diff variant_effect_predictor/Bio/Tools/Phylo/PAML/Result.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Phylo/PAML/Result.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,396 @@
+# Result.pm,v 1.3 2002/06/20 18:50:39 amackey Exp
+#
+# BioPerl module for Bio::Tools::Phylo::PAML::Result
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich, Aaron Mackey
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Phylo::PAML::Result - A PAML result set object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich, Aaron Mackey
+
+Email [e-mail]
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Phylo::PAML::Result;
+use vars qw(@ISA);
+use strict;
+
+
+use Bio::Root::Root;
+use Bio::AnalysisResultI;
+@ISA = qw(Bio::Root::Root Bio::AnalysisResultI);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Phylo::PAML::Result(%data);
+ Function: Builds a new Bio::Tools::Phylo::PAML::Result object
+ Returns : Bio::Tools::Phylo::PAML::Result
+ Args    : -trees => array reference of L<Bio::Tree::TreeI> objects
+           -MLmatrix => ML matrix
+           .... MORE ARGUMENTS LISTED HERE BY AARON AND JASON 
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+
+  my ($trees,$mlmat,$seqs,$ngmatrix,
+      $codonpos,$codonfreq,$version) = $self->_rearrange([qw(TREES MLMATRIX 
+						    SEQS NGMATRIX
+						    CODONPOS CODONFREQ
+						    VERSION)], @args);
+  $self->reset_seqs;
+  if( $trees ) {
+      if(ref($trees) !~ /ARRAY/i ) { 
+	  $self->warn("Must have provided a valid array reference to initialize trees");
+      } else { 
+	  foreach my $t ( @$trees ) {
+	      $self->add_tree($t);
+	  }
+      }
+  }
+  $self->{'_treeiterator'} = 0;
+
+  if( $mlmat ) {
+      if( ref($mlmat) !~ /ARRAY/i ) {
+	  $self->warn("Must have provided a valid array reference to initialize MLmatrix");
+      } else { 
+	  $self->set_MLmatrix($mlmat);
+      }
+  } 
+  if( $seqs ) { 
+      if( ref($seqs) !~ /ARRAY/i ) {
+	  $self->warn("Must have provided a valid array reference to initialize seqs");
+      } else {
+	  foreach my $s ( @$seqs ) {
+	      $self->add_seq($s);
+	  }
+      }
+  }
+  if( $ngmatrix ) {
+      if( ref($ngmatrix) !~ /ARRAY/i ) {
+	  $self->warn("Must have provided a valid array reference to initialize NGmatrix");
+      } else { 
+	  $self->set_NGmatrix($ngmatrix);
+      }
+  } 
+  
+  if( $codonfreq ) {
+      
+  
+  }
+
+  if( $codonpos ) {
+      if( ref($codonpos) !~ /ARRAY/i ) {
+	  $self->warn("Must have provided a valid array reference to initialize codonpos");
+      } else { 
+	  $self->set_codon_pos_basefreq(@$codonpos);
+      }
+  }
+
+  $self->version($version) if defined $version;
+
+  return $self;
+}
+
+=head2 next_tree
+
+ Title   : next_tree
+ Usage   : my $tree = $factory->next_tree;
+ Function: Get the next tree from the factory
+ Returns : L<Bio::Tree::TreeI>
+ Args    : none
+
+=cut
+
+sub next_tree{
+   my ($self,@args) = @_;
+   return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;
+}
+
+=head2 rewind_tree
+
+ Title   : rewind_tree_iterator
+ Usage   : $result->rewind_tree()
+ Function: Rewinds the tree iterator so that next_tree can be 
+           called again from the beginning
+ Returns : none
+ Args    : none
+
+=cut
+
+sub rewind_tree_iterator {
+    shift->{'_treeiterator'} = 0;
+}
+
+=head2 add_tree
+
+ Title   : add_tree
+ Usage   : $result->add_tree($tree);
+ Function: Adds a tree 
+ Returns : integer which is the number of trees stored
+ Args    : L<Bio::Tree::TreeI>
+
+=cut
+
+sub add_tree{
+   my ($self,$tree) = @_;
+   if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
+       push @{$self->{'_trees'}},$tree;
+   }
+   return scalar @{$self->{'_trees'}};
+}
+
+
+=head2 set_MLmatrix
+
+ Title   : set_MLmatrix
+ Usage   : $result->set_MLmatrix($mat)
+ Function: Set the ML Matrix
+ Returns : none
+ Args    : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is 
+	   lower triangle pairwise)
+
+
+=cut
+
+sub set_MLmatrix{
+   my ($self,$mat) = @_;
+   return unless ( defined $mat );
+   if( ref($mat) !~ /ARRAY/i ) {
+       $self->warn("Did not provide a valid 2D Array reference for set_MLmatrix");
+       return;
+   }
+   $self->{'_mlmatrix'} = $mat;
+}
+
+=head2 get_MLmatrix
+
+ Title   : get_MLmatrix
+ Usage   : my $mat = $result->get_MLmatrix()
+ Function: Get the ML matrix
+ Returns : 2D Array reference
+ Args    : none
+
+
+=cut
+
+sub get_MLmatrix{
+   my ($self,@args) = @_;
+   return $self->{'_mlmatrix'};
+}
+
+=head2 set_NGmatrix
+
+ Title   : set_NGmatrix
+ Usage   : $result->set_NGmatrix($mat)
+ Function: Set the Nei & Gojobori Matrix
+ Returns : none
+ Args    : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is 
+	   lower triangle pairwise)
+
+
+=cut
+
+sub set_NGmatrix{
+   my ($self,$mat) = @_;
+   return unless ( defined $mat );
+   if( ref($mat) !~ /ARRAY/i ) {
+       $self->warn("Did not provide a valid 2D Array reference for set_NGmatrix");
+       return;
+   }
+   $self->{'_ngmatrix'} = $mat;
+}
+
+=head2 get_NGmatrix
+
+ Title   : get_NGmatrix
+ Usage   : my $mat = $result->get_NGmatrix()
+ Function: Get the Nei & Gojobori matrix
+ Returns : 2D Array reference
+ Args    : none
+
+
+=cut
+
+sub get_NGmatrix{
+   my ($self,@args) = @_;
+   return $self->{'_ngmatrix'};
+}
+
+
+=head2 add_seq
+
+ Title   : add_seq
+ Usage   : $obj->add_seq($seq)
+ Function: Add a Bio::PrimarySeq to the Result
+ Returns : none
+ Args    : Bio::PrimarySeqI
+See also : L<Bio::PrimarySeqI>
+
+=cut
+
+sub add_seq{
+   my ($self,$seq) = @_;
+   if( $seq ) { 
+       unless( $seq->isa("Bio::PrimarySeqI") ) {
+	   $self->warn("Must provide a valid Bio::PrimarySeqI to add_seq");
+	   return;
+       }
+       push @{$self->{'_seqs'}},$seq;
+   }
+
+}
+
+=head2 reset_seqs
+
+ Title   : reset_seqs
+ Usage   : $result->reset_seqs
+ Function: Reset the OTU seqs stored
+ Returns : none
+ Args    : none
+
+
+=cut
+
+sub reset_seqs{
+   my ($self) = @_;
+   $self->{'_seqs'} = [];
+}
+
+=head2 get_seqs
+
+ Title   : get_seqs
+ Usage   : my @otus = $result->get_seqs
+ Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit)
+ Returns : Array of Bio::PrimarySeq
+ Args    : None
+See also : L<Bio::PrimarySeq>
+
+=cut
+
+sub get_seqs{
+   my ($self) = @_;
+   return @{$self->{'_seqs'}};
+}
+
+=head2 set_codon_pos_basefreq
+
+ Title   : set_codon_pos_basefreq
+ Usage   : $result->set_codon_pos_basefreq(@freqs)
+ Function: Set the codon position base frequencies
+ Returns : none
+ Args    : Array of length 3 where each slot has a hashref 
+           keyed on DNA base
+
+
+=cut
+
+sub set_codon_pos_basefreq {
+    my ($self,@codonpos) = @_;
+    if( scalar @codonpos != 3 ) { 
+	$self->warn("invalid array to set_codon_pos_basefreq, must be an array of length 3");
+	return;
+    }
+    foreach my $pos ( @codonpos ) { 
+	if( ref($pos) !~ /HASH/i ||
+	    ! exists $pos->{'A'} ) { 
+	    $self->warn("invalid array to set_codon_pos_basefreq, must be an array with hashreferences keyed on DNA bases, C,A,G,T");
+	}
+    }
+    $self->{'_codonposbasefreq'} = [@codonpos];
+}
+
+=head2 get_codon_pos_basefreq
+
+ Title   : get_codon_pos_basefreq
+ Usage   : my @basepos = $result->get_codon_pos_basefreq;
+ Function: Get the codon position base frequencies
+ Returns : Array of length 3 (each codon position), each 
+           slot is a hashref keyed on DNA bases, the values are
+           the frequency of the base at that position for all sequences
+ Args    : none
+ Note    : The array starts at 0 so position '1' is in position '0' 
+           of the array
+
+=cut
+
+sub get_codon_pos_basefreq{
+   my ($self) = @_;
+   return @{$self->{'_codonposbasefreq'}};
+}
+
+=head2 version
+
+ Title   : version
+ Usage   : $obj->version($newval)
+ Function: Get/Set version
+ Returns : value of version
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub version{
+   my $self = shift;
+   $self->{'_version'} = shift if @_;
+   return $self->{'_version'};
+}
+
+1;