Remove unused code

bioperl · Dec 6, 2011 · ff5b2ec · ff5b2ec
1 parent b047cb4
commit ff5b2ec
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Showing 2 changed files with 48 additions and 13 deletions.
diff --git a/lib/Bio/Tools/Run/Phylo/FastTree.pm b/lib/Bio/Tools/Run/Phylo/FastTree.pm
@@ -224,7 +224,6 @@ sub _run {
 
     # If -nt is not set check the alphabet of the input
     $self->_alphabet($file) if ( ! $self->nt );
-    $self->nt(1) if ( $self->_alphabet eq 'dna' );
 
     my $exe       = $self->executable || return;
     my $param_str = $self->arguments . " " . $self->_setparams($file);
@@ -275,11 +274,15 @@ sub _write_alignfile {
 
     my $out = Bio::AlignIO->new(
         -file   => ">$tempfile",
-        -format => 'fasta'
+        -format => 'phylip'
     );
     $out->write_aln($align);
     $out->close();
+    undef($out);
     close($tfh);
+    undef($tfh);
+
+    die "Alignment file $tempfile was not created" if ( ! -e $tempfile );
 
     $tempfile;
 }
@@ -288,24 +291,32 @@ sub _write_alignfile {
 
  Title   : _alphabet
  Usage   : my $alphabet = $self->_alphabet;
- Function: Get the alphabet of the input
+ Function: Get the alphabet of the input alignment, defaults to 'dna'
  Returns : 'dna' or 'protein'
- Args    : 
+ Args    : Alignment file
 
 =cut
 
 sub _alphabet {
     my ($self,$file) = @_;
+
+    if ( $file ) {
+	if ( -e $file ) {
+	    my $in = Bio::AlignIO->new(-file => $file);
+	    my $aln = $in->next_aln;
+	    # arbitrary, the first one
+	    my $seq = $aln->get_seq_by_pos(1);
+	    my $alphabet = $seq->alphabet;
+	    $self->{_alphabet} = $alphabet;
+
+	    $self->nt(1) if ( $alphabet eq 'dna' );
+	} else {
+	    die "File $file can not be found";
+	}
+    }
 
-    return $self->{_alphabet} if $self->{_alphabet};
-
-    my $in = Bio::AlignIO->new(-file => $file);
-    my $aln = $in->next_aln;
-    # arbitrary, the first one
-    my $seq = $aln->get_seq_by_pos(1);
-    $self->{_alphabet} = $seq->alphabet;
-
-    $self->{'_alphabet'};
+    # default is 'dna'    
+    return $self->{'_alphabet'} || 'dna';
 }
 
 =head2  _setparams

diff --git a/lib/Bio/Tools/Run/Phylo/Phyml.pm b/lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -920,6 +920,29 @@ sub bootstrap {
     return $self->{_bootstrap};
 }
 
+=head2 command
+
+ Title   : command
+ Usage   : $factory->command(...);
+ Function: 
+ Returns : string
+ Args    : None to get, integer to set. 
+
+=cut
+
+sub command {
+    my ( $self, $value ) = @_;
+    if ( defined($value) ) {
+        if ($value =~ /$PROGRAM_NAME/ ) {
+            $self->{_command} = $value;
+        }
+        else {
+            $self->throw("$value is not a $PROGRAM_NAME command");
+        }
+    }
+    return $self->{_command} || '';
+}
+
 =head2 Internal methods
 
 These methods are private and should not be called outside this class.
@@ -942,6 +965,7 @@ sub _run {
         $output_stat_file = '_phyml_stat.txt';
     }
 
+    $self->command($command);
     $self->debug("Phyml command = $command\n");
     `$command`;