[Bioperl-guts-l] bioperl commit

Jason Stajich jason at pub.open-bio.org
Tue Jun 22 14:11:06 EDT 2004


jason
Tue Jun 22 14:11:05 EDT 2004
Update of /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer
In directory pub.open-bio.org:/tmp/cvs-serv21161

Modified Files:
	HTMLResultWriter.pm TextResultWriter.pm 
Log Message:
deal with HMMER output okay

bioperl-live/Bio/SearchIO/Writer HTMLResultWriter.pm,1.32,1.33 TextResultWriter.pm,1.13,1.14
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.pm	2003/11/25 17:52:36	1.32
+++ /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/HTMLResultWriter.pm	2004/06/22 18:11:05	1.33
@@ -225,7 +225,8 @@
 	     $alg =~ /(WABA|EXONERATE)/i ) {
 	$qtype      = $dbtype = '';
 	$type = $dbseqtype  = 'NUCLEOTIDE';
-    } elsif( $alg =~ /(FAST|BLAST)P/  || $alg =~ /SSEARCH/i ) {
+    } elsif( $alg =~ /(FAST|BLAST)P/  || 
+	     $alg =~ /SSEARCH|HMM(PFAM|SEARCH)/i ) {
 	$qtype      = $dbtype = '';
 	$type = $dbseqtype  = 'PROTEIN';
     } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) {

===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/TextResultWriter.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/TextResultWriter.pm	2003/11/25 17:52:36	1.13
+++ /home/repository/bioperl/bioperl-live/Bio/SearchIO/Writer/TextResultWriter.pm	2004/06/22 18:11:05	1.14
@@ -217,7 +217,8 @@
 	     $alg =~ /(WABA|EXONERATE)/i ) {
 	$qtype      = $dbtype = '';
 	$type = $dbseqtype  = 'NUCLEOTIDE';
-    } elsif( $alg =~ /(FAST|BLAST)P/  || $alg =~ /SSEARCH/i ) {
+    } elsif( $alg =~ /(FAST|BLAST)P/  || 
+	     $alg =~ /SSEARCH|(HMM|SEARCH|PFAM)/i ) {
 	$qtype      = $dbtype = '';
 	$type = $dbseqtype  = 'PROTEIN';
     } elsif( $alg =~ /(FAST|BLAST)[XY]/i ) {



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