final fixes?

svn path=/bioperl-live/branches/branch-06/; revision=1592

Bio/PrimarySeqI.pm

@@ -496,6 +496,9 @@ sub trunc{
            codon table id (optional) defaults to 1
            Final argument set to 1 means do not edit amino terminal codon
 
+         Ok. We screwed up here. The main trunk is now ahead of this with
+         a cleaner interface EB.
+
 =cut
 
 sub translate {

Bio/Seq.pm

@@ -572,8 +572,8 @@ sub add_SeqFeature {
 	   $self->throw("$feat is not a SeqFeatureI and that's what we expect...");
        }
 
-       if( $feat->can("seq") ) {
-	   $fseq = $feat->seq;
+       if( $feat->can("entire_seq") ) {
+	   $fseq = $feat->entire_seq;
 	   $aseq = $self->primary_seq;
 
 	   if( defined $aseq ) {
@@ -588,12 +588,35 @@ sub add_SeqFeature {
 		   }
 	       }
 	   } # end of if aseq
-       } # end of if the feat can seq
+       } # end of if the feat can entire_seq
 
        push(@{$self->{'_as_feat'}},$feat);
    }
 }
 
+=head2 feature_count
+
+ Title   : feature_count
+ Usage   : $seq-feature_count()
+ Function: Return the number of SeqFeatures attached to a sequence
+ Example :
+ Returns : number of SeqFeatures
+ Args    : none
+
+=cut
+
+sub feature_count {
+    my ($self) = @_;
+
+    if (defined($self-{'_as_feat'})) {
+	return ($#{$self-{'_as_feat'}} + 1);
+    } else {
+	return 0;
+    }
+}
+
+
+
 =head2 top_SeqFeatures
 
  Title   : top_SeqFeatures
@@ -738,7 +761,7 @@ sub molecule {
 =head2 add_date
 
  Title   : add_date
- Usage   : $self->add_domment($ref)
+ Usage   : $self->add_date($ref)
  Function: adds a date
  Example :
  Returns : 

Bio/SimpleAlign.pm

@@ -958,7 +958,7 @@ sub read_MSF{
    # alignment section
 
    while( <$fh> ) {
-       /^\s+(\S+)\s+(.*)$/ && do {
+       /^\s*(\S+)\s+(.*)$/ && do {
 	   $name = $1;
 	   $str = $2;
 	   if( ! exists $hash{$name} ) {
@@ -1585,7 +1585,7 @@ sub write_MSF {
     #
     # ok - heavy handed, but there you go.
     #
-    print "\n//\n";
+    print $file "\n//\n";
 
     while( $count < $length ) {
 
@@ -1621,7 +1621,7 @@ sub write_MSF {
 	    print $file "\n";
 	} # end of each sequence
 
-	print "\n\n";
+	print $file "\n\n";
 
 	$count = $tempcount;
     }				

Bio/Tools/pSW.pm

@@ -1,4 +1,3 @@
-## $Id$
 
 #
 # BioPerl module for Bio::Tools::pSW
@@ -187,8 +186,8 @@ sub pairwise_alignment{
     $self->set_memory_and_report();
     # create engine objects 
 
-    $t1  = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->str());
-    $t2  = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->str());
+    $t1  = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->seq());
+    $t2  = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->seq());
     $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext);
     if( ! defined $aln || $aln == 0 ) {
 	$self->throw("Unable to build an alignment");
@@ -203,8 +202,8 @@ sub pairwise_alignment{
 
     # we are going to need the sequences as arrays for convience
 
-    @str1 = $seq1->seq();
-    @str2 = $seq2->seq();
+    @str1 = split(//, $seq1->seq());
+    @str2 = split(//, $seq2->seq());
 
     # get out start points
 
@@ -253,17 +252,17 @@ sub pairwise_alignment{
 
     $tstr = join('',@ostr1);
     $tid = $seq1->id();
-    $out->addSeq(Bio::Seq->new( -seq=> $tstr,
-			       -start => $start1,
-			       -end   => $end1,
-			       -id=>$tid ));
+    $out->addSeq(Bio::LocatableSeq->new( -seq=> $tstr,
+					 -start => $start1,
+					 -end   => $end1,
+					 -id=>$tid ));
 
     $tstr = join('',@ostr2);
     $tid = $seq2->id();
-    $out->addSeq(Bio::Seq->new( -seq=> $tstr,
-			       -start => $start2,
-			       -end => $end2,
-			       -id=> $tid ));
+    $out->addSeq(Bio::LocatableSeq->new( -seq=> $tstr,
+					 -start => $start2,
+					 -end => $end2,
+					 -id=> $tid ));
 
     # give'm back the alignment
 
@@ -283,9 +282,9 @@ sub align_and_show {
 
     $self->set_memory_and_report();
 
-    $t1  = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->str());
+    $t1  = &Bio::Ext::Align::new_Sequence_from_strings($seq1->id(),$seq1->seq());
 
-    $t2  = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->str());
+    $t2  = &Bio::Ext::Align::new_Sequence_from_strings($seq2->id(),$seq2->seq());
     $aln = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($t1,$t2,$self->{'matrix'},-$self->gap,-$self->ext);
     if( ! defined $aln || $aln == 0 ) {
 	$self->throw("Unable to build an alignment");

Changes

@@ -1,5 +1,32 @@
 Revision history for Bioperl core modules
 
+0.6.2  
+
+   There are very few functionality changes but a large
+   number of software improvements/bug fixes across the package.
+
+   o The EMBL/GenBank parsing are improved.
+
+   o The Swissprot reading is improved. Swissprot writing
+     is disabled as it doesn't work at all. This needs to
+     wait for 0.7 release
+
+   o Old syntax calls have been replaced with more modern syntax
+
+   o Modules that did not work at all, in particular the Sim4
+     set have been removed
+
+   o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
+     have improved compliance with interface specs and documentation
+
+   o Mailing list documentation updated throughout the distribution
+
+   o Most minor bug fixes have happened.
+
+   o The scripts in /examples now work and have the modern syntax
+     rather than the deprecated syntax
+
+
 0.6.1  Sun April 2 2000
 
    o Sequences can have Sequence Features attached to them

Makefile.PL

@@ -75,7 +75,7 @@ use ExtUtils::MakeMaker;
 $do_autoload_finesse = 0;
 $NAME     = 'Bio';
 $DISTNAME = "bioperl";
-$VERSION  = "0.06.0";
+$VERSION  = "0.06.2";
 
 if( $do_autoload_finesse == 1 ) {
     fatal("Autoload finessing does not work at the moment!");