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From: <tr...@us...> - 2003-02-12 17:00:41
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv7897 Added Files: AUTHORS NEWS Log Message: needed by autosomethingorother --- NEW FILE: AUTHORS --- See http://base.thep.lu.se/ --- NEW FILE: NEWS --- See ChangeLog in the CVS. |
|
From: <ku...@us...> - 2003-02-12 16:21:18
|
Update of /cvsroot/basedb/basedb In directory sc8-pr-cvs1:/tmp/cvs-serv21391 Modified Files: configure.ac Log Message: Changed default $prefix Index: configure.ac =================================================================== RCS file: /cvsroot/basedb/basedb/configure.ac,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** configure.ac 12 Feb 2003 12:23:28 -0000 1.4 --- configure.ac 12 Feb 2003 16:21:15 -0000 1.5 *************** *** 39,42 **** --- 39,44 ---- AM_INIT_AUTOMAKE(base,1.2.0RC2,bas...@li...) + AC_PREFIX_DEFAULT(/usr/local/base) + # Checks for programs. AC_PROG_CXX |
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From: <tr...@us...> - 2003-02-12 16:18:03
|
Update of /cvsroot/basedb/basedb/src/lib
In directory sc8-pr-cvs1:/tmp/cvs-serv19904/src/lib
Modified Files:
basefile.cc
Log Message:
adressed problem with pubsetbuf
Index: basefile.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/src/lib/basefile.cc,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** basefile.cc 11 Feb 2003 14:47:36 -0000 1.2
--- basefile.cc 12 Feb 2003 16:17:54 -0000 1.3
***************
*** 20,27 ****
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
#include <string.h>
#include <iostream>
! #include "basefile.h"
istream &getline(istream &i, vector<char> &v, char delim = '\n')
--- 20,32 ----
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
+ #ifdef HAVE_CONFIG_H
+ #include <config.h>
+ #endif
+
#include <string.h>
#include <iostream>
! #include <basefile.h>
!
istream &getline(istream &i, vector<char> &v, char delim = '\n')
***************
*** 122,126 ****
error = EOR;
dataEnd = true;
! #if !defined __GNUC__ || __GNUC__ >= 3
s.rdbuf()->pubsetbuf(&inbuf[0], inbuflen);
#endif
--- 127,131 ----
error = EOR;
dataEnd = true;
! #ifdef HAVE_PUBSETBUF
s.rdbuf()->pubsetbuf(&inbuf[0], inbuflen);
#endif
***************
*** 129,133 ****
BaseFileReader::~BaseFileReader()
{
! #if !defined __GNUC__ || __GNUC__ >= 3
str.rdbuf()->pubsetbuf(NULL, 0);
#endif
--- 134,138 ----
BaseFileReader::~BaseFileReader()
{
! #ifdef HAVE_PUBSETBUF
str.rdbuf()->pubsetbuf(NULL, 0);
#endif
|
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From: <tr...@us...> - 2003-02-12 16:18:03
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering
In directory sc8-pr-cvs1:/tmp/cvs-serv19904/plugins/src/clustering
Modified Files:
main.cc
Log Message:
adressed problem with pubsetbuf
Index: main.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/main.cc,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** main.cc 1 Feb 2003 12:52:50 -0000 1.1
--- main.cc 12 Feb 2003 16:17:53 -0000 1.2
***************
*** 1,2 ****
--- 1,6 ----
+ #ifdef HAVE_CONFIG_H
+ #include <config.h>
+ #endif
+
#include <stdlib.h>
#include <string.h>
***************
*** 10,14 ****
#endif
! #include "basefile.h"
#include "BaseClustering.h"
#include "StoreMergeReporter.h"
--- 14,18 ----
#endif
! #include <basefile.h>
#include "BaseClustering.h"
#include "StoreMergeReporter.h"
***************
*** 17,20 ****
--- 21,28 ----
using namespace std;
+ #ifdef HAVE_PUBSETBUF
+ char coutbuf[4096];
+ #endif
+
double get_opt(string s, map<string, string> opts);
void readandcluster(BaseFileReader& bfr, const map<string,string>& opts,
***************
*** 24,30 ****
int main(int argc, char **argv)
{
! #if !defined __GNUC__ || __GNUC__ >= 3
! char buf[4096];
! cout.rdbuf()->pubsetbuf(buf, sizeof(buf));
#endif
--- 32,37 ----
int main(int argc, char **argv)
{
! #ifdef HAVE_PUBSETBUF
! cout.rdbuf()->pubsetbuf(coutbuf, sizeof(coutbuf));
#endif
***************
*** 91,94 ****
--- 98,104 ----
}
cerr << "No spots section found\n";
+ #ifdef HAVE_PUBSETBUF
+ cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
return 1;
}
|
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From: <tr...@us...> - 2003-02-12 16:18:03
|
Update of /cvsroot/basedb/basedb/www In directory sc8-pr-cvs1:/tmp/cvs-serv19904/www Modified Files: gene_export.phtml Log Message: adressed problem with pubsetbuf Index: gene_export.phtml =================================================================== RCS file: /cvsroot/basedb/basedb/www/gene_export.phtml,v retrieving revision 1.31 retrieving revision 1.32 diff -C2 -d -r1.31 -r1.32 *** gene_export.phtml 22 Jan 2003 08:01:58 -0000 1.31 --- gene_export.phtml 12 Feb 2003 16:17:54 -0000 1.32 *************** *** 134,137 **** --- 134,138 ---- // rest of eternity. set_time_limit(300); + ob_implicit_flush(1); $format = max(1, min(7, (int)$i_fmt)); *************** *** 169,172 **** --- 170,174 ---- $prog->setUsedColumns($i_cols); $prog->setUsedFields($i_fields); + ob_implicit_flush(1); } |
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From: <tr...@us...> - 2003-02-12 16:18:03
|
Update of /cvsroot/basedb/basedb/src/assayImporter In directory sc8-pr-cvs1:/tmp/cvs-serv19904/src/assayImporter Modified Files: assayImporter.cc Log Message: adressed problem with pubsetbuf Index: assayImporter.cc =================================================================== RCS file: /cvsroot/basedb/basedb/src/assayImporter/assayImporter.cc,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** assayImporter.cc 11 Feb 2003 14:47:16 -0000 1.3 --- assayImporter.cc 12 Feb 2003 16:17:54 -0000 1.4 *************** *** 20,23 **** --- 20,28 ---- // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. // + + #ifdef HAVE_CONFIG_H + #include <config.h> + #endif + #include <cstdlib> #include <cstdio> *************** *** 26,30 **** #include <map> ! #include "basefile.h" istream &getline(istream &i, vector<char> &v, char delim = '\n'); --- 31,39 ---- #include <map> ! #include <basefile.h> ! ! #ifdef HAVE_PUBSETBUF ! char coutbuf[4096]; ! #endif istream &getline(istream &i, vector<char> &v, char delim = '\n'); *************** *** 233,245 **** } ! #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; --- 242,251 ---- } ! #ifdef HAVE_PUBSETBUF ! cout.rdbuf()->pubsetbuf(coutbuf, sizeof(coutbuf)); #endif int rc = assayImport(datain, cin, channels, extraout) ? 0 : 1; ! #ifdef HAVE_PUBSETBUF cout.rdbuf()->pubsetbuf(NULL, 0); #endif return rc; |
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From: <tr...@us...> - 2003-02-12 16:18:03
|
Update of /cvsroot/basedb/basedb/plugins/src/normalizers
In directory sc8-pr-cvs1:/tmp/cvs-serv19904/plugins/src/normalizers
Modified Files:
lowess_renorm.cc medianratio.cc
Log Message:
adressed problem with pubsetbuf
Index: lowess_renorm.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/lowess_renorm.cc,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** lowess_renorm.cc 11 Feb 2003 14:46:05 -0000 1.2
--- lowess_renorm.cc 12 Feb 2003 16:17:53 -0000 1.3
***************
*** 20,23 ****
--- 20,28 ----
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
+
+ #ifdef HAVE_CONFIG_H
+ #include <config.h>
+ #endif
+
#include <stdlib.h>
#include <string.h>
[...99 lines suppressed...]
***************
*** 120,127 ****
}
! #if !defined __GNUC__ || __GNUC__ >= 3
cout.rdbuf()->pubsetbuf(NULL, 0);
#endif
}
--- 129,137 ----
}
! #ifdef HAVE_PUBSETBUF
cout.rdbuf()->pubsetbuf(NULL, 0);
#endif
+ return 0;
}
Index: medianratio.cc
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/medianratio.cc,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** medianratio.cc 1 Feb 2003 12:52:52 -0000 1.1
--- medianratio.cc 12 Feb 2003 16:17:54 -0000 1.2
***************
*** 20,23 ****
--- 20,27 ----
// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
+ #ifdef HAVE_CONFIG_H
+ #include <config.h>
+ #endif
+
#include <stdlib.h>
#include <string.h>
***************
[...115 lines suppressed...]
***************
*** 106,109 ****
--- 110,126 ----
cout << "\n";
}
+ return true;
+ }
+
+ int main()
+ {
+ #ifdef HAVE_PUBSETBUF
+ cout.rdbuf()->pubsetbuf(coutbuf, sizeof(coutbuf));
+ #endif
+ int ok = dothings();
+ return !ok;
+ #ifdef HAVE_PUBSETBUF
+ cout.rdbuf()->pubsetbuf(NULL, 0);
+ #endif
}
|
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From: <tr...@us...> - 2003-02-12 16:17:20
|
Update of /cvsroot/basedb/basedb/include/local_distr
In directory sc8-pr-cvs1:/tmp/cvs-serv19639/include/local_distr
Modified Files:
raw_columns.inc.php
Log Message:
added comment
Index: raw_columns.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/local_distr/raw_columns.inc.php,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** raw_columns.inc.php 3 Feb 2003 08:56:10 -0000 1.15
--- raw_columns.inc.php 12 Feb 2003 16:17:15 -0000 1.16
***************
*** 21,24 ****
--- 21,37 ----
//
+ // This file defines site-specific things that have to do with the
+ // RawBioAssayData table. That table has a fairly small set of mandatory
+ // columns. In addition to these, a site admin may add columns and add
+ // information about them here so that BASE can know what to do with them.
+ // Note that this file MUST match your RawBioAssayData table's structure.
+ // You can add column to an existing BASE installation (although the
+ // ALTER TABLE command may take a long time depending on the size of
+ // the table), but deleting/renaming columns can only be done for fresh
+ // (empty) BASE installation, since things may refer to the columns.
+
+ // This is the GPR version of raw_columns.inc.php, with most columns from
+ // the GPR format, plus a few other columns.
+
require_once("extracols.inc.php");
***************
*** 35,38 ****
--- 48,53 ----
// Note that for PostgreSQL the order of the columns here must be the
// exact same as that in the table, and all columns must be present.
+ // This implies that those restrictions must always hold (because of
+ // RDBMS independence).
// The columns that are always present in RawBioAssayData are:
// rawBioAssay, position, element, reporter, x, y, block, numRow, numCol.
|
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From: <tr...@us...> - 2003-02-12 16:16:55
|
Update of /cvsroot/basedb/basedb/include/common
In directory sc8-pr-cvs1:/tmp/cvs-serv19298/include/common
Modified Files:
basefile_spots.inc.php
Log Message:
fixed problem with averaged serial basefile by adding group by stuff
Index: basefile_spots.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/common/basefile_spots.inc.php,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** basefile_spots.inc.php 22 Jan 2003 08:01:14 -0000 1.5
--- basefile_spots.inc.php 12 Feb 2003 16:16:48 -0000 1.6
***************
*** 136,147 ****
$fieldCols[] = array($c, false, "", 0, 0, 1);
if($prog->getSerialFormat()) // Serial format
{
$fieldCols = array_merge($columnCols, $fieldCols);
$columnCols = array();
- }
- if($prog->getSerialFormat()) // Serial format
- {
$searchbuffer = false;
BioAssay::prepareExportSearch($valuesearch, $searchbuffer,
--- 136,152 ----
$fieldCols[] = array($c, false, "", 0, 0, 1);
+ /* if(!$fieldCols || !$columnCols)
+ {
+ SBFCwrite("# There must be at least one column and ".
+ "one field specified\n");
+ unset($GLOBALS["SBFCfd"]);
+ return;
+ }*/
+
if($prog->getSerialFormat()) // Serial format
{
$fieldCols = array_merge($columnCols, $fieldCols);
$columnCols = array();
$searchbuffer = false;
BioAssay::prepareExportSearch($valuesearch, $searchbuffer,
***************
*** 165,171 ****
else // Normal format.
{
- // BioAssaySet::prepareGeneSearch($genesearch, $columnCols, 0,
- // 0, $geneavg);
-
$genes = $set->exportGeneSearch($genesearch, $columnCols, $geneavg);
$genesearch->reset();
--- 170,173 ----
***************
*** 204,211 ****
if(!isset($SBFCgenes[$m][$p]))
{
! error_log("Missing gene for mol/pos $m/$p");
return;
}
$g =& $SBFCgenes[$m][$p];
if($g)
{
--- 206,214 ----
if(!isset($SBFCgenes[$m][$p]))
{
! error_log("Missing gene for reporter/pos $m/$p");
return;
}
$g =& $SBFCgenes[$m][$p];
+
if($g)
{
|
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From: <tr...@us...> - 2003-02-12 16:16:55
|
Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv19298/include/classes
Modified Files:
bioassay.inc.php search.inc.php program.inc.php
Log Message:
fixed problem with averaged serial basefile by adding group by stuff
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/bioassay.inc.php,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** bioassay.inc.php 11 Feb 2003 14:43:06 -0000 1.32
--- bioassay.inc.php 12 Feb 2003 16:16:45 -0000 1.33
***************
*** 537,541 ****
// The %% will be replaced correspondingly.
function valueSearchExpressions($channels, $average, $forExport = false,
! $setid = 0)
{
static $a = false, $ca = -1;
--- 537,541 ----
// The %% will be replaced correspondingly.
function valueSearchExpressions($channels, $average, $forExport = false,
! $setid = 0, $forExportDisplay = false)
{
[...190 lines suppressed...]
! }
! else if($groupby)
{
$buffer[2] .= "GROUP BY ".implode(", ", $groupby);
}
$buffer[8] =& $unwantedCols;
***************
*** 1036,1040 ****
// and over. Reporters that do not appear in the assays will be
// skipped. This is MUCH better than trying to get all the data
! // in a single query, at least for MYSQL.
$marr = array_keys($genes);
for(reset($marr); list(, $m) = each($marr); )
--- 1050,1054 ----
// and over. Reporters that do not appear in the assays will be
// skipped. This is MUCH better than trying to get all the data
! // in a single query, at least for MySQL.
$marr = array_keys($genes);
for(reset($marr); list(, $m) = each($marr); )
Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/search.inc.php,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** search.inc.php 2 Feb 2003 18:03:03 -0000 1.30
--- search.inc.php 12 Feb 2003 16:16:47 -0000 1.31
***************
*** 655,659 ****
--- 655,663 ----
{
if(!$this->extraColumns)
+ {
+ if($isFirst)
+ return "NULL";
return "";
+ }
$a = "";
for(reset($this->extraColumns);
Index: program.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/program.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** program.inc.php 22 Jan 2003 08:01:00 -0000 1.12
--- program.inc.php 12 Feb 2003 16:16:47 -0000 1.13
***************
*** 114,121 ****
--- 114,125 ----
function getUsedColumns()
{
+ if($this->usedColumns == "")
+ return array();
return array_flip(explode("\t", $this->usedColumns));
}
function getUsedFields()
{
+ if($this->usedFields == "")
+ return array();
return array_flip(explode("\t", $this->usedFields));
}
***************
*** 254,258 ****
$chans = $this->minChannels;
$avg = $this->geneAverages;
! $expr = BioAssay::valueSearchExpressions($chans, $avg, true);
for($i = 0; $i < count($expr); $i++)
{
--- 258,263 ----
$chans = $this->minChannels;
$avg = $this->geneAverages;
! $expr = BioAssay::valueSearchExpressions($chans, $avg,
! true, 0, true);
for($i = 0; $i < count($expr); $i++)
{
|
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From: <ku...@us...> - 2003-02-12 12:24:01
|
Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv1896
Modified Files:
Makefile.am configure.ac
Log Message:
Continued fixing of automake/autoconfig/configure ...
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/Makefile.am,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile.am 12 Feb 2003 00:59:05 -0000 1.2
--- Makefile.am 12 Feb 2003 12:23:28 -0000 1.3
***************
*** 7,9 ****
prefixdir = $(prefix)
! prefix_DATA = example_config.inc.php
--- 7,9 ----
prefixdir = $(prefix)
! dist_prefix_DATA = example_config.inc.php
Index: configure.ac
===================================================================
RCS file: /cvsroot/basedb/basedb/configure.ac,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** configure.ac 12 Feb 2003 00:59:05 -0000 1.3
--- configure.ac 12 Feb 2003 12:23:28 -0000 1.4
***************
*** 37,41 ****
AM_CONFIG_HEADER(config.h)
! AM_INIT_AUTOMAKE(BASE,1.2.0,bas...@li...)
# Checks for programs.
--- 37,41 ----
AM_CONFIG_HEADER(config.h)
! AM_INIT_AUTOMAKE(base,1.2.0RC2,bas...@li...)
# Checks for programs.
***************
*** 345,348 ****
--- 345,349 ----
plugins/src/Makefile
plugins/src/clustering/Cgraph/Makefile
+ plugins/src/clustering/Cgraph/include/Makefile
plugins/src/clustering/Cgraph/source/Makefile
plugins/src/clustering/Makefile
***************
*** 353,356 ****
--- 354,358 ----
src/Makefile
src/assayImporter/Makefile
+ src/include/Makefile
src/jobRunner/Makefile
src/lib/Makefile
|
|
From: <ku...@us...> - 2003-02-12 12:23:33
|
Update of /cvsroot/basedb/basedb/www/img
In directory sc8-pr-cvs1:/tmp/cvs-serv1896/www/img
Modified Files:
Makefile.am
Log Message:
Continued fixing of automake/autoconfig/configure ...
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/www/img/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 12 Feb 2003 00:23:34 -0000 1.1
--- Makefile.am 12 Feb 2003 12:23:30 -0000 1.2
***************
*** 5,9 ****
wwwimgdir = $(prefix)/www/img
! wwwimg_DATA = \
1.gif ell.gif ex_t.gif newlogo.png p384_4.gif sti.gif baselogo.jpg \
ex_i.gif help.png p384_1.gif s0.gif stl.gif baseplotlogo.png \
--- 5,9 ----
wwwimgdir = $(prefix)/www/img
! dist_wwwimg_DATA = \
1.gif ell.gif ex_t.gif newlogo.png p384_4.gif sti.gif baselogo.jpg \
ex_i.gif help.png p384_1.gif s0.gif stl.gif baseplotlogo.png \
|
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From: <ku...@us...> - 2003-02-12 12:23:33
|
Update of /cvsroot/basedb/basedb/src In directory sc8-pr-cvs1:/tmp/cvs-serv1896/src Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/src/Makefile.am,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** Makefile.am 11 Feb 2003 23:36:08 -0000 1.2 --- Makefile.am 12 Feb 2003 12:23:29 -0000 1.3 *************** *** 3,7 **** ## $Id$ ! SUBDIRS = lib assayImporter jobRunner sectionCounter bin_PROGRAMS = baseftpd ftpdspawner spotImageChopper tifftopnm --- 3,7 ---- ## $Id$ ! SUBDIRS = include lib assayImporter jobRunner sectionCounter bin_PROGRAMS = baseftpd ftpdspawner spotImageChopper tifftopnm |
|
From: <ku...@us...> - 2003-02-12 12:23:33
|
Update of /cvsroot/basedb/basedb/www/plotapplet
In directory sc8-pr-cvs1:/tmp/cvs-serv1896/www/plotapplet
Modified Files:
Makefile.am
Log Message:
Continued fixing of automake/autoconfig/configure ...
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/www/plotapplet/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 12 Feb 2003 00:23:34 -0000 1.1
--- Makefile.am 12 Feb 2003 12:23:30 -0000 1.2
***************
*** 5,9 ****
wwwplotappletdir = $(prefix)/www/plotapplet
! wwwplotapplet_DATA = \
plot_assay.phtml plot_raw.phtml show_tmp.phtml plot.jar \
read_data.phtml store_tmp.phtml
--- 5,9 ----
wwwplotappletdir = $(prefix)/www/plotapplet
! dist_wwwplotapplet_DATA = \
plot_assay.phtml plot_raw.phtml show_tmp.phtml plot.jar \
read_data.phtml store_tmp.phtml
|
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From: <ku...@us...> - 2003-02-12 12:23:33
|
Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv1896/www
Modified Files:
Makefile.am
Log Message:
Continued fixing of automake/autoconfig/configure ...
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/www/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 12 Feb 2003 00:23:32 -0000 1.1
--- Makefile.am 12 Feb 2003 12:23:30 -0000 1.2
***************
*** 7,11 ****
wwwdir = $(prefix)/www
! www_SCRIPTS = \
admin_main.phtml arraybatch_edit.phtml arraybatch_list.phtml \
array_main.phtml array_popup.phtml arrayslide_edit.phtml \
--- 7,11 ----
wwwdir = $(prefix)/www
! www_HEADERS = \
admin_main.phtml arraybatch_edit.phtml arraybatch_list.phtml \
array_main.phtml array_popup.phtml arrayslide_edit.phtml \
|
|
From: <ku...@us...> - 2003-02-12 12:23:32
|
Update of /cvsroot/basedb/basedb/plugins/src/pca
In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/pca
Modified Files:
Makefile.am
Added Files:
gnuplot_i.h
Log Message:
Continued fixing of automake/autoconfig/configure ...
--- NEW FILE: gnuplot_i.h ---
/*-------------------------------------------------------------------------*/
/**
@file gnuplot_i.h
@author N. Devillard
@date Sep 1998
@version $Revision: 1.1 $
@brief C interface to gnuplot.
gnuplot is a freely available, command-driven graphical display tool for
Unix. It compiles and works quite well on a number of Unix flavours as
well as other operating systems. The following module enables sending
display requests to gnuplot through simple C calls.
*/
/*--------------------------------------------------------------------------*/
/*
$Id: gnuplot_i.h,v 1.1 2003/02/12 12:23:29 kurri Exp $
[...352 lines suppressed...]
Plots out a curve of given equation. The general form of the
equation is y=f(x), you only provide the f(x) side of the equation.
Example:
@code
gnuplot_ctrl *h ;
char eq[80] ;
h = gnuplot_init() ;
strcpy(eq, "sin(x) * cos(2*x)") ;
gnuplot_plot_equation(h, eq, "sine wave", normal) ;
gnuplot_close(h) ;
@endcode
*/
/*--------------------------------------------------------------------------*/
void gnuplot_plot_equation(gnuplot_ctrl * h, char * equation, char * title) ;
#endif
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/pca/Makefile.am,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Makefile.am 11 Feb 2003 23:24:25 -0000 1.4
--- Makefile.am 12 Feb 2003 12:23:29 -0000 1.5
***************
*** 10,12 ****
pca_LDADD = $(GSL_LIB) $(BLAS_LIB)
! INCLUDES = -Ignuplot_i-2.6/src
--- 10,12 ----
pca_LDADD = $(GSL_LIB) $(BLAS_LIB)
! EXTRA_DIST = gnuplot_i.h
|
|
From: <ku...@us...> - 2003-02-12 12:23:32
|
Update of /cvsroot/basedb/basedb/src/include In directory sc8-pr-cvs1:/tmp/cvs-serv1896/src/include Added Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... --- NEW FILE: Makefile.am --- ## Process this file with automake to produce Makefile.in ## ## $Id: Makefile.am,v 1.1 2003/02/12 12:23:30 kurri Exp $ EXTRA_DIST = basefile.h shhopt.h |
|
From: <ku...@us...> - 2003-02-12 12:23:32
|
Update of /cvsroot/basedb/basedb/plugins/src/mds In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/mds Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/mds/Makefile.am,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Makefile.am 11 Feb 2003 23:24:23 -0000 1.3 --- Makefile.am 12 Feb 2003 12:23:29 -0000 1.4 *************** *** 12,13 **** --- 12,15 ---- INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) + + EXTRA_DIST = MDSWrapper.h fastsqrt.h mds_algo.h |
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From: <ku...@us...> - 2003-02-12 12:23:32
|
Update of /cvsroot/basedb/basedb/plugins/src/normalizers In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/normalizers Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/Makefile.am,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** Makefile.am 11 Feb 2003 23:24:24 -0000 1.2 --- Makefile.am 12 Feb 2003 12:23:29 -0000 1.3 *************** *** 17,18 **** --- 17,20 ---- INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) + + EXTRA_DIST = lowess.hh median.hh microarr_point.hh |
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From: <ku...@us...> - 2003-02-12 12:23:32
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/source In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/clustering/Cgraph/source Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/source/Makefile.am,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Makefile.am 11 Feb 2003 23:24:23 -0000 1.3 --- Makefile.am 12 Feb 2003 12:23:29 -0000 1.4 *************** *** 13,14 **** --- 13,18 ---- INCLUDES = -I/usr/include/X11 -I../include + + EXTRA_DIST = \ + cgaxes.h cgfont.h cglobals.h common.h PS_font_names.h \ + version.h |
|
From: <ku...@us...> - 2003-02-12 12:23:31
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/include In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/clustering/Cgraph/include Added Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... --- NEW FILE: Makefile.am --- ## Process this file with automake to produce Makefile.in ## ## $Id: Makefile.am,v 1.1 2003/02/12 12:23:29 kurri Exp $ EXTRA_DIST = cgraph.h |
|
From: <ku...@us...> - 2003-02-12 12:23:31
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/clustering/Cgraph Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/Makefile.am,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** Makefile.am 6 Feb 2003 00:43:34 -0000 1.2 --- Makefile.am 12 Feb 2003 12:23:28 -0000 1.3 *************** *** 1,3 **** ! # $Id$ ! SUBDIRS = source --- 1,5 ---- ! ## Process this file with automake to produce Makefile.in ! ## ! ## $Id$ ! SUBDIRS = include source |
|
From: <ku...@us...> - 2003-02-12 12:23:31
|
Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv1896/include/web
Modified Files:
Makefile.am
Log Message:
Continued fixing of automake/autoconfig/configure ...
Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/Makefile.am,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Makefile.am 12 Feb 2003 00:54:47 -0000 1.1
--- Makefile.am 12 Feb 2003 12:23:28 -0000 1.2
***************
*** 5,9 ****
includewebdir = $(prefix)/include/web
! includeweb_SCRIPTS = \
array_common.inc.php assay_common.inc.php clust_common.inc.php \
experiment_common.inc.php gene_common.inc.php help.inc.php \
--- 5,9 ----
includewebdir = $(prefix)/include/web
! includeweb_HEADERS = \
array_common.inc.php assay_common.inc.php clust_common.inc.php \
experiment_common.inc.php gene_common.inc.php help.inc.php \
|
|
From: <ku...@us...> - 2003-02-12 12:23:31
|
Update of /cvsroot/basedb/basedb/plugins/src/clustering In directory sc8-pr-cvs1:/tmp/cvs-serv1896/plugins/src/clustering Modified Files: Makefile.am Log Message: Continued fixing of automake/autoconfig/configure ... Index: Makefile.am =================================================================== RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Makefile.am,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** Makefile.am 11 Feb 2003 23:24:22 -0000 1.3 --- Makefile.am 12 Feb 2003 12:23:28 -0000 1.4 *************** *** 9,13 **** plugin_PROGRAMS = basehclust drawassaytree drawgenetree drawmatrix findsubtree ! plugin_SCRIPTS = clusteringscript basehclust_SOURCES = \ --- 9,13 ---- plugin_PROGRAMS = basehclust drawassaytree drawgenetree drawmatrix findsubtree ! dist_plugin_SCRIPTS = clusteringscript basehclust_SOURCES = \ *************** *** 34,35 **** --- 34,42 ---- INCLUDES = -I@top_srcdir@/$(BASE_INCLUDE_LOCATION) -ICgraph/include + + EXTRA_DIST = \ + Algorithms.h AllClosestPairs.h AssayAnnotation.h AssayTree.h \ + BaseClustering.h BruteForce.h ClosestPairs.h Cluster.h ClusterTree.h \ + CongaLine.h Distances.h Error.h FastPair.h GeneTree.h MergeNode.h \ + MergeReporter.h MultiConga.h Neighbors.h NoClusteringCP.h PointSet.h \ + Quadtree.h SortedArray.h StoreMergeReporter.h Vector.h |
|
From: <ku...@us...> - 2003-02-12 12:22:11
|
Update of /cvsroot/basedb/basedb/documentation/faq
In directory sc8-pr-cvs1:/tmp/cvs-serv1581
Modified Files:
general.tex
Log Message:
Index: general.tex
===================================================================
RCS file: /cvsroot/basedb/basedb/documentation/faq/general.tex,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** general.tex 1 Feb 2003 20:38:57 -0000 1.5
--- general.tex 12 Feb 2003 12:22:08 -0000 1.6
***************
*** 62,68 ****
software}{http://www.gnu.org/philosophy/free-software-for-freedom.html}.
! Does open-source mean that one can propose extensions to the software
! and that it gets included in a next release, if indeed accepted by the
! developers?
I've never heard of any software license, proprietary or otherwise,
--- 62,68 ----
software}{http://www.gnu.org/philosophy/free-software-for-freedom.html}.
! \textit{Does open-source mean that one can propose extensions to the
! software and that it gets included in a next release, if indeed
! accepted by the developers?}
I've never heard of any software license, proprietary or otherwise,
|
