggedValueFactory" class = "py-name" href = "#" onclick = "return doclink('link-104', 'taggedValueFactory', 'link-104');" > taggedValueFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > line< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L532" > < / a > < tt class = "py-lineno" > 532< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L533" > < / a > < tt class = "py-lineno" > 533< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-105" class = "py-name" targets = "Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append" > < a title = "obitools.align.Alignement.append
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obitools.table.Table.append
obitools.table.TableRow.append
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obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-105', 'append', 'link-105');">append< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L534" > < / a > < tt class = "py-lineno" > 534< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L535" > < / a > < tt class = "py-lineno" > 535< / tt > < tt class = "py-line" > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > tag< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > =< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-name" > taggedvalue< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< / div > < a name = "L536" > < / a > < tt class = "py-lineno" > 536< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOEntry.parseStanzaName" > < / a > < div id = "OBOEntry.parseStanzaName-def" > < a name = "L537" > < / a > < tt class = "py-lineno" > 537< / tt > < a class = "py-toggle" href = "#" id = "OBOEntry.parseStanzaName-toggle" onclick = "return toggle('OBOEntry.parseStanzaName');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOEntry-class.html#parseStanzaName" > parseStanzaName< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > stanza< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOEntry.parseStanzaName-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOEntry.parseStanzaName-expanded" > < a name = "L538" > < / a > < tt class = "py-lineno" > 538< / tt > < tt class = "py-line" > < tt class = "py-name" > sm< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-106" class = "py-name" targets = "Class obitools.obo.parser.OBOEntry=obitools.obo.parser.OBOEntry-class.html" > < a title = "obitools.obo.parser.OBOEntry" class = "py-name" href = "#" onclick = "return doclink('link-106', 'OBOEntry', 'link-106');" > OBOEntry< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-107" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry._match_stanza_name" class = "py-name" href = "#" onclick = "return doclink('link-107', '_match_stanza_name', 'link-103');" > _match_stanza_name< / a > < / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > search< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L539" > < / a > < tt class = "py-lineno" > 539< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > sm< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L540" > < / a > < tt class = "py-lineno" > 540< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > sm< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > group< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L541" > < / a > < tt class = "py-lineno" > 541< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L542" > < / a > < tt class = "py-lineno" > 542< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < a name = "L543" > < / a > < tt class = "py-lineno" > 543< / tt > < tt class = "py-line" > < / tt >
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< a name = "L544" > < / a > < tt class = "py-lineno" > 544< / tt > < tt class = "py-line" > < tt id = "link-108" class = "py-name" targets = "Static Method obitools.obo.parser.OBOEntry.parseStanzaName()=obitools.obo.parser.OBOEntry-class.html#parseStanzaName" > < a title = "obitools.obo.parser.OBOEntry.parseStanzaName" class = "py-name" href = "#" onclick = "return doclink('link-108', 'parseStanzaName', 'link-108');" > parseStanzaName< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > staticmethod< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-109" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry.parseStanzaName" class = "py-name" href = "#" onclick = "return doclink('link-109', 'parseStanzaName', 'link-108');" > parseStanzaName< / a > < / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L545" > < / a > < tt class = "py-lineno" > 545< / tt > < tt class = "py-line" > < / tt >
< a name = "L546" > < / a > < tt class = "py-lineno" > 546< / tt > < tt class = "py-line" > < / tt >
< a name = "L547" > < / a > < tt class = "py-lineno" > 547< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm" > < / a > < div id = "OBOTerm-def" > < a name = "L548" > < / a > < tt class = "py-lineno" > 548< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm-toggle" onclick = "return toggle('OBOTerm');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > class< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html" > OBOTerm< / a > < tt class = "py-op" > (< / tt > < tt class = "py-base-class" > OBOEntry< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "OBOTerm-expanded" > < a name = "L549" > < / a > < tt class = "py-lineno" > 549< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L550" > < / a > < tt class = "py-lineno" > 550< / tt > < tt class = "py-line" > < tt class = "py-docstring" > A stanza named 'Term'. It inherits from the class OBOEntry.< / tt > < / tt >
< a name = "L551" > < / a > < tt class = "py-lineno" > 551< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "OBOTerm.__init__" > < / a > < div id = "OBOTerm.__init__-def" > < a name = "L552" > < / a > < tt class = "py-lineno" > 552< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm.__init__-toggle" onclick = "return toggle('OBOTerm.__init__');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#__init__" > __init__< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-param" > stanza< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm.__init__-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm.__init__-expanded" > < a name = "L553" > < / a > < tt class = "py-lineno" > 553< / tt > < tt class = "py-line" > < / tt >
< a name = "L554" > < / a > < tt class = "py-lineno" > 554< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## use of the OBOEntry constructor.< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L555" > < / a > < tt class = "py-lineno" > 555< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-110" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry" class = "py-name" href = "#" onclick = "return doclink('link-110', 'OBOEntry', 'link-106');" > OBOEntry< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-111" class = "py-name" > < a title = "obitools.BioSequence.__init__
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obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
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obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
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obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
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obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-111', '__init__', 'link-17');">__init__< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L556" > < / a > < tt class = "py-lineno" > 556< / tt > < tt class = "py-line" > < / tt >
< a name = "L557" > < / a > < tt class = "py-lineno" > 557< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt class = "py-name" > stanzaName< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'Term'< / tt > < / tt >
< a name = "L558" > < / a > < tt class = "py-lineno" > 558< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'id'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'id'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "An OBOTerm must have an id"< / tt > < / tt >
< a name = "L559" > < / a > < tt class = "py-lineno" > 559< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'name'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'name'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "An OBOTerm must have a name"< / tt > < / tt >
< a name = "L560" > < / a > < tt class = "py-lineno" > 560< / tt > < tt class = "py-line" > < / tt >
< a name = "L561" > < / a > < tt class = "py-lineno" > 561< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'def'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'def'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "Only one definition is allowed for an OBO term"< / tt > < / tt >
< a name = "L562" > < / a > < tt class = "py-lineno" > 562< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'comment'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'comment'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-number" > 1< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "Only one comment is allowed for an OBO term"< / tt > < / tt >
< a name = "L563" > < / a > < tt class = "py-lineno" > 563< / tt > < tt class = "py-line" > < / tt >
< a name = "L564" > < / a > < tt class = "py-lineno" > 564< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'union_of'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'union_of'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > > =< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "Only one union relationship is allowed for an OBO term"< / tt > < / tt >
< a name = "L565" > < / a > < tt class = "py-lineno" > 565< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'intersection_of'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > len< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'intersection_of'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > > =< / tt > < tt class = "py-number" > 2< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-string" > "Only one intersection relationship is allowed for an OBO term"< / tt > < / tt >
< a name = "L566" > < / a > < tt class = "py-lineno" > 566< / tt > < tt class = "py-line" > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L567" > < / a > < tt class = "py-lineno" > 567< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-112" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._isObsolete()=obitools.obo.parser.OBOTerm-class.html#_isObsolete" > < a title = "obitools.obo.parser.OBOTerm._isObsolete" class = "py-name" href = "#" onclick = "return doclink('link-112', '_isObsolete', 'link-112');" > _isObsolete< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< a name = "L568" > < / a > < tt class = "py-lineno" > 568< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'is_a'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L569" > < / a > < tt class = "py-lineno" > 569< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'relationship'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L570" > < / a > < tt class = "py-lineno" > 570< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'inverse_of'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L571" > < / a > < tt class = "py-lineno" > 571< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'disjoint_from'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L572" > < / a > < tt class = "py-lineno" > 572< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'union_of'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L573" > < / a > < tt class = "py-lineno" > 573< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'intersection_of'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < / tt >
< a name = "L574" > < / a > < tt class = "py-lineno" > 574< / tt > < tt class = "py-line" > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L575" > < / a > < tt class = "py-lineno" > 575< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'replace_by'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-113" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm._isObsolete" class = "py-name" href = "#" onclick = "return doclink('link-113', '_isObsolete', 'link-112');" > _isObsolete< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L576" > < / a > < tt class = "py-lineno" > 576< / tt > < tt class = "py-line" > < tt class = "py-keyword" > assert< / tt > < tt class = "py-string" > 'consider'< / tt > < tt class = "py-keyword" > not< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > or< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-114" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm._isObsolete" class = "py-name" href = "#" onclick = "return doclink('link-114', '_isObsolete', 'link-112');" > _isObsolete< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L577" > < / a > < tt class = "py-lineno" > 577< / tt > < tt class = "py-line" > < / tt >
< a name = "L578" > < / a > < tt class = "py-lineno" > 578< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## make-up functions. < / tt > < / tt >
< a name = "OBOTerm._getDefinition" > < / a > < div id = "OBOTerm._getDefinition-def" > < a name = "L579" > < / a > < tt class = "py-lineno" > 579< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getDefinition-toggle" onclick = "return toggle('OBOTerm._getDefinition');" > -< / a > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getDefinition" > _getDefinition< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getDefinition-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getDefinition-expanded" > < a name = "L580" > < / a > < tt class = "py-lineno" > 580< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-string" > 'def'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L581" > < / a > < tt class = "py-lineno" > 581< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'def'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L582" > < / a > < tt class = "py-lineno" > 582< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < a name = "L583" > < / a > < tt class = "py-lineno" > 583< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getId" > < / a > < div id = "OBOTerm._getId-def" > < a name = "L584" > < / a > < tt class = "py-lineno" > 584< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getId-toggle" onclick = "return toggle('OBOTerm._getId');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getId" > _getId< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getId-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getId-expanded" > < a name = "L585" > < / a > < tt class = "py-lineno" > 585< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'id'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< / div > < a name = "L586" > < / a > < tt class = "py-lineno" > 586< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getName" > < / a > < div id = "OBOTerm._getName-def" > < a name = "L587" > < / a > < tt class = "py-lineno" > 587< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getName-toggle" onclick = "return toggle('OBOTerm._getName');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getName" > _getName< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getName-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getName-expanded" > < a name = "L588" > < / a > < tt class = "py-lineno" > 588< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'name'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< / div > < a name = "L589" > < / a > < tt class = "py-lineno" > 589< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getComment" > < / a > < div id = "OBOTerm._getComment-def" > < a name = "L590" > < / a > < tt class = "py-lineno" > 590< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getComment-toggle" onclick = "return toggle('OBOTerm._getComment');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getComment" > _getComment< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getComment-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getComment-expanded" > < a name = "L591" > < / a > < tt class = "py-lineno" > 591< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-string" > 'comment'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L592" > < / a > < tt class = "py-lineno" > 592< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'comment'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < / tt >
< a name = "L593" > < / a > < tt class = "py-lineno" > 593< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < a name = "L594" > < / a > < tt class = "py-lineno" > 594< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getAltIds" > < / a > < div id = "OBOTerm._getAltIds-def" > < a name = "L595" > < / a > < tt class = "py-lineno" > 595< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getAltIds-toggle" onclick = "return toggle('OBOTerm._getAltIds');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getAltIds" > _getAltIds< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getAltIds-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getAltIds-expanded" > < a name = "L596" > < / a > < tt class = "py-lineno" > 596< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-string" > 'alt_id'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L597" > < / a > < tt class = "py-lineno" > 597< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-115" class = "py-name" targets = "Method obitools.eutils.EFetch.get()=obitools.eutils.EFetch-class.html#get" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-115', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'alt_id'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L598" > < / a > < tt class = "py-lineno" > 598< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < a name = "L599" > < / a > < tt class = "py-lineno" > 599< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getIsA" > < / a > < div id = "OBOTerm._getIsA-def" > < a name = "L600" > < / a > < tt class = "py-lineno" > 600< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getIsA-toggle" onclick = "return toggle('OBOTerm._getIsA');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getIsA" > _getIsA< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getIsA-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getIsA-expanded" > < a name = "L601" > < / a > < tt class = "py-lineno" > 601< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-116" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-116', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'is_a'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L602" > < / a > < tt class = "py-lineno" > 602< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getSynonym" > < / a > < div id = "OBOTerm._getSynonym-def" > < a name = "L603" > < / a > < tt class = "py-lineno" > 603< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getSynonym-toggle" onclick = "return toggle('OBOTerm._getSynonym');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getSynonym" > _getSynonym< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._getSynonym-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getSynonym-expanded" > < a name = "L604" > < / a > < tt class = "py-lineno" > 604< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-string" > 'synonym'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L605" > < / a > < tt class = "py-lineno" > 605< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-117" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-117', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'synonym'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< a name = "L606" > < / a > < tt class = "py-lineno" > 606< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > None< / tt > < / tt >
< / div > < a name = "L607" > < / a > < tt class = "py-lineno" > 607< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getSubset" > < / a > < div id = "OBOTerm._getSubset-def" > < a name = "L608" > < / a > < tt class = "py-lineno" > 608< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getSubset-toggle" onclick = "return toggle('OBOTerm._getSubset');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getSubset" > _getSubset< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getSubset-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getSubset-expanded" > < a name = "L609" > < / a > < tt class = "py-lineno" > 609< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-118" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-118', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'subset'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L610" > < / a > < tt class = "py-lineno" > 610< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getXref" > < / a > < div id = "OBOTerm._getXref-def" > < a name = "L611" > < / a > < tt class = "py-lineno" > 611< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getXref-toggle" onclick = "return toggle('OBOTerm._getXref');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getXref" > _getXref< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getXref-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getXref-expanded" > < a name = "L612" > < / a > < tt class = "py-lineno" > 612< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-119" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-119', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'xref'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L613" > < / a > < tt class = "py-lineno" > 613< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getUnion" > < / a > < div id = "OBOTerm._getUnion-def" > < a name = "L614" > < / a > < tt class = "py-lineno" > 614< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getUnion-toggle" onclick = "return toggle('OBOTerm._getUnion');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getUnion" > _getUnion< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getUnion-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getUnion-expanded" > < a name = "L615" > < / a > < tt class = "py-lineno" > 615< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-120" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-120', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'union_of'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L616" > < / a > < tt class = "py-lineno" > 616< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getIntersection" > < / a > < div id = "OBOTerm._getIntersection-def" > < a name = "L617" > < / a > < tt class = "py-lineno" > 617< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getIntersection-toggle" onclick = "return toggle('OBOTerm._getIntersection');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getIntersection" > _getIntersection< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getIntersection-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getIntersection-expanded" > < a name = "L618" > < / a > < tt class = "py-lineno" > 618< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-121" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-121', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'intersection_of'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L619" > < / a > < tt class = "py-lineno" > 619< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getDisjonction" > < / a > < div id = "OBOTerm._getDisjonction-def" > < a name = "L620" > < / a > < tt class = "py-lineno" > 620< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getDisjonction-toggle" onclick = "return toggle('OBOTerm._getDisjonction');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getDisjonction" > _getDisjonction< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getDisjonction-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getDisjonction-expanded" > < a name = "L621" > < / a > < tt class = "py-lineno" > 621< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-122" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-122', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'disjoint_from'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L622" > < / a > < tt class = "py-lineno" > 622< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._isObsolete" > < / a > < div id = "OBOTerm._isObsolete-def" > < a name = "L623" > < / a > < tt class = "py-lineno" > 623< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._isObsolete-toggle" onclick = "return toggle('OBOTerm._isObsolete');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_isObsolete" > _isObsolete< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOTerm._isObsolete-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._isObsolete-expanded" > < a name = "L624" > < / a > < tt class = "py-lineno" > 624< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-string" > 'is_obsolete'< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-keyword" > and< / tt > < tt class = "py-name" > str< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-string" > 'is_obsolete'< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > [< / tt > < tt class = "py-number" > 0< / tt > < tt class = "py-op" > ]< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > 'true'< / tt > < / tt >
< / div > < a name = "L625" > < / a > < tt class = "py-lineno" > 625< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getReplaceBy" > < / a > < div id = "OBOTerm._getReplaceBy-def" > < a name = "L626" > < / a > < tt class = "py-lineno" > 626< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getReplaceBy-toggle" onclick = "return toggle('OBOTerm._getReplaceBy');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getReplaceBy" > _getReplaceBy< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getReplaceBy-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getReplaceBy-expanded" > < a name = "L627" > < / a > < tt class = "py-lineno" > 627< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-123" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-123', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'replace_by'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L628" > < / a > < tt class = "py-lineno" > 628< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOTerm._getConsider" > < / a > < div id = "OBOTerm._getConsider-def" > < a name = "L629" > < / a > < tt class = "py-lineno" > 629< / tt > < a class = "py-toggle" href = "#" id = "OBOTerm._getConsider-toggle" onclick = "return toggle('OBOTerm._getConsider');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser.OBOTerm-class.html#_getConsider" > _getConsider< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > self< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< / div > < div id = "OBOTerm._getConsider-collapsed" style = "display:none;" pad = "+++" indent = "++++++++" > < / div > < div id = "OBOTerm._getConsider-expanded" > < a name = "L630" > < / a > < tt class = "py-lineno" > 630< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt class = "py-name" > list< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > set< / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > self< / tt > < tt class = "py-op" > .< / tt > < tt id = "link-124" class = "py-name" > < a title = "obitools.eutils.EFetch.get" class = "py-name" href = "#" onclick = "return doclink('link-124', 'get', 'link-115');" > get< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-string" > 'consider'< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > )< / tt > < / tt >
2008-04-15 16:58:36 +00:00
< / div > < a name = "L631" > < / a > < tt class = "py-lineno" > 631< / tt > < tt class = "py-line" > < / tt >
< a name = "L632" > < / a > < tt class = "py-lineno" > 632< / tt > < tt class = "py-line" > < tt class = "py-comment" > ## automatically make-up !< / tt > < / tt >
2008-04-29 11:07:08 +00:00
< a name = "L633" > < / a > < tt class = "py-lineno" > 633< / tt > < tt class = "py-line" > < tt class = "py-comment" > < / tt > < tt id = "link-125" class = "py-name" > < a title = "obitools.BioSequence.definition
2008-04-15 16:58:36 +00:00
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
2008-04-29 11:07:08 +00:00
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-125', 'definition', 'link-41');">definition< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-126" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getDefinition()=obitools.obo.parser.OBOTerm-class.html#_getDefinition" > < a title = "obitools.obo.parser.OBOTerm._getDefinition" class = "py-name" href = "#" onclick = "return doclink('link-126', '_getDefinition', 'link-126');" > _getDefinition< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L634" > < / a > < tt class = "py-lineno" > 634< / tt > < tt class = "py-line" > < tt id = "link-127" class = "py-name" targets = "Variable obitools.BioSequence.id=obitools.BioSequence-class.html#id,Variable obitools.cns.quality.QualitySequence.id=obitools.cns.quality.QualitySequence-class.html#id,Variable obitools.obo.parser.OBOTerm.id=obitools.obo.parser.OBOTerm-class.html#id" > < a title = "obitools.BioSequence.id
2008-04-15 16:58:36 +00:00
obitools.cns.quality.QualitySequence.id
2008-04-29 11:07:08 +00:00
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-127', 'id', 'link-127');">id< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-128" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getId()=obitools.obo.parser.OBOTerm-class.html#_getId" > < a title = "obitools.obo.parser.OBOTerm._getId" class = "py-name" href = "#" onclick = "return doclink('link-128', '_getId', 'link-128');" > _getId< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L635" > < / a > < tt class = "py-lineno" > 635< / tt > < tt class = "py-line" > < tt id = "link-129" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.name=obitools.obo.parser.OBOTerm-class.html#name" > < a title = "obitools.obo.parser.OBOTerm.name" class = "py-name" href = "#" onclick = "return doclink('link-129', 'name', 'link-129');" > name< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-130" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getName()=obitools.obo.parser.OBOTerm-class.html#_getName" > < a title = "obitools.obo.parser.OBOTerm._getName" class = "py-name" href = "#" onclick = "return doclink('link-130', '_getName', 'link-130');" > _getName< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L636" > < / a > < tt class = "py-lineno" > 636< / tt > < tt class = "py-line" > < tt id = "link-131" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm.comment
obitools.zipfile.ZipInfo.comment" class="py-name" href="#" onclick="return doclink('link-131', 'comment', 'link-23');">comment< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-132" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getComment()=obitools.obo.parser.OBOTerm-class.html#_getComment" > < a title = "obitools.obo.parser.OBOTerm._getComment" class = "py-name" href = "#" onclick = "return doclink('link-132', '_getComment', 'link-132');" > _getComment< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L637" > < / a > < tt class = "py-lineno" > 637< / tt > < tt class = "py-line" > < tt id = "link-133" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.alt_ids=obitools.obo.parser.OBOTerm-class.html#alt_ids" > < a title = "obitools.obo.parser.OBOTerm.alt_ids" class = "py-name" href = "#" onclick = "return doclink('link-133', 'alt_ids', 'link-133');" > alt_ids< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-134" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getAltIds()=obitools.obo.parser.OBOTerm-class.html#_getAltIds" > < a title = "obitools.obo.parser.OBOTerm._getAltIds" class = "py-name" href = "#" onclick = "return doclink('link-134', '_getAltIds', 'link-134');" > _getAltIds< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L638" > < / a > < tt class = "py-lineno" > 638< / tt > < tt class = "py-line" > < tt id = "link-135" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.is_a=obitools.obo.parser.OBOTerm-class.html#is_a" > < a title = "obitools.obo.parser.OBOTerm.is_a" class = "py-name" href = "#" onclick = "return doclink('link-135', 'is_a', 'link-135');" > is_a< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-136" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getIsA()=obitools.obo.parser.OBOTerm-class.html#_getIsA" > < a title = "obitools.obo.parser.OBOTerm._getIsA" class = "py-name" href = "#" onclick = "return doclink('link-136', '_getIsA', 'link-136');" > _getIsA< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L639" > < / a > < tt class = "py-lineno" > 639< / tt > < tt class = "py-line" > < tt id = "link-137" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.synonyms=obitools.obo.parser.OBOTerm-class.html#synonyms" > < a title = "obitools.obo.parser.OBOTerm.synonyms" class = "py-name" href = "#" onclick = "return doclink('link-137', 'synonyms', 'link-137');" > synonyms< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-138" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getSynonym()=obitools.obo.parser.OBOTerm-class.html#_getSynonym" > < a title = "obitools.obo.parser.OBOTerm._getSynonym" class = "py-name" href = "#" onclick = "return doclink('link-138', '_getSynonym', 'link-138');" > _getSynonym< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L640" > < / a > < tt class = "py-lineno" > 640< / tt > < tt class = "py-line" > < tt id = "link-139" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.subsets=obitools.obo.parser.OBOTerm-class.html#subsets" > < a title = "obitools.obo.parser.OBOTerm.subsets" class = "py-name" href = "#" onclick = "return doclink('link-139', 'subsets', 'link-139');" > subsets< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-140" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getSubset()=obitools.obo.parser.OBOTerm-class.html#_getSubset" > < a title = "obitools.obo.parser.OBOTerm._getSubset" class = "py-name" href = "#" onclick = "return doclink('link-140', '_getSubset', 'link-140');" > _getSubset< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L641" > < / a > < tt class = "py-lineno" > 641< / tt > < tt class = "py-line" > < tt id = "link-141" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.xrefs=obitools.obo.parser.OBOTerm-class.html#xrefs" > < a title = "obitools.obo.parser.OBOTerm.xrefs" class = "py-name" href = "#" onclick = "return doclink('link-141', 'xrefs', 'link-141');" > xrefs< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-142" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getXref()=obitools.obo.parser.OBOTerm-class.html#_getXref" > < a title = "obitools.obo.parser.OBOTerm._getXref" class = "py-name" href = "#" onclick = "return doclink('link-142', '_getXref', 'link-142');" > _getXref< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L642" > < / a > < tt class = "py-lineno" > 642< / tt > < tt class = "py-line" > < tt id = "link-143" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.union_of=obitools.obo.parser.OBOTerm-class.html#union_of" > < a title = "obitools.obo.parser.OBOTerm.union_of" class = "py-name" href = "#" onclick = "return doclink('link-143', 'union_of', 'link-143');" > union_of< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-144" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getUnion()=obitools.obo.parser.OBOTerm-class.html#_getUnion" > < a title = "obitools.obo.parser.OBOTerm._getUnion" class = "py-name" href = "#" onclick = "return doclink('link-144', '_getUnion', 'link-144');" > _getUnion< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L643" > < / a > < tt class = "py-lineno" > 643< / tt > < tt class = "py-line" > < tt id = "link-145" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.intersection_of=obitools.obo.parser.OBOTerm-class.html#intersection_of" > < a title = "obitools.obo.parser.OBOTerm.intersection_of" class = "py-name" href = "#" onclick = "return doclink('link-145', 'intersection_of', 'link-145');" > intersection_of< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-146" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getIntersection()=obitools.obo.parser.OBOTerm-class.html#_getIntersection" > < a title = "obitools.obo.parser.OBOTerm._getIntersection" class = "py-name" href = "#" onclick = "return doclink('link-146', '_getIntersection', 'link-146');" > _getIntersection< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L644" > < / a > < tt class = "py-lineno" > 644< / tt > < tt class = "py-line" > < tt id = "link-147" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.disjoint_from=obitools.obo.parser.OBOTerm-class.html#disjoint_from" > < a title = "obitools.obo.parser.OBOTerm.disjoint_from" class = "py-name" href = "#" onclick = "return doclink('link-147', 'disjoint_from', 'link-147');" > disjoint_from< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-148" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getDisjonction()=obitools.obo.parser.OBOTerm-class.html#_getDisjonction" > < a title = "obitools.obo.parser.OBOTerm._getDisjonction" class = "py-name" href = "#" onclick = "return doclink('link-148', '_getDisjonction', 'link-148');" > _getDisjonction< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L645" > < / a > < tt class = "py-lineno" > 645< / tt > < tt class = "py-line" > < tt id = "link-149" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.is_obsolete=obitools.obo.parser.OBOTerm-class.html#is_obsolete" > < a title = "obitools.obo.parser.OBOTerm.is_obsolete" class = "py-name" href = "#" onclick = "return doclink('link-149', 'is_obsolete', 'link-149');" > is_obsolete< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-150" class = "py-name" > < a title = "obitools.obo.parser.OBOTerm._isObsolete" class = "py-name" href = "#" onclick = "return doclink('link-150', '_isObsolete', 'link-112');" > _isObsolete< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L646" > < / a > < tt class = "py-lineno" > 646< / tt > < tt class = "py-line" > < tt id = "link-151" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.replace_by=obitools.obo.parser.OBOTerm-class.html#replace_by" > < a title = "obitools.obo.parser.OBOTerm.replace_by" class = "py-name" href = "#" onclick = "return doclink('link-151', 'replace_by', 'link-151');" > replace_by< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-152" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getReplaceBy()=obitools.obo.parser.OBOTerm-class.html#_getReplaceBy" > < a title = "obitools.obo.parser.OBOTerm._getReplaceBy" class = "py-name" href = "#" onclick = "return doclink('link-152', '_getReplaceBy', 'link-152');" > _getReplaceBy< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
< a name = "L647" > < / a > < tt class = "py-lineno" > 647< / tt > < tt class = "py-line" > < tt id = "link-153" class = "py-name" targets = "Variable obitools.obo.parser.OBOTerm.consider=obitools.obo.parser.OBOTerm-class.html#consider" > < a title = "obitools.obo.parser.OBOTerm.consider" class = "py-name" href = "#" onclick = "return doclink('link-153', 'consider', 'link-153');" > consider< / a > < / tt > < tt class = "py-op" > =< / tt > < tt class = "py-name" > property< / tt > < tt class = "py-op" > (< / tt > < tt id = "link-154" class = "py-name" targets = "Method obitools.obo.parser.OBOTerm._getConsider()=obitools.obo.parser.OBOTerm-class.html#_getConsider" > < a title = "obitools.obo.parser.OBOTerm._getConsider" class = "py-name" href = "#" onclick = "return doclink('link-154', '_getConsider', 'link-154');" > _getConsider< / a > < / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > ,< / tt > < tt class = "py-name" > None< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< / div > < a name = "L648" > < / a > < tt class = "py-lineno" > 648< / tt > < tt class = "py-line" > < / tt >
< a name = "L649" > < / a > < tt class = "py-lineno" > 649< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOEntryFactory" > < / a > < div id = "OBOEntryFactory-def" > < a name = "L650" > < / a > < tt class = "py-lineno" > 650< / tt > < a class = "py-toggle" href = "#" id = "OBOEntryFactory-toggle" onclick = "return toggle('OBOEntryFactory');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#OBOEntryFactory" > OBOEntryFactory< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > stanza< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
< / div > < div id = "OBOEntryFactory-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "OBOEntryFactory-expanded" > < a name = "L651" > < / a > < tt class = "py-lineno" > 651< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L652" > < / a > < tt class = "py-lineno" > 652< / tt > < tt class = "py-line" > < tt class = "py-docstring" > Dispatcher of stanza.< / tt > < / tt >
< a name = "L653" > < / a > < tt class = "py-lineno" > 653< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L654" > < / a > < tt class = "py-lineno" > 654< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @param stanza: a stanza composed of several lines.< / tt > < / tt >
< a name = "L655" > < / a > < tt class = "py-lineno" > 655< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @type stanza: text< / tt > < / tt >
< a name = "L656" > < / a > < tt class = "py-lineno" > 656< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L657" > < / a > < tt class = "py-lineno" > 657< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @return: an C{OBOTerm} | C{OBOEntry} instance< / tt > < / tt >
< a name = "L658" > < / a > < tt class = "py-lineno" > 658< / tt > < tt class = "py-line" > < tt class = "py-docstring" > < / tt > < / tt >
< a name = "L659" > < / a > < tt class = "py-lineno" > 659< / tt > < tt class = "py-line" > < tt class = "py-docstring" > @note: The dispatcher treats differently the stanza which are OBO "Term"< / tt > < / tt >
< a name = "L660" > < / a > < tt class = "py-lineno" > 660< / tt > < tt class = "py-line" > < tt class = "py-docstring" > and the others.< / tt > < / tt >
< a name = "L661" > < / a > < tt class = "py-lineno" > 661< / tt > < tt class = "py-line" > < tt class = "py-docstring" > '''< / tt > < / tt >
< a name = "L662" > < / a > < tt class = "py-lineno" > 662< / tt > < tt class = "py-line" > < / tt >
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< a name = "L663" > < / a > < tt class = "py-lineno" > 663< / tt > < tt class = "py-line" > < tt class = "py-name" > stanzaType< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-155" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry" class = "py-name" href = "#" onclick = "return doclink('link-155', 'OBOEntry', 'link-106');" > OBOEntry< / a > < / tt > < tt class = "py-op" > .< / tt > < tt id = "link-156" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry.parseStanzaName" class = "py-name" href = "#" onclick = "return doclink('link-156', 'parseStanzaName', 'link-108');" > parseStanzaName< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L664" > < / a > < tt class = "py-lineno" > 664< / tt > < tt class = "py-line" > < / tt >
< a name = "L665" > < / a > < tt class = "py-lineno" > 665< / tt > < tt class = "py-line" > < tt class = "py-keyword" > if< / tt > < tt class = "py-name" > stanzaType< / tt > < tt class = "py-op" > ==< / tt > < tt class = "py-string" > "Term"< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< a name = "L666" > < / a > < tt class = "py-lineno" > 666< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-157" class = "py-name" targets = "Class obitools.obo.parser.OBOTerm=obitools.obo.parser.OBOTerm-class.html" > < a title = "obitools.obo.parser.OBOTerm" class = "py-name" href = "#" onclick = "return doclink('link-157', 'OBOTerm', 'link-157');" > OBOTerm< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L667" > < / a > < tt class = "py-lineno" > 667< / tt > < tt class = "py-line" > < tt class = "py-keyword" > else< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< a name = "L668" > < / a > < tt class = "py-lineno" > 668< / tt > < tt class = "py-line" > < tt class = "py-keyword" > return< / tt > < tt id = "link-158" class = "py-name" > < a title = "obitools.obo.parser.OBOEntry" class = "py-name" href = "#" onclick = "return doclink('link-158', 'OBOEntry', 'link-106');" > OBOEntry< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > stanza< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< / div > < a name = "L669" > < / a > < tt class = "py-lineno" > 669< / tt > < tt class = "py-line" > < / tt >
< a name = "OBOEntryIterator" > < / a > < div id = "OBOEntryIterator-def" > < a name = "L670" > < / a > < tt class = "py-lineno" > 670< / tt > < a class = "py-toggle" href = "#" id = "OBOEntryIterator-toggle" onclick = "return toggle('OBOEntryIterator');" > -< / a > < tt class = "py-line" > < tt class = "py-keyword" > def< / tt > < a class = "py-def-name" href = "obitools.obo.parser-module.html#OBOEntryIterator" > OBOEntryIterator< / a > < tt class = "py-op" > (< / tt > < tt class = "py-param" > file< / tt > < tt class = "py-op" > )< / tt > < tt class = "py-op" > :< / tt > < / tt >
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< / div > < div id = "OBOEntryIterator-collapsed" style = "display:none;" pad = "+++" indent = "++++" > < / div > < div id = "OBOEntryIterator-expanded" > < a name = "L671" > < / a > < tt class = "py-lineno" > 671< / tt > < tt class = "py-line" > < tt class = "py-name" > entries< / tt > < tt class = "py-op" > =< / tt > < tt id = "link-159" class = "py-name" targets = "Function obitools.obo.parser.stanzaIterator()=obitools.obo.parser-module.html#stanzaIterator" > < a title = "obitools.obo.parser.stanzaIterator" class = "py-name" href = "#" onclick = "return doclink('link-159', 'stanzaIterator', 'link-159');" > stanzaIterator< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > file< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< a name = "L672" > < / a > < tt class = "py-lineno" > 672< / tt > < tt class = "py-line" > < tt class = "py-keyword" > for< / tt > < tt class = "py-name" > e< / tt > < tt class = "py-keyword" > in< / tt > < tt class = "py-name" > entries< / tt > < tt class = "py-op" > :< / tt > < / tt >
< a name = "L673" > < / a > < tt class = "py-lineno" > 673< / tt > < tt class = "py-line" > < tt class = "py-keyword" > print< / tt > < tt class = "py-name" > e< / tt > < / tt >
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< a name = "L674" > < / a > < tt class = "py-lineno" > 674< / tt > < tt class = "py-line" > < tt class = "py-keyword" > yield< / tt > < tt id = "link-160" class = "py-name" targets = "Function obitools.obo.parser.OBOEntryFactory()=obitools.obo.parser-module.html#OBOEntryFactory" > < a title = "obitools.obo.parser.OBOEntryFactory" class = "py-name" href = "#" onclick = "return doclink('link-160', 'OBOEntryFactory', 'link-160');" > OBOEntryFactory< / a > < / tt > < tt class = "py-op" > (< / tt > < tt class = "py-name" > e< / tt > < tt class = "py-op" > )< / tt > < / tt >
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< / div > < a name = "L675" > < / a > < tt class = "py-lineno" > 675< / tt > < tt class = "py-line" > < / tt > < script type = "text/javascript" >
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