Show gaeval_lists.php syntax highlighted
<?php
if(empty($SITEDEF_H)){require('SITEDEF.php');}
if(empty($PARAM_H)){require('getPARAM.php');}
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/TWO_COLUMN_HEADER/" . $SSI_QUERYSTRING);
?>
<link rel='stylesheet' type='text/css' href='GLquery.css' />
<SCRIPT LANGUAGE='JavaScript' SRC='GLquery.js'></SCRIPT>
<div id="mainWLS" align="center">
<H2>GAEVAL analysis of <?php echo "$COMMONORGN"; ?> transcript annotations</H2>
<?php
import_request_variables("gp","cp_");
require('GAEVALconf.php');
$SQL_svars = array('geneId' =>'geneId',
'integrity' =>'integrity',
'introns_confirmed' =>'introns_confirmed',
'introns_unsupported' =>'introns_unsupported',
'cds_size' =>'cds_size',
'utr5_size' =>'utr5_size',
'utr3_size' =>'utr3_size',
'exon_coverage' =>'exon_coverage'
);
$DEFAULT_COLUMN_ORDER = array('geneId' => 0,
'integrity' => 1,
'custom_integrity' => 2,
'introns_confirmed' => 3,
'introns_unsupported' => 4,
'exon_coverage' => 5,
'utr5_size' => 6,
'cds_size' => 7,
'utr3_size' => 8
);
$DEFAULT_COLUMN_HEADER = array('geneId' =>'Annotation',
'integrity' =>'Standard Integrity',
'custom_integrity' =>'Custom Integrity',
'introns_confirmed' =>'Introns Confirmed',
'introns_unsupported' =>'Intons Unsupported',
'cds_size' =>'CDS Size',
'utr5_size' =>'5`UTR Size',
'utr3_size' =>'3`UTR Size',
'exon_coverage' =>'%Coverage'
);
function by_display($a,$b){
global $DEFAULT_COLUMN_ORDER;
return ($DEFAULT_COLUMN_ORDER[$a] > $DEFAULT_COLUMN_ORDER[$b])?1:-1;
}
if($cp_ANNsrc){
mysql_connect($GAEVAL_DB_HOST,$GAEVAL_DB_USER,$GAEVAL_DB_PASS);
mysql_select_db($GAEVAL_DB_NAME);
if($cp_GAEVALsearch == "Retrieve annotations"){
$GAEVAL_TBLS = explode(":",$cp_ANNsrc);
$SQL_where = array();
$SQL_having = array();
$SQL_orderby = array();
switch ($cp_AIgroup){
case 1:
$SQL_where[] = "(integrity BETWEEN " . min($cp_AIscore1,$cp_AIscore2) . " AND " . max($cp_AIscore1,$cp_AIscore2) . " )";
break;
case 2:
$SQL_svars['custom_integrity'] = "($cp_AICparam1 * IF((introns_confirmed + introns_unsupported),(introns_confirmed / (introns_confirmed + introns_unsupported)),LEAST(1,(cds_size / 400))) + ($cp_AICparam2 * exon_coverage) + ($cp_AICparam3 * LEAST(1,(utr5_size / 200))) + ($cp_AICparam4 * LEAST(1,(utr3_size / 200)))) as custom_integrity";
$SQL_having[] = "(( custom_integrity ) BETWEEN " . min($cp_AICscore1,$cp_AICscore2) . " AND " . max($cp_AICscore1,$cp_AICscore2) . " )";
$cp_resultCols['custom_integrity'] = 'custom_integrity';
break;
}
switch ($cp_ISgroup){
case 1:
$SQL_where[] = "(((introns_confirmed * 100) / (introns_confirmed + introns_unsupported)) BETWEEN " . min($cp_ISpct1,$cp_ISpct2) . " AND " . max($cp_ISpct1,$cp_ISpct2) . " )";
break;
case 2:
$SQL_where[] = "((introns_confirmed BETWEEN " . min($cp_ISconf1,$cp_ISconf2) . " AND " . max($cp_ISconf1,$cp_ISconf2) . " )&&(introns_unsupported BETWEEN " . min($cp_ISuns1,$cp_ISuns2) . " AND " . max($cp_ISuns1,$cp_ISuns2) . " ))";
break;
}
switch ($cp_SCSgroup){
case 1:
$SQL_where[] = "(exon_coverage BETWEEN " . min($cp_SCSpct1,$cp_SCSpct2) . " AND " . max($cp_SCSpct1,$cp_SCSpct2) . " )";
break;
}
$SQL_cmd = "Select SQL_CALC_FOUND_ROWS " . implode(",",$SQL_svars) . " FROM $GAEVAL_TBLS[1] JOIN $GAEVAL_TBLS[0] USING (uid) ";
if(count($SQL_where)){
$SQL_cmd .= " WHERE " . implode("&&",$SQL_where);
}
if(count($SQL_having)){
$SQL_cmd .= " HAVING " . implode("&&",$SQL_having);
}
for($x=0;$x<count($cp_sortCol);$x++){
if(array_key_exists($cp_sortCol[$x],$SQL_svars) && (!array_key_exists($cp_sortCol[$x],$SQL_orderby))){
$SQL_orderby[$cp_sortCol[$x]] = "$cp_sortCol[$x] $cp_sortCol_ORT[$x]";
}
}
$SQL_cmd .= " ORDER BY " . implode(",",$SQL_orderby);
}elseif($cp_SQL_cmd){
$SQL_cmd = $cp_SQL_cmd;
}else{
$SQL_cmd = 0;
}
if($SQL_cmd){
$PRIMARY_SQL = $SQL_cmd;
if($cp_returnLIMIT){
$SQL_cmd .= " LIMIT ${cp_resultOFFSET},${cp_returnLIMIT} ";
}
// echo $SQL_cmd;
$result = mysql_query($SQL_cmd);
$pageCNT = mysql_num_rows($result);
$res2 = mysql_query("SELECT FOUND_ROWS()");
$rCNT = mysql_fetch_row($res2);
if($cp_returnLIMIT){
$PAGE_SELECTION = "<SELECT NAME='resTOC' ID='resTOC' ONCHANGE='goto_page(this);'>\n";
for($x=0;$x<=($rCNT[0] / $cp_returnLIMIT);$x++){
if(($x * $cp_returnLIMIT) == $cp_resultOFFSET){
$PAGE_SELECTION .= "<OPTION VALUE=$x SELECTED>Page " . ($x +1) . " Annotations ( " . ($x * $cp_returnLIMIT + 1) . " - " . ($x * $cp_returnLIMIT + $pageCNT) . " ) of $rCNT[0] </OPTION>\n";
}else{
$PAGE_SELECTION .= "<OPTION VALUE=$x >Page " . ($x +1) . " Annotations ( " . ($x * $cp_returnLIMIT + 1) . " - " . ($x * $cp_returnLIMIT + $pageCNT) . " ) of $rCNT[0] </OPTION>\n";
}
}
$PAGE_SELECTION .= "</SELECT>\n";
}else{
$PAGE_SELECTION = "Annotations ( 1 - $rCNT[0] ) of $rCNT[0]";
}
echo "<H3 CLASS='GAEVALresultHeader'>GAEVAL Search Results -- $PAGE_SELECTION </H3>\n";
uasort($cp_resultCols,'by_display');
echo "<TABLE ID='GAEVALresults'>\n<TR>";
foreach($cp_resultCols as $col){ echo "<TH>$DEFAULT_COLUMN_HEADER[$col]</TH>"; }
echo "</TR>\n";
while($row = mysql_fetch_assoc($result)){
echo "<TR>";
foreach($cp_resultCols as $col){ echo "<TD>$row[$col]</TD>"; }
echo "</TR>\n";
}
echo "</TABLE>\n<H3 CLASS='GAEVALresultHeader'></H3>\n";
// print new inline stylesheet to close the query selection list
echo "<STYLE>\n";
echo "UL.AIgroup, UL.ISgroup, UL.SCSgroup, UL.INCgroup { display:none; }\n";
echo "IMG#AIopen, IMG#ISopen, IMG#SCSopen, IMG#INCopen { display:none; }\n";
echo "IMG#AIclosed, IMG#ISclosed, IMG#SCSclosed, IMG#INCclosed { display:inline; }\n";
echo "</STYLE>\n";
mysql_free_result($result);
mysql_free_result($res2);
}
}
// Check form values and initialize defaults
if(!isset($cp_ANNsrc)){
$src = array_values($GAEVAL_SOURCES);
$cp_ANNsrc = $src[0];
}
if(!isset($cp_returnLIMIT)){ $cp_returnLIMIT = 50; }
if(!isset($cp_AIgroup)){ $cp_AIgroup = 0; }
if(!isset($cp_AIscore1)){ $cp_AIscore1 = 0; }
if(!isset($cp_AIscore2)){ $cp_AIscore2 = 1; }
if(!isset($cp_AICscore1)){ $cp_AICscore1 = 0; }
if(!isset($cp_AICscore2)){ $cp_AICscore2 = 1; }
if(!isset($cp_AICparam1)){ $cp_AICparam1 = 0.60; }
if(!isset($cp_AICparam2)){ $cp_AICparam2 = 0.30; }
if(!isset($cp_AICparam3)){ $cp_AICparam3 = 0.05; }
if(!isset($cp_AICparam4)){ $cp_AICparam4 = 0.05; }
if(!isset($cp_ISpct1)){ $cp_ISpct1 = 0; }
if(!isset($cp_ISpct2)){ $cp_ISpct2 = 100; }
if(!isset($cp_ISconf1)){ $cp_ISconf1 = 0; }
if(!isset($cp_ISconf2)){ $cp_ISconf2 = 1000; }
if(!isset($cp_ISuns1)){ $cp_ISuns1 = 0; }
if(!isset($cp_ISuns2)){ $cp_ISuns2 = 1000; }
if(!isset($cp_SCSpct1)){ $cp_SCSpct1 = 0; }
if(!isset($cp_SCSpct2)){ $cp_SCSpct2 = 100; }
?>
<INPUT TYPE='text' NAME='resultOFFSET' ID='resultOFFSET' VALUE=0 STYLE='display:none;' />
<INPUT TYPE='text' NAME='SQL_cmd' ID='SQL_cmd' VALUE=<?php echo "'$PRIMARY_SQL'" ?> STYLE='display:none;' />
<UL ID='GAEVALquery'>
<!-- -->
<LI><INPUT TYPE='submit' name='GAEVALsearch' value="Retrieve annotations" /> from annotation source
<SELECT NAME='ANNsrc'>
<?php
foreach($GAEVAL_SOURCES as $srcID => $src){
$select = ($cp_ANNsrc == $src)?"SELECTED":"";
echo "<OPTION VALUE='${src}' $select>${srcID}</OPTION>";
}
?>
</SELECT>
<SPAN CLASS='pageDisplay'>[ Show <SELECT CLASS='pageDisplay' NAME='returnLIMIT' ID='returnLIMIT'>
<?php
foreach(array(50,100,500,1000,5000) as $val){
$select = ($cp_returnLIMIT == $val)?"SELECTED":"";
echo "<OPTION VALUE=$val $select>${val}</OPTION>";
}
$select = ($cp_returnLIMIT == 0)?"SELECTED":"";
echo "<OPTION VALUE=0 $select>ALL</OPTION>";
?>
</SELECT> results per page ]
</SPAN>
</LI>
<LI><IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow2.png'"; ?> CLASS='menubutton' ID='AIclosed' ONCLICK='openMENU("AI");'>
<IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow.png'"; ?> CLASS='menubutton' ID='AIopen' ONCLICK='closeMENU("AI");'>Annotation Integrity Filter
<UL class='AIgroup' ID='AIoptions'>
<LI><INPUT TYPE='radio' NAME='AIgroup' VALUE='0' ONCHANGE='AIenable(this.value);' <?php if($cp_AIgroup == 0){ echo "CHECKED"; } ?>>Do NOT filter by integrity score!</INPUT></LI>
<LI><INPUT TYPE='radio' NAME='AIgroup' VALUE='1' ONCHANGE='AIenable(this.value);' <?php if($cp_AIgroup == 1){ echo "CHECKED"; } ?>>Select annotations with Integrity Scores
<P ID='AIcustom'>Between <INPUT TYPE='text' NAME='AIscore1' ID='AIscore1' VALUE=<?php printf("'%.2f'",${cp_AIscore1}); ?> SIZE=4 <?php if($cp_AIgroup != 1){ echo "DISABLED"; } ?> /> and <INPUT TYPE='text' NAME='AIscore2' ID='AIscore2' VALUE=<?php printf("'%.2f'",${cp_AIscore2}); ?> SIZE=4 <?php if($cp_AIgroup != 1){ echo "DISABLED"; } ?> />
</P></INPUT></LI>
<LI><INPUT TYPE='radio' NAME='AIgroup' VALUE='2' ONCHANGE='AIenable(this.value);' <?php if($cp_AIgroup == 2){ echo "CHECKED"; } ?>>Select annotations with CUSTOM Integrity Scores
<P ID='AIcustom'>
Between <INPUT TYPE='text' NAME='AICscore1' ID='AICscore1' VALUE=<?php printf("'%.2f'",${cp_AICscore1}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /> and <INPUT TYPE='text' NAME='AICscore2' ID='AICscore2' VALUE=<?php printf("'%.2f'",${cp_AICscore2}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /><BR>
CUSTOM Annotation Integrity = (<INPUT TYPE='text' NAME='AICparam1' ID='AICparam1' VALUE=<?php printf("'%.2f'",${cp_AICparam1}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /> * alpha) +
(<INPUT TYPE='text' NAME='AICparam2' ID='AICparam2' VALUE=<?php printf("'%.2f'",${cp_AICparam2}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /> * beta) +
(<INPUT TYPE='text' NAME='AICparam3' ID='AICparam3' VALUE=<?php printf("'%.2f'",${cp_AICparam3}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /> * delta) +
(<INPUT TYPE='text' NAME='AICparam4' ID='AICparam4' VALUE=<?php printf("'%.2f'",${cp_AICparam4}); ?> SIZE=4 <?php if($cp_AIgroup != 2){ echo "DISABLED"; } ?> /> * gamma)
</P></INPUT></LI>
</UL>
</LI>
<LI><IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow2.png'"; ?> CLASS='menubutton' ID='ISclosed' ONCLICK='openMENU("IS");'>
<IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow.png'"; ?> CLASS='menubutton' ID='ISopen' ONCLICK='closeMENU("IS");'>Annotation Support Filter (Intron Support)
<UL class='ISgroup' ID='ISoptions'>
<LI><INPUT TYPE='radio' NAME='ISgroup' VALUE='0' ONCHANGE='ISenable(this.value);' <?php if($cp_ISgroup == 0){ echo "CHECKED"; } ?> >Do NOT filter by intron support!</INPUT></LI>
<LI><INPUT TYPE='radio' NAME='ISgroup' VALUE='1' ONCHANGE='ISenable(this.value);' <?php if($cp_ISgroup == 1){ echo "CHECKED"; } ?> >Select annotations with a percentage of confirmed introns
<P ID='AIcustom'>Between <INPUT TYPE='text' NAME='ISpct1' ID='ISpct1' VALUE=<?php printf("'%3d'",${cp_ISpct1}); ?> SIZE=3 <?php if($cp_ISgroup != 1){ echo "DISABLED"; } ?> />% and <INPUT TYPE='text' NAME='ISpct2' ID='ISpct2' VALUE=<?php printf("'%3d'",${cp_ISpct2}); ?> SIZE=3 <?php if($cp_ISgroup != 1){ echo "DISABLED"; } ?> />%
</P></INPUT></LI>
<LI><INPUT TYPE='radio' NAME='ISgroup' VALUE='2' ONCHANGE='ISenable(this.value);' <?php if($cp_ISgroup == 2){ echo "CHECKED"; } ?> >Select annotations with
<P ID='AIcustom'>Between <INPUT TYPE='text' NAME='ISconf1' ID='ISconf1' VALUE=<?php printf("'%4d'",${cp_ISconf1}); ?> SIZE=4 <?php if($cp_ISgroup != 2){ echo "DISABLED"; } ?> /> and <INPUT TYPE='text' NAME='ISconf2' ID='ISconf2' VALUE=<?php printf("'%4d'",${cp_ISconf2}); ?> SIZE=4 <?php if($cp_ISgroup != 2){ echo "DISABLED"; } ?> /> introns confirmed<BR>
AND<BR>
Between <INPUT TYPE='text' NAME='ISuns1' ID='ISuns1' VALUE=<?php printf("'%4d'",${cp_ISuns1}); ?> SIZE=4 <?php if($cp_ISgroup != 2){ echo "DISABLED"; } ?> /> and <INPUT TYPE='text' NAME='ISuns2' ID='ISuns2' VALUE=<?php printf("'%4d'",${cp_ISuns2}); ?> SIZE=4 <?php if($cp_ISgroup != 2){ echo "DISABLED"; } ?> /> introns unsupported
</P></INPUT></LI>
</UL>
</LI>
<LI><IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow2.png'"; ?> CLASS='menubutton' ID='SCSclosed' ONCLICK='openMENU("SCS");'>
<IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow.png'"; ?> CLASS='menubutton' ID='SCSopen' ONCLICK='closeMENU("SCS");'>Annotation Support Filter (Sequence Coverage)
<UL class='SCSgroup' ID='SCSoptions'>
<LI><INPUT TYPE='radio' NAME='SCSgroup' VALUE='0' ONCHANGE='SCSenable(this.value);' <?php if($cp_SCSgroup == 0){ echo "CHECKED"; } ?> >Do NOT filter by sequence coverage!</INPUT></LI>
<LI><INPUT TYPE='radio' NAME='SCSgroup' VALUE='1' ONCHANGE='SCSenable(this.value);' <?php if($cp_SCSgroup == 1){ echo "CHECKED"; } ?> >Select annotations with a percent sequence coverage
<P ID='AIcustom'>Between <INPUT TYPE='text' NAME='SCSpct1' ID='SCSpct1' VALUE=<?php printf("'%3d'",${cp_SCSpct1}); ?> SIZE=3 <?php if($cp_SCSgroup != 1){ echo "DISABLED"; } ?> />% and <INPUT TYPE='text' NAME='SCSpct2' ID='SCSpct2' VALUE=<?php printf("'%3d'",${cp_SCSpct2}); ?> SIZE=3 <?php if($cp_SCSgroup != 1){ echo "DISABLED"; } ?> />%
</P></INPUT></LI>
</UL>
</LI>
<!-- -->
<LI><IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow2.png'"; ?> CLASS='menubutton' ID='INCclosed' ONCLICK='openMENU("INC");'>
<IMG SRC=<?php echo "'${IMAGEDIR}GDBmenuArrow.png'"; ?> CLASS='menubutton' ID='INCopen' ONCLICK='closeMENU("INC");'>Annotation Incongruence Filter
<UL class='INCgroup' ID='INCoptions'>
<LI><INPUT TYPE='checkbox' NAME='INC_altsp' VALUE='altsp' UNCHECKED>Alternative splicing filter</INPUT></LI>
<LI><INPUT TYPE='checkbox' NAME='INC_altcps' VALUE='altcps' UNCHECKED>Alternative polyadenylation site selection</INPUT></LI>
<LI><INPUT TYPE='checkbox' NAME='INC_fus' VALUE='fus' UNCHECKED>Split annotation filter</INPUT></LI>
<LI><INPUT TYPE='checkbox' NAME='INC_fis' VALUE='fis' UNCHECKED>Merged annotation filter</INPUT></LI>
<LI><INPUT TYPE='checkbox' NAME='INC_pcis' VALUE='pcis' UNCHECKED>Polycistronic transcript filter</INPUT></LI>
</UL>
</LI>
</UL>
<P ID='resultCols'>Display result columns<BR>
<?php
foreach(array_keys($DEFAULT_COLUMN_ORDER) as $col){
$select = ((!count($cp_resultCols))||($cp_resultCols[$col]))?"CHECKED":"";
if((!count($cp_resultCols))&&($col == 'custom_integrity')){ $select = ""; }
echo "<INPUT TYPE='checkbox' NAME='resultCols[$col]' VALUE='$col' ${select}>$DEFAULT_COLUMN_HEADER[$col]</INPUT><BR>\n";
}
?>
</P>
<P ID='sortCols'>Sort by columns<BR>
<?php
for($x=0;$x<5;$x++){
echo ($x + 1) . ".<SELECT NAME='sortCol[${x}]'>\n";
foreach(array_keys($DEFAULT_COLUMN_ORDER) as $col){
$select = ($cp_sortCol[$x] == $col)?"SELECTED":"";
echo "<OPTION VALUE='$col' $select>$DEFAULT_COLUMN_HEADER[$col]</OPTION>";
}
echo "</SELECT><BR>\n";
}
?>
</P>
</div>
<?php
require('SSI_GDBprep.php');
virtual("${CGIPATH}SSI_GDBgui.pl/STANDARD_FOOTER/" . $SSI_QUERYSTRING);
?>
See more files for this project here