[Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Domcut.pm, 1.15, 1.16 GOR4.pm, 1.14, 1.15 HNN.pm, 1.14, 1.15 Mitoprot.pm, 1.10, 1.11 NetPhos.pm, 1.14, 1.15

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:20 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Tools/Analysis/Protein

Modified Files:
	Domcut.pm GOR4.pm HNN.pm Mitoprot.pm NetPhos.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: HNN.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/HNN.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** HNN.pm	17 Nov 2006 15:28:28 -0000	1.14
--- HNN.pm	14 Jun 2007 14:16:17 -0000	1.15
***************
*** 20,24 ****
    #get a Bio::Seq or Bio::PrimarySeq
    use Bio::PrimarySeq;
!   my $seq = new Bio::PrimarySeq
        (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
         -primary_id=>'test'); # a Bio::PrimarySeqI object
--- 20,24 ----
    #get a Bio::Seq or Bio::PrimarySeq
    use Bio::PrimarySeq;
!   my $seq = Bio::PrimarySeq->new
        (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
         -primary_id=>'test'); # a Bio::PrimarySeqI object

Index: NetPhos.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/NetPhos.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** NetPhos.pm	26 Sep 2006 22:03:18 -0000	1.14
--- NetPhos.pm	14 Jun 2007 14:16:17 -0000	1.15
***************
*** 256,260 ****
      my $seq_fasta;
      my $stringfh = new IO::String($seq_fasta);
!     my $seqout = new Bio::SeqIO(-fh => $stringfh,
                                  -format => 'fasta');
      $seqout->write_seq($self->seq);
--- 256,260 ----
      my $seq_fasta;
      my $stringfh = new IO::String($seq_fasta);
!     my $seqout = Bio::SeqIO->new(-fh => $stringfh,
                                  -format => 'fasta');
      $seqout->write_seq($self->seq);

Index: Domcut.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/Domcut.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Domcut.pm	26 Sep 2006 22:03:18 -0000	1.15
--- Domcut.pm	14 Jun 2007 14:16:17 -0000	1.16
***************
*** 18,22 ****
    #get a  Bio::PrimarySeq
    use Bio::PrimarySeq;
!   my $seq = new Bio::PrimarySeq
       (-seq=>'IKLCVNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object
--- 18,22 ----
    #get a  Bio::PrimarySeq
    use Bio::PrimarySeq;
!   my $seq = Bio::PrimarySeq->new
       (-seq=>'IKLCVNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object

Index: Mitoprot.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/Mitoprot.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Mitoprot.pm	27 Sep 2006 15:13:57 -0000	1.10
--- Mitoprot.pm	14 Jun 2007 14:16:17 -0000	1.11
***************
*** 17,21 ****
  
    use Bio::PrimarySeq;
!   my $seq = new Bio::PrimarySeq
      (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object
--- 17,21 ----
  
    use Bio::PrimarySeq;
!   my $seq = Bio::PrimarySeq->new
      (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object

Index: GOR4.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/GOR4.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** GOR4.pm	17 Nov 2006 15:14:55 -0000	1.14
--- GOR4.pm	14 Jun 2007 14:16:17 -0000	1.15
***************
*** 19,23 ****
    #get a Bio::Seq or Bio::PrimarySeq
    use Bio::PrimarySeq;
!   $seq = new Bio::PrimarySeq
      (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object
--- 19,23 ----
    #get a Bio::Seq or Bio::PrimarySeq
    use Bio::PrimarySeq;
!   $seq = Bio::PrimarySeq->new
      (-seq=>'IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL',
       -primary_id=>'test'); # a Bio::PrimarySeqI object



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