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new version of the documentation with a part generated using doxygen and

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breathe
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Celine Mercier
2015-05-11 17:20:59 +02:00
parent 428431932f
commit 476f30659d
3 changed files with 23 additions and 17 deletions
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37
doc/source/formats.rst
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@ -4,23 +4,23 @@ Formats
********************************************* *********************************************
The Obitools3 Data Management System (ObiDMS) The OBItools3 Data Management System (OBIDMS)
********************************************* *********************************************
An ObiDMS directory consists of : An OBIDMS directory consists of :
* ObiDMS column files * OBIDMS column files
* an ObiDMS history file * 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 * a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
on most systems) containing metadata on most systems) containing metadata
* one column of data of the same type * one column of data of the same type
ObiDMS column files are read-only. OBIDMS column files are read-only.
File name File name
@ -38,7 +38,7 @@ Example : ``count_0003``
Header Header
------ ------
The header of an ObiDMS column contains : The header of an OBIDMS column contains :
* Endian byte order * Endian byte order
* PAGESIZE value / Size of the header * PAGESIZE value / Size of the header
@ -59,7 +59,7 @@ A column of data of the same type.
Versioning 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. of the column file.
The first version of a column file is numbered 0001, and each new version increments that 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 Mandatory columns
----------------- -----------------
Some columns must exist in an ObiDMS directory : Some columns must exist in an OBIDMS directory :
* sequence identifiers column * 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 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. 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 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. one view contain the same number of lines in the same order.
OBIIntColumn header file
========================
.. doxygenfile:: obiintcolumn.h

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doc/source/guidelines.rst
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@ -79,7 +79,7 @@ Programming languages
********************* *********************
C99 : C99 :
* All the low-level input/output functions (e.g. all the `ObiDMS <formats.html#the-obitools3-data-management-system-obidms>`_ functions) * All the low-level input/output functions (e.g. all the `OBIDMS <formats.html#the-obitools3-data-management-system-obidms>`_ functions)
* Computing-intensive code (e.g. alignment or pattern matching) * Computing-intensive code (e.g. alignment or pattern matching)
`Cython <cython.org>`_ : `Cython <cython.org>`_ :

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doc/source/index.rst
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@ -13,7 +13,6 @@ OBITools3 documentation
Formats <formats> Formats <formats>
Indices and tables Indices and tables
------------------ ------------------