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[basedb-cvs] basedb/www assay_plotter.phtml,1.7,1.8 bioassay.inc.php,1.38,1.39 experiment_plotter.phtml,1.11,1.12 item.inc.php,1.28,1.29 misc.inc.php,1.36,1.37 raw.inc.php,1.38,1.39 searchhtml.inc.php,1.40,1.41 spotinfo.phtml,1.9,1.10 test.phtml,1.47,1.48 trans_create.phtml,1.25,1.26
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From: <tr...@us...> - 2002-09-12 11:45:29
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Update of /cvsroot/basedb/basedb/www
In directory usw-pr-cvs1:/tmp/cvs-serv27760
Modified Files:
assay_plotter.phtml bioassay.inc.php experiment_plotter.phtml
item.inc.php misc.inc.php raw.inc.php searchhtml.inc.php
spotinfo.phtml test.phtml trans_create.phtml
Log Message:
added SNR to plot and filtering, plus some misc stuff
Index: assay_plotter.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/assay_plotter.phtml,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** assay_plotter.phtml 29 Aug 2002 16:51:33 -0000 1.7
--- assay_plotter.phtml 12 Sep 2002 11:45:25 -0000 1.8
***************
*** 61,65 ****
// Limit the width and height
if($format == "txt") $minmax = array(24, 97, 40, 12, 46, 25);
! else if($format == "png") $minmax = array(40, 1280, 640, 30, 960, 480);
else $minmax = array(0, 1280, 640, 0, 960, 480);
--- 61,65 ----
// Limit the width and height
if($format == "txt") $minmax = array(24, 97, 40, 12, 46, 25);
! else if($format == "png") $minmax = array(40, 1280, 800, 30, 960, 600);
else $minmax = array(0, 1280, 640, 0, 960, 480);
***************
*** 88,96 ****
$assayColsY = array_merge($assayColsX, array("Histogram"));
$annotCols = array("(raw) Block", "(raw) Flags", "log2(ratio)",
! "Plate N", "Plate N-1");
$plotAnnot = isset($i_annot) ? max(-1, min(count($annotCols) - 1,
(int)$i_annot)) : -1;
! $colorScale = $plotAnnot == 2;
if(!isset($i_ploty)) $i_ploty = 0;
--- 88,102 ----
$assayColsY = array_merge($assayColsX, array("Histogram"));
$annotCols = array("(raw) Block", "(raw) Flags", "log2(ratio)",
! "Plate N", "Plate N-1",
! "log2 SNR(means)", "log2 SNR(medians)",
! "log2 SNR(Ch1 mean)", "log2 SNR(Ch2 mean)",
! "log2 SNR(Ch1 median)", "log2 SNR(Ch2 median)"
! );
! $withColorScale = array(0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1);
! $withColorScale[-1] = 0;
$plotAnnot = isset($i_annot) ? max(-1, min(count($annotCols) - 1,
(int)$i_annot)) : -1;
! $colorScale = $withColorScale[$plotAnnot];
if(!isset($i_ploty)) $i_ploty = 0;
Index: bioassay.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/bioassay.inc.php,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** bioassay.inc.php 11 Sep 2002 10:35:12 -0000 1.38
--- bioassay.inc.php 12 Sep 2002 11:45:25 -0000 1.39
***************
*** 310,314 ****
"Growth (LIMS)",
"Bands (LIMS)",
! "Seq ver. (LIMS)"
);
}
--- 310,316 ----
"Growth (LIMS)",
"Bands (LIMS)",
! "Seq ver. (LIMS)",
! "Raw SNR(Ch1 mean)", "Raw SNR(Ch2 mean)",
[...113 lines suppressed...]
}
! if($third == 3 || $third == 4)
{
$extra .= " p.name AS `C`";
***************
*** 1141,1145 ****
$arr = array();
while($row =& db_fetch_row($res))
! $arr[] = $row;
return $arr;
}
--- 1180,1187 ----
$arr = array();
while($row =& db_fetch_row($res))
! {
! if(isset($row[0]) && isset($row[1]))
! $arr[] = $row;
! }
return $arr;
}
Index: experiment_plotter.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/experiment_plotter.phtml,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** experiment_plotter.phtml 5 Aug 2002 11:29:33 -0000 1.11
--- experiment_plotter.phtml 12 Sep 2002 11:45:26 -0000 1.12
***************
*** 89,93 ****
$rawCols = array("Mean(Mean FG)", "Mean(Mean BG)",
"% flagged", "Mean(Median FG)", "Mean(Median BG)",
! "Mean(Ch1 total int.)", "Mean(Ch2 total int.)");
$rawColsX = array("Raw data sets");
$annotCols = array("Owner", "Array print", "Hybridization date");
--- 89,96 ----
$rawCols = array("Mean(Mean FG)", "Mean(Mean BG)",
"% flagged", "Mean(Median FG)", "Mean(Median BG)",
! "Mean(Ch1 total int.)", "Mean(Ch2 total int.)",
! "Mean(SNR(Ch1 mean))", "Mean(SNR(Ch2 mean))",
! "Mean(SNR(Ch1 median))", "Mean(SNR(Ch2 median))"
! );
$rawColsX = array("Raw data sets");
$annotCols = array("Owner", "Array print", "Hybridization date");
***************
*** 382,387 ****
else
{
! fwrite($fd, "set title \"".addslashes(ereg_replace("[^[:print:]]",
! "", $annotCols[$plotAnnot].", ".$exp->getName()))."\"\n");
// Find all annotations and group the data points by them.
--- 385,390 ----
else
{
! fwrite($fd, "set title \"".addslashes(printable(
! $annotCols[$plotAnnot].", ".$exp->getName()))."\"\n");
// Find all annotations and group the data points by them.
***************
*** 407,412 ****
for(reset($rawnames); list($i, $n) = each($rawnames); )
{
! fwrite($fd, "set label \" ".addslashes(ereg_replace(
! "[^[:print:]]", "", $n))."\" at $i,0 $justify rotate\n");
}
--- 410,415 ----
for(reset($rawnames); list($i, $n) = each($rawnames); )
{
! fwrite($fd, "set label \" ".addslashes(printable($n)).
! "\" at $i,0 $justify rotate\n");
}
***************
*** 417,421 ****
if($ann == "") $ann = "not annotated";
fwrite($fd, ($f ? "plot" : ",")." '-' title \"".
! addslashes(ereg_replace("[^[:print:]]", "", $ann))."\"");
}
fwrite($fd, "\n");
--- 420,424 ----
if($ann == "") $ann = "not annotated";
fwrite($fd, ($f ? "plot" : ",")." '-' title \"".
! addslashes(printable($ann))."\"");
}
fwrite($fd, "\n");
Index: item.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/item.inc.php,v
retrieving revision 1.28
retrieving revision 1.29
diff -C2 -d -r1.28 -r1.29
*** item.inc.php 10 Sep 2002 23:05:33 -0000 1.28
--- item.inc.php 12 Sep 2002 11:45:26 -0000 1.29
***************
*** 32,38 ****
class Item
{
! var $type, $id, $name, $descr, $owner, $addedDate, $visible;
! function Item($type, $name, $descr, $owner, $addedDate, $id, $visible = 1)
{
$this->type = $type;
--- 32,39 ----
class Item
{
[...81 lines suppressed...]
! }
else
{
$query = "SELECT i.* FROM $this->type i, Shared$this->type s ".
! "WHERE s.item = i.id AND s.owner IN (0, $owner) ".
! "AND i.id = $id ".
! $this->sqlRemoved("i", $removed);
}
return $this->readQuery($query);
}
! function readOwned($id, $owner, $removed = NULL)
{
$id = (int)$id;
$owner = (int)$owner;
$query = "SELECT i.* FROM $this->type i ".
! "WHERE i.owner = $owner AND i.id = $id ".
! $this->sqlRemoved("i", $removed);
return $this->readQuery($query);
}
Index: misc.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/misc.inc.php,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** misc.inc.php 10 Sep 2002 23:06:00 -0000 1.36
--- misc.inc.php 12 Sep 2002 11:45:26 -0000 1.37
***************
*** 85,88 ****
--- 85,90 ----
else
{
+ // A Location header must have an absolute path. There will
+ // be no violation of the HTTP standard on my watch.
if($url == "" || substr($url, 0, 1) != "/")
$url = $config["urlpath"].$url;
Index: raw.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/raw.inc.php,v
retrieving revision 1.38
retrieving revision 1.39
diff -C2 -d -r1.38 -r1.39
*** raw.inc.php 10 Sep 2002 23:06:28 -0000 1.38
--- raw.inc.php 12 Sep 2002 11:45:26 -0000 1.39
***************
*** 706,710 ****
$arr = array();
while($row =& db_fetch_row($res))
! $arr[] = $row;
return $arr;
}
--- 706,713 ----
$arr = array();
while($row =& db_fetch_row($res))
! {
! if(isset($row[0]) && isset($row[1]))
! $arr[] = $row;
! }
return $arr;
}
***************
*** 716,719 ****
--- 719,723 ----
// 3 = mean median fg, 4 = mean median bg,
// 5 = mean ch1 int., 6 = mean ch2 int.
+ // 7-10 = mean SNR(ch[1/2] [mean/median])
// fg and bg are (ch1 fg + ch2 fg) etc.
// $grouping: -1 = none, 0 = user name, 1 = print name, 2 = hybe day
***************
*** 721,730 ****
{
$expid = (int)$expid;
! $what = max(0, min(6, (int)$what));
$grouping = max(-1, min(2, (int)$grouping));
if($what != 2)
{
! $whats = array("rbad.`FCh1Mean`+rbad.`FCh2Mean`",
"rbad.`BCh1Mean`+rbad.`BCh2Mean`",
"",
--- 725,735 ----
{
$expid = (int)$expid;
! $what = max(0, min(10, (int)$what));
$grouping = max(-1, min(2, (int)$grouping));
if($what != 2)
{
! $whats = array(
! "rbad.`FCh1Mean`+rbad.`FCh2Mean`",
"rbad.`BCh1Mean`+rbad.`BCh2Mean`",
"",
***************
*** 732,736 ****
"rbad.`BCh1Median`+rbad.`BCh2Median`",
"rbad.`FCh1Mean`*rbad.`FPixels`",
! "rbad.`FCh2Mean`*rbad.`FPixels`");
$wot = "AVG($whats[$what]), STDDEV($whats[$what]+0.0)*".
"SQRT(COUNT(*)/(COUNT(*)+1.0))";
--- 737,746 ----
"rbad.`BCh1Median`+rbad.`BCh2Median`",
"rbad.`FCh1Mean`*rbad.`FPixels`",
! "rbad.`FCh2Mean`*rbad.`FPixels`",
! "(rbad.`FCh1Mean`-rbad.`BCh1Mean`) / rbad.`BCh1SD`",
! "(rbad.`FCh2Mean`-rbad.`BCh2Mean`) / rbad.`BCh2SD`",
! "(rbad.`FCh1Median`-rbad.`BCh1Median`) rbad.`BCh1SD`",
! "(rbad.`FCh2Median`-rbad.`BCh2Median`) / rbad.`BCh2SD`"
! );
$wot = "AVG($whats[$what]), STDDEV($whats[$what]+0.0)*".
"SQRT(COUNT(*)/(COUNT(*)+1.0))";
***************
*** 747,751 ****
"WHERE rbad.`rawBioAssay` = r.id AND r.id = pr.`rawBioAssay` ".
"AND pr.experiment = $expid GROUP BY name, id ORDER BY name";
-
$res = query($query);
$arr = array();
--- 757,760 ----
Index: searchhtml.inc.php
===================================================================
RCS file: /cvsroot/basedb/basedb/www/searchhtml.inc.php,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** searchhtml.inc.php 10 Sep 2002 23:06:30 -0000 1.40
--- searchhtml.inc.php 12 Sep 2002 11:45:26 -0000 1.41
***************
*** 280,284 ****
}
! if(!$noform) echo "<form method=post action='$PHP_SELF'>\n";
echo "<tr><th>".webHelp(87)." Field</th><th>Op</th>".
--- 280,285 ----
}
! if(!$noform)
! echo "<form method=post action='$PHP_SELF'>\n";
echo "<tr><th>".webHelp(87)." Field</th><th>Op</th>".
Index: spotinfo.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/spotinfo.phtml,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** spotinfo.phtml 5 Aug 2002 11:19:01 -0000 1.9
--- spotinfo.phtml 12 Sep 2002 11:45:26 -0000 1.10
***************
*** 69,76 ****
function sigNoise(&$v, &$e1, &$e2)
{
! if($v === false || ($e1 === false && $e2 === false)) return "-";
! if($e1 === false) $noise = $e2;
else if($e2 === false) $noise = $e1;
! else $noise = sqrt($e1*$e1 + $e2*$e2);
if($noise == 0) return "inf";
return sprintf("%.2f", $v / $noise);
--- 69,77 ----
function sigNoise(&$v, &$e1, &$e2)
{
! if($v === false || (/*$e1 === false &&*/ $e2 === false)) return "-";
! /* if($e1 === false) $noise = $e2;
else if($e2 === false) $noise = $e1;
! else $noise = sqrt($e1*$e1 + $e2*$e2);*/
! $noise =& $e2;
if($noise == 0) return "inf";
return sprintf("%.2f", $v / $noise);
Index: test.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/test.phtml,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** test.phtml 7 Sep 2002 11:36:32 -0000 1.47
--- test.phtml 12 Sep 2002 11:45:26 -0000 1.48
***************
*** 26,32 ****
header("content-type: text/plain");
require_once("init.inc.php");
! echo "Testing db...\n";
ob_implicit_flush(1);
$s = array(0, 0, 0);
--- 26,35 ----
header("content-type: text/plain");
+ echo "old PHP_SELF: $_SERVER[PHP_SELF]\n";
require_once("init.inc.php");
! echo "new PHP_SELF: $PHP_SELF\n";
!
! /*echo "Testing db...\n";
ob_implicit_flush(1);
$s = array(0, 0, 0);
***************
*** 71,75 ****
echo "db_fetch_assoc2: $s[1] s\n";
echo "&db_fetch_assoc2: $s[2] s\n";
!
?>
--- 74,78 ----
echo "db_fetch_assoc2: $s[1] s\n";
echo "&db_fetch_assoc2: $s[2] s\n";
! */
?>
Index: trans_create.phtml
===================================================================
RCS file: /cvsroot/basedb/basedb/www/trans_create.phtml,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** trans_create.phtml 10 Sep 2002 23:06:30 -0000 1.25
--- trans_create.phtml 12 Sep 2002 11:45:26 -0000 1.26
***************
*** 242,246 ****
ob_implicit_flush(0);
echo "<p>\n";
! if($err != "") echo "<span class=red>Error: <?= $err ?></span><p>\n";
?>
<a class=large href="<?= html($location, 0) ?>">Return to BASE</a>
--- 242,247 ----
ob_implicit_flush(0);
echo "<p>\n";
! if($err != "")
! echo "<span class=red>Error: $err</span><p>\n";
?>
<a class=large href="<?= html($location, 0) ?>">Return to BASE</a>
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