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[Sashimi-commit] SF.net SVN: sashimi:[9482] trunk/trans_proteomic_pipeline/src/Parsers/ Algorithm2XML/tpp2mzid/tpp2mzid.cpp

[<mho...@us...>]

Revision: 9482
          http://sourceforge.net/p/sashimi/code/9482
Author:   mhoopmann
Date:     2026-04-18 16:55:38 +0000 (Sat, 18 Apr 2026)
Log Message:
-----------
[tpp2mzid] - fixed error caused by case where search to be converted had no PSMs to convert.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/tpp2mzid/tpp2mzid.cpp

Modified: trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/tpp2mzid/tpp2mzid.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/tpp2mzid/tpp2mzid.cpp	2026-04-16 06:39:35 UTC (rev 9481)
+++ trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/tpp2mzid/tpp2mzid.cpp	2026-04-18 16:55:38 UTC (rev 9482)
@@ -101,7 +101,7 @@
   NeoPepXMLParser pep;
   NeoProtXMLParser prot;
 
-  cout << "tpp2mzid v0.9.15 (August 22 2023), copyright Mike Hoopmann, Institute for Systems Biology." << endl;
+  cout << "tpp2mzid v0.9.16 (April 18 2026), copyright Mike Hoopmann, Institute for Systems Biology." << endl;
   cout << "Built using mzIMLTools: " << m.getMzIMLToolsVersion() << endl;
   cout << "Built using NeoPepXMLParser: " << pep.versionNeo() << endl;
   cout << "Built using NeoProtXMLParser: " << prot.versionNeo() << endl;
@@ -498,6 +498,9 @@
       addPTMProphetToSIP(&m.analysisProtocolCollection.spectrumIdentificationProtocol[b],m_sip);
     }
 
+
+    if(mrs->spectrum_query.size()==0) continue;
+
     CSpectrumIdentificationList* m_sil = NULL;
     CSpectrumIdentification* m_si = m.addSpectrumIdentification(m_sd->id, m_db->id, m_sip->id, m_sil);
 

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[Sashimi-commit] SF.net SVN: sashimi:[9481] trunk/trans_proteomic_ pipeline/perl/cgi-bin

[<rea...@us...>]

Revision: 9481
          http://sourceforge.net/p/sashimi/code/9481
Author:   real_procopio
Date:     2026-04-16 06:39:35 +0000 (Thu, 16 Apr 2026)
Log Message:
-----------
[error handling] Improve error reporting and code cleanup

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl
    trunk/trans_proteomic_pipeline/perl/cgi-bin/mascotout.pl
    trunk/trans_proteomic_pipeline/perl/cgi-bin/plotpp.pl
    trunk/trans_proteomic_pipeline/perl/cgi-bin/promastcgi.pl
    trunk/trans_proteomic_pipeline/perl/cgi-bin/show_tmp_pngfile.pl

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2026-04-16 06:37:19 UTC (rev 9480)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2026-04-16 06:39:35 UTC (rev 9481)
@@ -7,7 +7,7 @@
 #                                                                           #
 # View and filter protXML result files in web browser                       #
 #                                                                           #
-# Copyright (C) 2013-2025 Luis Mendoza                                      #
+# Copyright (C) 2013-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/mascotout.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/mascotout.pl	2026-04-16 06:37:19 UTC (rev 9480)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/mascotout.pl	2026-04-16 06:39:35 UTC (rev 9481)
@@ -1,8 +1,9 @@
 #!perl
-use FindBin qw($Bin);
+use FindBin qw($Bin $Script);
 use lib "$Bin/../lib/perl";
 use tpplib_perl; # exported TPP lib function points
 my $TPPVersionInfo = tpplib_perl::getTPPVersionInfo();
+my $page_title = $Script;
 
 print "Content-type: text/html\n\n";
 
@@ -31,10 +32,10 @@
     }
 
 } else {
-    print "\n\n<font style='border:3px solid red;color:red'>ERROR: Count not open file: $tarfile does not exist</font>\n\n";
+    print "\n\n\n\n<span style='padding:20px 100px;border:3px solid red;color:red'>ERROR: Could not open file: $tarfile does not exist</span>\n\n\n\n";
 }
 
-print "\n\n<hr size='1' noshade>";
-print "<font color='#999999'>$page_title\n$TPPVersionInfo</font>\n";
+print "\n<hr size='1' noshade>";
+print "<span style='color:#999999'>$page_title\n$TPPVersionInfo</span>\n";
 print "</PRE>\n</body>\n</html>";
 exit;

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/plotpp.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/plotpp.pl	2026-04-16 06:37:19 UTC (rev 9480)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/plotpp.pl	2026-04-16 06:39:35 UTC (rev 9481)
@@ -8,7 +8,7 @@
 # Write incoming data as a json object to a file for later visualization    #
 #  using flot                                                               #
 #                                                                           #
-# Copyright (C) 2017-2023 Luis Mendoza                                      #
+# Copyright (C) 2017-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -392,15 +392,15 @@
     my $file = $cgi_query->param('file') || '';
 
     my $html_response = "Content-type:text/html\n\n";
+    my $error_response = "<span style='color:red'>Unable to process request</span>";
 
     if (!$file || !open(FILE, "$file")) {
-	$html_response .= "<span style='color:red'>Could not find or open file $file for deletion</span>";
-	return $html_response;
+	return $html_response.$error_response;
     }
 
     my $go_ahead_and_delete = 0;
     while (<FILE>) {
-	if (/^#DATA:/) {
+	if (/^#DATA:$/) {
 	    $go_ahead_and_delete++;
 	    last;
 	}
@@ -407,14 +407,11 @@
     }
     close FILE;
 
-    if (!$go_ahead_and_delete) {
-	$html_response .= "<span style='color:red'>File $file is of incorrect type; did not delete</span>";
+    if ($go_ahead_and_delete && unlink $file) {
+        $html_response .= "--DELETEOK--";
     }
-    elsif (unlink $file) {
-	$html_response .= "--DELETEOK--";
-    }
     else {
-	$html_response .= "<span style='color:red'>Could not delete file $file</span>";
+        $html_response .= $error_response;
     }
 
     return $html_response;

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/promastcgi.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/promastcgi.pl	2026-04-16 06:37:19 UTC (rev 9480)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/promastcgi.pl	2026-04-16 06:39:35 UTC (rev 9481)
@@ -7,7 +7,7 @@
 #                                                                           #
 # Submits a sequence to the promast sequence mapping utility; returns JSON  #
 #                                                                           #
-# Copyright (C) 2021-2023 Luis Mendoza                                      #
+# Copyright (C) 2021-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -37,19 +37,14 @@
 
 
 # Globals
-my $exe_path   = tpplib_perl::getHomePath() . 'bin/promast.pl';
+my $exe_path = tpplib_perl::getHomePath() . 'bin/promast.pl';
 my $command;
 
-my $base_path  = '/net/dblocal/wwwspecial/peptideatlas/map';
-my %opts;
+my $q = new CGI;
+my $cgi_action = $q->url_param('action') || undef;
 
-# Get basic cgi parameters
-my $q =	new CGI;
-my $cgi_sessionid = $q->param('ssid')   || &getNewRandomString(10);
-my $cgi_action    = $q->param('action') || undef;
+my $json_response = "Content-type:application/json\n\n";
 
-
-my $json_response = "Content-type:application/json\n\n";
 &performSearch() if ($cgi_action eq 'beginSearch');
 
 if ($command) {
@@ -63,6 +58,9 @@
     $json_response .= $mapped;
   }
 }
+else {
+  &reportError("There was a problem with promast");
+}
 
 print $json_response;
 exit(0);
@@ -70,11 +68,13 @@
 
 
 ###############################################################################
-# Send Error
+# Send Error (and exits)
 ###############################################################################
 sub reportError {
   my $msg = shift || 'unknown error...';
 
+  $msg =~ s/\n/<br>/g;
+
   $json_response .= "{\"message\" : \"$msg\", \"status\" : \"ERROR\"}";
 
   print $json_response;
@@ -86,94 +86,41 @@
 # Run peptide sequence matching
 ###############################################################################
 sub performSearch {
-  my $dbase = $q->param('db')      || undef;
-  my $input = $q->param('peptide') || undef;
-  my $mztol = $q->param('mztol')   || undef;
-  my $fuzzy = $q->param('fuzzy')   || 0;
+  my $dbase = $q->url_param('db')      || undef;
+  my $input = $q->url_param('peptide') || undef;
+  my $mztol = $q->url_param('mztol')   || undef;
+  my $fuzzy = $q->url_param('fuzzy')   || 0;
 
-#    my $peplist = decode_entities($q->param('peptides')) || '';
-  my $peplist = $q->param('peptides') || '';
-
-  my $numpep = 0;
-  if ($peplist) {
-    $input = "$base_path/tmp/$cgi_sessionid.peplist";
-    open(POUT, ">>$input") || do {
-    &reportError("Cannot create file $input : $!");
-    $peplist = ''; # skips writing to file
-    };
-
-  PEPLIST:
-    for (split "\n", $peplist) {
-      s/[\r\n]//g;
-      s/^\s+//g;
-      s/\s+$//g;
-      next unless $_;
-
-      for (split /\s+/) {
-	if (++$numpep > 5000) {
-	  &reportError("Too many sequences requested!  Please limit requests to 5000 entries.");
-	  last PEPLIST;
-	}
-	print POUT "$_\n";
-      }
-    }
-    close (POUT);
-    $opts{'output'} = "multi";
-  }
-  else {
-    $opts{'output'} = "single";
-  }
-
   # Validate user input
   unless (defined($input)) { 
-    &reportError("Please specify a peptide sequence or list to search");
+    &reportError("Please specify a peptide sequence to search");
   }
 
+  if ($input !~ /^[A-Z]+$/) {
+    &reportError("Please specify a valid peptide sequence");
+  }
+
   if (defined($mztol) && $mztol !~ /^[\d|\.]+$/ ) {
     &reportError("Precursor m/z tolerance must be a number!");
   }
 
+  if ($fuzzy !~ /^\d$/) {
+    &reportError("Incorrect parameter passed");
+  }
+
   if (! -f $dbase) {
     &reportError("Database not available!");
   }
 
 
-  # Assemble command:
-  # promast
-  # -c
-  # -U
-  # -u
-  # -f <fuzzy>
-  # -m <mztol>
-  # <index file>
-  # <sequence>
-
+  # Assemble command
   my $options = "-E -c -u -o json";
   if ($fuzzy > 0) {
     $options .= " -U";      
     $options .= " -f $fuzzy";
     $options .= " -m $mztol" if defined($mztol);
-    $opts{'output'} = "fuzzy";
   }
 
   $command = "$exe_path $options $dbase $input";
   return;
 }
-
-
-###############################################################################
-# getNewRandomString
-###############################################################################
-sub getNewRandomString {
-  my $len = shift;
-
-  srand;
-  my $string = "";
-  my @charList = ('A'..'Z',0..9);
-  for (my $i = 0; $i<$len; $i++) {
-    $string .= $charList[int(rand 36)];
-  }
-
-  return $string;
-}
-

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/show_tmp_pngfile.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/show_tmp_pngfile.pl	2026-04-16 06:37:19 UTC (rev 9480)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/show_tmp_pngfile.pl	2026-04-16 06:39:35 UTC (rev 9481)
@@ -4,9 +4,8 @@
 # a little CGI script to pump a temp graphic file to stdout, then delete it
 #
 
-
 my $serverroot = $ENV{WEBSERVER_ROOT};
-$serverroot =~ s/\\/\//g;  # get those path seps pointing right!
+$serverroot =~ s|\\|/|g;  # get those path seps pointing right!
 
 
 my @qvars = split '&', $ENV{QUERY_STRING};
@@ -15,48 +14,42 @@
 my $retain = 0;
 
 foreach my $v (@qvars) {
-    my @var = split '=', $v;
-    if ($#var > 0) {
-	if ($var[0] eq "file") {
-	    $fname = $var[1];
-	}
-	if ($var[0] eq "keep") {
-	    $retain = $var[1];
-	}
-	
-
+  my @var = split '=', $v;
+  if ($#var > 0) {
+    if ($var[0] eq "file") {
+      $fname = $var[1];
     }
-
-
+    elsif ($var[0] eq "keep") {
+      $retain = $var[1];
+    }
+  }
 } 
 
-
-
-
-$fname =~ s/\\/\//g;  # get those path seps pointing right!
+$fname =~ s|\\|/|g;  # get those path seps pointing right!
 my $fullpath = $fname ;
-$fullpath =~ s/\/\//\//g;  # eliminate double slashes
+$fullpath =~ s|//|/|g;  # eliminate double slashes
 
 if (not -e $fullpath) { # prepend serverroot
-	$fullpath = $serverroot . $fname ;
+  $fullpath = $serverroot . $fname ;
 }
 
-if (not ($fname =~ m/\.png$/)) { # make sure nobody's trying to delete non-png files
-	print "Content-type: html/text\n\n";
-	print "wrong filetype";
-} elsif (-e $fullpath)  {  # if it exists, show it then delete it
-	# show it
-	my $qt = "'";
-	$qt = '"' if  ($^O eq 'MSWin32' );
-	my $quotedpath = $qt.$fullpath.$qt;
-	print "Content-type: image/png\n\n";
-	system("cat $quotedpath"); 
-	# kill it
-	if ($retain == 0) {
-	    system("rm $quotedpath"); 
-	}
-} else { # issue warning
-	print "Content-type: html/text\n\n";
-	print "The temporary image file $fullpath has already been deleted.  ";
-	print "Try using the Copy function in your browser instead.";
+if ($fname !~ /\.png$/) { # make sure nobody's trying to delete non-png files
+  print "Content-type: html/text\n\n";
+  print "wrong filetype";
 }
+elsif (-e $fullpath)  {  # if it exists, show it then delete it
+  # show it
+  my $qt = $^O eq 'MSWin32' ? '"' : "'";
+  my $quotedpath = $qt.$fullpath.$qt;
+  print "Content-type: image/png\n\n";
+  system("cat $quotedpath"); 
+  # kill it
+  if ($retain == 0) {
+    system("rm $quotedpath"); 
+  }
+}
+else { # issue warning
+  print "Content-type: html/text\n\n";
+  print "The temporary image file $fullpath has already been deleted.  ";
+  print "Try using the Copy function in your browser instead.";
+}

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[Sashimi-commit] SF.net SVN: sashimi:[9480] trunk/trans_proteomic_ pipeline

[<rea...@us...>]

Revision: 9480
          http://sourceforge.net/p/sashimi/code/9480
Author:   real_procopio
Date:     2026-04-16 06:37:19 +0000 (Thu, 16 Apr 2026)
Log Message:
-----------
[deprecation]
- Remove ancient protXML viewer, and any remaining references to it
- Replace cgi-based help page for PepXMLViewer with static HTML
- Rebalance Petunia tools menu

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/Makefile
    trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl
    trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp
    trunk/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/html/PepXMLViewer.html

Added Paths:
-----------
    trunk/trans_proteomic_pipeline/html/show_pipeline_help.html

Removed Paths:
-------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/protxml2html.pl
    trunk/trans_proteomic_pipeline/perl/cgi-bin/show_pipeline_help.pl

Added: trunk/trans_proteomic_pipeline/html/show_pipeline_help.html
===================================================================
--- trunk/trans_proteomic_pipeline/html/show_pipeline_help.html	                        (rev 0)
+++ trunk/trans_proteomic_pipeline/html/show_pipeline_help.html	2026-04-16 06:37:19 UTC (rev 9480)
@@ -0,0 +1,150 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <title>PepXML Viewer: Help</title>
+    <link rel="stylesheet" type="text/css" href="css/tpp.css" ></link>
+    <link rel="icon" type="text/x-icon" href="images/pep-xml.ico">
+  </head>
+
+  <body>
+
+    <div id="tppWrapper">
+
+      <div class="tppbanner" banner-bg-text="pepXML Help">&nbsp;&nbsp;TPP: PepXML Viewer help</div>
+
+      <div style="max-width:950px;padding-top:60px;padding-left:30px;background-color:#fff;">
+
+      <h1 class="section">Getting Started</h1>
+      <p>
+	This program is used to view PepXML files, which contain
+	information about peptides derived from MS/MS (MS level 2)
+	data.  In the Trans Proteomic Pipeline, these files are
+	iteratively modified by various programs as processing
+	progresses.  A basic PepXML file might only contain
+	search-engine results, converted, for example, from Comet, X!Tandem,
+        Spectrast, SEQUEST or MASCOT.
+	A more complex file (or the same file after more
+	processing steps) might contain information about Peptide
+	Prophet-assigned peptide probabilities and/or peptide quantitation
+	info (derived from XPRESS, ASAPratio, LIBRA, etc.)
+      </p>
+	 
+      <p> 
+	When the viewer program runs, it creates an "index" file with
+	a name similar to the xml file you're viewing.  This file
+	contains information for quickly moving through the (larger)
+	PepXML file.  You may safely delete these at any time;
+	however, the next time you invoke the viewer on this file, you
+	may notice a delay as the index file is rebuilt.
+      </p>
+
+
+      <h1 class="section">Understanding the Interface: Overview</h1>
+      <p>
+	The page has five menus and a data section.  
+      </p>
+      <ul>
+	<li><b>Summary</b>: general information about the file you're
+	  viewing, including stats based on the filtering options
+	  you've selected.  Keep an eye here and you see the number
+	  of peptides in the current subset change as you apply
+	  various filters.</li>
+
+	<li><b>Display Options</b>: any option (besides column selection)
+          that doesn't change the number of peptides in the
+	  current subset.  Here you'll find options like number of
+	  rows per page to display, sort order, highlighting, and so
+	  forth.  Data can be sorted by index (number), spectrum
+	  name, peptide, search scores, probability (when
+	  relevant), XPRESS quantitation either descending or
+	  ascending (when relevant), and ASAPRatio quantiation
+	  either descending or ascending (when relevant). After
+	  making selection, push the "Update Page" button.</li>
+
+	<li><b>Pick Columns</b>: column selection and ordering. Here
+	  you'll see lists of displayed and undisplayed columns.
+	  Click on a column name (hold 'control' and click to select
+	  multiple names at one time) and move them up or down, or
+	  hide or display them.</li>
+
+	<li><b>Filtering Options</b>: here you'll find choices to pare
+	  down your currently displayed subset.  The options here,
+	  like in Display Options, will change based on the
+	  information contained in a specific PepXML file.  Data can
+	  be filtered by probability (when relevant), precursor ion
+	  charge, search scores, XPRESS quantitation (when
+	  relevant), and ASAPRatio quantitation (when relevant).  In
+	  the latter cases, 'require valid ASAP Ratio' excluses
+	  those entries lacking a ratio, or having a negative ratio;
+	  a minimum and maximum ratio can also be set.  In addition,
+	  when both XPRESS and ASAPRatio data are available,
+	  checking ' Require xpress ratio within asap mean +/-
+	  error' excludes all results for which the two ratios
+	  differ by more than one standard deviation.  After making
+	  selection, push the 'Update Page' button, or press the enter
+	  key from a text box. Filter options remain set until the
+	  'Restore Original' button (found under 'Other Actions').</li>
+
+	<li><b>Other Actions:</b> 'Update Page' refreshes the display with
+	  new options you've selected.  'Export Spreadsheet'
+	  generates a tab-delimited file closely mimic the view of
+	  the data in your browser, corresponding the the current
+	  subset.  A link to the generated excel spreadsheet is
+	  displayed at the bottom of the 'Summary' section.
+	  'Generate Pep3D' runs that program with the current PepXML file
+	  as input.  'Additional Analysis Info' is a link to the models
+          summary page, which also provides details
+	  of MS/MS analysis, including for each input file, search
+	  engine, and record of each analysis.  To the far right,
+	  the 'Restore Original' button will discard any display
+	  or filter options and restore the entire subset.</li>
+
+	<li><b>Data Table</b>: this is where your data is displayed.
+	  Each link brings you to another window with more
+	  infomation.  See below for more information.</li>
+
+      </ul>
+
+	
+      <h1 class="section">Working with the Data</h1>
+      <p>
+	Information about most of the typical columns can be found
+	here.  Note that not all of these columns will be
+	available if your PepXML file was not processed with a
+	specific program.  Some entries in the data table also
+	contain links which provide additional infomation.
+      </p>
+
+      <ul>
+	<li><b>index</b> (entry number): unique search result id</li>
+	<li><b>probability</b>: probability that search result is correct
+	  (e.g. as determined by PeptideProphet), with link to
+	  probability analysis results.  Note that these links
+	  will be the same within one PepXML file.</li>
+	<li><b>spectrum</b>: links to comprehensive search results
+	  (including runner up peptides, if avaliable).  You can
+	  highlight and filter this text.</li>
+	<li><b>search scores</b>: specific for each search engine contributing to dataset.</li>
+	<li><b>matched ions</b>: the fraction of peptide theoretical
+	  fragment ions present in spectrum.  Link to MS/MS
+	  spectrum with assigned fragment ions.</li>
+	<li><b>peptide</b>: Best match from search engine for a given
+	  spectrum.  Linked to Blast launcher.  Note that you can
+	  highlight and filter this text.</li>
+	<li><b>protein(s)</b>: Link to database sequence viewre.  Hover the mouse over
+	  this link for a description, if avaliable.  Addtional
+	  proteins containing assigned peptide are listed out, if
+	  "multiple protein hits" : "list of all hits" is selected
+	  in display options.</li>
+	<li><b>XPRESS</b>: Quantitation with link to ion trace.</li>
+	<li><b>ASAPRatio</b>: Quantitation with link to ion trace.</li>
+	<li>PeptideProphet <b>F score</b>: composite score incorporating several search scores.</li>
+      </ul>
+      </div>
+
+      <footer id="tppPageFooter"><strong>Trans-Proteomic Pipeline</strong>:: PepXMLViewer Help<br/>_TPP_BUILDID_<br/></footer>
+
+    </div>
+  </body>
+</html>
+

Modified: trunk/trans_proteomic_pipeline/perl/Makefile
===================================================================
--- trunk/trans_proteomic_pipeline/perl/Makefile	2026-04-02 04:31:30 UTC (rev 9479)
+++ trunk/trans_proteomic_pipeline/perl/Makefile	2026-04-16 06:37:19 UTC (rev 9480)
@@ -207,10 +207,8 @@
 install :: $(INSTALL_CGI)/mascotout.pl
 install :: $(INSTALL_CGI)/plotpp.pl
 install :: $(INSTALL_CGI)/promastcgi.pl
-install :: $(INSTALL_CGI)/protxml2html.pl
 install :: $(INSTALL_CGI)/ProtXMLViewer.pl
 install :: $(INSTALL_CGI)/qsir.pl
-install :: $(INSTALL_CGI)/show_pipeline_help.pl
 install :: $(INSTALL_CGI)/show_tmp_pngfile.pl
 install :: $(INSTALL_CGI)/tpp_files.pl
 install :: $(INSTALL_CGI)/Seq2MS_json.pl

Deleted: trunk/trans_proteomic_pipeline/perl/cgi-bin/protxml2html.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/protxml2html.pl	2026-04-02 04:31:30 UTC (rev 9479)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/protxml2html.pl	2026-04-16 06:37:19 UTC (rev 9480)
@@ -1,11129 +0,0 @@
-#!perl
-#############################################################################
-# Program       : protxml2html.pl                                           #
-# Author        : Andrew Keller <ak...@sy...>                #
-# Date          : 3.28.03                                                   #
-# SVN Info      : $Id$
-#                                                                           #
-# ProteinProphet                                                            #
-#                                                                           #
-# Program       : ProteinProphet T.M.                                       #
-# Author        : Andrew Keller <ak...@sy...>                #
-# Date          : 11.27.02                                                  #
-#                                                                           #
-#                                                                           #
-# Copyright (C) 2003 Andrew Keller                                          #
-#                                                                           #
-# This library is free software; you can redistribute it and/or             #
-# modify it under the terms of the GNU Lesser General Public                #
-# License as published by the Free Software Foundation; either              #
-# version 2.1 of the License, or (at your option) any later version.        #
-#                                                                           #
-# This library 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 Lesser General Public          #
-# License along with this library; if not, write to the Free Software       #
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA #
-#                                                                           #
-# Andrew Keller                                                             #
-# Insitute for Systems Biology                                              #
-# 1441 North 34th St.                                                       #
-# Seattle, WA  98103  USA                                                   #
-# ak...@sy...                                                #
-#                                                                           #
-#############################################################################
-use strict;
-use FindBin qw($Bin);
-use lib "$Bin/../lib/perl";
-use POSIX;
-use File::Spec; # use perl libs instead of depending on /^\/ as fullpath indicator
-use tpplib_perl; # exported TPP lib function points
-
-
-print "Content-type: text/html\n\n" if(@ARGV == 0 || ! ($ARGV[0] eq '-file'));
-
-my %box;
-%box = &tpplib_perl::read_query_string if $ENV{'REQUEST_METHOD'}; # Read keys and values
-
-
-#############################################################################
-#         C O N F I G U R A T I O N    A R E A
-#
-# ISB-CYGWIN Release?
-#   This is a kludge to hardcode isb-cygwin specific
-#   defaults for the following parameters.  In the
-#   future these defaults should be automatically filled
-#   in by a true build system.  See the code which immediately
-#   follows this section for isb-cygwin defults.
-#
-########################################
-# ALL NON-ISB USERS: SET THIS VALUE TO 0
-my $ISB_VERSION = 0;
-########################################
-
-my $WINDOWS_CYGWIN = -f '/bin/cygpath';
-$ISB_VERSION = $WINDOWS_CYGWIN;
-
-# USE OUTSIDE OF ISB, UNCOMMENT THIS LINE
-#my $DISTR_VERSION = 1;
-
-# USE INSIDE ISB, UNCOMMENT THIS LINE
-my $DISTR_VERSION = 0; 
-
-# forward declare variables
-my $CGI_HOME;		# Full path web server home directory
-my $HELP_DIR;		# Where all help png's are kept
-my $xslt;		# Full path reference to a stylesheet processor 
-my $DTD_FILE;		# Full path reference to ProteinProphet_v1.7.dtd
-my $SERVER_ROOT = '';	
-my $TOP_PATH;
-
-# Why define this? We never use this variable...oh but *we* do.  We cleverly 
-# rewrite paths in the perl code using simple text subsitutions via a perl
-# one-liner buried within the TPP make files.  See the "perl_paths" 
-# target/directory.  Now the real question is what value should it have.
-my $base_dir;
-
-$TOP_PATH = tpplib_perl::getHomePath();
-$CGI_HOME = tpplib_perl::getCgiUrl();
-$HELP_DIR = tpplib_perl::getHtmlUrl() . "images/help";
-
-$xslt = 'xsltproc -novalid'; # disconnect dtd check (since only has web server reference name)
-
-
-#
-# Cygwin Configuration
-#
-if ( ($^O eq 'cygwin' )||($^O eq 'MSWin32' )) {
-
-    if(exists $ENV{'WEBSERVER_ROOT'}) {
-	my ($serverRoot) = ($ENV{'WEBSERVER_ROOT'} =~ /(\S+)/);
-	if ( $WINDOWS_CYGWIN && $serverRoot =~ /\:/ ) {
-	    $serverRoot = `cygpath '$serverRoot'`;
-	    ($serverRoot) = ($serverRoot =~ /(\S+)/);
-	}
-	if ($^O eq 'MSWin32' ) {
-	    $serverRoot =~ s/\\/\//g;  # get those path seps pointing right!
-	}
-	# make sure ends with '/'
-	$serverRoot .= '/' if($serverRoot !~ /\/$/);
-	$SERVER_ROOT = $serverRoot;
-	if($SERVER_ROOT eq '') {
-	    die "cannot find WEBSERVER_ROOT environment variable\n";
-	}
-    }
-    else {
-	die "cannot find WEBSERVER_ROOT environment variable\n";
-    }
-}
-# end configuration
-
-
-
-#
-# gather TPP version info
-#
-my $TPPVersionInfo = tpplib_perl::getTPPVersionInfo() || 'version n/a';
-my $TPPhostname = "http://" . tpplib_perl::get_tpp_hostname();
-
-my $LC_SERVER_ROOT = lc $SERVER_ROOT; # lower case
-
-my $GO_ONTOLOGY_CGI = 'goOntology';
-
-
-my $HTML = 0;
-my $HTML_ORIENTATION = 1; # whether or not
-my $SHTML = 1; # whether or not to use SSI to launch cgi instead of traditional written html file
-my $ICAT = 0;
-my $GLYC = 0;
-my $EXCEL = 0;    # Generate XLS file from command-line (arg = EXCEL) -- outputs to file
-my $HTMLGEN = 0;  # Generate HTML file from command-line (arg = HTML) -- outputs to stdout
-my $NOGAGGLE = 0; # If set, do not generate Gaggle files (command-line arg = NOGAGGLE)
-
-my $SINGLE_HITS = 0;
-my $DISPLAY_MODS = 1;
-my $MOD_MASS_ERROR = 0.5;
-
-# get rid of these all
-my $CALCULATE_PIES = $ISB_VERSION; #whether to calc pies on the fly
-my %prot_entries = (); # for pies, prob for each protein entry
-
-# write out new xsl stylesheet
-my $xmlfile;
-my $xslfile;
-my $pngfile = '';
-my $htmlfile;
-my $excelfile;
-
-my $gaggleNameValueFile;
-my $gaggleNameValueSize;
-
-my $gaggleNameListFile;
-my $gaggleNameListSize;
-
-my $gaggleMatrixFile;
-my $gaggleMatrixSize;
-
-my $sort_index = -1;
-my $start_string = 'start';
-my $start_string_comment = '<!--' . $start_string . '-->';
-my $USE_INDEX = 1; # whether to use explicit @index rather than num siblings
-$USE_INDEX = 1 if(scalar(@ARGV) >= 2 && $ARGV[1] eq 'index');
-
-my $RESULT_TABLE_PRE = '<table ';
-my $RESULT_TABLE = 'cellpadding="0" bgcolor="white" class="results">';
-my $RESULT_TABLE_SUF = '</table>';
-
-my $checked = 'CHECKED="yes"';
-
-my $inital_xsl = 0;
-my $MAX_NUM_ENTRIES = 2000; # if more than that, will filter at min prob
-my $MIN_PROT_PROB = 0.1;
-# in some environments, form info is transmitted as $ARGV[0]
-
-
-my $entry_delimiter = 8; # empty cell height for delimiting successive entries
-
-my $initiate = 0;
-if(scalar(@ARGV) > 1 && $ARGV[0] eq '-file' && $ARGV[1] =~ /^(\S+\.)xml(\.gz)?$/) { # take file name from arg
-	$xmlfile = $ARGV[1];
-	if ($^O eq 'MSWin32' ) {
-		$xmlfile =~ s/\\/\//g;  # get those path seps pointing right!
-	}
-	$xmlfile =~ /^(\S+\.)xml(\.gz)?$/; # reevaluate $1
-	$xslfile = $1 . 'xsl';
-	$excelfile = $1 . 'xls';
-	$pngfile = $1 . 'png';
-	$gaggleNameValueFile = $1 . 'nv.ggl';
-	$gaggleNameListFile = $1 . 'nl.ggl';
-	$gaggleMatrixFile = $1 . 'mx.ggl';
-	if($SHTML) {
-	    $htmlfile = $1 . 'shtml';
-	}
-	else {
-	    $htmlfile = $1 . 'htm';
-	}
-
-	# check for icat
-	for(my $k = 2; $k <= $#ARGV; $k++) {
-	    $ICAT = 1 if($ARGV[$k] eq 'ICAT');
-	    $GLYC = 1 if($ARGV[$k] eq 'GLYC');
-	    $EXCEL= 1 if($ARGV[$k] eq 'EXCEL');
-	    $HTMLGEN = 1 if($ARGV[$k] eq 'HTML');
-	    $NOGAGGLE = 1 if($ARGV[$k] eq 'NOGAGGLE');
-	}
-
-	$initiate = 1 unless ($EXCEL || $HTMLGEN);
-
-}
-elsif(exists $box{'xmlfile'} && $box{'xmlfile'} =~ /^(\S+\.)xml(\.gz)?$/) {
-    $xmlfile = $box{'xmlfile'};
-	if ($^O eq 'MSWin32' ) {
-		$xmlfile =~ s/\\/\//g;  # get those path seps pointing right!
-	}
-	$xmlfile =~ /^(\S+\.)xml(\.gz)?$/; # reevaluate $1
-    $xslfile = $1 . 'xsl';
-    $excelfile = $1 . 'xls';
-    $pngfile = $1 . 'png';
-    $gaggleNameValueFile = $1 . 'nv.ggl';
-    $gaggleNameListFile = $1 . 'nl.ggl';
-    $gaggleMatrixFile = $1 . 'mx.ggl';
-    if($SHTML) {
-	$htmlfile = $1 . 'shtml';
-    }
-    else {
-	$htmlfile = $1 . 'htm';
-    }
-} # if
-
-
-my $go_level = 0;
-my %go_prots = ();
-$go_level = $box{'go_level'} if(exists $box{'go_level'});
-
-my $NEW_XML_FORMAT = 1;
-# cancel DISPLAY_MODS for inappropriate directories running old version
-$DISPLAY_MODS = 0 if(! useXMLFormatLinks($xmlfile));
-
-$| = 1; # autoflush
-
-my $restore_view = exists $box{'restore_view'} && $box{'restore_view'} eq 'yes';
-
-$ICAT = 1 if(exists $box{'icat_mode'} && $box{'icat_mode'} eq 'yes');
-$GLYC = 1 if(exists $box{'glyc_mode'} && $box{'glyc_mode'} eq 'yes');
-my $pre_existing_xsl = 0;
-
-
-if(0 && $restore_view && ! -e $xslfile) {
-    print "Error: Cannot find stylesheet for most recent view of dataset.  Please recreate.\n\n";
-    exit(1);
-}
-
-if(exists $box{'custom_settings'}) {
-    if($box{'custom_settings'} eq 'current') {
-	writeCustomizedSettings($xmlfile, 0, \%box);
-    }
-    elsif($box{'custom_settings'} eq 'default') {
-	writeCustomizedSettings($xmlfile, 1, \%box);
-
-	# full/short menu settings
-	my $menu = exists $box{'menu'} ? $box{'menu'} : '';
-	my $full_menu = exists $box{'full_menu'} ? $box{'full_menu'} : '';
-	my $short_menu = exists $box{'short_menu'} ? $box{'short_menu'} : '';
-
-	%box = %{getCustomizedSettings($xmlfile)}; # immediately get default settings
-	$box{'menu'} = $menu if(! ($menu eq '')); 
-	$box{'full_menu'} = $full_menu if(! ($full_menu eq '')); 
-	$box{'short_menu'} = $short_menu if(! ($short_menu eq '')); 
-	
-    }
-}
-
-
-if(exists $box{'outfile'}) {
-
-    my $init_outfile = $box{'outfile'}; # for later
-    # if windows name, convert it to cywin
-    if($WINDOWS_CYGWIN && $box{'outfile'} =~ /\\/) {
-	$box{'outfile'} = `cygpath '$box{'outfile'}'`;
-	if($box{'outfile'} =~ /^(\S+)\s?/) {
-	    $box{'outfile'} = $1;
-	}
-    } # windows 
-    my $outfile = $box{'outfile'} . '.xml';
-
-    if($box{'outfile'} eq '') {
-	print " please go back and specify filename for displayed data\n";
-	exit(1);
-    }
-    # check to make sure not same as self and steal full path from xmlfile
-    else {
-	# steal directory from xml fle
-	if(!File::Spec->file_name_is_absolute($outfile)) {
-	    my ($vol,$dirs,$files) = File::Spec->splitpath($xmlfile);
-	    $outfile = File::Spec->catpath($vol,$dirs,$outfile);
-	    if($outfile =~ /^(\S+)\.xml(\.gz)?$/) {
-		$box{'outfile'} = $1;
- 	    }
-	}
-
-	my $index = index($xmlfile, $outfile);
-	if((File::Spec->file_name_is_absolute($outfile) && $outfile eq $xmlfile) ||
-	   ($index >= 0 && $index + (length $outfile) == (length $xmlfile))) {
-	    if($HTML_ORIENTATION && $xmlfile =~ /^(\S+\.)xml(\.gz)?$/) {
-		if($SHTML) {
-		    print " please go back and specify a filename for displayed data other than $init_outfile.shtml\n";
-		}
-		else {
-		    print " please go back and specify a filename for displayed data other than $init_outfile.htm\n";
-		}
-	    }
-	    else {
-		print " please go back and specify a filename for displayed data other than $init_outfile\n";
-	    }
-	    exit(1);
-	}
-	if(-e $outfile) {
-
-	    if($HTML_ORIENTATION && $outfile =~ /^(\S+\.)xml(\.gz)?$/) {
-		if($SHTML) {
-		    print " $init_outfile.shtml already exists.  Please go back and specify an alternative filename for displayed data\n";
-		}
-		else {
-		    print " $init_outfile.htm already exists.  Please go back and specify an alternative filename for displayed data\n";
-		}
-	    }
-	    else {
-		print " $init_outfile already exists.  Please go back and specify an alternative filename for displayed data\n";
-	    }
-	    exit(1);
-	}
-
-	my $suffix = $HTML_ORIENTATION ? '.htm' : '.xml';
-
-	$suffix = '.shtml' if($SHTML);
-	my $newhtmlfile = $box{'outfile'} . '.htm';
-	$newhtmlfile = $box{'outfile'} . $suffix if($SHTML);
-	writeXMLFile($box{'outfile'}, \%box, $xslt, $xmlfile); # both temporary xsl file and xmlfile....
-	initialize($xslt, $box{'outfile'} . '.xml', $box{'outfile'} . '.xsl', \%box, $newhtmlfile, 0);
-
-	# make local reference
-	my $local_datafile = $box{'outfile'} . $suffix;
-
-	if(! $ISB_VERSION) {
-
-	    $local_datafile = $box{'outfile'} . '.xml'; # BSP until shtml fixed
-
-	    # this should be just like after analysis: use local datafile link, but windows name for shtml file
-
-	    if((length $SERVER_ROOT) <= (length $local_datafile) && 
-	       index((lc $local_datafile), ($LC_SERVER_ROOT)) == 0) {
-		$local_datafile = '/' . substr($local_datafile, (length $SERVER_ROOT));
-	    }
-	    else {
-		die "problem (pr1): $local_datafile is not mounted under webserver root: $SERVER_ROOT\n";
-	    }
-	    my $windows_outfile = $outfile;
-	    if($WINDOWS_CYGWIN) {
-		$windows_outfile = `cygpath -w '$outfile'`;
-		if($windows_outfile =~ /^(\S+)\s?/) {
-		    $windows_outfile = $1;
-		}
-	    }
-	    # use windows path here
-	    print " data written to $windows_outfile<br><br>\n";
-	    if (!exists $ENV{'WEBSERVER_TMP'}) { # if working in tmpdir, don't give misleading info
-		print ' direct your browser to <a target="Win1" href="' .  $local_datafile . '">' . "http://" . $TPPhostname . $local_datafile . '</a>' . "\n\n"; 
-	    }
-	} # if iis & cygwin
-	else { # unix
-	    if (!exists $ENV{'WEBSERVER_TMP'}) { # if working in tmpdir, don't give misleading info
-		print ' data written to <a target="Win1" href="' .  $local_datafile . '">' . $local_datafile . '</a>', "\n\n";
-	    }
-	}
-
-    }
-}
-else {
-    if(!$xmlfile) {
-	print " No xml file specified; please use the -file option\n";
-	&printUsage();
-	exit(1);
-    }
-
-    if($initiate) {
-	initialize($xslt, $xmlfile, $xslfile, \%box, $htmlfile, 0);
-	print "\n protein probabilities written to file ";
-
-	if(! $ISB_VERSION) {
-	    my $local_ref = $HTML_ORIENTATION ? $htmlfile : $xmlfile;
-	    my $windows_ref = $xmlfile;
-	    if($WINDOWS_CYGWIN) {
-		# get windows name
-		$windows_ref = `cygpath -w '$xmlfile'`;
-	    }
-	    if($windows_ref =~ /^(\S+)\s?/) {
-		$windows_ref = $1;
-		print $windows_ref;
-	    }
-	    if((length $SERVER_ROOT) <= (length $local_ref) && 
-	       index((lc $local_ref), ($LC_SERVER_ROOT)) == 0) {
-		$local_ref = '/' . substr($local_ref, (length $SERVER_ROOT));
-		print "\n direct your browser to http://" . $TPPhostname . $local_ref if($HTML_ORIENTATION);
-	    }
-	    else {
-		die "problem (pr2): $local_ref is not mounted under webserver root: $SERVER_ROOT\n";
-	    }
-	} # if iis & cygwin
-	elsif($HTML_ORIENTATION) {
-	    print $htmlfile;
-	}
-	else {
-	    print $xmlfile;
-	}
-	print "\n\n";
-    }
-    elsif ($EXCEL) {
-	print "Writing results to tab-delimited file: $excelfile\n";
-	writeTabDelimData($excelfile, $xslt, $xmlfile);
-	print "Done!\n";
-
-    }
-    elsif ($HTMLGEN) {
-	my $outfile = $htmlfile;
-	$outfile =~ s/shtml$/html/i;
-	print "Writing results to html file: $outfile\n";
-
-	open(HTMLOUT, ">$outfile") or die "cannot open $outfile $!\n";
-	my $ fh= select HTMLOUT;
-	my $nrows = 0;
-	my $ncols = 0;
-	unless ($NOGAGGLE) {
-	    writeGaggleNameValueData($gaggleNameValueFile, $xslt, $xmlfile);
-	    $nrows = writeGaggleNameListData($gaggleNameListFile, $xslt, $xmlfile);
-	    $ncols = writeGaggleMatrixData($gaggleMatrixFile, $xslt, $xmlfile);
-	}
-	writeXSLFile($xslfile, \%box, 0, $nrows, $ncols) if(! $restore_view);
-	printHTML($xslt, $xmlfile, $xslfile, \%box);
-	select $fh;
-	print "Done!\n";
-
-    }
-    else {
-	if($restore_view) {
-
-	    if(-e $xslfile) {
-		$pre_existing_xsl = 1;
-		%box = %{readXSLFile($xslfile)};
-
-	    }
-	    else {
-		%box = %{initialize($xslt, $xmlfile, $xslfile, \%box, $htmlfile, 1)}; # write the xsl file
-	    }
-	}
-	else {
-	    %box = %{getCustomizedSettings($xmlfile)} if(exists $box{'restore'} && $box{'restore'} eq 'yes'); # no longer need to keep track of 'restore'
-	}
-	$go_level = $box{'go_level'} if(exists $box{'go_level'});
-
-	if(exists $box{'excel'} && $box{'excel'} eq 'yes') {
-	    writeTabDelimData($excelfile, $xslt, $xmlfile);
-	    print "\n"; # write something to prevent cgi timeout
-	}
-
-	if(exists $box{'action'} && $box{'action'} eq 'Recompute p-values') {
-	    if ($^O eq 'linux') {
-		system($TOP_PATH."bin/ASAPRatioPvalueParser $xmlfile");
-	    }
-	    else {
-		system("ASAPRatioPvalueParser $xmlfile");
-	    }
-	}
-	writeGaggleNameValueData($gaggleNameValueFile, $xslt, $xmlfile);
-	my $nrows = writeGaggleNameListData($gaggleNameListFile, $xslt, $xmlfile);
-	my $ncols = writeGaggleMatrixData($gaggleMatrixFile, $xslt, $xmlfile);
-	writeXSLFile($xslfile, \%box, 0, $nrows, $ncols) if(! $restore_view);
-	printHTML($xslt, $xmlfile, $xslfile, \%box);
-    }
-}
-
-sub useXMLFormatLinks {
-    (my $file) = @_;
-    return $NEW_XML_FORMAT;
-}
-
-
-sub getGoOntology {
-(my $proteins, my $go_level) = @_;
-# first string together hidden info for ChenWei's program
-#return "making pie chart...\n";
-# new interface for chen wei
-# goOntology <full path curr dir> <web server dir> <level> <prot1> <wt1> <prot2> <wt2> ..
-# goOntology <level> <file> <curr dir> <web server dir>
-
-# need to specify the full path name and webserver name for directories
-my $dir = '';
-if($xmlfile =~ /^(\S+\/)\S+\.xml/) {
-    $dir = $1;
-}
-my $local_dir = $dir;
-
-my $go_file = $dir . 'go_prots.txt';
-
-open(OUT, ">$go_file") or die "cannot open $go_file $!\n";
-foreach(keys %{$proteins}) {
-    if(/^IPI\:(\S+)\.\d$/) {
-	print OUT "$1\t${$proteins}{$_}\n";
-    }
-    else {
-	print OUT "$_\t${$proteins}{$_}\n";
-    }
-}
-
-
-close(OUT);
-
-
-if(! $ISB_VERSION) {
-
-    if(exists $ENV{'WEBSERVER_ROOT'}) {
-	# make sure ends with '/'
-	my ($serverRoot) = ($ENV{'WEBSERVER_ROOT'} =~ /(\S+)/);
-	if ( $serverRoot =~ /\:/ ) {
-	    $serverRoot = `cygpath '$serverRoot'`;
-	    ($serverRoot) = ($serverRoot =~ /(\S+)/);
-	}
-	if ($^O eq 'MSWin32' ) {
-		$serverRoot =~ s/\\/\//g;  # get those path seps pointing right!
-	}
-	# make sure ends with '/'
-	$serverRoot .= '/' if($serverRoot !~ /\/$/);
-	if((length $serverRoot) <= (length $dir)) {
-	    $local_dir = '/' . substr($local_dir, (length $serverRoot));
-	}else {
-	    die "problem (pr3): >$local_dir< is not mounted under webserver root: >$serverRoot<\n";
-	}
-    }
-} # if not ISB version
-my $hide = 0;
-if($go_level > 100) { # hide
-    $go_level = $go_level - 100;
-    $hide = 1;
-}
-if($CALCULATE_PIES) {
-    print "<HR/><font color=\"green\">Go Ontology Information: Level $go_level</font><p/>";
-    my $command = '/regis/data3/search/akeller/GO_ONTOLOGY/Go.exe ' . $go_level . ' ' . $go_file . ' /regis/data3/search/akeller/GO_ONTOLOGY/';
-    $command .= ' HIDE' if($hide);
-    system($command);
-    unlink($go_file) if(-e $go_file);
-# write output to file, which will be hyperlinked at top of output
-
-} # if calc pies
-
-
-}
-
-
-sub writeXMLFile {
-(my $file, my $boxptr, my $xslt, my $xml) = @_;
-
-my $tempxslfile = $file . '.tmp.xsl';
-
-
-open(OUT, ">$tempxslfile");
-print OUT '<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:protx="http://regis-web.systemsbiology.net/protXML">', "\n";
-
-print OUT '<xsl:output method="xml" version="1.0" encoding="UTF-8" indent="yes"/>', "\n";
-
-
-print OUT '<xsl:template match="node() | @*">', "\n";
-print OUT '<xsl:copy>', "\n";
-
-
-print OUT '<xsl:apply-templates select="*[not(self::protx:protein_group or self::protx:protein or self::protx:peptide)] | @*"/>';
-
-print OUT '<xsl:text>' . "\n" . '</xsl:text>';
-
-my $minprob = exists ${$boxptr}{'min_prob'} && ! (${$boxptr}{'min_prob'} eq '') ? ${$boxptr}{'min_prob'} : 0;
-my $minntt = exists ${$boxptr}{'min_ntt'} && ! (${$boxptr}{'min_ntt'} eq '') ? ${$boxptr}{'min_ntt'} : 0;
-
-my $maxnmc = exists ${$boxptr}{'max_nmc'} && ! (${$boxptr}{'max_nmc'} eq '') ? ${$boxptr}{'max_nmc'} : -1;
-my $pep_aa = exists ${$boxptr}{'pep_aa'} && ! (${$boxptr}{'pep_aa'} eq '') ? ${$boxptr}{'pep_aa'} : '';
-my $exclude_1 = exists ${$boxptr}{'ex1'} && ${$boxptr}{'ex1'} eq 'yes' ? ${$boxptr}{'ex1'} : '';
-my $exclude_2 = exists ${$boxptr}{'ex2'} && ${$boxptr}{'ex2'} eq 'yes' ? ${$boxptr}{'ex2'} : '';
-my $exclude_3 = exists ${$boxptr}{'ex3'} && ${$boxptr}{'ex3'} eq 'yes' ? ${$boxptr}{'ex3'} : '';
-
-my @inclusions = exists ${$boxptr}{'inclusions'} ? split(' ', ${$boxptr}{'inclusions'}) : ();
-my @exclusions = exists ${$boxptr}{'exclusions'} ? split(' ', ${$boxptr}{'exclusions'}) : ();
-my @pinclusions = exists ${$boxptr}{'pinclusions'} ? split(' ', ${$boxptr}{'pinclusions'}) : ();
-my @pexclusions = exists ${$boxptr}{'pexclusions'} ? split(' ', ${$boxptr}{'pexclusions'}) : ();
-
-# other variables needed?
-my $min_asap = exists ${$boxptr}{'min_asap'} && ! ${$boxptr}{'min_asap'} eq '' ? ${$boxptr}{'min_asap'} : 0;
-my $max_asap = exists ${$boxptr}{'max_asap'} && ! ${$boxptr}{'max_asap'} eq '' ? ${$boxptr}{'max_asap'} : 0;
-my $min_xpress = exists ${$boxptr}{'min_xpress'} && ! ${$boxptr}{'min_xpress'} eq '' ? ${$boxptr}{'min_xpress'} : 0;
-my $max_xpress = exists ${$boxptr}{'max_xpress'} && ! ${$boxptr}{'max_xpress'} eq '' ? ${$boxptr}{'max_xpress'} : 0;
-my $show_groups = exists ${$boxptr}{'show_groups'} && ! ${$boxptr}{'show_groups'} eq '' ? ${$boxptr}{'show_groups'} : '';
-my $min_pepprob = exists ${$boxptr}{'min_pepprob'} && ! ${$boxptr}{'min_pepprob'} eq '' ? ${$boxptr}{'min_pepprob'} : 0;
-my $filter_asap = exists ${$boxptr}{'filter_asap'} && ! ${$boxptr}{'filter_asap'} eq '' ? ${$boxptr}{'filter_asap'} : '';
-
-my $show_ggl = exists ${$boxptr}{'show_ggl'} && ${$boxptr}{'show_ggl'} eq 'yes' ? ${$boxptr}{'show_ggl'} : '';
-
-my $filter_xpress = exists ${$boxptr}{'filter_xpress'} ? ${$boxptr}{'filter_xpress'} : '';
-my $show_adjusted_asap = (! exists ${$boxptr}{'show_adjusted_asap'} && ! exists ${$boxptr}{'adj_asap'}) || (${$boxptr}{'show_adjusted_asap'} eq 'yes') ?  ${$boxptr}{'show_adjusted_asap'} : '';
-#my $show_adjusted_asap = (${$boxptr}{'show_adjusted_asap'} eq 'yes') ?  ${$boxptr}{'show_adjusted_asap'} : '';
-my $max_pvalue_display = exists ${$boxptr}{'max_pvalue'} && ! (${$boxptr}{'max_pvalue'} eq '') ? ${$boxptr}{'max_pvalue'} : 1.0;
-my $asap_xpress = exists ${$boxptr}{'asap_xpress'} ? ${$boxptr}{'asap_xpress'} : '';
-my $quant_light2heavy = ! exists ${$boxptr}{'quant_light2heavy'} || ${$boxptr}{'quant_light2heavy'} eq 'true' ? 'true' : 'false';
-
-
-# add filter_xpress and asap_xpress capabilities here....
-
-
-# apply-templates select="protx:protein_group"
-# SHOW GROUPS
-if(! ($show_groups eq '')) {
-    print OUT '<xsl:apply-templates select="protx:protein_group[@probability &gt;=\'' . $minprob . '\'';
-    print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/ASAPRatio/@ratio_mean &gt;= \'0\' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@ratio_standard_dev &gt;= \'0\'' if(! ($filter_asap eq ''));
-    print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean &gt;= \'0\' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev &gt;= \'0\'' if(! ($filter_xpress eq ''));
-
-    print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &gt;= \'' . $min_xpress . '\'' if($min_xpress > 0);
-    print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &lt;= \'' . $max_xpress . '\'' if($max_xpress > 0);
-
-    if($show_adjusted_asap eq '' || ! exists ${$boxptr}{'adj_asap'}) {
-	print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &gt;= \'' . $min_asap . '\'' if($min_asap > 0);
-	print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &lt;= \'' . $max_asap . '\'' if($max_asap > 0);
-
-	print OUT ' and (not(protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']) or not(protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']) or ((protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev - protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy).'ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev &gt;= \'0\') and (protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev - protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev &gt;= \'0\')))' if(! ($asap_xpress eq ''));
-
-    }
-    else { # use adjusted values
-	print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@' . getRatioPrefix($quant_light2heavy) . 'adj_ratio_mean &gt;= \'' . $min_asap . '\'' if($min_asap > 0);
-	print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@' . getRatioPrefix($quant_light2heavy) . 'adj_ratio_mean &lt;= \'' . $max_asap . '\'' if($max_asap > 0);
-	print OUT ' and (not(protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']) or not(protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']) or ((protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev - protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_standard_dev &gt;= \'0\') and (protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_standard_dev - protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev &gt;= \'0\')))' if(! ($asap_xpress eq ''));
-
-    }
-    print OUT ' and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:protein[@group_sibling_id = \'a\']/protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@decimal_pvalue &lt;= \'' . $max_pvalue_display . '\'' if($max_pvalue_display < 1.0);
-    for(my $e = 0; $e <= $#exclusions; $e++) {
-	print OUT ' and not(@group_number=\'' . $exclusions[$e] . '\')';
-    }
-    print OUT ']"/>';
-
-    if(@inclusions) {
-	my $first = 1;
-	foreach(@inclusions) {
-	    if($first) {
-		print OUT '<xsl:apply-templates select="protx:protein_group[@group_number=\'' . $_ . '\'';
-		$first = 0;
-	    }
-	    else {
-		print OUT ' or @group_number=\'' . $_ . '\'';
-	    }
-	}
-	print OUT ']"/>';
-    } # if have some inclusions
-} # show groups
-# HIDE GROUPS
-else {
-    print OUT '<xsl:apply-templates select="protx:protein_group[@probability &gt;=\'' . $minprob . '\'';
-    print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean &gt;= \'0\' and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev &gt;= \'0\']' if(! ($filter_asap eq ''));
-    print OUT ' and protx:protein[protx:analysis_result[@analysis=\'xpress\'] and protx:XPressRatio/@ratio_mean &gt;= \'0\' and protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev &gt;= \'0\']' if(! ($filter_xpress eq ''));
-    print OUT ' and protx:protein[protx:analysis_result[@analysis=\'xpress\'] and protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &gt;= \'' . $min_xpress . '\']' if($min_xpress > 0);
-    print OUT ' and protx:protein[protx:analysis_result[@analysis=\'xpress\'] and protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &lt;= \'' . $max_xpress . '\']' if($max_xpress > 0);
-    if($show_adjusted_asap eq '' || ! exists ${$boxptr}{'adj_asap'}) {
-	print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &gt;= \'' . $min_asap . '\']' if($min_asap > 0);
-	print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@' . getRatioPrefix($quant_light2heavy) . 'ratio_mean &lt;= \'' . $max_asap . '\']' if($max_asap > 0);
-	print OUT ' and (not(protx:protein/protx:analysis_result[@analysis=\'asapratio\']) or not(protx:protein/protx:analysis_result[@analysis=\'xpress\']) or protx:protein[protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev - protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean + protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev &gt;= \'0\' and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean + protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev - protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:analysis_result[@analysis=\'xpress\']protx:XPressRatio/@ratio_standard_dev &gt;= \'0\'])' if(! ($asap_xpress eq ''));
-    }
-    else { # show adjusted
-	print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@' . getRatioPrefix($quant_light2heavy) . 'adj_ratio_mean &gt;= \'' . $min_asap . '\']' if($min_asap > 0);
-	print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@' . getRatioPrefix($quant_light2heavy) . 'adj_ratio_mean &lt;= \'' . $max_asap . '\']' if($max_asap > 0);
-	print OUT ' and (not(protx:protein/protx:analysis_result[@analysis=\'asapratio_pvalue\']) or not(protx:protein/protx:analysis_result[@analysis=\'xpress\']) or protx:protein[protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean + protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev - protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean + protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_standard_dev &gt;= \'0\' and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean + protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_standard_dev - protx:analysis_result[@analysis=\'xpress\']protx:XPressRatio/@ratio_mean + protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_standard_dev &gt;= \'0\'])' if(! ($asap_xpress eq ''));
-    }
-    print OUT ' and protx:protein[protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@decimal_pvalue &lt;= \'' . $max_pvalue_display . '\]' if($max_pvalue_display < 1.0);
-    foreach(@exclusions) {
-	print OUT ' and not(@group_number=\'' . $_ . '\')';
-    }
-    print OUT ']"/>';
-
-if(@inclusions) {
-    my $first = 1;
-    foreach(@inclusions) {
-	if($first) {
-	    print OUT '<xsl:apply-templates select="protx:protein_group[@group_number=\'' . $_ . '\'';
-	    $first = 0;
-	}
-	else {
-	    print OUT ' or @group_number=\'' . $_ . '\'';
-	}
-    }
-    print OUT ']"/>';
-} # if have some inclusions
-}
-# apply-templates select="protx:protein"
-if(! ($show_groups eq '')) {
-    print OUT '<xsl:apply-templates select="protx:protein"/>';
-}
-# HIDE GROUPS
-else {
-
-# make sure there are no pexclusions or pinclusions
-    print OUT '<xsl:apply-templates select="protx:protein[@probability &gt;=\'' . $minprob . '\'';
-    print OUT ' and protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean &gt;= \'0\' and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_standard_dev &gt;= \'0\'' if(! ($filter_asap eq ''));
-    print OUT ' and protx:analysis_result[@analysis=\'xpress\'] and protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean &gt;= \'' . $min_xpress . '\'' if($min_xpress > 0);
-    print OUT ' and protx:analysis_result[@analysis=\'xpress\'] and protx:analysis_result[@analysis=\'xpress\']/protx:XPressRatio/@ratio_mean &lt;= \'' . $max_xpress . '\'' if($max_xpress > 0);
-    if($show_adjusted_asap eq '' || ! exists ${$boxptr}{'adj_asap'}) {
-	print OUT ' and protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean &gt;= \'' . $min_asap . '\'' if($min_asap > 0);
-	print OUT ' and protx:analysis_result[@analysis=\'asapratio\'] and protx:analysis_result[@analysis=\'asapratio\']/protx:ASAPRatio/@'. getRatioPrefix($quant_light2heavy) .'ratio_mean &lt;= \'' . $max_asap . '\'' if($max_asap > 0);
-    }
-    else { # show adjusted
-	print OUT ' and protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean &gt;= \'' . $min_asap . '\'' if($min_asap > 0);
-	print OUT ' and protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@adj_ratio_mean &lt;= \'' . $max_asap . '\'' if($max_asap > 0);
-    }
-    print OUT ' and protx:analysis_result[@analysis=\'asapratio_pvalue\'] and protx:analysis_result[@analysis=\'asapratio_pvalue\']/protx:ASAPRatio_pvalue/@decimal_pvalue &lt;= \'' . $max_pvalue_display . '\'' if($max_pvalue_display < 1.0);
-
-    foreach(@pexclusions) {
-	if(/^(\d+)([a-z,A-Z])$/) {
-	    print OUT ' and not(parent::node()/@group_number=\'' . $1 . '\' and @group_sibling_id=\'' . $2 . '\')';
-	}
-    }
-
-    print OUT ']"/>';
-    if(@pinclusions > 0) {
-	my $first = 1;
-	foreach(@pinclusions) {
-	    if(/^(\d+)([a-z,A-Z])$/) {
-		if($first) {
-		    $first = 0;
-		    print OUT '<xsl:apply-templates select="protx:protein[(parent::node()/@group_number=\'' . $1 . '\' and @group_sibling_id=\'' . $2 . '\')';
-		}
-		else {
-		    print OUT ' or (parent::node()/@group_number=\'' . $1 . '\' and @group_sibling_id=\'' . $2 . '\')';
-		}
-	    }
-	}
-	print OUT ']"/>';
-
-    }
-
-}
-
-print OUT '<xsl:apply-templates select="protx:peptide[@nsp_adjusted_probability &gt;= \'' . $min_pepprob . '\'';
-print OUT ' and @n_enzymatic_termini &gt;=\''. $minntt . '\'' if($minntt > 0);
-print OUT ' and not(@charge=\'1\')' if(! ($exclude_1 eq ''));
-print OUT ' and not(@charge=\'2\')' if(! ($exclude_2 eq ''));
-print OUT ' and not(@charge=\'3\')' if(! ($exclude_3 eq ''));
-print OUT ']"/>';
-
-# apply-templates select="peptide"
-
-
-print OUT '</xsl:copy>';
-print OUT '</xsl:template>', "\n";
-print OUT '</xsl:stylesheet>', "\n";
-close(OUT);
-
-my $outfile = $file . '.xml'; #'tempfile.xml';
-
-
-# now compute filter
-my $filter = '';
-if($minprob > 0) {
-    if($show_groups eq '') {
-	$filter .= 'min_prot_prob=\'' . $minprob . '\' ';
-    }
-    else { # group
-	$filter .= 'min_group_prob=\'' . $minprob . '\' ';
-    }
-}
-$filter .= 'exclude_illegal_XPRESSRatios=\'Y\' ' if($filter_xpress);
-$filter .= 'exclude_illegal_ASAPRatios=\'Y\' ' if($filter_asap);
-my $asap_prefix = $show_adjusted_asap eq '' || ! exists ${$boxptr}{'adj_asap'} ? '' : 'adj_';
-$filter .= 'asap_xpress_consistency=\'Y\' ' if(! ($asap_xpress eq ''));
-$filter .= 'min_' . getRatioPrefix($quant_light2heavy) . 'xpress=\'' . $min_xpress . '\' ' if($min_xpress > 0);
-$filter .= 'max_' . getRatioPrefix($quant_light2heavy) . 'xpress=\'' . $max_xpress . '\' ' if($max_xpress > 0);
-$filter .= $asap_prefix . 'min_' . getRatioPrefix($quant_light2heavy) . 'asap=\'' . $min_asap . '\' ' if($min_asap > 0);
-$filter .= $asap_prefix . 'max_' . getRatioPrefix($quant_light2heavy) . 'asap=\'' . $max_asap . '\' ' if($max_asap > 0);
-$filter .= 'max_pvalue=\'' . $max_pvalue_display . '\' ' if($max_pvalue_display < 1.0);
-$filter .= 'min_pepprob=\'' . $min_pepprob . '\' ' if($min_pepprob > 0);
-$filter .= 'minntt=\'' . $minntt . '\' ' if($minntt > 0);
-$filter .= 'maxnmc=\'' . $maxnmc . '\' ' if($maxnmc >= 0);
-$filter .= 'exclude_1+_peptides=\'Y\' ' if($exclude_1);
-$filter .= 'exclude_2+_peptides=\'Y\' ' if($exclude_2);
-$filter .= 'exclude_3+_peptides=\'Y\' ' if($exclude_3);
-$filter .= 'group_entry_inclusions=\'' . join(',', @inclusions) . '\' ' if(@inclusions > 0);
-$filter .= 'group_entry_exclusions=\'' . join(',', @exclusions) . '\' ' if(@exclusions > 0);
-$filter .= 'protein_entry_inclusions=\'' . join(',', @pinclusions) . '\' ' if(@pinclusions > 0);
-$filter .= 'protein_entry_exclusions=\'' . join(',', @pexclusions) . '\' ' if(@pexclusions > 0);
-
-
-# if $xmlfile is gzipped, returns tmpfile name, else returns $xmlfile
-my $tmp_xml = tpplib_perl::uncompress_to_tmpfile($xml);
-
-if($xslt =~ /xsltproc/) {
-    open XALAN, "$xslt $tempxslfile $tmp_xml |" or print "cannot open $xslt\n";;
-}
-else {
-    open XALAN, "$xslt $tmp_xml $tempxslfile |" or print "cannot open $xslt\n";;
-}
-open(XML, ">$outfile");
-
-my $start = 1;
-my $counter = 1;
-my $parentfile = $xmlfile;
-if($HTML_ORIENTATION && $xmlfile =~ /^(\S+\.)xml(\.gz)?$/) {
-    if($SHTML) {
-	$parentfile = $1 . 'shtml';
-    }
-    else {
-	$parentfile = $1 . 'htm';
-    }
-}
-
-# make local reference
-my $local_parent = $parentfile;
-my $windows_parent = '';
-if(! $ISB_VERSION) {
-    if((length $SERVER_ROOT) <= (length $local_parent) && 
-       index((lc $local_parent), ($LC_SERVER_ROOT)) == 0) {
-	$local_parent = '/' . substr($local_parent, (length $SERVER_ROOT));
-	if($WINDOWS_CYGWIN) {
-	    $windows_parent = `cygpath -w '$outfile'`;
-	    if($windows_parent =~ /^(\S+)\s?/) {
-		$windows_parent = $1;
-	    }
-	}
-    }
-    else {
-	die "problem (pr4): $local_parent is not mounted under webserver root: $SERVER_ROOT\n";
-    }
-} # if iis & cygwin
-
-
-# check for stylesheet reference
-my $xsltproc = $xslt =~ /xsltproc/;
-my $doctype = 0;
-while(<XALAN>) {
-    if($start && /^(\<\?xml\-stylesheet type\=\"text\/xsl\" href\=\")\S+(\"\?\>.*)$/) {
-	my $local_xslfile = $file . '.xsl';
-
-	if(! $ISB_VERSION) {
-	    if((length $SERVER_ROOT) <= (length $local_xslfile) && 
-	       index((lc $local_xslfile), ($LC_SERVER_ROOT)) == 0) {
-		$local_xslfile = '/' . substr($local_xslfile, (length $SERVER_ROOT));
-	    }
-	    else {
-		die "problem (pr5): $local_xslfile is not mounted under webserver root: $SERVER_ROOT\n";
-	    }
-	} # if iis & cygwin
-	print XML $1 . $local_xslfile . $2;
-	$start = 0;
-    }
-    elsif($start && ! $doctype && /^\<protx\:protein\_summary/) {
-	my $local_xslfile = $file . '.xsl';
-
-	if(! $ISB_VERSION) {
-	    if((length $SERVER_ROOT) <= (length $local_xslfile) && 
-	       index((lc $local_xslfile), ($LC_SERVER_ROOT)) == 0) {
-		$local_xslfile = '/' . substr($local_xslfile, (length $SERVER_ROOT));
-	    }
-	    else {
-		die "problem (pr6): $local_xslfile is not mounted under webserver root: $SERVER_ROOT\n";
-	    }
-	} # if iis & cygwin
-	print XML '<?xml-stylesheet type="text/xsl" href="' . $local_xslfile . '"? xmlns:protx="http://regis-web.systemsbiology.net/protXML">' . "\n";
-	print XML;
-	$start = 0;
-    }
-    # make replacements to num predicted correct prots and parent data file, as well as sens / err data
-    elsif(/^(.*dataset\_derivation generation\_no\=\")(\d+)(\".*)$/) {
-	my $first = $1;
-	my $second = $2;
-	my $third = $3;
-	if(! ($filter eq '')) { # then there is something to do
-	    if($xslt =~ /xsltproc/) {
-		my $update = $first . ($second+1) . '">';
-		my $next = $second + 1;
-		my $rest = $third;
-
-		if($third =~ /^(\"\>.*?)(\<data\_filter\s+.*)/) {
-		    print XML $first . ($second+1) . $1 . "\n";
-		    print XML '<data_filter number="' . ($second+1) . '" parent_file="' . $local_parent;
-		    print XML '" windows_parent="' . $windows_parent if($WINDOWS_CYGWIN);
-		    print XML '" description="' . $filter . '"/>', "\n";
-		    print XML $2 . "\n";
-		}
-		else {
-		    print XML $first . ($second+1) . $third, "\n";
-		    # now add current filter
-		    print XML '<data_filter number="' . ($second+1) . '" parent_file="' . $local_parent;
-		    print XML '" windows_parent="' . $windows_parent if($WINDOWS_CYGWIN);
-		    print XML '" description="' . $filter . '"/>', "\n";
-		}
-	    } # xsltproc
-	    else {
-		print XML $first . ($second+1) . $third, "\n";
-		# now add current filter
-		print XML '<data_filter number="' . ($second+1) . '" parent_file="' . $local_parent;
-		print XML '" windows_parent="' . $windows_parent if($WINDOWS_CYGWIN);
-		print XML '" description="' . $filter . '"/>', "\n";
-	    }
-
-	}
-	else {
-	    print XML;
-	}
-    }
-
-    elsif($USE_INDEX && /^(.*\<protx\:protein_group.*?group_number\=\")\d+(\".*)$/) {
-	print XML $1 . $counter++ . $2;
-    }
-    else {
-	if($start && /DOCTYPE/) {
-	    $doctype = 1;
-	}
-	print XML;
-    }
-}
-
-close(XML);
-close(XALAN);
-unlink($tmp_xml) if ($tmp_xml ne $xml); # did we decompress protxml.gz?
-
-
-$inital_xsl = $counter > $MAX_NUM_ENTRIES;
-unlink($tempxslfile) if(-e $tempxslfile);
-unlink("$outfile.tmp") if(-e "$outfile.tmp");
-${$boxptr}{'restore'} = 'yes'; # for new xsl
-${$boxptr}{'xmlfile'} = $file . '.xml';
-if(exists $box{'xmlfile'} && $box{'xmlfile'} =~ /^(\S+\.)xml(\.gz)?$/) {
-    $xmlfile = $box{'xmlfile'};
-    $xslfile = $1 . 'xsl';
-    $excelfile = $1 . 'xls';
-}
-
-}
-
-
-sub writeTabDelimData {
-    (my $outfile, my $engine, my $xml) = @_;
-    my $tempxslfile = $xmlfile . '.tmp.xsl';
-    my $tempfile = $xmlfile . '.tmp.xls';
-
-    my $text = exists $box{'text1'} ? $box{'text1'} : '';
-    my @select_aas = ();
-    if(exists $box{'pep_aa'} && ! ($box{'pep_aa'} eq '')) {
-	for(my $k = 0; $k < (length $box{'pep_aa'}); $k++) {
-	    my $next = substr($box{'pep_aa'}, $k);
-	    if($next =~ /^[a-z,A-Z](\d\d+)/) {
-		my $mass = $1;
-		push(@select_aas, substr($box{'pep_aa'}, $k, 1) . '[' . $mass . ']');
-		$k += (length $mass);
-	    }
-	    else {
-		push(@select_aas, substr($box{'pep_aa'}, $k, 1));
-	    }
-	}
-    }
-
-    unlink($tempxslfile) if(-e $tempxslfile);
-    unlink($tempfile) if(-e $tempfile);
-    writeXSLFile($tempxslfile, \%box, 1, 0, 0);
-
-    if($xslt =~ /xsltproc/) {
-	system("$engine $tempxslfile $xml > $tempfile");
-    }
-    else {
-	system("$engine $xml $tempxslfile > $tempfile");
-    }
-    open(OUT, ">$outfile") or die "cannot open $outfile $!\n";
-    open(IN, "$tempfile") or die "cannot open $tempfile $!\n";
-    my $start = 0;
-    my $active = 0;
-    my $prot_ind = -1;
-    my $pep_ind = -1;
-    my $first = 1;
-    while(<IN>) {
-	if(index($_, $start_string_comment) >= 0) {   
-	    $start = 1;
-	}
-	elsif($start) {
-	    if(/\S/) {
-		$active = 1;
-	    }
-	    if(/^\<\/form/ || /^\<\/table/) {
-		$start = 0;
-	    }
-	    elsif($active) {
-		if(@select_aas > 0 || ! ($text eq '')) {
-		    chomp();
-		    my @parsed = split('\t');
-		    if($first) {
-			for(my $p = 0; $p <= $#parsed; $p++) {
-			    if($prot_ind == -1 && $parsed[$p] eq 'protein') {
-				$prot_ind = $p;
-			    }
-			    elsif($pep_ind == -1 && $parsed[$p] eq 'peptide sequence') {
-				$pep_ind = $p;
-			    }
-			}
-			print OUT "$_\n";
-			$first = 0; # done
-		    }
-		    else {
-			my $ok = 1;
-			for(my $p = 0; $p <= $#parsed; $p++) {
-			    for(my $s = 0; $s <= $#select_aas; $s++) {
-				$ok &&= $pep_ind >= @parsed || $pep_ind == -1 || $p != $pep_ind || index($parsed[$p], $select_aas[$s]) >= 0;
-			    }
-			    $ok &&= $prot_ind >= @parsed || $prot_ind == -1 || $p != $prot_ind || index($parsed[$p], $text) >= 0; # =~ /$text/;
-			}
-			print OUT "$_\n" if($ok);
-		    } # not first
-		}
-		else {
-		    print OUT;
-		}
-	    }
-	}
-	elsif(0 && ! $start && /^\<font color\=\"green\"\>(\S.*)\<\/font\>/) {
-	    print OUT "$1\n";
-	}
-    }
-    close(IN);
-    close(OUT);
-    unlink($tempfile) if(-e $tempfile);
-    unlink($tempxslfile) if(-e $tempxslfile);
-
-    chmod 0666, $outfile;
-}
-
-sub writeGaggleNameListData {
- (my $outfile, my $engine, my $xml) = @_;
- my $tempxslfile = $xmlfile . '.tmp.nl.ggl.xsl';
- my $tempfile = $xmlfile . '.tmp.nl.ggl';
-
- my $text = exists $box{'text1'} ? $box{'text1'} : '';
- my @select_aas = ();
- if(exists $box{'pep_aa'} && ! ($box{'pep_aa'} eq '')) {
-     for(my $k = 0; $k < (length $box{'pep_aa'}); $k++) {
-	 my $next = substr($box{'pep_aa'}, $k);
-	 if($next =~ /^[a-z,A-Z](\d\d+)/) {
-	     my $mass = $1;
-	     push(@select_aas, substr($box{'pep_aa'}, $k, 1) . '[' . $mass . ']');
-	     $k += (length $mass);
-	 }
-	 else {
-	     push(@select_aas, substr($box{'pep_aa'}, $k, 1));
-	 }
-     }
- }
-
-
- unlink($tempxslfile) if(-e $tempxslfile);
- unlink($tempfile) if(-e $tempfile);
- writeGaggleNameListXSLFile($tempxslfile, \%box);
-
- if($xslt =~ /xsltproc/) {
-     system("$engine $tempxslfile $xml > $tempfile");
- }
- else {
-     system("$engine $xml $tempxslfile > $tempfile");
- }
-
- open(OUT, ">$outfile") or die "cannot open $outfile $!\n";
- open(IN, "$tempfile") or die "cannot open $tempfile $!\n";
- my $nrows = 0;
- my $start = 0;
- my $active = 0;
- my $prot_ind = -1;
- my $pep_ind = -1;
- my $first = 1;
- while(<IN>) {
-     if(index($_, $start_string_comment) >= 0) {   
-	 $start = 1;
-     }
-     elsif($start) {
-	 if(/\S/) {
-	     $active = 1;
-	 }
-	 if(/^\<\/form/ || /^\<\/table/) {
-	     $start = 0;
-	 }
-	 elsif($active) {
-	     if(@select_aas > 0 || ! ($text eq '')) {
-		 chomp();
-		 my @parsed = split('\t');
-		 if($first) {
-		     for(my $p = 0; $p <= $#parsed; $p++) {
-			 if($prot_ind == -1 && $parsed[$p] eq 'protein') {
-			     $prot_ind = $p;
-			 }
-			 elsif($pep_ind == -1 && $parsed[$p] eq 'peptide sequence') {
-			     $pep_ind = $p;
-			 }
-		     }
-		     print OUT "$_\n";
-		     $first = 0; # done
-		 }
-		 else {
-		     my $ok = 1;
-		     for(my $p = 0; $p <= $#parsed; $p++) {
-			 for(my $s = 0; $s <= $#select_aas; $s++) {
-			     $ok &&= $pep_ind >= @parsed || $pep_ind == -1 || $p != $pep_ind || index($parsed[$p], $select_aas[$s]) >= 0;
-			 }
-			 $ok &&= $prot_ind >= @parsed || $prot_ind == -1 || $p != $prot_ind || index($parsed[$p], $text) >= 0; # =~ /$text/;
-		     }
-		     if( $ok ) { print OUT "$_\n"; } 
-		 } # not first
-	     } 
-	     else {
-		 print OUT;
-		 $nrows++;
-	     }
-	 }
-     }
-     elsif(0 && ! $start && /^\<font color\=\"green\"\>(\S.*)\<\/font\>/) {
-	 print OUT "$1\n";
-     }
- }
-
- close(IN);
- close(OUT);
- unlink($tempfile) if(-e $tempfile);
- unlink($tempxslfile) if(-e $tempxslfile);
-
- chmod 0666, $outfile;
- return $nrows;
-}
-
-sub writeGaggleNameValueData {
- (my $outfile, my $engine, my $xml) = @_;
- my $tempxslfile = $xmlfile . '.tmp.nv.ggl.xsl';
- my $tempfile = $xmlfile . '.tmp.nv.ggl';
-
- my $text = exists $box{'text1'} ? $box{'text1'} : '';
- my @select_aas = ();
- if(exists $box{'pep_aa'} && ! ($box{'pep_aa'} eq '')) {
-     for(my $k = 0; $k < (length $box{'pep_aa'}); $k++) {
-	 my $next = substr($box{'pep_aa'}, $k);
-	 if($next =~ /^[a-z,A-Z](\d\d+)/) {
-	     my $mass = $1;
-	     push(@select_aas, substr($box{'pep_aa'}, $k, 1) . '[' . $mass . ']');
-	     $k += (length $mass);
-	 }
-	 else {
-	     push(@select_aas, substr($box{'pep_aa'}, $k, 1));
-	 }
-     }
- }
-
-
- unlink($tempxslfile) if(-e $tempxslfile);
- unlink($tempfile) if(-e $tempfile);
- writeGaggleNameValueXSLFile($tempxslfile, \%box);
-
- if($xslt =~ /xsltproc/) {
-     system("$engine $tempxslfile $xml > $tempfile");
- }
- else {
-     system("$engine $xml $tempxslfile > $tempfile");
- }
-
- open(OUT, ">$outfile") or die "cannot open $outfile $!\n";
- open(IN, "$tempfile") or die "cannot open $tempfile $!\n";
-
- my $nrows = 0;
- my $start = 0;
- my $active = 0;
- my $prot_ind = -1;
- my $pep_ind = -1;
- my $first = 1;
- while(<IN>) {
-     if(index($_, $start_string_comment) >= 0) {   
-	 $start = ...
 
[truncated message content]

[Sashimi-commit] SF.net SVN: sashimi:[9479] trunk/trans_proteomic_pipeline/perl/cgi-bin/ ProtXMLViewer.pl

[<rea...@us...>]

Revision: 9479
          http://sourceforge.net/p/sashimi/code/9479
Author:   real_procopio
Date:     2026-04-02 04:31:30 +0000 (Thu, 02 Apr 2026)
Log Message:
-----------
[ProtXMLViewer] Make sure file exists before attempting to create models file

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2026-04-02 03:18:39 UTC (rev 9478)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2026-04-02 04:31:30 UTC (rev 9479)
@@ -3125,7 +3125,7 @@
     $models_file =~ s/.prot.xml$/.prot-MODELS.html/;
 
     my $models_exe = tpplib_perl::getHomePath() . 'bin/tpp_models.pl';
-    `$models_exe $opts{'infile'}` if (!-e $models_file);  # attempt, but disregard any errors
+    `$models_exe $opts{'infile'}` if (!-e $models_file && -f $opts{'infile'});  # attempt, but disregard any errors
 
     if (-e $models_file) {
 	my $data_dir = tpplib_perl::getDataPath();

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Sashimi-commit] SF.net SVN: sashimi:[9478] trunk/trans_proteomic_ pipeline/perl/cgi-bin/madcaps.pl

[<rea...@us...>]

Revision: 9478
          http://sourceforge.net/p/sashimi/code/9478
Author:   real_procopio
Date:     2026-04-02 03:18:39 +0000 (Thu, 02 Apr 2026)
Log Message:
-----------
[madcaps] Validate digestion parameters

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/madcaps.pl

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/madcaps.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/madcaps.pl	2026-04-02 00:46:49 UTC (rev 9477)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/madcaps.pl	2026-04-02 03:18:39 UTC (rev 9478)
@@ -8,7 +8,7 @@
 #  Multiple Alignment, Digestion, Coverage, and Annotations of              #
 #    Protein Sequences                                                      #
 #                                                                           #
-# Copyright (C) 2017-2024 Luis Mendoza                                      #
+# Copyright (C) 2017-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -50,7 +50,6 @@
 my %opts;
 my %aamass;
 
-
 my %index;  # not used (yet)
 
 
@@ -118,7 +117,7 @@
 	"   ",
         '<input id="browse_button" title="Browse filesystem" onclick="tpp_selectFile(this,\'db_fullpathid\',null,\'\');" type="button" value="Browse">',
 	br,br,
-	'Enter protein accessions and (optional) peptide sequences, one per line in no particular order: ',
+	'Enter protein accessions and (optional) peptide sequences, one per line (in no particular order): ',
 	br,
 	'<textarea name="bigform" style="white-space:pre;" rows="30" cols="120">';
 
@@ -1150,6 +1149,16 @@
     $opts{'max_nmc'} = $cgi_query->param('max_nmc') || 0;
     $opts{'min_peplen'} = $cgi_query->param('min_peplen') || 7;
 
+    if ($opts{'min_pepmass'} !~ /^\d+\.?\d*$/) {
+      $opts{'min_pepmass'} = 600;
+    }
+    if ($opts{'max_pepmass'} !~ /^\d+\.?\d*$/) {
+      $opts{'max_pepmass'} = 4000;
+    }
+    if ($opts{'max_nmc'} !~ /^\d+$/) {
+      $opts{'max_nmc'} = 0;
+    }
+
     param('min_pepmass',$opts{'min_pepmass'});
     param('max_pepmass',$opts{'max_pepmass'});
     param('max_nmc',$opts{'max_nmc'});

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Sashimi-commit] SF.net SVN: sashimi:[9477] trunk/trans_proteomic_ pipeline/perl/bin

[<rea...@us...>]

Revision: 9477
          http://sourceforge.net/p/sashimi/code/9477
Author:   real_procopio
Date:     2026-04-02 00:46:49 +0000 (Thu, 02 Apr 2026)
Log Message:
-----------
[ProteoMapper] v1.7.0: Ignore specified mass tolerance if not doing fuzzy matching; Accept U and O in input sequences; Correctly capture error code from system call to find number of cores; Some cleanup

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/bin/clips.pl
    trunk/trans_proteomic_pipeline/perl/bin/promast.pl

Modified: trunk/trans_proteomic_pipeline/perl/bin/clips.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/bin/clips.pl	2026-02-26 03:01:35 UTC (rev 9476)
+++ trunk/trans_proteomic_pipeline/perl/bin/clips.pl	2026-04-02 00:46:49 UTC (rev 9477)
@@ -8,7 +8,7 @@
 #                                                                           #
 # Generate reverse index of n-AA keys, for use in mapping observed          #
 #  peptide sequences to all proteins                                        #
-# Copyright (C) 2018-2023 Luis Mendoza                                      #
+# Copyright (C) 2018-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -38,7 +38,7 @@
 use FindBin qw($Bin);
 use lib "$Bin/../lib/perl";
 
-my $VersionInfo = "stand-alone 1.5";
+my $VersionInfo = "stand-alone 1.7.0";
 my $rc = eval {
   require tpplib_perl; # exported TPP lib function points
   tpplib_perl->import();
@@ -202,10 +202,7 @@
 	    $protvar[$1] .= $2;
 	}
 
-
 	my $new = 0;
-
-
 	if ($new) {
 	    my @variants = @protvar[1..$pepkeysize];
 	    my %ret = ();
@@ -214,7 +211,6 @@
 	    &assemble_variants_NEW('', $alias, 1, \@variants, \%ret);
 
 	    my $pos = 1;
-
 	    for (my $i = $pepkeysize+1; $i <= length($protseq); $i++) {
 		$pos++;
 
@@ -256,8 +252,6 @@
 }
 
 
-
-
 ####################################################################################
 sub assemble_variants_NEW {    # recurse me...recurse me, my friend...
 ####################################################################################
@@ -272,8 +266,6 @@
 	if (1+length($str) == $pepkeysize) {
 	    $index{"$str$aa"} .= ":$prt,$pos";    # format:  PROT,POS    #### speed this up with arrays??
 
-
-
 	    ###$index{"$str$aa"} .= ":$prt,".($pos+1);    # format:  PROT,POS    #### speed this up with arrays??
 	    ## $index{"$str$aa"} .= ":".($pos+1).".$prt"; # format:  POS.PROT (allows numerical treatment)
 	    ## $ret{"$str$aa"} = 1;
@@ -284,8 +276,6 @@
 
 #	    print "==$str$aa\n";
 
-
-
 	}
 	else {
 	    &assemble_variants_NEW("$str$aa", $prt, $pos, $varaas, $prestr);
@@ -293,12 +283,6 @@
     }
 }
 
-
-
-
-
-
-
 ####################################################################################
 sub assemble_variants {    # recurse me...recurse me, my friend...
 ####################################################################################

Modified: trunk/trans_proteomic_pipeline/perl/bin/promast.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/bin/promast.pl	2026-02-26 03:01:35 UTC (rev 9476)
+++ trunk/trans_proteomic_pipeline/perl/bin/promast.pl	2026-04-02 00:46:49 UTC (rev 9477)
@@ -7,7 +7,7 @@
 # SVN Info      : $Id$
 #                                                                           #
 # Find all instances of input peptide sequence(s) by index lookup           #
-# Copyright (C) 2018-2023 Luis Mendoza                                      #
+# Copyright (C) 2018-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -45,7 +45,7 @@
 my @btimes;
 push @btimes, Benchmark->new; #0 :: exec start time
 
-my $VersionInfo = "stand-alone 1.6.0";
+my $VersionInfo = "stand-alone 1.7.0";
 my $rc = eval {
   require tpplib_perl;  # exported TPP lib function points
   tpplib_perl->import();
@@ -175,6 +175,10 @@
     if ($p =~ /X/) {
       print STDERR "...with wildcards";
       print STDERR " (ignoring fuzzy matching)" if $options{'f'};
+      if ($options{'m'}) {
+	print STDERR " (ignoring mass tolerance)";
+	$options{'m'} = undef;
+      }
       &expand_wildcards('',$p);
     }
     elsif ($options{'f'}) {
@@ -1153,7 +1157,7 @@
 sub dispatchPeps {
 ####################################################################################
   chomp(my $ncores = `getconf _NPROCESSORS_ONLN`);
-  if ($@) {
+  if ($?) {
     $ncores = $ENV{"NUMBER_OF_PROCESSORS"} || 1;
   }
   my $batches = 1 + int (scalar(keys %peps) / 5000);
@@ -1211,7 +1215,7 @@
       delete $peps{$pep};
       next;
     }
-    if ($pep =~ /[JUZBOX]/ ||
+    if ($pep =~ /[JZBX]/ ||  # changed to also accept U, O
 	$pep !~ /^[A-Z]+$/ ) {
       print STDERR "Warning: ignoring peptide containing non-AA characters: $pep\n";
       delete $peps{$pep};

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Sashimi-commit] SF.net SVN: sashimi:[9476] trunk/trans_proteomic_ pipeline/src/Parsers/RefreshParser/RefreshParser.cpp

[<rea...@us...>]

Revision: 9476
          http://sourceforge.net/p/sashimi/code/9476
Author:   real_procopio
Date:     2026-02-26 03:01:35 +0000 (Thu, 26 Feb 2026)
Log Message:
-----------
[cleanup] Re-tab RefreshParser.cpp for clarity

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cpp

Modified: trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cpp	2026-02-26 01:12:48 UTC (rev 9475)
+++ trunk/trans_proteomic_pipeline/src/Parsers/RefreshParser/RefreshParser.cpp	2026-02-26 03:01:35 UTC (rev 9476)
@@ -313,815 +313,813 @@
 	  if(strcmp(interact_file_lines[line_num-1]->sequence, tag->getAttributeValue("peptide"))) {
 	    cerr << "Error: " << interact_file_lines[line_num-1]->sequence << " does not match " << tag->getAttributeValue("peptide") << endl;
 #else
-	  if(strcmp(interact_file_lines[line_num-1]->sequence, tag->getAttributeValue("stripped_peptide"))) {
-	    cerr << "Error: " << interact_file_lines[line_num-1]->sequence << " does not match " << tag->getAttributeValue("stripped_peptide") << endl;
+	    if(strcmp(interact_file_lines[line_num-1]->sequence, tag->getAttributeValue("stripped_peptide"))) {
+	      cerr << "Error: " << interact_file_lines[line_num-1]->sequence << " does not match " << tag->getAttributeValue("stripped_peptide") << endl;
 #endif
 
-	    tag->write(cerr);
-	    exit(1);
+	      tag->write(cerr);
+	      exit(1);
+	    }
+
 	  }
+	  else if(use_default_min_ntt_ && tag->isStart() && ! strcmp(tag->getName(), "enzymatic_search_constraint") &&
+		  ! strcasecmp(tag->getAttributeValue("enzyme"), (*enzymes_)[enzyme_index_])) {
+	    min_num_tol_term_ = atoi(tag->getAttributeValue("min_number_termini"));
 
-	}
-	else if(use_default_min_ntt_ && tag->isStart() && ! strcmp(tag->getName(), "enzymatic_search_constraint") &&
-		! strcasecmp(tag->getAttributeValue("enzyme"), (*enzymes_)[enzyme_index_])) {
-	  min_num_tol_term_ = atoi(tag->getAttributeValue("min_number_termini"));
+	  }
+	  else if ( ! strcmp(tag->getName(), "mod_aminoacid_mass") && tag->getAttributeValue("alt_aa")) {
+	    char* alt_aa = new char[strlen(tag->getAttributeValue("alt_aa"))+1];
+	    strcpy(alt_aa, tag->getAttributeValue("alt_aa"));
+	    int pos = atoi(tag->getAttributeValue("position"));
 
-	}
-	else if ( ! strcmp(tag->getName(), "mod_aminoacid_mass") && tag->getAttributeValue("alt_aa")) {
-	  char* alt_aa = new char[strlen(tag->getAttributeValue("alt_aa"))+1];
-	  strcpy(alt_aa, tag->getAttributeValue("alt_aa"));
-	  int pos = atoi(tag->getAttributeValue("position"));
-	    
-	  if (!interact_file_lines[line_num-1]->alt_sequence) {
-	    interact_file_lines[line_num-1]->alt_sequence  = new char[strlen(interact_file_lines[line_num-1]->sequence)+1];
-	    strcpy(interact_file_lines[line_num-1]->alt_sequence, interact_file_lines[line_num-1]->sequence_I2L);
-	    interact_file_lines[line_num-1]->alt_sequence[pos-1] = *alt_aa;
+	    if (!interact_file_lines[line_num-1]->alt_sequence) {
+	      interact_file_lines[line_num-1]->alt_sequence  = new char[strlen(interact_file_lines[line_num-1]->sequence)+1];
+	      strcpy(interact_file_lines[line_num-1]->alt_sequence, interact_file_lines[line_num-1]->sequence_I2L);
+	      interact_file_lines[line_num-1]->alt_sequence[pos-1] = *alt_aa;
+	    }
+	    delete[] alt_aa;
 	  }
-	  delete[] alt_aa;
-	}
-	else if(tag->isStart() && ! strcmp(tag->getName(), "sample_enzyme")) {
-	  char* nextenz = new char[strlen(tag->getAttributeValue("name"))+1];
-	  strcpy(nextenz, tag->getAttributeValue("name"));
-	  int enzIdx = enzymes_->findByStringValue(nextenz);
-	  if (enzIdx == -1) {
-	    //not an enzyme already stored
-	    enzymes_->insertAtEnd(nextenz);
-	    enzyme_digestions_->insertAtEnd(new ProteolyticEnzyme(tag));
-	    enzyme_index_ = enzyme_digestions_->length()-1;
-	    enzyme_data = True;
-	    if(use_default_min_ntt_ && min_num_tol_term_ < 0)
-	      min_num_tol_term_ = 0;
+	  else if(tag->isStart() && ! strcmp(tag->getName(), "sample_enzyme")) {
+	    char* nextenz = new char[strlen(tag->getAttributeValue("name"))+1];
+	    strcpy(nextenz, tag->getAttributeValue("name"));
+	    int enzIdx = enzymes_->findByStringValue(nextenz);
+	    if (enzIdx == -1) {
+	      //not an enzyme already stored
+	      enzymes_->insertAtEnd(nextenz);
+	      enzyme_digestions_->insertAtEnd(new ProteolyticEnzyme(tag));
+	      enzyme_index_ = enzyme_digestions_->length()-1;
+	      enzyme_data = True;
+	      if(use_default_min_ntt_ && min_num_tol_term_ < 0)
+		min_num_tol_term_ = 0;
+	    }
+	    else {
+	      //already listed
+	      delete [] nextenz;
+	      enzyme_index_ = enzIdx;
+	      if(use_default_min_ntt_ && min_num_tol_term_ < 0)
+		min_num_tol_term_ = 0;
+	    }
 	  }
-	  else {
-	    //already listed
-	    delete [] nextenz;
-	    enzyme_index_ = enzIdx;
-	    if(use_default_min_ntt_ && min_num_tol_term_ < 0)
-	      min_num_tol_term_ = 0;
+
+	  if(enzyme_data) {
+	    if(tag->isEnd() && ! strcmp(tag->getName(), "sample_enzyme")) {
+	      (*enzyme_digestions_)[enzyme_index_]->fixSpecificity();
+	      enzyme_data = False;
+	    }
+	    else if(strcmp(tag->getName(), "sample_enzyme")) {
+	      (*enzyme_digestions_)[enzyme_index_]->enterSpecificity(tag);
+	    }
 	  }
-	}
-	  
-	if(enzyme_data) {
-	  if(tag->isEnd() && ! strcmp(tag->getName(), "sample_enzyme")) {
-	    (*enzyme_digestions_)[enzyme_index_]->fixSpecificity();
-	    enzyme_data = False;
-	  }
-	  else if(strcmp(tag->getName(), "sample_enzyme")) {
-	    (*enzyme_digestions_)[enzyme_index_]->enterSpecificity(tag);
-	  }
-	    
-	}
 
-	delete tag;
-      } // if not null
+	  delete tag;
+	} // if not null
 
-      data = strchr(data+1, '<');
-    } // next tag
+	data = strchr(data+1, '<');
+      } // next tag
 
-  } // next line
-  fin.close();
+    } // next line
+    fin.close();
 
-  num_interact_lines = line_num; 
-  interact_file_lines = (interact_data_line_t**)realloc(interact_file_lines, sizeof(interact_data_line_t*)* num_interact_lines);
+    num_interact_lines = line_num; 
+    interact_file_lines = (interact_data_line_t**)realloc(interact_file_lines, sizeof(interact_data_line_t*)* num_interact_lines);
 
-  // now do the db search
+    // now do the db search
 
-  uniq_lines = num_interact_lines;
-  uniq_interact_data = build_uniq_kwlist(interact_file_lines,&uniq_lines);
+    uniq_lines = num_interact_lines;
+    uniq_interact_data = build_uniq_kwlist(interact_file_lines,&uniq_lines);
 
 #ifndef __LGPL__
-  if ( !(kwset = kwsalloc((char *) 0)) )
-    printf("Error initializing the keyword set!\n");
+    if ( !(kwset = kwsalloc((char *) 0)) )
+      printf("Error initializing the keyword set!\n");
  
-  fprintf(stderr,"  - Building Commentz-Walter keyword tree...");
-  const char* prev_seq = "";
-  const char* prev_alt = "";
-  int tot_added = 0;
-  Array<int>* alt_index_map = new Array<int>();
-  for ( i = 0; i < uniq_lines; i++ ) {
-    interact_line = (interact_data_line_t *)uniq_interact_data[i];
+    fprintf(stderr,"  - Building Commentz-Walter keyword tree...");
+    const char* prev_seq = "";
+    const char* prev_alt = "";
+    int tot_added = 0;
+    Array<int>* alt_index_map = new Array<int>();
+    for ( i = 0; i < uniq_lines; i++ ) {
+      interact_line = (interact_data_line_t *)uniq_interact_data[i];
 
-    if ( interact_line->sequence_I2L != NULL ) {
-      if (  strcmp( interact_line->sequence_I2L,prev_seq) != 0 ) {
+      if ( interact_line->sequence_I2L != NULL ) {
+	if (  strcmp( interact_line->sequence_I2L,prev_seq) != 0 ) {
 
-	prev_seq = interact_line->sequence_I2L;
+	  prev_seq = interact_line->sequence_I2L;
+	  if ( kwsincr(kwset, 
+		       interact_line->sequence_I2L,
+		       strlen(interact_line->sequence_I2L)) != 0 ) 
+	    printf("Error adding %s to the keyword structure!\n",
+		   interact_line->sequence_I2L);
+
+	  alt_index_map->insertAtEnd(i);
+
+	  tot_added++;
+	}
+      }
+
+      if ( interact_line->alt_sequence != NULL ) {
 	if ( kwsincr(kwset, 
-		     interact_line->sequence_I2L,
-		     strlen(interact_line->sequence_I2L)) != 0 ) 
+		     interact_line->alt_sequence,
+		     strlen(interact_line->alt_sequence)) != 0 ) 
 	  printf("Error adding %s to the keyword structure!\n",
-		 interact_line->sequence_I2L);
+		 interact_line->alt_sequence);
 
 	alt_index_map->insertAtEnd(i);
-
 	tot_added++;
       }
     }
 
-    if ( interact_line->alt_sequence != NULL ) {
-      if ( kwsincr(kwset, 
-		   interact_line->alt_sequence,
-		   strlen(interact_line->alt_sequence)) != 0 ) 
-	printf("Error adding %s to the keyword structure!\n",
-	       interact_line->alt_sequence);
-      
-      alt_index_map->insertAtEnd(i);
-      tot_added++;
-    }
-  }
+    /* Prep the keyword trie for searching */
+    if ( kwsprep (kwset) != 0 )
+      printf("Error prepping the structure for a search!\n");
+#else
+    /* SPARE Parts Section */
+    kwset_t kwset;
+    kwmap_t kwmap; // preserves order of uniq_lines
+    int n_kwsets;
+    int max_kwset_size = min(5000,uniq_lines); //limit to avoid trie width explosion, also may adjust downward dynamically
+    std::vector<STRINGFINDER_pep *> finder_pep;
+    std::vector<STRINGFINDER_std *> finder_std;
+    fprintf(stdout,"  - Building Commentz-Walter keyword tree for %ld unique peptides...",uniq_lines);
+    bool bUsePeptideAlphabet = true; // use smaller alphabet if posssible
+    bool firstpass = true; // we may have to retry on trie width exception
+    while (true) { // dynamic sizing of tries
+      std::vector<kwset_t> kwsets; // break large jobs into multiple sets
+      n_kwsets = (uniq_lines/max_kwset_size)+((uniq_lines%max_kwset_size)!=0);
+      kwsets.resize(n_kwsets);
+      try {
+	peptideAlphabet::init(); // initialize lookup tables, etc
+	const char *badStr=NULL;
+	for ( i = 0; i < uniq_lines; i++ ) {
+	  interact_line = (interact_data_line_t *)uniq_interact_data[i];
 
-  /* Prep the keyword trie for searching */
-  if ( kwsprep (kwset) != 0 )
-    printf("Error prepping the structure for a search!\n");
-#else
-  /* SPARE Parts Section */
-  kwset_t kwset;
-  kwmap_t kwmap; // preserves order of uniq_lines
-  int n_kwsets;
-  int max_kwset_size = min(5000,uniq_lines); //limit to avoid trie width explosion, also may adjust downward dynamically
-  std::vector<STRINGFINDER_pep *> finder_pep;
-  std::vector<STRINGFINDER_std *> finder_std;
-  fprintf(stdout,"  - Building Commentz-Walter keyword tree for %ld unique peptides...",uniq_lines);
-  bool bUsePeptideAlphabet = true; // use smaller alphabet if posssible
-  bool firstpass = true; // we may have to retry on trie width exception
-  while (true) { // dynamic sizing of tries
-    std::vector<kwset_t> kwsets; // break large jobs into multiple sets
-    n_kwsets = (uniq_lines/max_kwset_size)+((uniq_lines%max_kwset_size)!=0);
-    kwsets.resize(n_kwsets);
-    try {
-      peptideAlphabet::init(); // initialize lookup tables, etc
-      const char *badStr=NULL;
-      for ( i = 0; i < uniq_lines; i++ ) {
-	interact_line = (interact_data_line_t *)uniq_interact_data[i];
-    
-	if ( interact_line->sequence != NULL ) {
-	  kwsets[i/max_kwset_size].insert(interact_line->sequence_I2L);
-	  if (bUsePeptideAlphabet && !peptideAlphabet::legal_string(interact_line->sequence_I2L)) {
-	    badStr = interact_line->sequence_I2L;
-	    bUsePeptideAlphabet = false;
+	  if ( interact_line->sequence != NULL ) {
+	    kwsets[i/max_kwset_size].insert(interact_line->sequence_I2L);
+	    if (bUsePeptideAlphabet && !peptideAlphabet::legal_string(interact_line->sequence_I2L)) {
+	      badStr = interact_line->sequence_I2L;
+	      bUsePeptideAlphabet = false;
+	    }
+	    if (firstpass && (i!=kwmap[interact_line->sequence_I2L])) { // will insert a record
+	      kwmap.find(interact_line->sequence_I2L)->second = i;
+	    }
 	  }
-	  if (firstpass && (i!=kwmap[interact_line->sequence_I2L])) { // will insert a record
-	    kwmap.find(interact_line->sequence_I2L)->second = i;
+
+	  if ( interact_line->alt_sequence != NULL ) {
+	    kwsets[i/max_kwset_size].insert(interact_line->alt_sequence);
+	    if (bUsePeptideAlphabet && !peptideAlphabet::legal_string(interact_line->alt_sequence)) {
+	      badStr = interact_line->alt_sequence;
+	      bUsePeptideAlphabet = false;
+	    }
+	    if (firstpass && (i!=kwmap[interact_line->alt_sequence])) { // will insert a record
+	      kwmap.find(interact_line->alt_sequence)->second = i;
+	    }
 	  }
 	}
-    
-	if ( interact_line->alt_sequence != NULL ) {
-	  kwsets[i/max_kwset_size].insert(interact_line->alt_sequence);
-	  if (bUsePeptideAlphabet && !peptideAlphabet::legal_string(interact_line->alt_sequence)) {
-	    badStr = interact_line->alt_sequence;
-	    bUsePeptideAlphabet = false;
+	/* Prep the keyword trie for searching */
+	if (bUsePeptideAlphabet) {
+	  firstpass = false; 
+	  for (int n=n_kwsets;n--;) {
+	    finder_pep.push_back(new STRINGFINDER_pep(kwsets[n])); 
 	  }
-	  if (firstpass && (i!=kwmap[interact_line->alt_sequence])) { // will insert a record
-	    kwmap.find(interact_line->alt_sequence)->second = i;
+	} else {
+	  if (firstpass) {
+	    cout << "warning: unexpected character in peptide sequence \"" << badStr << "\", using more general but less efficient search " << endl;
 	  }
+	  firstpass = false; 
+	  for (int n=n_kwsets;n--;) {
+	    finder_std.push_back(new STRINGFINDER_std(kwsets[n])); 
+	  }
 	}
-      }
-      /* Prep the keyword trie for searching */
-      if (bUsePeptideAlphabet) {
-	firstpass = false; 
-	for (int n=n_kwsets;n--;) {
-	  finder_pep.push_back(new STRINGFINDER_pep(kwsets[n])); 
+	break; // success
+      } // end try
+      catch (...) {
+	// go back and try it again with smaller trie width
+	max_kwset_size /= 2; 
+	if (bUsePeptideAlphabet) {
+	  for (size_t n=finder_pep.size();n--;) {
+	    delete finder_pep[n];
+	  }
+	  finder_pep.clear();
+	} else {
+	  for (size_t n=finder_std.size();n--;) {
+	    delete finder_std[n];
+	  }
+	  finder_std.clear();
 	}
-      } else {
-	if (firstpass) {
-	  cout << "warning: unexpected character in peptide sequence \"" << badStr << "\", using more general but less efficient search " << endl;
-	}
-	firstpass = false; 
-	for (int n=n_kwsets;n--;) {
-	  finder_std.push_back(new STRINGFINDER_std(kwsets[n])); 
-	}
       }
-      break; // success
-    } // end try
-    catch (...) {
-      // go back and try it again with smaller trie width
-      max_kwset_size /= 2; 
-      if (bUsePeptideAlphabet) {
-	for (size_t n=finder_pep.size();n--;) {
-	  delete finder_pep[n];
-	} 
-	finder_pep.clear();
-      } else {
-	for (size_t n=finder_std.size();n--;) {
-	  delete finder_std[n];
-	}
-	finder_std.clear();
-      }
     }
-  }
 #endif //__LGPL__
-  /* Perform the search */
-  fprintf(stdout,"\n  - Searching the tree...");
-  if ( ! (fp = fopen(database_,"r"))){
-    std::string rdb(resolve_root(database_));
-    const char *trythis = rdb.c_str();
-    if (strcmp(trythis, database_)) {
-      int err = errno;
-      if (! (fp = fopen(trythis,"r"))) {
-	printf("error: could not open database file \"%s\" (%s)\n", database_, strerror(err));
-	printf("also tried \"%s\" (%s)\n", trythis, strerror(errno));
+    /* Perform the search */
+    fprintf(stdout,"\n  - Searching the tree...");
+    if ( ! (fp = fopen(database_,"r"))){
+      std::string rdb(resolve_root(database_));
+      const char *trythis = rdb.c_str();
+      if (strcmp(trythis, database_)) {
+	int err = errno;
+	if (! (fp = fopen(trythis,"r"))) {
+	  printf("error: could not open database file \"%s\" (%s)\n", database_, strerror(err));
+	  printf("also tried \"%s\" (%s)\n", trythis, strerror(errno));
+	} else {
+	  printf("opening \"%s\" as \"%s\"\n",database_,trythis);
+	}
       } else {
-	printf("opening \"%s\" as \"%s\"\n",database_,trythis);
+	printf("error: could not open database file \"%s\" (%s)\n", database_, strerror(errno));
       }
-    } else {
-      printf("error: could not open database file \"%s\" (%s)\n", database_, strerror(errno));
+      if (!fp) {
+	exit(-1);
+      }
     }
-    if (!fp) {
-      exit(-1);
-    }
-  }
 
-  int iLenSeq;
+    int iLenSeq;
 
-  char *szBuf_ = (char*) malloc(sizeof(char)*line_width_);
-  char *szSeq_ = (char*) malloc(sizeof(char)*MAX_SEQ);
-  char *szHdr_ = (char*) malloc(sizeof(char)*MAX_HEADER_LEN); 
-  char *szOutputDb_ = (char*) malloc(sizeof(char)*SIZE_FILE);
-  int* sort_idx = NULL;
-  int max_num_hits = 0;
+    char *szBuf_ = (char*) malloc(sizeof(char)*line_width_);
+    char *szSeq_ = (char*) malloc(sizeof(char)*MAX_SEQ);
+    char *szHdr_ = (char*) malloc(sizeof(char)*MAX_HEADER_LEN); 
+    char *szOutputDb_ = (char*) malloc(sizeof(char)*SIZE_FILE);
+    int* sort_idx = NULL;
+    int max_num_hits = 0;
 
-  szBuf_[0] = '\0';
-  szSeq_[0] = '\0';
-  szHdr_[0] = '\0';
-  szOutputDb_[0] = '\0';
+    szBuf_[0] = '\0';
+    szSeq_[0] = '\0';
+    szHdr_[0] = '\0';
+    szOutputDb_[0] = '\0';
 
-  while (fgets(szBuf_, line_width_, fp))
-    {
-      if (szBuf_[0]=='>')
-	{
-	  int cAA;
-	 
-	  strncpy(szHdr_, szBuf_, MAX_HEADER_LEN);
-	  szHdr_[MAX_HEADER_LEN-1] = '\0';
-	  if(strlen(szBuf_) < MAX_HEADER_LEN)
-	    szHdr_[strlen(szBuf_)-1] = '\0';
-	 
-	  // now get rid of quotations
-	  char* quotematch = strchr(szHdr_, '"');
-	  while(quotematch != NULL) {
-	    memmove(quotematch,quotematch+1,strlen(quotematch));
-	    quotematch = strchr(quotematch, '"');
-	  } // while
+    while (fgets(szBuf_, line_width_, fp))
+      {
+	if (szBuf_[0]=='>')
+	  {
+	    int cAA;
 
-	  iLenSeq=0;
+	    strncpy(szHdr_, szBuf_, MAX_HEADER_LEN);
+	    szHdr_[MAX_HEADER_LEN-1] = '\0';
+	    if(strlen(szBuf_) < MAX_HEADER_LEN)
+	      szHdr_[strlen(szBuf_)-1] = '\0';
 
-	  while ( (cAA=fgetc(fp)) ) {
-	    if (isalpha(cAA) || cAA=='*') {
-	      if (cAA == 'I')
-		cAA = 'L';
-	      if (cAA == '*')
-		cAA = '-';
+	    // now get rid of quotations
+	    char* quotematch = strchr(szHdr_, '"');
+	    while(quotematch != NULL) {
+	      memmove(quotematch,quotematch+1,strlen(quotematch));
+	      quotematch = strchr(quotematch, '"');
+	    } // while
 
-	      szSeq_[iLenSeq++]=cAA;
-	      if (iLenSeq > MAX_SEQ) {
-		printf(" Error - sequence larger than MAX_SEQ\n\n");
-		printf("%s\n\n", szHdr_);
-		fclose(fp);
-		exit(1);
+	    iLenSeq=0;
+
+	    while ( (cAA=fgetc(fp)) ) {
+	      if (isalpha(cAA) || cAA=='*') {
+		if (cAA == 'I')
+		  cAA = 'L';
+		if (cAA == '*')
+		  cAA = '-';
+
+		szSeq_[iLenSeq++]=cAA;
+		if (iLenSeq > MAX_SEQ) {
+		  printf(" Error - sequence larger than MAX_SEQ\n\n");
+		  printf("%s\n\n", szHdr_);
+		  fclose(fp);
+		  exit(1);
+		}
 	      }
-	    }
-	    else if (feof(fp) || cAA=='>') {
-	      int iReturn;
-	      iReturn=ungetc(cAA, fp);
+	      else if (feof(fp) || cAA=='>') {
+		int iReturn;
+		iReturn=ungetc(cAA, fp);
 
-	      if (iReturn!=cAA) {
-		printf("Error with ungetc.\n\n");
-		fclose(fp);
-		exit(1);
+		if (iReturn!=cAA) {
+		  printf("Error with ungetc.\n\n");
+		  fclose(fp);
+		  exit(1);
+		}
+		break;
 	      }
-	      break;
 	    }
-	  }
 
-	  szSeq_[iLenSeq]='\0';
-	 
+	    szSeq_[iLenSeq]='\0';
+
 #ifdef __LGPL__	 
-	  /* SPARE Parts */
-	  glob_matches.clear(); // nothing found yet
-	  if (bUsePeptideAlphabet) {
-	    for (int n=n_kwsets;n--;) {
-	      finder_pep[n]->match(szSeq_,spareparts_callback); // any proteins match?
+	    /* SPARE Parts */
+	    glob_matches.clear(); // nothing found yet
+	    if (bUsePeptideAlphabet) {
+	      for (int n=n_kwsets;n--;) {
+		finder_pep[n]->match(szSeq_,spareparts_callback); // any proteins match?
+	      }
+	    } else {
+	      for (int n=n_kwsets;n--;) {
+		finder_std[n]->match(szSeq_,spareparts_callback); // any proteins match?
+	      }
 	    }
-	  } else {
-	    for (int n=n_kwsets;n--;) {
-	      finder_std[n]->match(szSeq_,spareparts_callback); // any proteins match?
-	    }
-	  }
-	  num_hits = (int)glob_matches.size();
-	  kwset_t::const_iterator iter = glob_matches.begin();
+	    num_hits = (int)glob_matches.size();
+	    kwset_t::const_iterator iter = glob_matches.begin();
 #else	  
-	  num_hits = kwsexec_multiple(kwset, szSeq_, strlen(szSeq_), &match);
+	    num_hits = kwsexec_multiple(kwset, szSeq_, strlen(szSeq_), &match);
 #endif //__LGPL__
 
-	  //DDS: sort the matched indices
-	  if (num_hits > 0) {
-	    if (num_hits>max_num_hits) {
-	      sort_idx = (int *)realloc(sort_idx,(max_num_hits=num_hits)*sizeof(int));
-	    }
+	    //DDS: sort the matched indices
+	    if (num_hits > 0) {
+	      if (num_hits>max_num_hits) {
+		sort_idx = (int *)realloc(sort_idx,(max_num_hits=num_hits)*sizeof(int));
+	      }
 
-	    for (i=0; i<num_hits; i++){
+	      for (i=0; i<num_hits; i++){
 #ifdef __LGPL__	 
-	      sort_idx[i] = kwmap.find(iter->c_str())->second;
-	      iter++;
+		sort_idx[i] = kwmap.find(iter->c_str())->second;
+		iter++;
 #else	  
-	      sort_idx[i] = match[i].index;
+		sort_idx[i] = match[i].index;
 #endif
-	    }
+	      }
 #ifndef __LGPL__
-	    free(match);
+	      free(match);
 #endif
-	    qsort(sort_idx, num_hits, sizeof(int), compare_indices);
-       
-	    // Process the hits for this protein sequence
-	    prev_index = -1;
-	   
-	    for ( i=0; i<num_hits; i++) {
-	      int this_index = sort_idx[i];
-	      this_index = (*alt_index_map)[this_index];
+	      qsort(sort_idx, num_hits, sizeof(int), compare_indices);
 
-	      const char* result = NULL;
+	      // Process the hits for this protein sequence
+	      prev_index = -1;
 
-	      if (uniq_interact_data[this_index]) {
-		result = strstr(szSeq_, ((interact_data_line_t *)
-					 uniq_interact_data[this_index])->sequence_I2L);
-	      }
-	      bool alt = false;
-	      if (!result) {
-		alt = true;
-		result = strstr(szSeq_, ((interact_data_line_t *)
-					 uniq_interact_data[this_index])->alt_sequence);
-	      }
+	      for ( i=0; i<num_hits; i++) {
+		int this_index = sort_idx[i];
+		this_index = (*alt_index_map)[this_index];
 
-	      //DDS: For this to work the indices must be sorted
-	      if ( this_index != prev_index ) {
-		if ( (new_db_ref = (db_ref_t *)malloc(sizeof(db_ref_t))) == NULL )
-		  printf("Error: Could not allocate memory for db_ref_t!\n");
+		const char* result = NULL;
 
-		// use space or | as delimiter of accession if IPI database
-		char cDelimiter;
+		if (uniq_interact_data[this_index]) {
+		  result = strstr(szSeq_, ((interact_data_line_t *)
+					   uniq_interact_data[this_index])->sequence_I2L);
+		}
+		bool alt = false;
+		if (!result) {
+		  alt = true;
+		  result = strstr(szSeq_, ((interact_data_line_t *)
+					   uniq_interact_data[this_index])->alt_sequence);
+		}
 
-		if (!strncmp(szHdr_, ">IPI", 4) && strchr(szHdr_, '|') != NULL && strchr(szHdr_, '|')<strchr(szHdr_,' ') )
-		  cDelimiter = '|';
-		else
-		  cDelimiter = ' ';
+		//DDS: For this to work the indices must be sorted
+		if ( this_index != prev_index ) {
+		  if ( (new_db_ref = (db_ref_t *)malloc(sizeof(db_ref_t))) == NULL )
+		    printf("Error: Could not allocate memory for db_ref_t!\n");
 
-		if ( strchr(szHdr_,cDelimiter) != NULL ) {
-		  new_db_ref->alias = make_substr(szHdr_,
-						  0,
-						  strchr(szHdr_,cDelimiter) - szHdr_ - 1);
+		  // use space or | as delimiter of accession if IPI database
+		  char cDelimiter;
 
-		  // get rid of windows control characters (^M, etc) by truncating at the first one
-		  size_t len = strlen(new_db_ref->alias);
-		  for (size_t i = 0; i < len; i++) {
-		    if (new_db_ref->alias[i] < 20 || new_db_ref->alias[i] > 126) {
-		      new_db_ref->alias[i] = 0;
-		      break;
+		  if (!strncmp(szHdr_, ">IPI", 4) && strchr(szHdr_, '|') != NULL && strchr(szHdr_, '|')<strchr(szHdr_,' ') )
+		    cDelimiter = '|';
+		  else
+		    cDelimiter = ' ';
+
+		  if ( strchr(szHdr_,cDelimiter) != NULL ) {
+		    new_db_ref->alias = make_substr(szHdr_,
+						    0,
+						    strchr(szHdr_,cDelimiter) - szHdr_ - 1);
+
+		    // get rid of windows control characters (^M, etc) by truncating at the first one
+		    size_t len = strlen(new_db_ref->alias);
+		    for (size_t i = 0; i < len; i++) {
+		      if (new_db_ref->alias[i] < 20 || new_db_ref->alias[i] > 126) {
+			new_db_ref->alias[i] = 0;
+			break;
+		      }
 		    }
-		  }
 
-		  new_db_ref->description = make_substr(szHdr_,
-							strchr(szHdr_,cDelimiter) - szHdr_,
-							(int)strlen(szHdr_));
+		    new_db_ref->description = make_substr(szHdr_,
+							  strchr(szHdr_,cDelimiter) - szHdr_,
+							  (int)strlen(szHdr_));
 
-		  // get rid of windows control characters (^M, etc) by truncating at the first one
-		  len = strlen(new_db_ref->description);
-		  for (size_t i = 0; i < len; i++) {
-		    if (new_db_ref->description[i] < 20 || new_db_ref->description[i] > 126) {
-		      new_db_ref->description[i] = 0;
-		      break;
+		    // get rid of windows control characters (^M, etc) by truncating at the first one
+		    len = strlen(new_db_ref->description);
+		    for (size_t i = 0; i < len; i++) {
+		      if (new_db_ref->description[i] < 20 || new_db_ref->description[i] > 126) {
+			new_db_ref->description[i] = 0;
+			break;
+		      }
 		    }
+
+		    // make sure no xml problem characters in prot descr
+		    for(int z = 0; z < (int) strlen(new_db_ref->description); z++)
+		      if(new_db_ref->description[z] == '&')
+			new_db_ref->description[z] = '+';
+		      else if(new_db_ref->description[z] == '"')
+			new_db_ref->description[z] = '\'';
+		      else if(new_db_ref->description[z] == '>')
+			new_db_ref->description[z] = ' ';
+		      else if(new_db_ref->description[z] == '<')
+			new_db_ref->description[z] = ' ';
+		      else if(new_db_ref->description[z] == '/')
+			new_db_ref->description[z] = '\\';
 		  }
+		  else {
+		    new_db_ref->alias = strdup(szHdr_);
 
-		  // make sure no xml problem characters in prot descr
-		  for(int z = 0; z < (int) strlen(new_db_ref->description); z++)
-		    if(new_db_ref->description[z] == '&')
-		      new_db_ref->description[z] = '+';
-		    else if(new_db_ref->description[z] == '"')
-		      new_db_ref->description[z] = '\'';
-		    else if(new_db_ref->description[z] == '>')
-		      new_db_ref->description[z] = ' ';
-		    else if(new_db_ref->description[z] == '<')
-		      new_db_ref->description[z] = ' ';
-		    else if(new_db_ref->description[z] == '/')
-		      new_db_ref->description[z] = '\\';
-		}
-		else {
-		  new_db_ref->alias = strdup(szHdr_);
-
-		  // get rid of windows control characters (^M, etc) by truncating at the first one
-		  size_t len = strlen(new_db_ref->alias);
-		  for (size_t i = 0; i < len; i++) {
-		    if (new_db_ref->alias[i] < 20 || new_db_ref->alias[i] > 126) {
-		      new_db_ref->alias[i] = 0;
-		      break;
+		    // get rid of windows control characters (^M, etc) by truncating at the first one
+		    size_t len = strlen(new_db_ref->alias);
+		    for (size_t i = 0; i < len; i++) {
+		      if (new_db_ref->alias[i] < 20 || new_db_ref->alias[i] > 126) {
+			new_db_ref->alias[i] = 0;
+			break;
+		      }
 		    }
+		    new_db_ref->description = (char *)malloc((2) * sizeof( char )); // allocate as done elsewhere
+		    new_db_ref->description[0] = 0;
 		  }
-		  new_db_ref->description = (char *)malloc((2) * sizeof( char )); // allocate as done elsewhere
-		  new_db_ref->description[0] = 0;
-		}
 
-		ref_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_refs;
-		ntt_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_ntts;
-		if(calc_prot_wt_)
-		  prot_wt_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_prot_wts;
+		  ref_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_refs;
+		  ntt_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_ntts;
+		  if(calc_prot_wt_)
+		    prot_wt_list = ((interact_data_line_t *)uniq_interact_data[this_index])->updated_prot_wts;
 
-		if ( uniq_interact_data[this_index]->updated_hits == 0 ){
-		  if ( (ref_list = (db_ref_t **)malloc( sizeof(db_ref_t *))) == NULL )
-		    printf("Error: Could not allocate memory for a new ref_list!\n");
-		  if ( (ntt_list = (int*)malloc( sizeof(int *))) == NULL )
-		    printf("Error: Could not allocate memory for a new ntt_list!\n");
-		  if (calc_prot_wt_ && (prot_wt_list = (double*)malloc( sizeof(double *))) == NULL )
-		    printf("Error: Could not allocate memory for a new prot_wt_list!\n");
-		}
-		else {
-		  if ( (ref_list = (db_ref_t **)realloc(ref_list,
-							(((interact_data_line_t *)
-							  uniq_interact_data[this_index])->updated_hits + 1) * 
-							sizeof(db_ref_t *))) == NULL ) 
-		    printf("Error: Could not reallocate memory for ref_list!\n");
-		  if ( (ntt_list = (int*)realloc(ntt_list,
-						 (((interact_data_line_t *)
-						   uniq_interact_data[this_index])->updated_hits + 1) * 
-						 sizeof(int *))) == NULL ) 
-		    printf("Error: Could not reallocate memory for ntt_list!\n");
-		  if (calc_prot_wt_ && (prot_wt_list = (double*)realloc(prot_wt_list,
-									(((interact_data_line_t *)
-									  uniq_interact_data[this_index])->updated_hits + 1) * 
-									sizeof(double *))) == NULL ) 
-		    printf("Error: Could not reallocate memory for prot_wt_list!\n");
-		}
-		ref_list[uniq_interact_data[this_index]->updated_hits] = new_db_ref;
-		ntt = -1;
+		  if ( uniq_interact_data[this_index]->updated_hits == 0 ){
+		    if ( (ref_list = (db_ref_t **)malloc( sizeof(db_ref_t *))) == NULL )
+		      printf("Error: Could not allocate memory for a new ref_list!\n");
+		    if ( (ntt_list = (int*)malloc( sizeof(int *))) == NULL )
+		      printf("Error: Could not allocate memory for a new ntt_list!\n");
+		    if (calc_prot_wt_ && (prot_wt_list = (double*)malloc( sizeof(double *))) == NULL )
+		      printf("Error: Could not allocate memory for a new prot_wt_list!\n");
+		  }
+		  else {
+		    if ( (ref_list = (db_ref_t **)realloc(ref_list,
+							  (((interact_data_line_t *)
+							    uniq_interact_data[this_index])->updated_hits + 1) * 
+							  sizeof(db_ref_t *))) == NULL ) 
+		      printf("Error: Could not reallocate memory for ref_list!\n");
+		    if ( (ntt_list = (int*)realloc(ntt_list,
+						   (((interact_data_line_t *)
+						     uniq_interact_data[this_index])->updated_hits + 1) * 
+						   sizeof(int *))) == NULL ) 
+		      printf("Error: Could not reallocate memory for ntt_list!\n");
+		    if (calc_prot_wt_ && (prot_wt_list = (double*)realloc(prot_wt_list,
+									  (((interact_data_line_t *)
+									    uniq_interact_data[this_index])->updated_hits + 1) * 
+									  sizeof(double *))) == NULL ) 
+		      printf("Error: Could not reallocate memory for prot_wt_list!\n");
+		  }
+		  ref_list[uniq_interact_data[this_index]->updated_hits] = new_db_ref;
+		  ntt = -1;
 
-		char prev, next;
-		ntt = 0;
-		bool firstpass = true;
-		if(result != NULL) {
-		  size_t seqlen=strlen(szSeq_);
-		  //DDS: Find all occurrences of the peptide in the protein
-		  while (result != NULL) { 
+		  char prev, next;
+		  ntt = 0;
+		  bool firstpass = true;
+		  if(result != NULL) {
+		    size_t seqlen=strlen(szSeq_);
+		    //DDS: Find all occurrences of the peptide in the protein
+		    while (result != NULL) { 
 
-		    size_t reslen = strlen(result);
-		    if(reslen == seqlen)
-		      prev = '-';
-		    else
-		      prev = (result-1)[0];
+		      size_t reslen = strlen(result);
+		      if(reslen == seqlen)
+			prev = '-';
+		      else
+			prev = (result-1)[0];
 
-		    // change M to - when it's first character in the Protein
-		    if(prev == 'M' && reslen >= seqlen - 1) {
-		      prev = '-';
-		    }
+		      // change M to - when it's first character in the Protein
+		      if(prev == 'M' && reslen >= seqlen - 1) {
+			prev = '-';
+		      }
 
-		    size_t nextlen=strlen(((interact_data_line_t *)
-					   uniq_interact_data[this_index])->sequence_I2L);
+		      size_t nextlen=strlen(((interact_data_line_t *)
+					     uniq_interact_data[this_index])->sequence_I2L);
 
-		    if(reslen == nextlen)
-		      next = '-';
-		    else
-		      next = result[nextlen]; // next aa
+		      if(reslen == nextlen)
+			next = '-';
+		      else
+			next = result[nextlen]; // next aa
 
-		    if (enzyme_digestions_->size() == 0) {
-		      cerr << "ERROR: <sample_enzyme> tag was not found in the pep.xml file." << endl;
-		      exit(1);
-		    }
+		      if (enzyme_digestions_->size() == 0) {
+			cerr << "ERROR: <sample_enzyme> tag was not found in the pep.xml file." << endl;
+			exit(1);
+		      }
 
-		    int new_ntt = (*enzyme_digestions_)[((interact_data_line_t *)
-							 uniq_interact_data[this_index])->enzyme_ind]->
-		      getNumTolTerm(prev, ((interact_data_line_t *) uniq_interact_data[this_index])->sequence_I2L, next);
+		      int new_ntt = (*enzyme_digestions_)[((interact_data_line_t *)
+							   uniq_interact_data[this_index])->enzyme_ind]->
+			getNumTolTerm(prev, ((interact_data_line_t *) uniq_interact_data[this_index])->sequence_I2L, next);
 
-		    if (firstpass || new_ntt > ntt) { // do this just once
-		      if (firstpass) {
-			new_db_ref->prev_aa = (char *)malloc(n_desired_prev_aas_+1);
-			new_db_ref->next_aa = (char *)malloc(n_desired_next_aas_+1);
-		      }
-		      // resize the prev AA string
+		      if (firstpass || new_ntt > ntt) { // do this just once
+			if (firstpass) {
+			  new_db_ref->prev_aa = (char *)malloc(n_desired_prev_aas_+1);
+			  new_db_ref->next_aa = (char *)malloc(n_desired_next_aas_+1);
+			}
+			// resize the prev AA string
 
-		      if (NULL != new_db_ref->prev_aa ) {
-			const char *aa=result;
-			int count = 0;
-			while ((count<n_desired_prev_aas_) && (aa>szSeq_)) {
-			  aa--;
-			  count++;
+			if (NULL != new_db_ref->prev_aa ) {
+			  const char *aa=result;
+			  int count = 0;
+			  while ((count<n_desired_prev_aas_) && (aa>szSeq_)) {
+			    aa--;
+			    count++;
+			  }
+			  char *w=new_db_ref->prev_aa;
+			  while (count--) {
+			    *w++ = *aa++;
+			  }
+			  *w = 0;
+			  if (!new_db_ref->prev_aa[0]) {
+			    strcpy(new_db_ref->prev_aa,"-");
+			  }
 			}
-			char *w=new_db_ref->prev_aa;
-			while (count--) {
-			  *w++ = *aa++;
+			// resize the follow AA string
+			if (NULL != new_db_ref->next_aa) {
+			  const char *aa=result+nextlen;
+			  int count = 0;
+			  while ((count<n_desired_next_aas_) && *aa) {
+			    aa++;
+			    count++;
+			  }
+			  char *w=new_db_ref->next_aa;
+			  aa=result+nextlen;
+			  while (count--) {
+			    *w++ = *aa++;
+			  }
+			  *w = 0;
+			  if (!new_db_ref->next_aa[0]) {
+			    strcpy(new_db_ref->next_aa,"-");
+			  }
 			}
-			*w = 0;
-			if (!new_db_ref->prev_aa[0]) {
-			  strcpy(new_db_ref->prev_aa,"-");
-			}
 		      }
-		      // resize the follow AA string
-		      if (NULL != new_db_ref->next_aa) {
-			const char *aa=result+nextlen;
-			int count = 0;
-			while ((count<n_desired_next_aas_) && *aa) {
-			  aa++;
-			  count++;
-			}
-			char *w=new_db_ref->next_aa;
-			aa=result+nextlen;
-			while (count--) {
-			  *w++ = *aa++;
-			}
-			*w = 0;
-			if (!new_db_ref->next_aa[0]) {
-			  strcpy(new_db_ref->next_aa,"-");
-			}
-		      }
+		      ntt = new_ntt > ntt ? new_ntt : ntt;		   
+		      result = strstr(result+strlen(((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L), 
+				      ((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L);
+		      firstpass = false;
 		    }
-		    ntt = new_ntt > ntt ? new_ntt : ntt;		   
-		    result = strstr(result+strlen(((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L), 
-				    ((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L);
-		    firstpass = false;
+		  } // if not null
+		  else {
+		    cout << "error: " << ((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L << " not found in " <<  szSeq_ << endl; 
+		    exit(1);
 		  }
-		} // if not null
-		else {
-		  cout << "error: " << ((interact_data_line_t *)uniq_interact_data[this_index])->sequence_I2L << " not found in " <<  szSeq_ << endl; 
-		  exit(1);
-		}
 
-		// now see if we can reuse existing text
-		consolidate_text_ptr(new_db_ref->alias,aliases);
-		consolidate_text_ptr(new_db_ref->description,descriptions);
-		consolidate_text_ptr(new_db_ref->prev_aa,prev_aas);
-		consolidate_text_ptr(new_db_ref->next_aa,next_aas);
+		  // now see if we can reuse existing text
+		  consolidate_text_ptr(new_db_ref->alias,aliases);
+		  consolidate_text_ptr(new_db_ref->description,descriptions);
+		  consolidate_text_ptr(new_db_ref->prev_aa,prev_aas);
+		  consolidate_text_ptr(new_db_ref->next_aa,next_aas);
 
-		ntt_list[uniq_interact_data[this_index]->updated_hits] = ntt;
+		  ntt_list[uniq_interact_data[this_index]->updated_hits] = ntt;
 
-		if(calc_prot_wt_)
-		  prot_wt_list[uniq_interact_data[this_index]->updated_hits] = ResidueMass::getProteinMass(szSeq_, monoisotopic);
+		  if(calc_prot_wt_)
+		    prot_wt_list[uniq_interact_data[this_index]->updated_hits] = ResidueMass::getProteinMass(szSeq_, monoisotopic);
 
-		uniq_interact_data[this_index]->updated_hits += 1;
-		((interact_data_line_t *)uniq_interact_data[this_index])->updated_refs = ref_list;
-		((interact_data_line_t *)uniq_interact_data[this_index])->updated_ntts = ntt_list;
+		  uniq_interact_data[this_index]->updated_hits += 1;
+		  ((interact_data_line_t *)uniq_interact_data[this_index])->updated_refs = ref_list;
+		  ((interact_data_line_t *)uniq_interact_data[this_index])->updated_ntts = ntt_list;
 
-		if(calc_prot_wt_)
-		  ((interact_data_line_t *)uniq_interact_data[this_index])->updated_prot_wts = prot_wt_list;
+		  if(calc_prot_wt_)
+		    ((interact_data_line_t *)uniq_interact_data[this_index])->updated_prot_wts = prot_wt_list;
 
-		prev_index = this_index;
-	      } // end if this_index != prev_index
-	    } // end for num_hits
-	  } // end if num_hits
-	} // while fgets database
-    } // while fin.getline
+		  prev_index = this_index;
+		} // end if this_index != prev_index
+	      } // end for num_hits
+	    } // end if num_hits
+	  } // while fgets database
+      } // while fin.getline
 #ifdef __LGPL__
-  /*SPARE Parts Section*/
-  for (int n=n_kwsets;n--;) {
-    if (bUsePeptideAlphabet)
-      delete finder_pep[n];
-    else
-      delete finder_std[n];
-  }
+    /*SPARE Parts Section*/
+    for (int n=n_kwsets;n--;) {
+      if (bUsePeptideAlphabet)
+	delete finder_pep[n];
+      else
+	delete finder_std[n];
+    }
 #else
-  kwsfree(kwset);
+    kwsfree(kwset);
 #endif
-  fclose( fp );
+    fclose( fp );
 
-  fprintf(stdout,"\n  - Linking duplicate entries...");
-  link_duplicates(interact_file_lines,num_interact_lines);
+    fprintf(stdout,"\n  - Linking duplicate entries...");
+    link_duplicates(interact_file_lines,num_interact_lines);
 
-  incr_time = time(NULL);
-  fprintf(stdout,"\n  - Printing results...");
+    incr_time = time(NULL);
+    fprintf(stdout,"\n  - Printing results...");
 
-  // second time through data
-  Tag* analysis_summary = new Tag("analysis_summary", True, True);
-  analysis_summary->setAttributeValue("analysis", getName());
-  analysis_summary->setAttributeValue("time", time_);
+    // second time through data
+    Tag* analysis_summary = new Tag("analysis_summary", True, True);
+    analysis_summary->setAttributeValue("analysis", getName());
+    analysis_summary->setAttributeValue("time", time_);
 
-  Tag* analysis_timestamp_start = new Tag("analysis_timestamp", True, False);
-  analysis_timestamp_start->setAttributeValue("analysis", getName());
-  analysis_timestamp_start->setAttributeValue("time", time_);
-  analysis_timestamp_start->setAttributeValue("id", "1");
+    Tag* analysis_timestamp_start = new Tag("analysis_timestamp", True, False);
+    analysis_timestamp_start->setAttributeValue("analysis", getName());
+    analysis_timestamp_start->setAttributeValue("time", time_);
+    analysis_timestamp_start->setAttributeValue("id", "1");
 
-  Tag* analysis_timestamp_stop = new Tag("analysis_timestamp", False, True);
+    Tag* analysis_timestamp_stop = new Tag("analysis_timestamp", False, True);
 
-  Tag* timestamp = new Tag("database_refresh_timestamp", True, True);
-  // get time info
-  timestamp->setAttributeValue("database", database_);
-  //  if(! use_default_min_ntt_) {
+    Tag* timestamp = new Tag("database_refresh_timestamp", True, True);
+    // get time info
+    timestamp->setAttributeValue("database", database_);
+    //  if(! use_default_min_ntt_) {
   
-  char next[20];
-  sprintf(next, "%d", min_num_tol_term_);
-  timestamp->setAttributeValue("min_num_enz_term", next);
+    char next[20];
+    sprintf(next, "%d", min_num_tol_term_);
+    timestamp->setAttributeValue("min_num_enz_term", next);
   
-  //}
-  // want to overwrite timestamp to summary.xml file......
+    //}
+    // want to overwrite timestamp to summary.xml file......
 
-  int index = 0;
-  double nextprob = -1.0;
+    int index = 0;
+    double nextprob = -1.0;
 
-  // construct a tmpfile name based on xmlfile
-  std::string outfile = make_tmpfile_name(xmlfile);
-  //cerr << "writing data to " << outfile << endl;
-  ofstream fout(outfile.c_str());
-  if(! fout) {
-    cerr << "cannot write output to file " << outfile << endl;
-    exit(1);
-  }
+    // construct a tmpfile name based on xmlfile
+    std::string outfile = make_tmpfile_name(xmlfile);
+    //cerr << "writing data to " << outfile << endl;
+    ofstream fout(outfile.c_str());
+    if(! fout) {
+      cerr << "cannot write output to file " << outfile << endl;
+      exit(1);
+    }
 
-  TagFilter* refresh_filter = new TagFilter("alternative_protein");
+    TagFilter* refresh_filter = new TagFilter("alternative_protein");
 
-  TagFilter* timestamp_filter = new TagFilter("analysis_timestamp");
-  timestamp_filter->enterRequiredAttributeVal("analysis", getName());
+    TagFilter* timestamp_filter = new TagFilter("analysis_timestamp");
+    timestamp_filter->enterRequiredAttributeVal("analysis", getName());
 
-  TagFilter* summary_filter = new TagFilter("analysis_summary");
-  summary_filter->enterRequiredAttributeVal("analysis", getName());
+    TagFilter* summary_filter = new TagFilter("analysis_summary");
+    summary_filter->enterRequiredAttributeVal("analysis", getName());
 
-  int result_index = 1;
-  char search_result[] = "spectrum_query";
-  char attr_name[] = "index";
+    int result_index = 1;
+    char search_result[] = "spectrum_query";
+    char attr_name[] = "index";
 
-  RACI fin2(xmlfile); // can read gzipped xml
-  if(! fin2) {
-    cerr << "RefreshParser(2): error opening " << xmlfile << endl;
-    exit(1);
-  }
+    RACI fin2(xmlfile); // can read gzipped xml
+    if(! fin2) {
+      cerr << "RefreshParser(2): error opening " << xmlfile << endl;
+      exit(1);
+    }
 
-  char current_database[500];
-  current_database[0] = 0;
-  Array<Tag*>* tags = NULL;
-  long line_index = 0L;
-  Boolean refreshed = False;
+    char current_database[500];
+    current_database[0] = 0;
+    Array<Tag*>* tags = NULL;
+    long line_index = 0L;
+    Boolean refreshed = False;
 
-  while(fin2.getline(nextline, line_width_)) {   
-    data = strchr(nextline, '<');
-    while(data != NULL) {
-      tag = new Tag(data);
-      refreshed = False;
+    while(fin2.getline(nextline, line_width_)) {   
+      data = strchr(nextline, '<');
+      while(data != NULL) {
+	tag = new Tag(data);
+	refreshed = False;
 
-      //tag->write(cout);
-      if(line_index > num_interact_lines) {
-	cerr << "error1" << endl;
-	exit(1);
-      }
-      if(tag != NULL && ! timestamp_filter->filter(tag) && ! refresh_filter->filter(tag) &&
-	 ! summary_filter->filter(tag)) {
-	if ( (tag->isStart() && ! strcmp(tag->getName(), "linked_peptide"))  || 
-	     (tag->isStart() && ! strcmp(tag->getName(), "search_hit") && 
-	      ! strcmp(tag->getAttributeValue("hit_rank"), "1") &&
-	      (!tag->getAttributeValue("is_rejected") || 
-	       strcmp(tag->getAttributeValue("is_rejected"), "1")) &&
-	      refresh(tag)) ) {
+	//tag->write(cout);
+	if(line_index > num_interact_lines) {
+	  cerr << "error1" << endl;
+	  exit(1);
+	}
+	if(tag != NULL && ! timestamp_filter->filter(tag) && ! refresh_filter->filter(tag) &&
+	   ! summary_filter->filter(tag)) {
+	  if ( (tag->isStart() && ! strcmp(tag->getName(), "linked_peptide"))  || 
+	       (tag->isStart() && ! strcmp(tag->getName(), "search_hit") && 
+		! strcmp(tag->getAttributeValue("hit_rank"), "1") &&
+		(!tag->getAttributeValue("is_rejected") || 
+		 strcmp(tag->getAttributeValue("is_rejected"), "1")) &&
+		refresh(tag)) ) {
 #ifdef USE_STD_MODS
-	  if(strcmp(interact_file_lines[line_index]->sequence, tag->getAttributeValue("peptide"))) {
-	    cerr << "error2 " << interact_file_lines[line_index]->sequence << " vs " << tag->getAttributeValue("peptide") << endl;
+	    if(strcmp(interact_file_lines[line_index]->sequence, tag->getAttributeValue("peptide"))) {
+	      cerr << "error2 " << interact_file_lines[line_index]->sequence << " vs " << tag->getAttributeValue("peptide") << endl;
 #else
-	  if(strcmp(interact_file_lines[line_index]->sequence, tag->getAttributeValue("stripped_peptide"))) {
-	    cerr << "error2 " << interact_file_lines[line_index]->sequence << " vs " << tag->getAttributeValue("stripped_peptide") << endl;
+	      if(strcmp(interact_file_lines[line_index]->sequence, tag->getAttributeValue("stripped_peptide"))) {
+		cerr << "error2 " << interact_file_lines[line_index]->sequence << " vs " << tag->getAttributeValue("stripped_peptide") << endl;
 #endif
-	    exit(1);
-	  }
+		exit(1);
+	      }
 	  
-	  tags = getRefreshTags(tag,
-				interact_file_lines[line_index++],
-				current_database);
-	  
-	  if(tags != NULL) {
-	    for(int k = 0; k < tags->length(); k++)
-	      if((*tags)[k] != NULL) {
-		RECORD((*tags)[k]);
-		delete (*tags)[k];
+	      tags = getRefreshTags(tag,
+				    interact_file_lines[line_index++],
+				    current_database);
+
+	      if(tags != NULL) {
+		for(int k = 0; k < tags->length(); k++)
+		  if((*tags)[k] != NULL) {
+		    RECORD((*tags)[k]);
+		    delete (*tags)[k];
+		  }
+		delete tags;
+		tags = NULL;
+		refreshed = True;
 	      }
-	    delete tags;
-	    tags = NULL;
-	    refreshed = True;
+	    }
+	    else if(tag->isStart() && ! strcmp(tag->getName(), "msms_pipeline_analysis")) {
+	      tag->write(fout);
+	      // here write the timestamp
+	      analysis_summary->write(fout);
+	    }
+	    else if(tag->isEnd() && ! strcmp(tag->getName(), "search_summary")) {
+	      tag->write(fout);
+	      // here write the timestamp
+	      analysis_timestamp_start->write(fout);
+	      timestamp->write(fout);
+	      analysis_timestamp_stop->write(fout);
+	    }
+	    else if(tag->isStart() && ! strcmp(tag->getName(), "search_database")) {
+	      memcpy(current_database, 
+		     tag->getAttributeValue("local_path"), 
+		     strlen(tag->getAttributeValue("local_path"))+1);
+	      RECORD(tag);
+	    }
+	    else {
+	      tag->write(fout);
+	    }
 	  }
-	}
-	else if(tag->isStart() && ! strcmp(tag->getName(), "msms_pipeline_analysis")) {
-	  tag->write(fout);
-	  // here write the timestamp
-	  analysis_summary->write(fout);
-	}
-	else if(tag->isEnd() && ! strcmp(tag->getName(), "search_summary")) {
-	  tag->write(fout);
-	  // here write the timestamp
-	  analysis_timestamp_start->write(fout);
-	  timestamp->write(fout);
-	  analysis_timestamp_stop->write(fout);
-	}
-	else if(tag->isStart() && ! strcmp(tag->getName(), "search_database")) {
-	  memcpy(current_database, 
-		 tag->getAttributeValue("local_path"), 
-		 strlen(tag->getAttributeValue("local_path"))+1);
-	  RECORD(tag);
-	}
-	else {
-	  tag->write(fout);
-	}
-      }
-      if(! refreshed && tag != NULL)
-	delete tag;
-      data = strchr(data+1, '<');
-    } // next tag
-  } // next line
-  fin2.close();
-  fout.close();
+	  if(! refreshed && tag != NULL)
+	    delete tag;
+	  data = strchr(data+1, '<');
+	} // next tag
+      } // next line
+      fin2.close();
+      fout.close();
 
-  delete [] nextline;
+      delete [] nextline;
 
-  if (num_mapped_ == 0)
-    fprintf(stdout,"\nERROR: no entries mapped! Please check input files.");
-  else
-    fprintf(stdout,"\n  - Mapped %d entries", num_mapped_);
-  if (num_not_mapped_ > 0)
-    fprintf(stdout,"\nWarning: could not map %d entries", num_not_mapped_);
+      if (num_mapped_ == 0)
+	fprintf(stdout,"\nERROR: no entries mapped! Please check input files.");
+      else
+	fprintf(stdout,"\n  - Mapped %d entries", num_mapped_);
+      if (num_not_mapped_ > 0)
+	fprintf(stdout,"\nWarning: could not map %d entries", num_not_mapped_);
 
-  fprintf(stdout,"\n\n");
+      fprintf(stdout,"\n\n");
 
-  if (testType!=NO_TEST) {
-    //
-    // regression test stuff - bpratt Insilicos LLC, Nov 2005
-    //
-    TagListComparator("RefreshParser",testType,test_tags,testFileName);
-    delete[] testFileName;
-    for(int k = test_tags.length(); k--;) {
-      delete test_tags[k];
-    }
-  }
+      if (testType!=NO_TEST) {
+	//
+	// regression test stuff - bpratt Insilicos LLC, Nov 2005
+	//
+	TagListComparator("RefreshParser",testType,test_tags,testFileName);
+	delete[] testFileName;
+	for(int k = test_tags.length(); k--;) {
+	  delete test_tags[k];
+	}
+      }
 
-  if(! overwrite(xmlfile, outfile.c_str(), "</msms_pipeline_analysis>")) {
-    cerr << "error: no RefreshParser data written to file " << xmlfile << endl;
-  }
+      if(! overwrite(xmlfile, outfile.c_str(), "</msms_pipeline_analysis>")) {
+	cerr << "error: no RefreshParser data written to file " << xmlfile << endl;
+      }
 
 
-  // clean up...
-  map <int*, int> freed_iptrs_map;
-  map <char*, int> *freed_cptrs_map = new map <char*, int>;
-  map <db_ref_t*, int> *freed_pptrs_map = new map <db_ref_t*, int>;
-  map <db_ref_t**, int> *freed_rptrs_map = new map <db_ref_t**, int>;
+      // clean up...
+      map <int*, int> freed_iptrs_map;
+      map <char*, int> *freed_cptrs_map = new map <char*, int>;
+      map <db_ref_t*, int> *freed_pptrs_map = new map <db_ref_t*, int>;
+      map <db_ref_t**, int> *freed_rptrs_map = new map <db_ref_t**, int>;
 
-  if (uniq_interact_data != NULL) {
-    for(int k = 0; k < uniq_lines; k++) {
-      if (uniq_interact_data[k] != NULL) {
-        if (uniq_interact_data[k]->updated_refs != NULL)
-          save_ptrs_to_free(uniq_interact_data[k],freed_rptrs_map,freed_pptrs_map,freed_cptrs_map);
-        uniq_interact_data[k]->updated_refs = NULL;
+      if (uniq_interact_data != NULL) {
+	for(int k = 0; k < uniq_lines; k++) {
+	  if (uniq_interact_data[k] != NULL) {
+	    if (uniq_interact_data[k]->updated_refs != NULL)
+	      save_ptrs_to_free(uniq_interact_data[k],freed_rptrs_map,freed_pptrs_map,freed_cptrs_map);
+	    uniq_interact_data[k]->updated_refs = NULL;
+	  }
+	}
+	free(uniq_interact_data);
+	uniq_interact_data = NULL;
       }
-    }
-    free(uniq_interact_data);
-    uniq_interact_data = NULL;
-  }
 
-  if (interact_file_lines != NULL) {
-    for(int k = 0; k < num_interact_lines; k++) {
-      if (interact_file_lines[k] != NULL) {
-	delete[] interact_file_lines[k]->sequence;
-	delete[] interact_file_lines[k]->sequence_I2L;
-	delete[] interact_file_lines[k]->db_ref;
-	if ( interact_file_lines[k]->alt_sequence != NULL )
-	  delete[] interact_file_lines[k]->alt_sequence;
+      if (interact_file_lines != NULL) {
+	for(int k = 0; k < num_interact_lines; k++) {
+	  if (interact_file_lines[k] != NULL) {
+	    delete[] interact_file_lines[k]->sequence;
+	    delete[] interact_file_lines[k]->sequence_I2L;
+	    delete[] interact_file_lines[k]->db_ref;
+	    if ( interact_file_lines[k]->alt_sequence != NULL )
+	      delete[] interact_file_lines[k]->alt_sequence;
 
-	if (interact_file_lines[k]->updated_ntts != NULL)
-	  freed_iptrs_map[interact_file_lines[k]->updated_ntts] = 1;
-	interact_file_lines[k]->updated_ntts = NULL;
+	    if (interact_file_lines[k]->updated_ntts != NULL)
+	      freed_iptrs_map[interact_file_lines[k]->updated_ntts] = 1;
+	    interact_file_lines[k]->updated_ntts = NULL;
 
-	if (interact_file_lines[k]->updated_refs != NULL)
-	  save_ptrs_to_free(interact_file_lines[k],freed_rptrs_map,freed_pptrs_map,freed_cptrs_map);
-	interact_file_lines[k]->updated_refs = NULL;
+	    if (interact_file_lines[k]->updated_refs != NULL)
+	      save_ptrs_to_free(interact_file_lines[k],freed_rptrs_map,freed_pptrs_map,freed_cptrs_map);
+	    interact_file_lines[k]->updated_refs = NULL;
 
-	free(interact_file_lines[k]);
-	interact_file_lines[k] = NULL;
+	    free(interact_file_lines[k]);
+	    interact_file_lines[k] = NULL;
+	  }
+	}
+	free(interact_file_lines);
+	interact_file_lines = NULL;
       }
-    }
-    free(interact_file_lines);
-    interact_file_lines = NULL;
-  }
 
-  for (map <int*, int>::const_iterator it = freed_iptrs_map.begin(); it != freed_iptrs_map.end(); it++)
-    free(it->first);
-  for (map <char*, int>::const_iterator it = (*freed_cptrs_map).begin(); it != (*freed_cptrs_map).end(); it++)
-    free(it->first);
-  for (map <db_ref_t*, int>::const_iterator it = (*freed_pptrs_map).begin(); it != (*freed_pptrs_map).end(); it++)
-    free(it->first);
-  for (map <db_ref_t**, int>::const_iterator it = (*freed_rptrs_map).begin(); it != (*freed_rptrs_map).end(); it++)
-    free(it->first);
-  delete freed_cptrs_map;
-  delete freed_pptrs_map;
-  delete freed_rptrs_map;
+      for (map <int*, int>::const_iterator it = freed_iptrs_map.begin(); it != freed_iptrs_map.end(); it++)
+	free(it->first);
+      for (map <char*, int>::const_iterator it = (*freed_cptrs_map).begin(); it != (*freed_cptrs_map).end(); it++)
+	free(it->first);
+      for (map <db_ref_t*, int>::const_iterator it = (*freed_pptrs_map).begin(); it != (*freed_pptrs_map).end(); it++)
+	free(it->first);
+      for (map <db_ref_t**, int>::const_iterator it = (*freed_rptrs_map).begin(); it != (*freed_rptrs_map).end(); it++)
+	free(it->first);
+      delete freed_cptrs_map;
+      delete freed_pptrs_map;
+      delete freed_rptrs_map;
 
-  delete alt_index_map;
-  delete analysis_summary;
-  delete analysis_timestamp_start;
-  delete analysis_timestamp_stop;
-  delete timestamp;
-  delete refresh_filter;
-  delete timestamp_filter;
-  delete summary_filter;
+      delete alt_index_map;
+      delete analysis_summary;
+      delete analysis_timestamp_start;
+      delete analysis_timestamp_stop;
+      delete timestamp;
+      delete refresh_filter;
+      delete timestamp_filter;
+      delete summary_filter;
 
-  free(sort_idx);
-  free(szBuf_);
-  free(szSeq_);
-  free(szHdr_);
-  free(szOutputDb_);
+      free(sort_idx);
+      free(szBuf_);
+      free(szSeq_);
+      free(szHdr_);
+      free(szOutputDb_);
 
-  aliases.clear();
-  descriptions.clear();
-  prev_aas.clear();
-  next_aas.clear();
-}
+      aliases.clear();
+      descriptions.clear();
+      prev_aas.clear();
+      next_aas.clear();
+    }
 
-
 void RefreshParser::setFilter(Tag* tag) {
   if(tag == NULL)
     return;

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Sashimi-commit] SF.net SVN: sashimi:[9475] trunk/trans_proteomic_ pipeline/extern

[<rea...@us...>]

Revision: 9475
          http://sourceforge.net/p/sashimi/code/9475
Author:   real_procopio
Date:     2026-02-26 01:12:48 +0000 (Thu, 26 Feb 2026)
Log Message:
-----------
[comet] v2026.01.0

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/Makefile

Added Paths:
-----------
    trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip

Removed Paths:
-------------
    trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip

Modified: trunk/trans_proteomic_pipeline/extern/Makefile
===================================================================
--- trunk/trans_proteomic_pipeline/extern/Makefile	2026-02-26 00:17:57 UTC (rev 9474)
+++ trunk/trans_proteomic_pipeline/extern/Makefile	2026-02-26 01:12:48 UTC (rev 9475)
@@ -414,7 +414,7 @@
 #
 # http://comet-ms.sourceforge.net/
 #
-COMET_VER := 2025030
+COMET_VER := 2026010
 COMET_ZIP := $(TPP_EXT)/comet_source_$(COMET_VER).zip
 COMET_SRC := $(BUILD_SRC)/comet_source_$(COMET_VER)
 .PHONY: comet comet-source comet-clean

Deleted: trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip
===================================================================
(Binary files differ)

Added: trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip
===================================================================
(Binary files differ)

Index: trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip
===================================================================
--- trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip	2026-02-26 00:17:57 UTC (rev 9474)
+++ trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip	2026-02-26 01:12:48 UTC (rev 9475)

Property changes on: trunk/trans_proteomic_pipeline/extern/comet_source_2026010.zip
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Sashimi-commit] SF.net SVN: sashimi:[9474] trunk/trans_proteomic_ pipeline/html/ref/unimod.json

[<rea...@us...>]

Revision: 9474
          http://sourceforge.net/p/sashimi/code/9474
Author:   real_procopio
Date:     2026-02-26 00:17:57 +0000 (Thu, 26 Feb 2026)
Log Message:
-----------
Latest Unimod data, up to id=2147

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/html/ref/unimod.json

Modified: trunk/trans_proteomic_pipeline/html/ref/unimod.json
===================================================================
--- trunk/trans_proteomic_pipeline/html/ref/unimod.json	2026-02-25 18:09:39 UTC (rev 9473)
+++ trunk/trans_proteomic_pipeline/html/ref/unimod.json	2026-02-26 00:17:57 UTC (rev 9474)
@@ -1415,6 +1415,16 @@
       ],
       "altst": []
     },
+    "b-type-ion": {
+      "recid": "2132",
+      "_iscommon": false,
+      "fname": "Dehydration of C-terminus as reaction inside the mass spectrometer",
+      "delta": "-18.010565",
+      "sites": [],
+      "altst": [
+        "C-term"
+      ]
+    },
     "Cys->Oxoalanine": {
       "recid": "402",
       "_iscommon": false,
@@ -1469,6 +1479,16 @@
         "N"
       ]
     },
+    "z-type-ion": {
+      "recid": "2143",
+      "_iscommon": false,
+      "fname": "Ammonia loss from N-terminus as reaction inside the mass spectrometer",
+      "delta": "-17.026549",
+      "sites": [],
+      "altst": [
+        "N-term"
+      ]
+    },
     "Met->Asn": {
       "recid": "1149",
       "_iscommon": false,
@@ -1988,6 +2008,16 @@
         "V"
       ]
     },
+    "Dehydromethionine": {
+      "recid": "2144",
+      "_iscommon": false,
+      "fname": "Intramolecular cyclization product of N-terminal methionine, forming a five-membered azasulfonium ion where the sulfur atom bonds to the amine group",
+      "delta": "-2.01565",
+      "sites": [],
+      "altst": [
+        "M"
+      ]
+    },
     "Met->Glu": {
       "recid": "1145",
       "_iscommon": false,
@@ -2079,6 +2109,16 @@
         "E"
       ]
     },
+    "c-type-ion": {
+      "recid": "2141",
+      "_iscommon": false,
+      "fname": "Cleavage at the N atom from the N+1 residue as reaction inside the mass spectrometer",
+      "delta": "-0.984016",
+      "sites": [],
+      "altst": [
+        "C-term"
+      ]
+    },
     "Glu->pyro-Glu+Methyl:2H(2)13C(1)": {
       "recid": "1827",
       "_iscommon": false,
@@ -2119,6 +2159,16 @@
         "K"
       ]
     },
+    "Cys->fGly-diol": {
+      "recid": "2129",
+      "_iscommon": false,
+      "fname": "formylglycinediol, activated in sulfatases",
+      "delta": "0.017759",
+      "sites": [],
+      "altst": [
+        "C"
+      ]
+    },
     "Gln->Lys": {
       "recid": "631",
       "_iscommon": false,
@@ -2621,6 +2671,16 @@
         "E"
       ]
     },
+    "Label:2H(8)": {
+      "recid": "2146",
+      "_iscommon": false,
+      "fname": "SILAC: Lysine_D8",
+      "delta": "8.050214",
+      "sites": [],
+      "altst": [
+        "K"
+      ]
+    },
     "Lys->His": {
       "recid": "1136",
       "_iscommon": false,
@@ -3250,6 +3310,17 @@
         "C-term"
       ]
     },
+    "Methyl:13C(1)2H(2)": {
+      "recid": "2140",
+      "_iscommon": false,
+      "fname": "Heavy-Methyl:13C(1)2H(2)",
+      "delta": "17.031558",
+      "sites": [],
+      "altst": [
+        "K",
+        "N-term"
+      ]
+    },
     "Methyl:2H(3)": {
       "recid": "298",
       "_iscommon": false,
@@ -3567,6 +3638,16 @@
         "C"
       ]
     },
+    "x-type-ion": {
+      "recid": "2142",
+      "_iscommon": false,
+      "fname": "Cleavage at the carbonyl from the N-1 residue as reaction inside the mass spectrometer",
+      "delta": "25.979265",
+      "sites": [],
+      "altst": [
+        "N-term"
+      ]
+    },
     "His->Tyr": {
       "recid": "581",
       "_iscommon": false,
@@ -5437,6 +5518,16 @@
         "W"
       ]
     },
+    "Cys->Ser-O-sulfate": {
+      "recid": "2131",
+      "_iscommon": false,
+      "fname": "Serine O-sulfate",
+      "delta": "63.979659",
+      "sites": [],
+      "altst": [
+        "C"
+      ]
+    },
     "Val->Tyr": {
       "recid": "1223",
       "_iscommon": false,
@@ -5835,6 +5926,16 @@
         "K"
       ]
     },
+    "Cys->sulfo-fGly-dio": {
+      "recid": "2130",
+      "_iscommon": false,
+      "fname": "Sulphated formylglycinediol, activated in sulfatases",
+      "delta": "78.966748",
+      "sites": [],
+      "altst": [
+        "C"
+      ]
+    },
     "Delta:Se(1)": {
       "recid": "423",
       "_iscommon": false,
@@ -7715,6 +7816,16 @@
         "K"
       ]
     },
+    "imidazolone": {
+      "recid": "2147",
+      "_iscommon": false,
+      "fname": "imidazolone from 3-DG",
+      "delta": "144.042259",
+      "sites": [],
+      "altst": [
+        "R"
+      ]
+    },
     "iTRAQ4plex115": {
       "recid": "533",
       "_iscommon": false,
@@ -8383,6 +8494,18 @@
         "N-term"
       ]
     },
+    "Phosphocholine": {
+      "recid": "2139",
+      "_iscommon": false,
+      "fname": "Serine/Threonine/Tyrosine of a protein becomes posttranslationally modified with a phosphocholine moiety.",
+      "delta": "165.05548",
+      "sites": [],
+      "altst": [
+        "T",
+        "S",
+        "Y"
+      ]
+    },
     "Tween20": {
       "recid": "1834",
       "_iscommon": false,
@@ -8654,6 +8777,21 @@
         "C"
       ]
     },
+    "PnTAG": {
+      "recid": "2135",
+      "_iscommon": false,
+      "fname": "6-Phosphonohexanoylation",
+      "delta": "178.039496",
+      "sites": [],
+      "altst": [
+        "Y",
+        "T",
+        "S",
+        "N-term",
+        "N-term",
+        "K"
+      ]
+    },
     "Galactosyl": {
       "recid": "907",
       "_iscommon": false,
@@ -9261,12 +9399,13 @@
       "delta": "224.152478",
       "sites": [],
       "altst": [
+        "S",
         "H",
         "N-term",
         "N-term",
         "K",
-        "S",
-        "T"
+        "T",
+        "Y"
       ]
     },
     "Brij58": {
@@ -9313,7 +9452,8 @@
         "T",
         "S",
         "H",
-        "N-term"
+        "N-term",
+        "Y"
       ]
     },
     "Xlink:DSPP[226]": {
@@ -9424,7 +9564,8 @@
         "T",
         "S",
         "H",
-        "N-term"
+        "N-term",
+        "Y"
       ]
     },
     "PyridoxalPhosphateH2": {
@@ -9437,6 +9578,21 @@
         "K"
       ]
     },
+    "DMA-PEG3": {
+      "recid": "2136",
+      "_iscommon": false,
+      "fname": "DimethylaminoPEG3ylation",
+      "delta": "231.147058",
+      "sites": [],
+      "altst": [
+        "K",
+        "N-term",
+        "N-term",
+        "S",
+        "T",
+        "Y"
+      ]
+    },
     "PropylNAGthiazoline": {
       "recid": "514",
       "_iscommon": false,
@@ -10029,7 +10185,8 @@
         "N-term",
         "N-term",
         "K",
-        "T"
+        "T",
+        "Y"
       ]
     },
     "IGBP": {
@@ -10163,7 +10320,8 @@
         "T",
         "S",
         "H",
-        "N-term"
+        "N-term",
+        "Y"
       ]
     },
     "PhosphoCytidine": {
@@ -10526,6 +10684,16 @@
         "K"
       ]
     },
+    "Desthiobiotin-Phenol": {
+      "recid": "2127",
+      "_iscommon": false,
+      "fname": "Desthiobiotin-Phenol",
+      "delta": "331.189592",
+      "sites": [],
+      "altst": [
+        "Y"
+      ]
+    },
     "LG-lactam-K": {
       "recid": "503",
       "_iscommon": false,
@@ -11007,6 +11175,16 @@
         "K"
       ]
     },
+    "HCCA-Lys": {
+      "recid": "2138",
+      "_iscommon": false,
+      "fname": "Lysine labelled with HCCA tag",
+      "delta": "412.211056",
+      "sites": [],
+      "altst": [
+        "K"
+      ]
+    },
     "PEO-Iodoacetyl-LC-Biotin": {
       "recid": "20",
       "_iscommon": false,
@@ -11419,6 +11597,16 @@
         "C"
       ]
     },
+    "Cys-vinyl sulfone amine probe addition": {
+      "recid": "2128",
+      "_iscommon": false,
+      "fname": "Michael addition of a vinyl sulfone amine desthiobiotin probe to cysteine",
+      "delta": "478.24612",
+      "sites": [],
+      "altst": [
+        "C"
+      ]
+    },
     "EQIGG": {
       "recid": "846",
       "_iscommon": false,
@@ -16783,9 +16971,9 @@
     }
   },
   "info": {
-    "datetime": "2024-08-14 21:38:47",
-    "generator": "./unimodxml2json.py",
+    "datetime": "2026-02-25 14:03:11",
+    "generator": "/users/lmendoza/bin/UNIMOD/./unimodxml2json.py",
     "source": "/proteomics/lmendoza/reference/unimod.xml",
-    "last_id": "2126"
+    "last_id": "2147"
   }
 }
\ No newline at end of file

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[Sashimi-commit] SF.net SVN: sashimi:[9473] trunk/trans_proteomic_ pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp

[<en...@us...>]

Revision: 9473
          http://sourceforge.net/p/sashimi/code/9473
Author:   eng_jk
Date:     2026-02-25 18:09:39 +0000 (Wed, 25 Feb 2026)
Log Message:
-----------
modify DatabaseParser to account for Comet .idx extension

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp

Modified: trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp	2025-12-09 06:49:19 UTC (rev 9472)
+++ trunk/trans_proteomic_pipeline/src/Parsers/DatabaseParser/DatabaseParser.cpp	2026-02-25 18:09:39 UTC (rev 9473)
@@ -65,6 +65,12 @@
 	    memcpy(current_database, 
 		   tag->getAttributeValue("local_path"), 
 		   strlen(tag->getAttributeValue("local_path"))+1);
+
+       // when parsing .idx from Comet index search, strip ".idx" extension from
+       // parsed attribute value to return original fasta for sequence matching
+       int len = strlen(current_database);
+       if (strcmp(current_database + len - 4, ".idx") == 0 && len >= 4)
+          current_database[len - 4] = '\0';
 	  }
 	  else if(tag->isStart() && ! strcmp(tag->getName(), "database_refresh_timestamp")) {
 	    strcpy(current_database, tag->getAttributeValue("database"));

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[Sashimi-commit] SF.net SVN: sashimi:[9472] trunk/trans_proteomic_ pipeline/extern

[<rea...@us...>]

Revision: 9472
          http://sourceforge.net/p/sashimi/code/9472
Author:   real_procopio
Date:     2025-12-09 06:49:19 +0000 (Tue, 09 Dec 2025)
Log Message:
-----------
[comet] v2025.03.0

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/Makefile

Added Paths:
-----------
    trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip

Removed Paths:
-------------
    trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip

Modified: trunk/trans_proteomic_pipeline/extern/Makefile
===================================================================
--- trunk/trans_proteomic_pipeline/extern/Makefile	2025-12-09 06:23:23 UTC (rev 9471)
+++ trunk/trans_proteomic_pipeline/extern/Makefile	2025-12-09 06:49:19 UTC (rev 9472)
@@ -414,7 +414,7 @@
 #
 # http://comet-ms.sourceforge.net/
 #
-COMET_VER := 2025011
+COMET_VER := 2025030
 COMET_ZIP := $(TPP_EXT)/comet_source_$(COMET_VER).zip
 COMET_SRC := $(BUILD_SRC)/comet_source_$(COMET_VER)
 .PHONY: comet comet-source comet-clean

Deleted: trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip
===================================================================
(Binary files differ)

Added: trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip
===================================================================
(Binary files differ)

Index: trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip
===================================================================
--- trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip	2025-12-09 06:23:23 UTC (rev 9471)
+++ trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip	2025-12-09 06:49:19 UTC (rev 9472)

Property changes on: trunk/trans_proteomic_pipeline/extern/comet_source_2025030.zip
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
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[Sashimi-commit] SF.net SVN: sashimi:[9471] trunk/trans_proteomic_pipeline/perl/tpp_gui/ tpp_gui.pl

[<rea...@us...>]

Revision: 9471
          http://sourceforge.net/p/sashimi/code/9471
Author:   real_procopio
Date:     2025-12-09 06:23:23 +0000 (Tue, 09 Dec 2025)
Log Message:
-----------
[Petunia] Updated path to Python in local UB24 (regis)

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl

Modified: trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl	2025-12-08 19:41:23 UTC (rev 9470)
+++ trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl	2025-12-09 06:23:23 UTC (rev 9471)
@@ -17492,11 +17492,14 @@
     $new_file .= $charList[int(rand 36)];
   }
 
+  my $py_lib_path = readconfig('pythonpath', "/proteomics/sw/python/Ubuntu24");
+
   open(SHCMD, ">$new_file") || &fatalError("CANNOT_CREATE_SHELL_COMMAND_FILE:$new_file:$!");
   chmod 0744, $new_file;
   print SHCMD "#!/bin/bash\n";
   print SHCMD "export PERL5LIB=/proteomics/sw/perl-u20/share/perl:/proteomics/sw/perl-u20/lib/perl5:/proteomics/sw/perl-u20/lib/x86_64-linux-gnu/perl\n";
   print SHCMD "export PATH=/proteomics/sw/bin:\$PATH\n";
+  print SHCMD "export PYTHONPATH=$py_lib_path\n";
   print SHCMD "#echo PATH == \$PATH\n";
   print SHCMD "export HOST=`/bin/hostname -s`\n";
   print SHCMD "#echo HOST == \$HOST\n";

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[Sashimi-commit] SF.net SVN: sashimi:[9470] trunk/trans_proteomic_ pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

[<en...@us...>]

Revision: 9470
          http://sourceforge.net/p/sashimi/code/9470
Author:   eng_jk
Date:     2025-12-08 19:41:23 +0000 (Mon, 08 Dec 2025)
Log Message:
-----------
Correct parsing of MS1 peaks for mzML files with ion mobility dimension.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

Modified: trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-04-30 00:57:04 UTC (rev 9469)
+++ trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-12-08 19:41:23 UTC (rev 9470)
@@ -1556,7 +1556,7 @@
    }
 
    if (scanHeaderMS.msLevel == (scanHeader.msLevel - 1))
-    {
+   {
       RAMPREAL *pPeaks;
       int n = 0;
       int bFirstDataPoint=1;
@@ -1565,19 +1565,23 @@
       double dLowMass = scanHeader.precursorMZ - 0.25;
       double dHighMass = scanHeader.precursorMZ + 0.25;
       
+      RAMPREAL fMass;
+      RAMPREAL fInten;
+      RAMPREAL fIonMob;
+
       // Open a scan
       pPeaks = readPeaks(fp_, index_[iScanNum]);
       printf("\nms1peaks = [");
       while (pPeaks != NULL && pPeaks[n] != -1)
-       {
-	 RAMPREAL fMass;
-	 RAMPREAL fInten;
-	 
-	 fMass = pPeaks[n];
+      {
+         fMass = pPeaks[n];
          n++;
          fInten = pPeaks[n];
          n++;
 
+         if ((fp_->fileType == 3 || fp_->fileType == 1) && fp_->mzML->getIonMobility())
+            fIonMob=pPeaks[n++];
+
          if (fInten > 0.0)
          {
             if (dLowMass<fMass && fMass<dHighMass)
@@ -1602,10 +1606,10 @@
 
       printf("\nms1scanLabel = \"%d, RT %0.2f\";\n", iScanNum, scanHeaderMS.retentionTime);
       pEnvironment.iMS1Scan = iScanNum;
-  }
+   }
    else
    {
-     printf("\nms1scanLabel = \" %d is not a valid precursor scan!\";\n",iScanNum);
+      printf("\nms1scanLabel = \" %d is not a valid precursor scan!\";\n",iScanNum);
       printf("ms1peaks= [[0.0,0.0]];\n");
    }
 }

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[Sashimi-commit] SF.net SVN: sashimi:[9469] trunk/trans_proteomic_ pipeline/html/js/showxic.js

[<rea...@us...>]

Revision: 9469
          http://sourceforge.net/p/sashimi/code/9469
Author:   real_procopio
Date:     2025-04-30 00:57:04 +0000 (Wed, 30 Apr 2025)
Log Message:
-----------
[showXIC] Display RT in minutes insetad of seconds (as per Lab request).  Minor style adjustment to max ppm

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/html/js/showxic.js

Modified: trunk/trans_proteomic_pipeline/html/js/showxic.js
===================================================================
--- trunk/trans_proteomic_pipeline/html/js/showxic.js	2025-04-29 23:39:01 UTC (rev 9468)
+++ trunk/trans_proteomic_pipeline/html/js/showxic.js	2025-04-30 00:57:04 UTC (rev 9469)
@@ -136,9 +136,9 @@
 		    hitdataset['data'] = [];
 		    peps[hit["modified"]] = hitdataset;
 		}
-		peps[hit["modified"]]['data'].push({'x':hit["rt"], 'y':0});
-		peps[hit["modified"]]['data'].push({'x':hit["rt"], 'y':0.9});
-		peps[hit["modified"]]['data'].push({'x':hit["rt"], 'y':0});
+		peps[hit["modified"]]['data'].push({'x':hit["rt"]/60, 'y':0});
+		peps[hit["modified"]]['data'].push({'x':hit["rt"]/60, 'y':0.9});
+		peps[hit["modified"]]['data'].push({'x':hit["rt"]/60, 'y':0});
 	    }
 
 	    for (let pep in peps) {
@@ -148,7 +148,7 @@
 
 	    tpp_clearElement("pepxml_hits_table",false);
 
-	    var fields1 = [ "rt","ppm" ];
+	    var fields1 = [ "ppm" ];
 	    var fields4 = [ "mz","diff","probability" ];
 	    var fields = [ "rt","scan","mz","diff","ppm","charge","modified","probability" ];
 	    var tr = document.createElement("tr");
@@ -175,7 +175,11 @@
 		    td.className = 'value';
                     if (field == 'charge')
 			td.append("+");
-		    if (fields1.includes(field))
+                    if (field == 'rt') {
+			td.append((Number(hit[field])/60).toFixed(3));
+			td.title = hit[field]+" seconds";
+		    }
+		    else if (fields1.includes(field))
 			td.append(Number(hit[field]).toFixed(1));
 		    else if (fields4.includes(field))
 			td.append(Number(hit[field]).toFixed(4));
@@ -250,8 +254,12 @@
     var url_params = "FILE="+mzfile;
     for (let param of _ParamsNumeric) {
 	var val = Number(document.getElementById("new_"+param).value.trim());
-	if (val && typeof val === 'number')
-	    url_params += "&"+param+"="+val;
+	if (val && typeof val === 'number') {
+	    if (param.endsWith('_RT'))
+		url_params += "&"+param+"="+val*60;
+	    else
+		url_params += "&"+param+"="+val;
+	}
 	else
 	    val = '';
 
@@ -332,7 +340,7 @@
 	pspan.append(span);
 
         span = document.createElement("li");
-        span.innerHTML = "<strong>Radius</strong> of each PPM circle is proportional to m/z difference <i>(max="+max_ppm+"ppm)</i>";
+        span.innerHTML = "<strong>Radius</strong> of each PPM circle is proportional to m/z difference (max=<i class='tpporange'>"+max_ppm+"ppm</i>)";
         pspan.append(span);
     }
 
@@ -374,7 +382,7 @@
 function plotXIC(mzfile,data) {
     var mzval = document.getElementById("new_MZ").value.trim();
     var subt = mzval==0 ? "Total Ion Current" : "Ion Current @ m/z = "+mzval;
-    var chart = new_chart(mzfile, subt, 'Time (seconds)');
+    var chart = new_chart(mzfile, subt, 'Time (minutes)');
 
     var dataset = {};
     dataset['label'] = "Intensity";
@@ -394,8 +402,8 @@
 	}
 
 	if (was_zero)
-	    dataset['data'].push({'x':point['time'], 'y':0});
-	dataset['data'].push({'x':point['time'], 'y':point['intensity']});
+	    dataset['data'].push({'x':point['time']/60, 'y':0});
+	dataset['data'].push({'x':point['time']/60, 'y':point['intensity']});
 
 	if (point['ppm'] && Math.abs(point['ppm']) > 0) {
 	    var ppm = Math.abs(point['ppm']);
@@ -403,7 +411,7 @@
 		max_ppm = ppm;
 	}
 
-	prev_rt = point['time'];
+	prev_rt = point['time']/60;
 	was_zero = false;
     }
     chart['data']['datasets'] = [dataset];
@@ -420,7 +428,7 @@
             if (point['ppm'] && Math.abs(point['ppm']) > 0) {
 		var ppm = Math.abs(point['ppm']);
                 var radius = 2+(25*ppm/max_ppm);
-                ppmdataset['data'].push({'x':point['time'], 'y':point['intensity'], 'r':radius, 'ppm':point['ppm']});
+                ppmdataset['data'].push({'x':point['time']/60, 'y':point['intensity'], 'r':radius, 'ppm':point['ppm']});
             }
 	}
 	chart['data']['datasets'].push(ppmdataset);
@@ -437,8 +445,8 @@
 	hitdataset['borderWidth'] = 4;
 	hitdataset['yAxisID'] = 'yabs';
         hitdataset['data'] = [];
-        hitdataset['data'].push({'x':_hit_data["RT"], 'y':0});
-        hitdataset['data'].push({'x':_hit_data["RT"], 'y':1});
+        hitdataset['data'].push({'x':_hit_data["RT"]/60, 'y':0});
+        hitdataset['data'].push({'x':_hit_data["RT"]/60, 'y':1});
 	chart['data']['datasets'].push(hitdataset);
         chart['options']['plugins']['legend']['display'] = true;
 	had_hit = true;

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[Sashimi-commit] SF.net SVN: sashimi:[9468] trunk/trans_proteomic_ pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

[<en...@us...>]

Revision: 9468
          http://sourceforge.net/p/sashimi/code/9468
Author:   eng_jk
Date:     2025-04-29 23:39:01 +0000 (Tue, 29 Apr 2025)
Log Message:
-----------
Add logic when finding correpsonding MS1 scan if scanHeader.precursorScanNum==0.
Previous code would fail as it would never find a scan number that matches the
scanHeader.precursorScanNum. It would hit the MAX_SCANS_TO_FIND_MS1_SIGNAL scan
range limit and complain the scan is not a valid precursor scan. The update now
handles scanHeader.precursorScanNum==0 by returning the first precursor scan
prior to the identification which is a better compromise than showing no
precursor scan. And I got rid of the MAX_SCANS_TO_FIND_MS1_SIGNAL range.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

Modified: trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-04-10 17:19:01 UTC (rev 9467)
+++ trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-04-29 23:39:01 UTC (rev 9468)
@@ -31,7 +31,6 @@
 #include "Search/SpectraST/SpectraSTLibEntry.hpp"
 
 #define PROTON_MASS 1.00727646688
-#define MAX_SCANS_TO_FIND_MS1_SIGNAL 500
 #define MZ_RANGE_MAX 2000.0   // for setting x-axis scale, ignored if any data are above this value
 #define TITLE "Lorikeet Spectrum Viewer // TPP"
 
@@ -1525,21 +1524,37 @@
      iScanNum = pEnvironment.iMS1Scan;
      readHeader(fp_, index_[iScanNum], &scanHeaderMS);
    }
-   else { 
-     // loop back through scans to find MS1 scan
-     iScanNum--;
-     while (i<MAX_SCANS_TO_FIND_MS1_SIGNAL)
-       {
-	 readHeader(fp_, index_[iScanNum], &scanHeaderMS);
-	 if (iScanNum < 1 || ( scanHeaderMS.msLevel == (scanHeader.msLevel - 1) && scanHeaderMS.acquisitionNum == scanHeader.precursorScanNum))
-	   {
-	     break;
-	   }
-	 iScanNum--;
-	 i++;
-       }
-   }   
+   else {
+      // loop back through scans to find MS1 scan
+      iScanNum--;
 
+      while (1)
+      {
+         readHeader(fp_, index_[iScanNum], &scanHeaderMS);
+
+         if (scanHeader.precursorScanNum != 0)
+         {
+            // This first if() below assumes scanHeader.precursorScanNum is set.
+            // Which means there's no point in also checking the msLevel
+            // here as it will be checked below at next if statement.
+            // Removing that check allows a break out of the while() loop
+            // when we get to the precursorScanNum.
+            if (iScanNum < 1 || scanHeaderMS.acquisitionNum == scanHeader.precursorScanNum)
+            {
+               break;
+            }
+         }
+         else if (iScanNum < 1 || scanHeaderMS.msLevel == (scanHeader.msLevel - 1))
+         {
+            // I see exmaples where scanHeader.precursorScanNum is set to 0.
+            // For such cases, break on the first msLevel-1 scan.  
+            break;
+         }
+
+         iScanNum--;
+      }
+   }
+
    if (scanHeaderMS.msLevel == (scanHeader.msLevel - 1))
     {
       RAMPREAL *pPeaks;

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[Sashimi-commit] SF.net SVN: sashimi:[9467] tags/release_7-3-0/

[<rea...@us...>]

Revision: 9467
          http://sourceforge.net/p/sashimi/code/9467
Author:   real_procopio
Date:     2025-04-10 17:19:01 +0000 (Thu, 10 Apr 2025)
Log Message:
-----------
Tagging 7.3.0 release

Added Paths:
-----------
    tags/release_7-3-0/

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[Sashimi-commit] SF.net SVN: sashimi:[9466] trunk/trans_proteomic_ pipeline/perl/cgi-bin/qsir.pl

[<rea...@us...>]

Revision: 9466
          http://sourceforge.net/p/sashimi/code/9466
Author:   real_procopio
Date:     2025-04-10 07:46:04 +0000 (Thu, 10 Apr 2025)
Log Message:
-----------
[qsir] Deal with Windoze paths...

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/qsir.pl

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/qsir.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/qsir.pl	2025-04-10 01:28:23 UTC (rev 9465)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/qsir.pl	2025-04-10 07:46:04 UTC (rev 9466)
@@ -36,6 +36,7 @@
 # $CGI::LIST_CONTEXT_WARN = 0; # turn off this for now
 
 my $cgi_query = CGI->new;
+my $in_windows = ($^O eq 'MSWin32');
 
 my %options = ();
 
@@ -142,6 +143,11 @@
   if ($element eq 'msms_run_summary') {
     my $msrun = $atts{'base_name'}.$atts{'raw_data'};
 
+    if ($in_windows) {
+      $msrun = lc($msrun);
+      $msrun =~ s|\\|/|g;
+    }
+
     if ($options{F} eq $msrun) {
       $foundmsrun = 1;
     }
@@ -261,6 +267,11 @@
     @files = @ARGV;
   }
 
+  if ($in_windows) {
+    $options{F} =lc($options{F});
+    $options{F} =~ s|\\|/|g;
+  }
+
   &printOpts() if $options{d};
 }
 

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[Sashimi-commit] SF.net SVN: sashimi:[9465] trunk/trans_proteomic_pipeline

[<rea...@us...>]

Revision: 9465
          http://sourceforge.net/p/sashimi/code/9465
Author:   real_procopio
Date:     2025-04-10 01:28:23 +0000 (Thu, 10 Apr 2025)
Log Message:
-----------
[ProtXMLViewer] Make Windows path comparisons case-insensitive; add [ + ] to Legend link for clarity.   [Quetzal] Point to main Quetzal for links from L-keet

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/html/js/coatl.js
    trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl

Modified: trunk/trans_proteomic_pipeline/html/js/coatl.js
===================================================================
--- trunk/trans_proteomic_pipeline/html/js/coatl.js	2025-04-09 07:38:34 UTC (rev 9464)
+++ trunk/trans_proteomic_pipeline/html/js/coatl.js	2025-04-10 01:28:23 UTC (rev 9465)
@@ -9,7 +9,7 @@
     //_Quetzal['windowName'] = 'Quetzal!';
     _Quetzal['windowName'] = '';
     _Quetzal['spectra'] = [];
-    _Quetzal['url'] = window.location.origin + '_QUETZAL_URL_';
+    _Quetzal['url'] = 'https://proteomecentral.proteomexchange.org/quetzal/';
 
     if (add_listener) {
 	window.addEventListener("message", (e) => {

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2025-04-09 07:38:34 UTC (rev 9464)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/ProtXMLViewer.pl	2025-04-10 01:28:23 UTC (rev 9465)
@@ -539,7 +539,7 @@
 
    # show legend
     print "<br/><br/><span class='annt'>";
-    print "<a style='margin-left:15px;' title='hide/show legend' href=\"javascript:toggleViz('boxpepslegend');\">&nbsp;&nbsp;&nbsp;Legend&nbsp;&nbsp;&nbsp;</a><br/>";
+    print "<a style='margin-left:15px;' title='hide/show legend' href=\"javascript:toggleViz('boxpepslegend');\">&nbsp;&nbsp;&nbsp;Legend&nbsp;[ + ]&nbsp;&nbsp;</a><br/>";
     print "<span id='boxpepslegend' style='display:none;'>";
     print "For each <b>protein</b> entry:";
     print "<li><b>Bar width</b> corresponds to peptide <b>length</b></li>";
@@ -948,9 +948,9 @@
 	my $data_dir = tpplib_perl::getDataPath();
 	my $data_url = tpplib_perl::getDataUrl();
 
-	if ($^O eq 'MSWin32') {  # work with C:/  and  c:/  etc...
-	    $data_dir = lcfirst($data_dir);
-	    $tsvfile = lcfirst($tsvfile);
+	if ($^O eq 'MSWin32') {  # work with paste-eating Windows FS
+	    $data_dir = lc($data_dir);
+	    $tsvfile = lc($tsvfile);
 	}
 	$tsvfile =~ s/$data_dir/$data_url/;
 

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[Sashimi-commit] SF.net SVN: sashimi:[9464] trunk/trans_proteomic_ pipeline

[<rea...@us...>]

Revision: 9464
          http://sourceforge.net/p/sashimi/code/9464
Author:   real_procopio
Date:     2025-04-09 07:38:34 +0000 (Wed, 09 Apr 2025)
Log Message:
-----------
[Windows installer] Skip check for old ARCH type; minor text change.   [Landing Page] Update link to Release Notes

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/html/index.html
    trunk/trans_proteomic_pipeline/installer_win32/innodependencyinstaller/scripts/products.iss
    trunk/trans_proteomic_pipeline/installer_win32/tpp.iss

Modified: trunk/trans_proteomic_pipeline/html/index.html
===================================================================
--- trunk/trans_proteomic_pipeline/html/index.html	2025-04-09 07:29:39 UTC (rev 9463)
+++ trunk/trans_proteomic_pipeline/html/index.html	2025-04-09 07:38:34 UTC (rev 9464)
@@ -40,7 +40,7 @@
 <h1 class="section">Resources</h1>
 <p>Externally available resources for TPP</p>
 <a class="tppinfobox c2" target="tppext" href="http://www.tppms.org"><h2>tppms.org</h2>Main landing page for TPP, with info and links</a>
-<a class="tppinfobox c2" target="tppext" href="http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.2.0_Release_Notes"><h2>Release Notes</h2>List of changes and updates for this TPP version</a>
+<a class="tppinfobox c2" target="tppext" href="http://tools.proteomecenter.org/wiki/index.php?title=TPP:7.3.0_Release_Notes"><h2>Release Notes</h2>List of changes and updates for this TPP version</a>
 <a class="tppinfobox c2" target="tppext" href="http://groups.google.com/group/spctools-discuss"><h2>spctools-discuss</h2>Main discussion group for TPP tools</a>
 <a class="tppinfobox c2" target="tppext" href="http://groups.google.com/group/spctools-announce"><h2>spctools-announce</h2>Group for general TPP announcements</a>
 

Modified: trunk/trans_proteomic_pipeline/installer_win32/innodependencyinstaller/scripts/products.iss
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/innodependencyinstaller/scripts/products.iss	2025-04-09 07:29:39 UTC (rev 9463)
+++ trunk/trans_proteomic_pipeline/installer_win32/innodependencyinstaller/scripts/products.iss	2025-04-09 07:38:34 UTC (rev 9464)
@@ -241,7 +241,7 @@
 
 function IsIA64: boolean;
 begin
-	Result := (not isForcedX86) and Is64BitInstallMode and (ProcessorArchitecture = paIA64);
+	Result := false;
 end;
 
 function GetString(x86, x64, ia64: String): String;

Modified: trunk/trans_proteomic_pipeline/installer_win32/tpp.iss
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/tpp.iss	2025-04-09 07:29:39 UTC (rev 9463)
+++ trunk/trans_proteomic_pipeline/installer_win32/tpp.iss	2025-04-09 07:38:34 UTC (rev 9464)
@@ -223,7 +223,7 @@
   LightMsgPage := CreateOutputMsgPage(wpWelcome,
     'TPP Installation Help', 'Getting installation assistance',
     'Welcome to the TPP installation process.  If you need assistance with ' +
-    'the installation or the TPP in general, please refer to our support and ' +
+    'the installation or TPP in general, please refer to our support and ' +
     'discussion newsgroup at:'#13#13 +
     'http://groups.google.com/group/spctools-discuss'#13#13 +
     'and the TPP Wiki at:'#13#13 +

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[Sashimi-commit] SF.net SVN: sashimi:[9463] trunk/trans_proteomic_pipeline/extern

[<rea...@us...>]

Revision: 9463
          http://sourceforge.net/p/sashimi/code/9463
Author:   real_procopio
Date:     2025-04-09 07:29:39 +0000 (Wed, 09 Apr 2025)
Log Message:
-----------
[Comet] Update to V.2025.01.1

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/Makefile

Added Paths:
-----------
    trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip

Removed Paths:
-------------
    trunk/trans_proteomic_pipeline/extern/comet_source_2024020.zip

Modified: trunk/trans_proteomic_pipeline/extern/Makefile
===================================================================
--- trunk/trans_proteomic_pipeline/extern/Makefile	2025-04-09 07:27:47 UTC (rev 9462)
+++ trunk/trans_proteomic_pipeline/extern/Makefile	2025-04-09 07:29:39 UTC (rev 9463)
@@ -414,7 +414,7 @@
 #
 # http://comet-ms.sourceforge.net/
 #
-COMET_VER := 2024020
+COMET_VER := 2025011
 COMET_ZIP := $(TPP_EXT)/comet_source_$(COMET_VER).zip
 COMET_SRC := $(BUILD_SRC)/comet_source_$(COMET_VER)
 .PHONY: comet comet-source comet-clean

Deleted: trunk/trans_proteomic_pipeline/extern/comet_source_2024020.zip
===================================================================
(Binary files differ)

Added: trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip
===================================================================
(Binary files differ)

Index: trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip
===================================================================
--- trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip	2025-04-09 07:27:47 UTC (rev 9462)
+++ trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip	2025-04-09 07:29:39 UTC (rev 9463)

Property changes on: trunk/trans_proteomic_pipeline/extern/comet_source_2025011.zip
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
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[Sashimi-commit] SF.net SVN: sashimi:[9462] trunk/trans_proteomic_ pipeline/extern/ProteoWizard/pwiz-src/VERSION

[<rea...@us...>]

Revision: 9462
          http://sourceforge.net/p/sashimi/code/9462
Author:   real_procopio
Date:     2025-04-09 07:27:47 +0000 (Wed, 09 Apr 2025)
Log Message:
-----------
[PWiz] Revert VERSION string for successful compilation in Windows...

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz-src/VERSION

Modified: trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz-src/VERSION
===================================================================
--- trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz-src/VERSION	2025-04-08 22:38:18 UTC (rev 9461)
+++ trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz-src/VERSION	2025-04-09 07:27:47 UTC (rev 9462)
@@ -1 +1 @@
-3.0.24305
\ No newline at end of file
+#define PWIZ_VERSION "3 0 24305 20f5d8c"
\ No newline at end of file

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[Sashimi-commit] SF.net SVN: sashimi:[9461] trunk/trans_proteomic_ pipeline/perl

[<rea...@us...>]

Revision: 9461
          http://sourceforge.net/p/sashimi/code/9461
Author:   real_procopio
Date:     2025-04-08 22:38:18 +0000 (Tue, 08 Apr 2025)
Log Message:
-----------
[TPP files] Replace backslashes with forward ones.   [Petunia] Point to updated Python in regis

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/cgi-bin/tpp_files.pl
    trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl

Modified: trunk/trans_proteomic_pipeline/perl/cgi-bin/tpp_files.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/cgi-bin/tpp_files.pl	2025-04-08 20:26:13 UTC (rev 9460)
+++ trunk/trans_proteomic_pipeline/perl/cgi-bin/tpp_files.pl	2025-04-08 22:38:18 UTC (rev 9461)
@@ -40,6 +40,8 @@
 my $in_windows = ($^O eq 'MSWin32');
 
 my $datadir = $cgi_query->param('datadir') || tpplib_perl::getDataPath();
+$datadir =~ s|\\|/|g;
+
 my $action  = $cgi_query->param('action')  || 'dirlist'; #default
 my $filter  = $cgi_query->param('filter')  || '';
 my $sortby  = $cgi_query->param('sort')    || 'fname_asc';

Modified: trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl	2025-04-08 20:26:13 UTC (rev 9460)
+++ trunk/trans_proteomic_pipeline/perl/tpp_gui/tpp_gui.pl	2025-04-08 22:38:18 UTC (rev 9461)
@@ -4501,7 +4501,7 @@
     # export LC_ALL=C
     # tdf2mzml.py <options>
     my $ld_lib_path = dirname($command{tdf2mzml});
-    my $py_lib_path = readconfig('pythonpath', "/proteomics/sw/python/Ubuntu20");
+    my $py_lib_path = readconfig('pythonpath', "/proteomics/sw/python/Ubuntu24");
     my @commands;
     for my $file (@file_list) {
         my $out_file = $file;

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[Sashimi-commit] SF.net SVN: sashimi:[9460] trunk/trans_proteomic_ pipeline/VERSION.mk

[<rea...@us...>]

Revision: 9460
          http://sourceforge.net/p/sashimi/code/9460
Author:   real_procopio
Date:     2025-04-08 20:26:13 +0000 (Tue, 08 Apr 2025)
Log Message:
-----------
[version] The winds of change...

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/VERSION.mk

Modified: trunk/trans_proteomic_pipeline/VERSION.mk
===================================================================
--- trunk/trans_proteomic_pipeline/VERSION.mk	2025-04-08 20:16:49 UTC (rev 9459)
+++ trunk/trans_proteomic_pipeline/VERSION.mk	2025-04-08 20:26:13 UTC (rev 9460)
@@ -6,6 +6,6 @@
 # use -a<N> for alpha, and -b<N> for beta builds, where <N> is incremented for
 # each new build.
 
-TPP_VERSION := 7.2.1dev
+TPP_VERSION := 7.3.0
 # What's the name of this TPP release
-TPP_RELEASE := Bombogenesis
+TPP_RELEASE := Trade Wind

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[Sashimi-commit] SF.net SVN: sashimi:[9459] trunk/trans_proteomic_ pipeline

[<rea...@us...>]

Revision: 9459
          http://sourceforge.net/p/sashimi/code/9459
Author:   real_procopio
Date:     2025-04-08 20:16:49 +0000 (Tue, 08 Apr 2025)
Log Message:
-----------
[Cuva/ShowXIC] Configuration tweaks for Windows

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/html/js/cuvalibre.js
    trunk/trans_proteomic_pipeline/html/js/showxic.js
    trunk/trans_proteomic_pipeline/installer_win32/tpp.iss

Modified: trunk/trans_proteomic_pipeline/html/js/cuvalibre.js
===================================================================
--- trunk/trans_proteomic_pipeline/html/js/cuvalibre.js	2025-04-08 20:11:23 UTC (rev 9458)
+++ trunk/trans_proteomic_pipeline/html/js/cuvalibre.js	2025-04-08 20:16:49 UTC (rev 9459)
@@ -69,7 +69,7 @@
     // /////
 
     document.body.style.cursor = "default";
-    window.history.replaceState(null, null, "//"+ window.location.hostname + window.location.pathname + '?file='+file);
+    window.history.replaceState(null, null, "//"+ window.location.host + window.location.pathname + '?file='+file);
 
     var chart = {};
     chart['type'] = 'scatter';

Modified: trunk/trans_proteomic_pipeline/html/js/showxic.js
===================================================================
--- trunk/trans_proteomic_pipeline/html/js/showxic.js	2025-04-08 20:11:23 UTC (rev 9458)
+++ trunk/trans_proteomic_pipeline/html/js/showxic.js	2025-04-08 20:16:49 UTC (rev 9459)
@@ -272,7 +272,7 @@
 		    url_params += "&"+param+"="+_hit_data[param];
 	    }
 	    document.title = "XIC: "+ mzfile.substring(mzfile.lastIndexOf('/') + 1);
-	    history.pushState({"mzfile":mzfile, "data":data, "hit":_hit_data}, document.title, "//"+ window.location.hostname + window.location.pathname + '?'+url_params);
+	    history.pushState({"mzfile":mzfile, "data":data, "hit":_hit_data}, document.title, "//"+ window.location.host + window.location.pathname + '?'+url_params);
 	    render_data(mzfile,data);
         })
         .catch(error => {

Modified: trunk/trans_proteomic_pipeline/installer_win32/tpp.iss
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/tpp.iss	2025-04-08 20:11:23 UTC (rev 9458)
+++ trunk/trans_proteomic_pipeline/installer_win32/tpp.iss	2025-04-08 20:16:49 UTC (rev 9459)
@@ -577,6 +577,16 @@
 		Seq2MSPage.Values[2],Seq2MSPage.Values[3],	
                 DataDirPage.Values[0] + '\params'
                 );
+    UpdateConf( ExpandConstant('{app}') + '\html\js\cuvalibre.js',
+                ExpandConstant('{app}'),
+                DataDirPage.Values[0],
+                ExpandConstant('{#TPP_BASEURL}'),
+                ExpandConstant('{#TPP_DATAURL}'),
+                TPPPortPage.Values[0],
+                Seq2MSPage.Values[0],Seq2MSPage.Values[1],
+                Seq2MSPage.Values[2],Seq2MSPage.Values[3],
+                DataDirPage.Values[0] + '\params'
+                );		
     UpdateConf( ExpandConstant('{app}') + '\html\js\plotpp.js',
                 ExpandConstant('{app}'),
                 DataDirPage.Values[0],
@@ -607,6 +617,16 @@
 		Seq2MSPage.Values[2],Seq2MSPage.Values[3],	
                 DataDirPage.Values[0] + '\params'
                 );
+    UpdateConf( ExpandConstant('{app}') + '\html\js\showxic.js',
+                ExpandConstant('{app}'),
+                DataDirPage.Values[0],
+                ExpandConstant('{#TPP_BASEURL}'),
+                ExpandConstant('{#TPP_DATAURL}'),
+                TPPPortPage.Values[0],
+                Seq2MSPage.Values[0],Seq2MSPage.Values[1],
+                Seq2MSPage.Values[2],Seq2MSPage.Values[3],
+                DataDirPage.Values[0] + '\params'
+                );
     UpdateConf( ExpandConstant('{app}') + '\html\js\tpp.js',
                 ExpandConstant('{app}'),
                 DataDirPage.Values[0],

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[Sashimi-commit] SF.net SVN: sashimi:[9458] trunk/trans_proteomic_ pipeline

[<rea...@us...>]

Revision: 9458
          http://sourceforge.net/p/sashimi/code/9458
Author:   real_procopio
Date:     2025-04-08 20:11:23 +0000 (Tue, 08 Apr 2025)
Log Message:
-----------
[Quetzal] Remove outdated code and related config; will re-add newer version at a later date

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/conf/httpd-2.4-tpp.conf
    trunk/trans_proteomic_pipeline/conf/httpd-tpp.conf
    trunk/trans_proteomic_pipeline/html/Makefile

Removed Paths:
-------------
    trunk/trans_proteomic_pipeline/html/quetzal/

Modified: trunk/trans_proteomic_pipeline/conf/httpd-2.4-tpp.conf
===================================================================
--- trunk/trans_proteomic_pipeline/conf/httpd-2.4-tpp.conf	2025-04-02 00:05:29 UTC (rev 9457)
+++ trunk/trans_proteomic_pipeline/conf/httpd-2.4-tpp.conf	2025-04-08 20:11:23 UTC (rev 9458)
@@ -111,11 +111,6 @@
     Options Includes MultiViews
 </Directory>
 
-# Redirect TPP :: QUETZAL
-Alias /_TPP_BASEURL_/quetzal  "_INSTALL_DIR_/html/quetzal"
-<Directory "_INSTALL_DIR_/html/quetzal">
-    Options Includes MultiViews
-</Directory>
 
 # Support legacy URLs that may appear in TPP outputted files
 Alias /ISB/schema /_TPP_BASEURL_/schema

Modified: trunk/trans_proteomic_pipeline/conf/httpd-tpp.conf
===================================================================
--- trunk/trans_proteomic_pipeline/conf/httpd-tpp.conf	2025-04-02 00:05:29 UTC (rev 9457)
+++ trunk/trans_proteomic_pipeline/conf/httpd-tpp.conf	2025-04-08 20:11:23 UTC (rev 9458)
@@ -109,11 +109,6 @@
     Options Includes MultiViews
 </Directory>
 
-# Redirect TPP :: QUETZAL
-Alias /_TPP_BASEURL_/quetzal  "_INSTALL_DIR_/html/quetzal"
-<Directory "_INSTALL_DIR_/html/quetzal">
-    Options Includes MultiViews
-</Directory>
 
 # Support legacy URLs that may appear in TPP outputted files
 Alias /ISB/schema /_TPP_BASEURL_/schema

Modified: trunk/trans_proteomic_pipeline/html/Makefile
===================================================================
--- trunk/trans_proteomic_pipeline/html/Makefile	2025-04-02 00:05:29 UTC (rev 9457)
+++ trunk/trans_proteomic_pipeline/html/Makefile	2025-04-08 20:11:23 UTC (rev 9458)
@@ -31,26 +31,8 @@
 # Include the TPP configuration and default rules
 include $(or $(SRC_DIR),$(abspath ..))/common.mk
 
-INSTALL_QUETZAL := $(INSTALL_WWW)/quetzal
-
-BUILD_QUETZAL := $(BUILD_WWW)/quetzal
-
 WWW_DIR := $(SRC_DIR)/html
 
-QZL_DIR := $(WWW_DIR)/quetzal
-
-QZL_TEXT :=  $(wildcard \
-   $(QZL_DIR)/js/*.js \
-   $(QZL_DIR)/js/chartJS/* \
-   $(QZL_DIR)/css/*.css \
-   $(QZL_DIR)/*.html \
-   $(QZL_DIR)/*.json \
-   )
-
-QZL_IMAGES := $(wildcard \
-   $(QZL_DIR)/images/*.png \
-   )
-
 WWW_TEXT := $(wildcard \
    $(WWW_DIR)/*.html \
    $(WWW_DIR)/js/*.js \
@@ -69,10 +51,7 @@
 WWW_TXT := $(subst $(WWW_DIR),$(BUILD_WWW),$(WWW_TEXT)) 
 WWW_IMG := $(subst $(WWW_DIR),$(BUILD_WWW),$(WWW_IMAGES))
 
-QZL_TXT := $(subst $(QZL_DIR),$(BUILD_QUETZAL),$(QZL_TEXT)) 
-QZL_IMG := $(subst $(QZL_DIR),$(BUILD_QUETZAL),$(QZL_IMAGES))
 
-
 # -- HELP ----------------------------------------------------------------------
 #
 help ::
@@ -87,8 +66,6 @@
 	@echo "Additional information for html:"
 	@echo "  WWW_TXT = $(WWW_TXT)"
 	@echo "  WWW_IMG = $(WWW_IMG)"
-	@echo "  QZL_TXT = $(QZL_TXT)"
-	@echo "  QZL_IMG = $(QZL_IMG)"
 	@echo
 
 
@@ -98,21 +75,15 @@
 # Top level
 .PHONY: html 
 all  : html
-html : $(WWW_TXT) $(WWW_IMG) $(QZL_TXT) $(QZL_IMG) 
+html : $(WWW_TXT) $(WWW_IMG) 
 
 # Which web server templates...
 ifeq ($(SYSTEM),mingw32)
-QUETZAL_URL := /tpp/quetzal/
 # ...windows installer will fill in TPP_BASEURL and TPP_DATADIR
 $(WWW_TXT) : $(BUILD_WWW)/% : $(WWW_DIR)/% | $(MKDIR)
 	cp $< $@
 	  sed $(SED_OPT) 's#_TPP_BUILDID_#$(TPP_BUILDID)#g' $@
-	  sed $(SED_OPT) 's#_QUETZAL_URL_#$(QUETZAL_URL)#g' $@
 
-$(QZL_TXT) : $(BUILD_QUETZAL)/% : $(QZL_DIR)/% | $(MKDIR)
-	cp $< $@
-	  sed $(SED_OPT) 's#_TPP_BUILDID_#$(TPP_BUILDID)#g' $@
-
 else
 # ...replace template values with TPP config
 $(WWW_TXT) : $(BUILD_WWW)/% : $(WWW_DIR)/% | $(MKDIR)
@@ -122,15 +93,7 @@
 	  sed $(SED_OPT) 's#_TPP_DATADIR_#$(TPP_DATADIR)#g' $@
 	  sed $(SED_OPT) 's#_SEQ2MS_SOURCE_URL_#$(SEQ2MS_SOURCE_URL)#g' $@
 	  sed $(SED_OPT) 's#_SEQ2MS_DEFAULT_MODEL_#$(SEQ2MS_DEFAULT_MODEL)#g' $@
-	  sed $(SED_OPT) 's#_QUETZAL_URL_#$(QUETZAL_URL)#g' $@
 
-
-$(QZL_TXT) : $(BUILD_QUETZAL)/% : $(QZL_DIR)/% | $(MKDIR)
-	cp $< $@
-	  sed $(SED_OPT) 's#_TPP_BUILDID_#$(TPP_BUILDID)#g' $@
-	  sed $(SED_OPT) 's#_TPP_BASEURL_#$(TPP_BASEURL)#g' $@
-	  sed $(SED_OPT) 's#_TPP_DATADIR_#$(TPP_DATADIR)#g' $@
-
 endif
 
 
@@ -137,21 +100,15 @@
 $(WWW_IMG) : $(BUILD_WWW)/% : $(WWW_DIR)/% | $(MKDIR)
 	cp $< $@
 
-$(QZL_IMG) : $(BUILD_QUETZAL)/% : $(QZL_DIR)/% | $(MKDIR)
-	cp $< $@
 
-
 # -- INSTALL -------------------------------------------------------------------
 #
 
 install :: $(subst $(BUILD_WWW),$(INSTALL_WWW),$(WWW_TXT)) 
 install :: $(subst $(BUILD_WWW),$(INSTALL_WWW),$(WWW_IMG)) 
-install :: $(subst $(BUILD_QUETZAL),$(INSTALL_QUETZAL),$(QZL_TXT))
-install :: $(subst $(BUILD_QUETZAL),$(INSTALL_QUETZAL),$(QZL_IMG))
 
 
 
-
 # -- CLEAN --------------------------------------------------------------------
 #
 .PHONY: html-clean

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