[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.