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[basedb-cvs] basedb/plugins/src/pca Makefile.am,1.3,1.4

From: <ku...@us...> - 2003-02-11 23:24:28

Update of /cvsroot/basedb/basedb/plugins/src/pca
In directory sc8-pr-cvs1:/tmp/cvs-serv325/src/pca

Modified Files:
	Makefile.am 
Log Message:
Changed single # comments to more correct double ## comments (automake
thing.
Changed install directory to $(prefix)/plugins_bin.


Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/pca/Makefile.am,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile.am	6 Feb 2003 01:31:20 -0000	1.3
--- Makefile.am	11 Feb 2003 23:24:25 -0000	1.4
***************
*** 1,5 ****
! # $Id$
  
! bin_PROGRAMS = pca
  
  pca_SOURCES  = PCA_v01.c gnuplot_i.c
--- 1,9 ----
! ## Process this file with automake to produce Makefile.in
! ##
! ## $Id$
  
! plugindir = $(prefix)/plugins_bin
! 
! plugin_PROGRAMS = pca
  
  pca_SOURCES  = PCA_v01.c gnuplot_i.c

[basedb-cvs] basedb/plugins/src/normalizers Makefile.am,1.1,1.2

From: <ku...@us...> - 2003-02-11 23:24:28

Update of /cvsroot/basedb/basedb/plugins/src/normalizers
In directory sc8-pr-cvs1:/tmp/cvs-serv325/src/normalizers

Modified Files:
	Makefile.am 
Log Message:
Changed single # comments to more correct double ## comments (automake
thing.
Changed install directory to $(prefix)/plugins_bin.


Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am	6 Feb 2003 00:43:34 -0000	1.1
--- Makefile.am	11 Feb 2003 23:24:24 -0000	1.2
***************
*** 1,5 ****
! # $Id$
  
! bin_PROGRAMS    = lowess medianratio
  noinst_PROGRAMS = lowess_test
  
--- 1,9 ----
! ## Process this file with automake to produce Makefile.in
! ##
! ## $Id$
  
! plugindir = $(prefix)/plugins_bin
! 
! plugin_PROGRAMS    = lowess medianratio
  noinst_PROGRAMS = lowess_test

[basedb-cvs] basedb/documentation/development plugins.txt,1.4,1.5

From: <tr...@us...> - 2003-02-11 14:53:59

Update of /cvsroot/basedb/basedb/documentation/development
In directory sc8-pr-cvs1:/tmp/cvs-serv13508

Modified Files:
	plugins.txt 
Log Message:
Added stuff about extra data columns (setExtraField)

Index: plugins.txt
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/development/plugins.txt,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** plugins.txt	10 Feb 2003 08:40:41 -0000	1.4
--- plugins.txt	11 Feb 2003 14:53:55 -0000	1.5
***************
*** 98,102 ****
  position_of_2016, quiality_of_2016, ratio_of_2017, intensity2_of_2017, ...
  (I included the quite redundant position field in this example by
! mistake.) The setExtraField header is used to tell BASE about 
  
  The names of available columns and fields are shown on the plugin
--- 98,102 ----
  position_of_2016, quiality_of_2016, ratio_of_2017, intensity2_of_2017, ...
  (I included the quite redundant position field in this example by
! mistake.) The setExtraFloats header is used to tell BASE about 
  
  The names of available columns and fields are shown on the plugin

[basedb-cvs] basedb .cvsignore,1.1,1.2

From: <tr...@us...> - 2003-02-11 14:53:20

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv13145

Modified Files:
	.cvsignore 
Log Message:
added some autogenerated files

Index: .cvsignore
===================================================================
RCS file: /cvsroot/basedb/basedb/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** .cvsignore	19 Jun 2002 18:37:23 -0000	1.1
--- .cvsignore	11 Feb 2003 14:53:13 -0000	1.2
***************
*** 1,3 ****
  .htaccess
  config.inc.php
! getconfig.inc.php
--- 1,13 ----
  .htaccess
  config.inc.php
! Makefile
! Makefile.in
! aclocal.m4
! config.cache
! config.guess
! config.h
! config.h.in
! config.log
! config.status
! config.sub
! configure

[basedb-cvs] basedb/src/include basefile.h,1.1,1.2

From: <tr...@us...> - 2003-02-11 14:47:43

Update of /cvsroot/basedb/basedb/src/include
In directory sc8-pr-cvs1:/tmp/cvs-serv9596/include

Modified Files:
	basefile.h 
Log Message:
Fixed broken pubsetbuf() with deallocated buffer

Index: basefile.h
===================================================================
RCS file: /cvsroot/basedb/basedb/src/include/basefile.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** basefile.h	1 Feb 2003 12:52:53 -0000	1.1
--- basefile.h	11 Feb 2003 14:47:35 -0000	1.2
***************
*** 75,78 ****
--- 75,79 ----
    public:
  	BaseFileReader(istream &s);
+ 	~BaseFileReader();
  
  	enum

[basedb-cvs] basedb/src/lib basefile.cc,1.1,1.2

From: <tr...@us...> - 2003-02-11 14:47:43

Update of /cvsroot/basedb/basedb/src/lib
In directory sc8-pr-cvs1:/tmp/cvs-serv9596/lib

Modified Files:
	basefile.cc 
Log Message:
Fixed broken pubsetbuf() with deallocated buffer

Index: basefile.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/src/lib/basefile.cc,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** basefile.cc	6 Feb 2003 00:43:35 -0000	1.1
--- basefile.cc	11 Feb 2003 14:47:36 -0000	1.2
***************
*** 2,6 ****
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002 Lao Saal, Carl Troein, Johan Vallon-Christersson
  //
  // This file is part of BASE.
--- 2,6 ----
  //
  // BioArray Software Environment (BASE) - homepage http://base.thep.lu.se/
! // Copyright (C) 2002,2003 Lao Saal, Carl Troein, Johan Vallon-Christersson
  //
  // This file is part of BASE.
***************
*** 124,127 ****
--- 124,134 ----
  #if !defined __GNUC__ || __GNUC__ >= 3
  	s.rdbuf()->pubsetbuf(&inbuf[0], inbuflen);
+ #endif
+ }
+ 
+ BaseFileReader::~BaseFileReader()
+ {
+ #if !defined __GNUC__ || __GNUC__ >= 3
+ 	str.rdbuf()->pubsetbuf(NULL, 0);
  #endif
  }

[basedb-cvs] basedb/src/assayImporter assayImporter.cc,1.2,1.3

From: <tr...@us...> - 2003-02-11 14:47:20

Update of /cvsroot/basedb/basedb/src/assayImporter
In directory sc8-pr-cvs1:/tmp/cvs-serv9397/assayImporter

Modified Files:
	assayImporter.cc 
Log Message:
Added import and display of extra bioassayset float columns

Index: assayImporter.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/src/assayImporter/assayImporter.cc,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** assayImporter.cc	11 Feb 2003 10:45:52 -0000	1.2
--- assayImporter.cc	11 Feb 2003 14:47:16 -0000	1.3
***************
*** 28,31 ****
--- 28,33 ----
  #include "basefile.h"
  
+ istream &getline(istream &i, vector<char> &v, char delim = '\n');
+ 
  using namespace std;		// Ugly, I know, so sue me.
  
***************
*** 36,42 ****
  	map<int,int> efFields, ostream &extraout)
[...108 lines suppressed...]
  		return 1;
  	}
! 	return assayImport(datain, cin, channels, extraout) ? 0 : 1;
  }
--- 232,246 ----
  		return 1;
  	}
! 
! #if !defined __GNUC__ || __GNUC__ >= 3
! 	char buf[4096], buf2[4096];
! 	cout.rdbuf()->pubsetbuf(buf, sizeof(buf));
! 	cin.rdbuf()->pubsetbuf(buf2, sizeof(buf2));
! #endif
! 	int rc = assayImport(datain, cin, channels, extraout) ? 0 : 1;
! #if !defined __GNUC__ || __GNUC__ >= 3
! 	cout.rdbuf()->pubsetbuf(NULL, 0);
! 	cin.rdbuf()->pubsetbuf(NULL, 0);
! #endif
! 	return rc;
  }

[basedb-cvs] basedb/plugins/src/normalizers lowess_renorm.cc,1.1,1.2

From: <tr...@us...> - 2003-02-11 14:46:09

Update of /cvsroot/basedb/basedb/plugins/src/normalizers
In directory sc8-pr-cvs1:/tmp/cvs-serv8658

Modified Files:
	lowess_renorm.cc 
Log Message:
Fixed broken pubsetbuf() with deallocated buffer

Index: lowess_renorm.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/lowess_renorm.cc,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** lowess_renorm.cc	1 Feb 2003 12:52:52 -0000	1.1
--- lowess_renorm.cc	11 Feb 2003 14:46:05 -0000	1.2
***************
*** 40,48 ****
  int main()
  {
- #if !defined __GNUC__ || __GNUC__ >= 3
-   char buf[4096];
-   cout.rdbuf()->pubsetbuf(buf, sizeof(buf));
- #endif
- 
    BaseFileReader bfr(cin);
    BaseFileSection sect;
--- 40,43 ----
***************
*** 59,62 ****
--- 54,62 ----
    cout << "BASEfile\n";
  
+ #if !defined __GNUC__ || __GNUC__ >= 3
+   char buf[4096];
+   cout.rdbuf()->pubsetbuf(buf, sizeof(buf));
+ #endif
+ 
    while(1)
    {
***************
*** 67,70 ****
--- 67,73 ----
            bfr.errText()<<"\n";
        }
+ #if !defined __GNUC__ || __GNUC__ >= 3
+       cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
        exit(bfr.getError());
      }
***************
*** 76,79 ****
--- 79,85 ----
      	 !sect2.findFieldList("assays", assays)){
        cerr << "lowess: Missing header columns/assayFields/assays\n";
+ #if !defined __GNUC__ || __GNUC__ >= 3
+       cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
        exit(1);
      }
***************
*** 81,84 ****
--- 87,93 ----
      if(assays.size() != 1){
        cerr << "lowess: Not exactly one assay in 'spots' section\n";
+ #if !defined __GNUC__ || __GNUC__ >= 3
+       cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
        exit(1);
      }
***************
*** 92,95 ****
--- 101,107 ----
        cerr << "lowess: Missing position/reporter/assayData columns "
        	"or intensity1/intensity2 fields\n";
+ #if !defined __GNUC__ || __GNUC__ >= 3
+       cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
        exit(1);
      }
***************
*** 107,110 ****
--- 119,127 ----
      cout << "\n";
    }
+ 
+ #if !defined __GNUC__ || __GNUC__ >= 3
+   cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
+ 
  }

[basedb-cvs] basedb/www assay_table.phtml,1.24,1.25 gene_explore.phtml,1.71,1.72

From: <tr...@us...> - 2003-02-11 14:44:00

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv7524

Modified Files:
	assay_table.phtml gene_explore.phtml 
Log Message:
Added import and display of extra bioassayset float columns

Index: assay_table.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/assay_table.phtml,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** assay_table.phtml	3 Feb 2003 08:54:11 -0000	1.24
--- assay_table.phtml	11 Feb 2003 14:43:56 -0000	1.25
***************
*** 180,184 ****
  		// Add the columns as non-shown to speed up the reporter list adding.
  		$columns = makeValueSearchColumns($ass->getChannels(), 0, 0, 0,
! 			$rawLevel, $repLevel);
  		// Clone the search because we'll do irreversible changes to it.
  		$search2 = $search;
--- 180,184 ----
  		// Add the columns as non-shown to speed up the reporter list adding.
  		$columns = makeValueSearchColumns($ass->getChannels(), 0, 0, 0,
! 			$rawLevel, $repLevel, $ass->getBioAssaySet());
  		// Clone the search because we'll do irreversible changes to it.
  		$search2 = $search;
***************
*** 199,203 ****
  
  	$columns = makeValueSearchColumns($ass->getChannels(), 1,
! 		count($cbRaws), $lims, $rawLevel, $repLevel);
  	$ass->addValueSearchColumns($search, $columns);
  
--- 199,203 ----
  
  	$columns = makeValueSearchColumns($ass->getChannels(), 1,
! 		count($cbRaws), $lims, $rawLevel, $repLevel, $ass->getBioAssaySet());
  	$ass->addValueSearchColumns($search, $columns);
  
***************
*** 245,249 ****
  
  function makeValueSearchColumns($channels, $show, $spots,
! 	$lims, $rawLevel, $repLevel)
  {
  	$cols = array(
--- 245,249 ----
  
  function makeValueSearchColumns($channels, $show, $spots,
! 	$lims, $rawLevel, $repLevel, $setid)
  {
  	$cols = array(
***************
*** 267,270 ****
--- 267,272 ----
  			"renderExploreRatio", $show);
  	}
+ 
+ 	addExtraDataColumnsToColumns($cols, $setid, $show);
  
  	$rawcols = RawBioAssayData::getAllShownColumns();

Index: gene_explore.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/gene_explore.phtml,v
retrieving revision 1.71
retrieving revision 1.72
diff -C2 -d -r1.71 -r1.72
*** gene_explore.phtml	4 Feb 2003 21:51:13 -0000	1.71
--- gene_explore.phtml	11 Feb 2003 14:43:57 -0000	1.72
***************
*** 373,377 ****
  		$average = $gpage == -1;
  		$columns = makeExploreSearchColumns($channels, $average, $annot != 0,
! 			$showBackend, $spotSize != 0, $rawLevel);
  		BioAssay::prepareExploreSearch($onesearch, $columns, 0, $expid,
  			$channels, $average, $setid);
--- 373,377 ----
  		$average = $gpage == -1;
  		$columns = makeExploreSearchColumns($channels, $average, $annot != 0,
! 			$showBackend, $spotSize != 0, $rawLevel, $setid);
  		BioAssay::prepareExploreSearch($onesearch, $columns, 0, $expid,
  			$channels, $average, $setid);
***************
*** 925,929 ****
  
  function makeExploreSearchColumns($channels, $average, $hasannot,
! 	$showBackend, $showSpot = false, $rawLevel = 3)
  {
  	$cols = array();
--- 925,929 ----
  
  function makeExploreSearchColumns($channels, $average, $hasannot,
! 	$showBackend, $showSpot = false, $rawLevel = 3, $setid)
  {
  	$cols = array();
***************
*** 947,950 ****
--- 947,952 ----
  			"renderExploreRatio", 1);
  	}
+ 
+ 	addExtraDataColumnsToColumns($cols, $setid, 1);
  
  	$rawcols = RawBioAssayData::getAllShownColumns();

[basedb-cvs] basedb/www arrayslide_edit.phtml,1.10,1.11

From: <tr...@us...> - 2003-02-11 14:43:53

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv7474

Modified Files:
	arrayslide_edit.phtml 
Log Message:
Added missing include

Index: arrayslide_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/arrayslide_edit.phtml,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** arrayslide_edit.phtml	30 Dec 2002 22:09:18 -0000	1.10
--- arrayslide_edit.phtml	11 Feb 2003 14:43:48 -0000	1.11
***************
*** 28,31 ****
--- 28,32 ----
  	require_once("links_common.inc.php");
  	require_once("htmlinit.inc.php");
+ 	require_once("hyb.inc.php");
  
  	verifyAccess(ArraySlide::globalRead());

[basedb-cvs] basedb/include/classes bioassay.inc.php,1.31,1.32 bioassayset.inc.php,1.21,1.22 jobhandler.inc.php,1.9,1.10

From: <tr...@us...> - 2003-02-11 14:43:17

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv7133/classes

Modified Files:
	bioassay.inc.php bioassayset.inc.php jobhandler.inc.php 
Log Message:
Added import and display of extra bioassayset float columns

Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** bioassay.inc.php	3 Feb 2003 20:13:17 -0000	1.31
--- bioassay.inc.php	11 Feb 2003 14:43:06 -0000	1.32
***************
*** 708,712 ****
  		{
  			$xct = $xctables[$arr["valueType"]];
! 			$tn = "xc_$xid";
  			$tables[$tn] = array(
  				"$config[dbDynamic]BioAssayExtra$xct$expid $tn",
--- 708,712 ----
  		{
  			$xct = $xctables[$arr["valueType"]];
! 			$tn = "baef_$xid";
  			$tables[$tn] = array(
  				"$config[dbDynamic]BioAssayExtra$xct$expid $tn",

Index: bioassayset.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassayset.inc.php,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** bioassayset.inc.php	10 Feb 2003 08:40:42 -0000	1.21
--- bioassayset.inc.php	11 Feb 2003 14:43:08 -0000	1.22
***************
*** 154,158 ****
  		if(!$this->extraColumns)
  			$this->extraColumns = ExtraDataColumn::getBriefForSet($this->id);
! 		return $this->hasExtraColumns;
  	}
  
--- 154,158 ----
  		if(!$this->extraColumns)
  			$this->extraColumns = ExtraDataColumn::getBriefForSet($this->id);
! 		return $this->extraColumns;
  	}
  
***************
*** 169,172 ****
--- 169,176 ----
  		$this->intensityMeasure = $val;
  	}
+ 	function setHasExtraColumns($val)
+ 	{
+ 		$this->hasExtraColumns = $val ? 1 : 0;
+ 	}
  
  	// Adds another extra data column for this bioassayset.
***************
*** 709,716 ****
  		for($i = 1; $i <= $channels; $i++)
  			$columns[] = "intensity$i";
! 		if(!db_tabfile_load($fname, $table, $columns))
  			return false;
  		return $this->updateGeneTable(false);
  	}
  }
  
--- 713,731 ----
  		for($i = 1; $i <= $channels; $i++)
  			$columns[] = "intensity$i";
! 		if(db_tabfile_load($fname, $table, $columns) < 1)
  			return false;
  		return $this->updateGeneTable(false);
  	}
+ 
+ 	function importExtraFloats($fname)
+ 	{
+ 		global $config;
+ 		$table = "$config[dbDynamic]BioAssayExtraFloat$this->experiment";
+ 		$columns = array("bioAssay", "position", "extraDataColumn",
+ 			"extraValue");
+ 		if(db_tabfile_load($fname, $table, $columns) < 1)
+ 			return false;
+ 		return true;
+ 	}
  }
  
***************
*** 948,957 ****
  		for(reset($arr), $i = 0; list($id, $a) = each($arr); $i++)
  		{
! 			$expr[] = array("_xc_$id", $types[$a["valueType"]],
! 				"%%.extraValue", $a["name"]);
! 			Search::bindExpressionToTable($expr[$i], "xc_$id");
  		}
  		return $expr;
  	}
  }
  
--- 963,976 ----
  		for(reset($arr), $i = 0; list($id, $a) = each($arr); $i++)
  		{
! 			$name = $a["name"];
! 			$expr[] = array("_xc_".printable($name), $types[$a["valueType"]],
! 				"%%.extraValue", $name);
! 			$tname = "baef_$id";
! 			$comm = "[Extra]";
! 			Search::bindExpressionToTable($expr[$i], $tname, $comm);
  		}
  		return $expr;
  	}
+ 
  }
  

Index: jobhandler.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/jobhandler.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** jobhandler.inc.php	10 Feb 2003 08:40:45 -0000	1.9
--- jobhandler.inc.php	11 Feb 2003 14:43:10 -0000	1.10
***************
*** 358,361 ****
--- 358,370 ----
  			unset($parents);
  		}
+ 
+ 		// Find the ids of the extra float columns
+ 		for(reset($extraFloats); list($ef) = each($extraFloats); )
+ 		{
+ 			$efid = ExtraDataColumn::getIdFromNameAndType($ef, 0, true);
+ 			if(!$efid)
+ 				return "Can't create extra float column '$ef'\n";
[...117 lines suppressed...]
+ 			unlink($tempfileextra);
  			return "assayImporter returned $rc: ".implode("\n", $res);
  		}
! 		$ok = $set->importBASEfile($tempfile2, $channels);
  		unlink($tempfile2);
! 		if(!$ok)
! 		{
! 			unlink($tempfileextra);
  			return "Failed to import assay data into database";
+ 		}
+ 
+ 		if($extraFloats)
+ 			$ok = $set->importExtraFloats($tempfileextra);
+ 		else
+ 			$ok = true;
+ 		unlink($tempfileextra);
+ 		if(!$ok)
+ 			return "Failed to import extra float columns into database";
  		return "";
  	}

[basedb-cvs] basedb/include/web assay_common.inc.php,1.2,1.3 experiment_common.inc.php,1.24,1.25 gene_common.inc.php,1.9,1.10

From: <tr...@us...> - 2003-02-11 14:43:17

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv7133/web

Modified Files:
	assay_common.inc.php experiment_common.inc.php 
	gene_common.inc.php 
Log Message:
Added import and display of extra bioassayset float columns

Index: assay_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/assay_common.inc.php,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** assay_common.inc.php	1 Feb 2003 23:04:15 -0000	1.2
--- assay_common.inc.php	11 Feb 2003 14:43:12 -0000	1.3
***************
*** 49,53 ****
  	return "[<a ".href("assay_table.phtml?i_a=$id", 2).">Table</a>] ".
  		"[<a class=popup href='assay_plotter.phtml?i_a=$id' ".
! 		"target='assayPlotter_$id'>HTML&nbsp;Plot&nbsp;tool</a>]".
  		"[<a class=popup href='plotapplet/plot_assay.phtml?i_a=$id' ".
  		"target='assayJavaPlot_$id'>Java&nbsp;Plot&nbsp;tool</a>]";
--- 49,53 ----
  	return "[<a ".href("assay_table.phtml?i_a=$id", 2).">Table</a>] ".
  		"[<a class=popup href='assay_plotter.phtml?i_a=$id' ".
! 		"target='assayPlotter_$id'>HTML&nbsp;Plot&nbsp;tool</a>] ".
  		"[<a class=popup href='plotapplet/plot_assay.phtml?i_a=$id' ".
  		"target='assayJavaPlot_$id'>Java&nbsp;Plot&nbsp;tool</a>]";

Index: experiment_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/experiment_common.inc.php,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** experiment_common.inc.php	10 Feb 2003 08:40:46 -0000	1.24
--- experiment_common.inc.php	11 Feb 2003 14:43:12 -0000	1.25
***************
*** 500,503 ****
--- 500,505 ----
  <tr><th>Total # of values</th><td><?= $set->getSpotCount() ?></td></tr>
  <tr><th>Total # of reporters</th><td><?= $set->getGeneCount() ?></td></tr>
+ <tr><th>Extra columns</th><td><?= $set->getHasExtraColumns() ? "Yes" : "No"
+ 	?></td></tr>
  <tr><td colspan=2 class=large><a <?=
  	href("gene_explore.phtml?i_set=$setid", 2) ?>

Index: gene_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/gene_common.inc.php,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** gene_common.inc.php	4 Feb 2003 21:51:11 -0000	1.9
--- gene_common.inc.php	11 Feb 2003 14:43:12 -0000	1.10
***************
*** 158,161 ****
--- 158,172 ----
  }
  
+ function addExtraDataColumnsToColumns(&$cols, $setid, $show = 1)
+ {
+ 	$xc = ExtraDataColumn::getBriefForSet($setid);
+ 	for(reset($xc); list($id, $arr) = each($xc); )
+ 	{
+ 		$name = $arr["name"];
+ 		$cols[] = array("_xc_".printable($name), false, html($name), 1,
+ 			"renderExploreIntensity", $show);
+ 	}
+ }
+ 
  
  ?>

[basedb-cvs] basedb/src/sectionCounter .cvsignore,NONE,1.1