diff --git a/doc/source/formats.rst b/doc/source/formats.rst index 37c459b..61e6ddf 100644 --- a/doc/source/formats.rst +++ b/doc/source/formats.rst @@ -4,23 +4,23 @@ Formats ********************************************* -The Obitools3 Data Management System (ObiDMS) +The OBItools3 Data Management System (OBIDMS) ********************************************* -An ObiDMS directory consists of : - * ObiDMS column files - * an ObiDMS history file +An OBIDMS directory consists of : + * OBIDMS column files + * an OBIDMS history file -ObiDMS column files +OBIDMS column files =================== -Each ObiDMS column file contains : +Each OBIDMS column file contains : * a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes on most systems) containing metadata * one column of data of the same type -ObiDMS column files are read-only. +OBIDMS column files are read-only. File name @@ -38,7 +38,7 @@ Example : ``count_0003`` Header ------ -The header of an ObiDMS column contains : +The header of an OBIDMS column contains : * Endian byte order * PAGESIZE value / Size of the header @@ -59,7 +59,7 @@ A column of data of the same type. Versioning ---------- -Since ObiDMS column files are read-only, any modification leads to the creation of a new version +Since OBIDMS column files are read-only, any modification leads to the creation of a new version of the column file. The first version of a column file is numbered 0001, and each new version increments that @@ -69,20 +69,27 @@ number by 1. Mandatory columns ----------------- -Some columns must exist in an ObiDMS directory : +Some columns must exist in an OBIDMS directory : * sequence identifiers column -ObiDMS history file +OBIDMS history file =================== -An ObiDMS history file consists of data that can be represented in the form of a directed acyclic -graph presenting the history of all the operations ever done in the ObiDMS directory. +An OBIDMS history file consists of data that can be represented in the form of a directed acyclic +graph presenting the history of all the operations ever done in the OBIDMS directory. -ObiDMS views +OBIDMS views ============ -An ObiDMS view corresponds to a list of ObiDMS columns and lines. A view includes one version +An OBIDMS view corresponds to a list of OBIDMS columns and lines. A view includes one version of each mandatory column. Only one version of each column is included. All the columns of one view contain the same number of lines in the same order. + + +OBIIntColumn header file +======================== + +.. doxygenfile:: obiintcolumn.h + diff --git a/doc/source/guidelines.rst b/doc/source/guidelines.rst index 0c61e04..253bb9f 100644 --- a/doc/source/guidelines.rst +++ b/doc/source/guidelines.rst @@ -79,7 +79,7 @@ Programming languages ********************* C99 : - * All the low-level input/output functions (e.g. all the `ObiDMS `_ functions) + * All the low-level input/output functions (e.g. all the `OBIDMS `_ functions) * Computing-intensive code (e.g. alignment or pattern matching) `Cython `_ : diff --git a/doc/source/index.rst b/doc/source/index.rst index 7dd81b8..17a0050 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -13,7 +13,6 @@ OBITools3 documentation Formats - Indices and tables ------------------