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

From: <tr...@us...> - 2003-02-13 10:28:37

Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/bin

Modified Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

Index: .cvsignore
===================================================================
RCS file: /cvsroot/basedb/basedb/bin/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** .cvsignore	3 Feb 2003 20:13:16 -0000	1.1
--- .cvsignore	13 Feb 2003 10:16:31 -0000	1.2
***************
*** 4,5 ****
--- 4,9 ----
  spotImageChopper
  tifftopnm
+ Makefile.in
+ Makefile
+ baseftpd
+ ftpdspawner

[basedb-cvs] basedb .cvsignore,1.2,1.3

From: <tr...@us...> - 2003-02-13 10:28:37

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv26240

Modified Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

Index: .cvsignore
===================================================================
RCS file: /cvsroot/basedb/basedb/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** .cvsignore	11 Feb 2003 14:53:13 -0000	1.2
--- .cvsignore	13 Feb 2003 10:16:30 -0000	1.3
***************
*** 12,13 ****
--- 12,16 ----
  config.sub
  configure
+ stamp-h
+ stamp-h.in
+ stamp-h1

[basedb-cvs] basedb/plugins/src/clustering/Cgraph/include .cvsignore,NONE,1.1

From: <tr...@us...> - 2003-02-13 10:27:56

Update of /cvsroot/basedb/basedb/plugins/src/clustering/Cgraph/include
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/plugins/src/clustering/Cgraph/include

Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile

[basedb-cvs] basedb/sql .cvsignore,NONE,1.1

From: <tr...@us...> - 2003-02-13 10:27:56

Update of /cvsroot/basedb/basedb/sql
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/sql

Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile

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

From: <tr...@us...> - 2003-02-13 10:27:55

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/www

Modified Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

Index: .cvsignore
===================================================================
RCS file: /cvsroot/basedb/basedb/www/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** .cvsignore	14 Aug 2002 16:46:22 -0000	1.1
--- .cvsignore	13 Feb 2003 10:16:37 -0000	1.2
***************
*** 1 ****
--- 1,3 ----
  getconfig.inc.php
+ Makefile
+ Makefile.in

[basedb-cvs] basedb/www/plotapplet .cvsignore,NONE,1.1

From: <tr...@us...> - 2003-02-13 10:27:54

Update of /cvsroot/basedb/basedb/www/plotapplet
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/www/plotapplet

Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile

[basedb-cvs] basedb/include/classes .cvsignore,NONE,1.1 array.inc.php,1.19,1.20

From: <tr...@us...> - 2003-02-13 10:27:41

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/include/classes

Modified Files:
	array.inc.php 
Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile

Index: array.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/array.inc.php,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** array.inc.php	2 Feb 2003 13:44:00 -0000	1.19
--- array.inc.php	13 Feb 2003 10:16:32 -0000	1.20
***************
*** 521,527 ****
  
  		$query = "SELECT e.block, e.x, e.y, r.`reporterId`, r.`geneName` ".
! 			"FROM Element e, Well w, Probe p, Reporter r ".
! 			"WHERE e.`arrayType` = $atid AND w.id = e.well ".
! 			"AND p.id = w.probe AND r.id = p.reporter ".
  			"ORDER BY block, x, y";
  		$res = query($query);
--- 521,528 ----
  
  		$query = "SELECT e.block, e.x, e.y, r.`reporterId`, r.`geneName` ".
! 			"FROM Element e LEFT JOIN Well w ON w.id = e.well ".
! 			"CROSS JOIN Probe p ON p.id = w.probe ".
! 			"CROSS JOIN Reporter r ON r.id = p.reporter ".
! 			"WHERE e.`arrayType` = $atid ".
  			"ORDER BY block, x, y";
  		$res = query($query);

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

From: <tr...@us...> - 2003-02-13 10:23:44

Update of /cvsroot/basedb/basedb/src/include
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/src/include

Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile

[basedb-cvs] basedb/www/img .cvsignore,NONE,1.1

From: <tr...@us...> - 2003-02-13 10:23:44

Update of /cvsroot/basedb/basedb/www/img
In directory sc8-pr-cvs1:/tmp/cvs-serv26240/www/img

Added Files:
	.cvsignore 
Log Message:
Ignoring Makefile.in but not Makefile.am

--- NEW FILE: .cvsignore ---
Makefile.in
Makefile
.xvpics

[basedb-cvs] basedb/www arraytype_gal.phtml,1.4,1.5

From: <tr...@us...> - 2003-02-13 08:58:27

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv20970

Modified Files:
	arraytype_gal.phtml 
Log Message:
Added error for reporter mapped designs

Index: arraytype_gal.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/arraytype_gal.phtml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** arraytype_gal.phtml	2 Feb 2003 13:44:01 -0000	1.4
--- arraytype_gal.phtml	13 Feb 2003 08:58:24 -0000	1.5
***************
*** 38,41 ****
--- 38,47 ----
  	else if(!$at->getPrinted())
  		$err = "That array design doesn't have a print map yet";
+ 	else if($at->getPrinted() == 2)
+ 	{
+ 		$err = "The array design has a reporter map rather than a print ".
+ 			"map. You can download that file directly from the array ".
+ 			"design page.";
+ 	}
  	else
  	{
***************
*** 51,56 ****
  		{
  			$b =& $blocks[$i];
! 			echo "\"Block$b[blockNum]=$b[xOrigin], $b[yOrigin], $b[featureDiameter], ".
! 				"$b[xFeatures], $b[xSpacing], $b[yFeatures], $b[ySpacing]\"\n";
  		}
  		unset($b);
--- 57,63 ----
  		{
  			$b =& $blocks[$i];
! 			echo "\"Block$b[blockNum]=$b[xOrigin], $b[yOrigin], ".
! 				"$b[featureDiameter], $b[xFeatures], $b[xSpacing], ".
! 				"$b[yFeatures], $b[ySpacing]\"\n";
  		}
  		unset($b);

[basedb-cvs] basedb/include/classes acquisition.inc.php,1.12,1.13 search.inc.php,1.31,1.32

From: <tr...@us...> - 2003-02-13 08:48:19

Update of /cvsroot/basedb/basedb/include/classes
In directory sc8-pr-cvs1:/tmp/cvs-serv17896/include/classes

Modified Files:
	acquisition.inc.php search.inc.php 
Log Message:
Added image set list and fixed ware links

Index: acquisition.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/acquisition.inc.php,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** acquisition.inc.php	3 Feb 2003 08:51:13 -0000	1.12
--- acquisition.inc.php	13 Feb 2003 08:47:45 -0000	1.13
***************
*** 86,100 ****
  	{
  		// Add more fields and operators here
! 		$fields = array();
  
  		$search->makeWhere($fields);
  		$search->addExtraWhere(Item::whereRemoved("ia", $removed));
  		$search->addExtraWhere(Item::whereShared("ia", $user));
! 		$search->addExtraWhere("ia.hybridization = ".(int)$hybid);
  
  		$query = "SELECT COUNT(*) ".
[...69 lines suppressed...]
  			"WHERE hw.id = ia.scanner AND ug.id = ia.owner ".
  			$search->getWhere()." ".$search->getExtraWhere()." ".
  			"GROUP BY ia.id $ss2 $ob ".$search->makeLimit();
--- 132,147 ----
  
  		$query = "SELECT ia.*, $ss1 COUNT(DISTINCT im.id) AS images, ".
! 			db_string_concat(array("hw.name", "' '", "hw.version")).
! 			" AS hardware, hw.removed AS `hardwareRemoved`, ".
! 			Item::whereShared("hw", $user)." AS `hardwareRead`, ".
! 			"h.name AS `hybName`, h.removed AS `hybRemoved`, ".
! 			Item::whereShared("h", $user)." AS `hybRead`, ".
  			"COUNT(DISTINCT r.id) AS raws, ug.name AS `userName` ".
! 			"FROM Hardware hw, UserGroup ug, Hybridization h, ".
! 			"ImageAcquisition ia ".
  			"LEFT JOIN Image im ON im.`imageAcquisition` = ia.id ".
  			"LEFT JOIN RawBioAssay r ON r.`imageAcquisition` = ia.id ".
  			"WHERE hw.id = ia.scanner AND ug.id = ia.owner ".
+ 			"AND h.id = ia.hybridization ".
  			$search->getWhere()." ".$search->getExtraWhere()." ".
  			"GROUP BY ia.id $ss2 $ob ".$search->makeLimit();

Index: search.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/classes/search.inc.php,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** search.inc.php	12 Feb 2003 16:16:47 -0000	1.31
--- search.inc.php	13 Feb 2003 08:47:45 -0000	1.32
***************
*** 111,120 ****
  //   sample, arraytype, extract, hybridization, plate, user, value, labeled,
  //   raw, exp, gene, array, reporter, upload, annottype, ware, protocol,
! //   label, program, rawdata
  //  For UserSearch:
  //   plate, sample, extract, labeled, hybridization, value, arraytype, well,
  //   wizzzard, raw, exp, user, gene, reporterlist, program, news, acq, acq_img,
  //   ware, acq_rba, platetype, print, array, reporter, upload, annottype,
! //   protocol, label, rawdata
  //  For BioAssaySearch:
  //   ge_gene, ge_onegene, bioassay
--- 111,120 ----
  //   sample, arraytype, extract, hybridization, plate, user, value, labeled,
  //   raw, exp, gene, array, reporter, upload, annottype, ware, protocol,
! //   label, program, rawdata, acquisition
  //  For UserSearch:
  //   plate, sample, extract, labeled, hybridization, value, arraytype, well,
  //   wizzzard, raw, exp, user, gene, reporterlist, program, news, acq, acq_img,
  //   ware, acq_rba, platetype, print, array, reporter, upload, annottype,
! //   protocol, label, rawdata, acquisition
  //  For BioAssaySearch:
  //   ge_gene, ge_onegene, bioassay

[basedb-cvs] basedb/www acquisition_list.phtml,NONE,1.1 Makefile.am,1.3,1.4 hyb_edit.phtml,1.52,1.53 left.phtml,1.67,1.68

From: <tr...@us...> - 2003-02-13 08:47:52

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv17896/www

Modified Files:
	Makefile.am hyb_edit.phtml left.phtml 
Added Files:
	acquisition_list.phtml 
Log Message:
Added image set list and fixed ware links

--- NEW FILE: acquisition_list.phtml ---
<?
// $Id: acquisition_list.phtml,v 1.1 2003/02/13 08:47:47 troein Exp $
//
// 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.
//
// BASE is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 2
// of the License, or (at your option) any later version.
//
// BASE is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
[...73 lines suppressed...]
			"<td>".wareArrLink("hard", $a)."</td>".
			"<td>".htmldate($a["scanDate"])."</td>".
			"<td>".html($a["userName"])."</td>".
			"<td>".groupAccessCheckbox($a["id"])."</td>".
			"<td>".groupInfo($a, $users)."</td>".
			"<td>".worldInfo($a)."</td>".
			"<td>".html($a["images"])."</td>".
			"<td>".implode(", ", $rlink)."</td>".
			"</tr>\n";
	}
	$cols = count($headerfields);

	if($acqs)
		groupAccessFooter($cols, $curUser);
	showDelLinks($cols);
?>
</table>
<?
	htmlEnd();
?>

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/www/Makefile.am,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile.am	12 Feb 2003 17:00:49 -0000	1.3
--- Makefile.am	13 Feb 2003 08:47:47 -0000	1.4
***************
*** 35,40 ****
    sampleannot_edit.phtml sampleannot_list.phtml sample_edit.phtml	\
    sample_list.phtml sampletissue_tree.phtml settings.phtml		\
!   showtext.phtml spotinfo.phtml test.phtml trans_create.phtml		\
    upload_list.phtml user_edit.phtml usergroup_edit.phtml		\
    usergroup_list.phtml user_list.phtml ware_edit.phtml ware_list.phtml	\
!   wizzzard_edit.phtml wizzzard_list.phtml
--- 35,40 ----
    sampleannot_edit.phtml sampleannot_list.phtml sample_edit.phtml	\
    sample_list.phtml sampletissue_tree.phtml settings.phtml		\
!   showtext.phtml spotinfo.phtml trans_create.phtml		\
    upload_list.phtml user_edit.phtml usergroup_edit.phtml		\
    usergroup_list.phtml user_list.phtml ware_edit.phtml ware_list.phtml	\
!   wizzzard_edit.phtml wizzzard_list.phtml acquisition_list.phtml

Index: hyb_edit.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/hyb_edit.phtml,v
retrieving revision 1.52
retrieving revision 1.53
diff -C2 -d -r1.52 -r1.53
*** hyb_edit.phtml	2 Feb 2003 15:31:52 -0000	1.52
--- hyb_edit.phtml	13 Feb 2003 08:47:47 -0000	1.53
***************
*** 443,447 ****
  		ImageAcquisition::prepareSearch($search, $hybid, $curUser, 0,
  			showDelValue());
! 		$headerfields = array("Name", "Scanner", "Version", "Scan date",
  			"Owner", "[<a href=javascript:selAll(1)>A</a>&nbsp;".
  			"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
--- 443,447 ----
  		ImageAcquisition::prepareSearch($search, $hybid, $curUser, 0,
  			showDelValue());
! 		$headerfields = array("Name", "Hybridization", "Scanner", "Scan date",
  			"Owner", "[<a href=javascript:selAll(1)>A</a>&nbsp;".
  			"<a href=javascript:selAll(0)>N</a>]", "Group", "World",
***************
*** 449,452 ****
--- 449,453 ----
  		$sortorder = array(1, 1, 1, -1, 1, 0, 0, 0, 1, 1);
  		$defsort = 0;
+ 		unset($headerfields[1]);
  		if($hyb->mayEdit($curUser))
  		{
***************
*** 482,498 ****
  				$rlink[] = html("");
  
- 			$scanner = html($a["scannerName"]);
- 			if($a["scannerShared"])
- 			{
- 				$scanner = "<a href='ware_edit.phtml".
- 					"?i_type=hard&i_w=$a[scanner]'>".
- 					$scanner."</a>";
- 			}
- 
  			echo "<tr bgcolor=$tdbg[$odd]>".
  				"<td><a ".href("hyb_image.phtml?i_acq=$a[id]", 2).">".
  					html($a["name"])."</a></td>".
! 				"<td>".$scanner."</td>".
! 				"<td>".html($a["scannerVersion"])."</td>".
  				"<td>".htmldate($a["scanDate"])."</td>".
  				"<td>".html($a["userName"])."</td>".
--- 483,490 ----
  				$rlink[] = html("");
  
  			echo "<tr bgcolor=$tdbg[$odd]>".
  				"<td><a ".href("hyb_image.phtml?i_acq=$a[id]", 2).">".
  					html($a["name"])."</a></td>".
! 				"<td>".wareArrLink("hard", $a)."</td>".
  				"<td>".htmldate($a["scanDate"])."</td>".
  				"<td>".html($a["userName"])."</td>".
***************
*** 504,508 ****
  				"</tr>\n";
  		}
! 		$cols = 10;
  		if($addscan != "")
  			echo "<tr><td colspan=$cols>$addscan</td></tr>\n";
--- 496,500 ----
  				"</tr>\n";
  		}
! 		$cols = count($headerfields);
  		if($addscan != "")
  			echo "<tr><td colspan=$cols>$addscan</td></tr>\n";

Index: left.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/left.phtml,v
retrieving revision 1.67
retrieving revision 1.68
diff -C2 -d -r1.67 -r1.68
*** left.phtml	3 Feb 2003 08:54:12 -0000	1.67
--- left.phtml	13 Feb 2003 08:47:48 -0000	1.68
***************
*** 201,204 ****
--- 201,205 ----
  	href="index.phtml?l=hyb&m=hyb_list.phtml">Hybridizations</a></td></tr>
  <tr><td><a target=main href="hyb_list.phtml">Hybridizations</a></td></tr>
+ <tr><td><a target=main href="acquisition_list.phtml">Image sets</a></td></tr>
  <tr><td><img src='img/1.gif' alt='' width=1 height=1></td></tr>
  <tr><td><a target=main href="ware_list.phtml?i_type=hard"

[basedb-cvs] basedb/include/web links_common.inc.php,1.13,1.14

From: <tr...@us...> - 2003-02-13 08:47:51

Update of /cvsroot/basedb/basedb/include/web
In directory sc8-pr-cvs1:/tmp/cvs-serv17896/include/web

Modified Files:
	links_common.inc.php 
Log Message:
Added image set list and fixed ware links

Index: links_common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/web/links_common.inc.php,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** links_common.inc.php	3 Feb 2003 08:54:11 -0000	1.13
--- links_common.inc.php	13 Feb 2003 08:47:47 -0000	1.14
***************
*** 295,299 ****
  		return html($arr["${type}ware"]).remMark($arr["${type}wareRemoved"]);
  	return "<a ".href("ware_edit.phtml?i_type=$type&i_w=".
! 		(int)$arr["featureSoftware"], 2).">".
  		html($arr["${type}ware"])."</a>".remMark($arr["${type}wareRemoved"]);
  }
--- 295,299 ----
  		return html($arr["${type}ware"]).remMark($arr["${type}wareRemoved"]);
  	return "<a ".href("ware_edit.phtml?i_type=$type&i_w=".
! 		(int)$arr[$type == "soft" ? "featureSoftware" : "scanner"], 2).">".
  		html($arr["${type}ware"])."</a>".remMark($arr["${type}wareRemoved"]);
  }

[basedb-cvs] basedb/include/common common.inc.php,1.18,1.19

From: <tr...@us...> - 2003-02-13 08:47:51

Update of /cvsroot/basedb/basedb/include/common
In directory sc8-pr-cvs1:/tmp/cvs-serv17896/include/common

Modified Files:
	common.inc.php 
Log Message:
Added image set list and fixed ware links

Index: common.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/include/common/common.inc.php,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** common.inc.php	1 Feb 2003 17:18:50 -0000	1.18
--- common.inc.php	13 Feb 2003 08:47:46 -0000	1.19
***************
*** 106,110 ****
  	// the config file but then it wasn't updated with each new version and
  	// that was... well, not a Good Thing.
! 	$config["codename"]			= "BASE 1.2.0RC1";
  
  	// Import variables into the global scope in a controlled fashion. Only
--- 106,110 ----
  	// the config file but then it wasn't updated with each new version and
  	// that was... well, not a Good Thing.
! 	$config["codename"]			= "BASE 1.2.0RC2";
  
  	// Import variables into the global scope in a controlled fashion. Only

[basedb-cvs] basedb README,1.20,1.21

From: <tr...@us...> - 2003-02-12 17:57:10

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv3538

Modified Files:
	README 
Log Message:
Updated to rc2

Index: README
===================================================================
RCS file: /cvsroot/basedb/basedb/README,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** README	12 Feb 2003 01:06:49 -0000	1.20
--- README	12 Feb 2003 17:57:02 -0000	1.21
***************
*** 2,6 ****
  this document.
  
! *** Installation documentation for BASE 1.2.0RC1
  
  First of all, a general disclaimer: It is assumed that you know what you're
--- 2,6 ----
  this document.
  
! *** Installation documentation for BASE 1.2.0RC2
  
[...268 lines suppressed...]
! to give us a chance to help you. Most importantly: What you did, what
! happened and was shown on the screen, and what appeared in the error log(s).
  
  
  
! The FTP server: (not working in 1.2.0RC1)
  
  Included with BASE is an FTP server which can be used to upload/download
--- 256,266 ----
  
  In general, when reporting a problem/bug, please include enough information
! to give us a chance to help you. Most importantly: What version of BASE you
! are using, what you did, what happened and was shown on the screen, and what
! appeared in the error log(s).
  
  
  
! The FTP server: (now working again, but this text is outdated)
  
  Included with BASE is an FTP server which can be used to upload/download

[basedb-cvs] basedb/plugins/src/merge_bioassays Makefile.am,1.2,1.3

From: <tr...@us...> - 2003-02-12 17:01:20

Update of /cvsroot/basedb/basedb/plugins/src/merge_bioassays
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/plugins/src/merge_bioassays

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/merge_bioassays/Makefile.am,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile.am	11 Feb 2003 23:24:23 -0000	1.2
--- Makefile.am	12 Feb 2003 17:00:47 -0000	1.3
***************
*** 3,7 ****
  ## $Id$
  
! plugindir = $(prefix)/plugins_bin
  
  plugin_PROGRAMS = merge_bioassays
--- 3,7 ----
  ## $Id$
  
! plugindir = $(prefix)/plugins/bin
  
  plugin_PROGRAMS = merge_bioassays

[basedb-cvs] basedb/plugins/src/mds Makefile.am,1.4,1.5

From: <tr...@us...> - 2003-02-12 17:01:20

Update of /cvsroot/basedb/basedb/plugins/src/mds
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/plugins/src/mds

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/mds/Makefile.am,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Makefile.am	12 Feb 2003 12:23:29 -0000	1.4
--- Makefile.am	12 Feb 2003 17:00:47 -0000	1.5
***************
*** 3,7 ****
  ## $Id$
  
! plugindir = $(prefix)/plugins_bin
  
  plugin_PROGRAMS = mds
--- 3,7 ----
  ## $Id$
  
! plugindir = $(prefix)/plugins/bin
  
  plugin_PROGRAMS = mds

[basedb-cvs] basedb/plugins/src/clustering Makefile.am,1.4,1.5

From: <tr...@us...> - 2003-02-12 17:01:20

Update of /cvsroot/basedb/basedb/plugins/src/clustering
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/plugins/src/clustering

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/clustering/Makefile.am,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** Makefile.am	12 Feb 2003 12:23:28 -0000	1.4
--- Makefile.am	12 Feb 2003 17:00:47 -0000	1.5
***************
*** 5,9 ****
  SUBDIRS	= Cgraph
  
! plugindir = $(prefix)/plugins_bin
  
  plugin_PROGRAMS = basehclust drawassaytree drawgenetree drawmatrix findsubtree
--- 5,9 ----
  SUBDIRS	= Cgraph
  
! plugindir = $(prefix)/plugins/bin
  
  plugin_PROGRAMS = basehclust drawassaytree drawgenetree drawmatrix findsubtree

[basedb-cvs] basedb Makefile.am,1.3,1.4 configure.ac,1.5,1.6

From: <tr...@us...> - 2003-02-12 17:01:19

Update of /cvsroot/basedb/basedb
In directory sc8-pr-cvs1:/tmp/cvs-serv7975

Modified Files:
	Makefile.am configure.ac 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/Makefile.am,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile.am	12 Feb 2003 12:23:28 -0000	1.3
--- Makefile.am	12 Feb 2003 17:00:46 -0000	1.4
***************
*** 3,9 ****
  ## $Id$
  
! SUBDIRS = src plugins include www
  
  prefixdir = $(prefix)
  
! dist_prefix_DATA = example_config.inc.php
--- 3,9 ----
  ## $Id$
  
! SUBDIRS = src plugins include www bin misc sql
  
  prefixdir = $(prefix)
  
! dist_prefix_DATA = README example_config.inc.php

Index: configure.ac
===================================================================
RCS file: /cvsroot/basedb/basedb/configure.ac,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** configure.ac	12 Feb 2003 16:21:15 -0000	1.5
--- configure.ac	12 Feb 2003 17:00:46 -0000	1.6
***************
*** 338,341 ****
--- 338,342 ----
  #AC_OUTPUT
  AC_OUTPUT([Makefile
+ 		 bin/Makefile
  		 include/Makefile
  		 include/classes/Makefile
***************
*** 344,347 ****
--- 345,349 ----
  		 include/local_distr/Makefile
  		 include/web/Makefile
+ 		 misc/Makefile
                   plugins/Makefile
                   plugins/src/Makefile
***************
*** 354,357 ****
--- 356,360 ----
                   plugins/src/normalizers/Makefile
                   plugins/src/pca/Makefile
+ 		 sql/Makefile
                   src/Makefile
                   src/assayImporter/Makefile

[basedb-cvs] basedb/www Makefile.am,1.2,1.3

From: <tr...@us...> - 2003-02-12 17:00:52

Update of /cvsroot/basedb/basedb/www
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/www

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/www/Makefile.am,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Makefile.am	12 Feb 2003 12:23:30 -0000	1.2
--- Makefile.am	12 Feb 2003 17:00:49 -0000	1.3
***************
*** 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		\
--- 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		\
***************
*** 15,19 ****
    assay_plotter.phtml assay_table.phtml assay_view.phtml		\
    bio_main.phtml closeme.phtml clust_image.phtml clust_index.phtml	\
!   clust_left.phtml clust_main.phtml clust_top.phtml codesize		\
    data_main.phtml download.phtml downtime.phtml				\
    example_getconfig.inc.php experiment_edit.phtml			\
--- 15,19 ----
    assay_plotter.phtml assay_table.phtml assay_view.phtml		\
    bio_main.phtml closeme.phtml clust_image.phtml clust_index.phtml	\
!   clust_left.phtml clust_main.phtml clust_top.phtml 			\
    data_main.phtml download.phtml downtime.phtml				\
    example_getconfig.inc.php experiment_edit.phtml			\

[basedb-cvs] basedb/sql Makefile.am,NONE,1.1

From: <tr...@us...> - 2003-02-12 17:00:51

Update of /cvsroot/basedb/basedb/sql
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/sql

Added Files:
	Makefile.am 
Log Message:
Added and removed files

--- NEW FILE: Makefile.am ---
## Process this file with automake to produce Makefile.in
##
## $Id: Makefile.am,v 1.1 2003/02/12 17:00:48 troein Exp $

sqldir = $(prefix)/sql

dist_sql_DATA = base_mysql.sql base_mysql_data.sql base_pgsql.sql

[basedb-cvs] basedb/plugins/src/pca Makefile.am,1.5,1.6

From: <tr...@us...> - 2003-02-12 17:00:51

Update of /cvsroot/basedb/basedb/plugins/src/pca
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/plugins/src/pca

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/pca/Makefile.am,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** Makefile.am	12 Feb 2003 12:23:29 -0000	1.5
--- Makefile.am	12 Feb 2003 17:00:48 -0000	1.6
***************
*** 3,7 ****
  ## $Id$
  
! plugindir = $(prefix)/plugins_bin
  
  plugin_PROGRAMS = pca
--- 3,7 ----
  ## $Id$
  
! plugindir = $(prefix)/plugins/bin
  
  plugin_PROGRAMS = pca

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

From: <tr...@us...> - 2003-02-12 17:00:50

Update of /cvsroot/basedb/basedb/plugins/src/normalizers
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/plugins/src/normalizers

Modified Files:
	Makefile.am 
Log Message:
Added and removed files

Index: Makefile.am
===================================================================
RCS file: /cvsroot/basedb/basedb/plugins/src/normalizers/Makefile.am,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Makefile.am	12 Feb 2003 12:23:29 -0000	1.3
--- Makefile.am	12 Feb 2003 17:00:47 -0000	1.4
***************
*** 3,7 ****
  ## $Id$
  
! plugindir = $(prefix)/plugins_bin
  
  plugin_PROGRAMS    = lowess medianratio
--- 3,7 ----
  ## $Id$
  
! plugindir = $(prefix)/plugins/bin
  
  plugin_PROGRAMS    = lowess medianratio

[basedb-cvs] basedb/bin Makefile.am,NONE,1.1

From: <tr...@us...> - 2003-02-12 17:00:50

Update of /cvsroot/basedb/basedb/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/bin

Added Files:
	Makefile.am 
Log Message:
Added and removed files

--- NEW FILE: Makefile.am ---
## Process this file with automake to produce Makefile.in
##
## $Id: Makefile.am,v 1.1 2003/02/12 17:00:46 troein Exp $

dist_bin_SCRIPTS = backup.sh base.server baseftpd.php checkDatabase.php \
  dbmigrate_107_to_12.php dbmigrate_to_107.php helpParser.php \
  jobController.php schema_mysql_to_pgsql.php startBase.php stopBase.php

[basedb-cvs] basedb/misc Makefile.am,NONE,1.1

From: <tr...@us...> - 2003-02-12 17:00:50

Update of /cvsroot/basedb/basedb/misc
In directory sc8-pr-cvs1:/tmp/cvs-serv7975/misc

Added Files:
	Makefile.am 
Log Message:
Added and removed files

--- NEW FILE: Makefile.am ---
## Process this file with automake to produce Makefile.in
##
## $Id: Makefile.am,v 1.1 2003/02/12 17:00:46 troein Exp $

miscdir = $(prefix)/misc

dist_misc_DATA = glyphplot.ps webhelp.txt welcome.html

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