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Qian Zhu committed 5f4f7b1

Partial docs for Seek tools

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tools/DBCombiner/stdafx.cpp

 /*!
  * \page DBCombiner DBCombiner
  * 
+ * Combines a set of DB files generated from different Sleipnir::CDatabase's
+ * into one DB file. 
+ *
+ * Perhaps for space reason, it is sometime not feasible to generate a Sleipnir::CDatabase
+ * covering all datasets on one machine or one partition. Consequently, people
+ * generate separate Sleipnir::CDatabase's on different machines
+ * first, and then join them one DB file at a time with DBCombiner.
+ *
  * 
  * \section sec_usage Usage
  * 
  * \code
  * DBCombiner -i <genes.txt> -x <db_list.txt> -d <input_dir> -D <output_dir> [-s]
  * \endcode
- * Combines multiple \c .db files listed in the \c db_list.txt into one \c .db file.
- * Perhaps for space reason, it is sometime not feasible to generate the CDatabase 
- * covering all datasets on one machine or one partition. Consequently, people 
- * generate separate CDatabases on different machines
- * first, and then join them one .db file at a time with DBCombiner.
- * Thus DBCombiner accepts CDatabase's that are generated separately. In order for
- * DBCombiner to work, only the \c db files covering the same genes may be
+ *
+ * Combines the DB files listed in the \c db_list.txt into one DB.
+ *
+ * DBCombiner accepts multiple Sleipnir::CDatabase's that are generated separately. In order for
+ * DBCombiner to work, only DB files covering the same genes may be
  * combined. 
- * The resulted \c .db file will cover datasets in the same order as the order of 
- * DB files in \c db_list.txt.
- * The \c -s option performs a splitting after the combining is done. 
- * It splits the combined CDatabaselet to one gene per \c .db file. 
- * This is required for SeekMiner, SeekServer.
+ * The order of DB files in \c db_list.txt is the the order that datasets
+ * will be covered in the combined file.
+ *
+ * The \c -s option further splits the combined Sleipnir::CDatabaselet into one gene per \c DB file.
+ * This \c -s must be enabled for Seek coexpression integrations. (\ref SeekMiner, \ref SeekServer).
  * 
  * Sample lines from the \c genes.txt file:
  * \code
  * /x/y/database2/00000004.db
  * /x/y/database3/00000004.db
  * \endcode
- * Note that \c database1, \c database2, \c database3 are three CDatabase's 
+ * Note that \c database1, \c database2, \c database3 are three Sleipnir::CDatabase's
  * generated for different datasets.
- * Note how we use the same ID 00000004 to ensure the \c db files cover
+ *
+ * Note how we use the same ID \c 00000004 to ensure that the DB files cover
  * the same genes.
+ *
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
  *	<td>-d</td>
  *	<td>None</td>
  *	<td>Directory</td>
- *	<td>Input directory containing DB files</td>
+ *	<td>Input directory containing \c *.db files</td>
  * </tr><tr>
  *	<td>-D</td>
  *	<td>None</td>
  *	<td>-x</td>
  *	<td>None</td>
  *	<td>Text file</td>
- *	<td>Input file containing a list of CDatabaselets to combine</td>
+ *	<td>Input file containing a list of Sleipnir::CDatabaselet's to combine</td>
  * </tr><tr>
  *	<td>-s</td>
  *	<td>None</td>
  *	<td>off</td>
- *	<td>If enabled, split the combined CDatabaselet to one gene per .db file</td>
+ *	<td>If enabled, split the combined Sleipnir::CDatabaselet to one gene per \c DB file</td>
  * </tr></table>
  */

tools/Data2DB/stdafx.cpp

  * Data2DB converts a collection of DAT/DAB files (Sleipnir::CDat) into a simple flatfile database
  * (Sleipnir::CDatabase).  DAT/DAB files organize data so that values for all gene pairs within a single
  * dataset can be accessed efficiently; database files organize data so that values from all datasets for
- * a single gene or gene pair can be accessed efficiently.  This is critical for real-time Bayesian inference and for Seek coexpression search
- * (e.g. by \ref BNServer, \ref SeekMiner, \ref SeekServer).
+ * a single gene or gene pair can be accessed efficiently.  This is critical for real-time Bayesian inference (e.g., by \ref BNServer) and for Seek coexpression search
+ * (e.g. by \ref SeekMiner, \ref SeekServer).
  * 
  * \section sec_usage Usage
  * 
  * \endcode
  * Construct a Sleipnir::CDatabase containing the data from DAB files that 
  * are specified in the \c dataset_file_list.txt. The genes are indexed according
- * to \c gene_map.txt. By default, there would be 1000 CDatabaselet's (\c .db) 
- * generated, with each CDatabaselet containing \a N / 1000 genes. Users can control
- * how many \c .db files to be generated (and indirectly how many genes 
- * are contained in each \c .db file) using the \c -f option.
+ * to \c gene_map.txt. By default, there would be 1000 Sleipnir::CDatabaselet's (DB files)
+ * generated, with each containing \a N / 1000 genes. Users can control
+ * the number of generated DB files (and indirectly the number of genes contained in each DB)
+ * using the \c -f option.
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  *	<td>-f</td>
  *	<td>1000</td>
  *	<td>Integer</td>
- *	<td>Number of separate database files to store in the output directory; values over 1000 are not
- *		recommended due to filesystem limitations.</td>
+ *	<td>Number of separate database files to store in the output directory</td>
  * </tr><tr>
  *	<td>-b</td>
  *	<td>-1</td>

tools/PCLServer/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page PCLServer PCLServer
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * PCLServer -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include PCLServer/PCLServer.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekAggregatedDataset/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekAggregatedDataset SeekAggregatedDataset
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekAggregatedDataset ...
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekAggregatedDataset/SeekAggregatedDataset.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>
  *	<td>Text file</td>
  *	<td>Tab-delimited text file containing two columns, numerical gene IDs (one-based) and unique gene
  *		names (matching those in the input DAT/DAB files).</td>
- * </tr><tr>
- *	<td>-d</td>
- *	<td>.</td>
- *	<td>Directory</td>
- *	<td>Input directory containing DB files</td>
- * </tr><tr>
- *	<td>-D</td>
- *	<td>.</td>
- *	<td>Directory</td>
- *	<td>Output directory in which database files will be stored.</td>
- * </tr><tr>
- *	<td>-x</td>
- *	<td>.</td>
- *	<td>Text file</td>
- *	<td>Input file containing list of CDatabaselets to combine</td>
  * </tr></table>
  */

tools/SeekEvaluator/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekEvaluator SeekEvaluator
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekEvaluator ...
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekEvaluator/SeekEvaluator.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekGeneRecommender/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekGeneRecommender SeekGeneRecommender
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekGeneRecommender -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekGeneRecommender/SeekGeneRecommender.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekPValue/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekPValue SeekPValue
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekPValue -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekPValue/SeekPValue.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekPrep/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekPrep SeekPrep
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekPrep -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekPrep/SeekPrep.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekReader/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekReader SeekReader
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekReader -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekReader/SeekReader.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekServer/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekServer SeekServer
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekServer -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekServer/SeekServer.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>

tools/SeekTest/stdafx.cpp

 #include "stdafx.h"
 
 /*!
- * \page DBCombiner DBCombiner
+ * \page SeekTest SeekTest
  * 
  * 
  * \section sec_usage Usage
  * \subsection ssec_usage_basic Basic Usage
  * 
  * \code
- * DBCombiner -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
+ * SeekTest -i <genes.txt> -x <db list> -d <input directory> -D <output_dir>
  * \endcode
  * 
  * 
  * \subsection ssec_usage_detailed Detailed Usage
  * 
- * \include DBCombiner/DBCombiner.ggo
+ * \include SeekTest/SeekTest.ggo
  * 
  * <table><tr>
  *	<th>Flag</th>