JPRED-2 Current state of the SVN trank

[jpred.git] / jpred / lib / DSSP / SCOP.pm

diff --git a/jpred/lib/DSSP/SCOP.pm b/jpred/lib/DSSP/SCOP.pm
index 5975c33..a05baca 100644 (file)
--- a/jpred/lib/DSSP/SCOP.pm
+++ b/jpred/lib/DSSP/SCOP.pm
@@ -32,56 +32,61 @@ Returns the DSSP::Position objects from within the range given. These are in the
 =cut
 
 sub get_range {
-       my ($self, $defn) = @_;
-
-       $defn =~ / / and croak "get_range('$defn') has a space in it, which isn't allowed";
-       my @ranges = split /,/, $defn;
-
-       my @data;
-       for (@ranges) {
-               my @range;
-               # A:1-200 or A:
-               if (/:/) {
-                       my ($chain, $range) = split /:/, $_;
-
-                       # A:1-200
-                       if ($range =~ /([[:alnum:]]+)-([[:alnum:]]+)/) {
-                               push @data, [ $self->select_positions($chain, $1, $2) ];
-                       }
-                       # Hmmmmm.
-                       elsif ($range) {
-                               confess "You shouldn't be here";
-                       }
-                       # A:
-                       else {
-                               push @data, [ $self->get_chain_defs($chain) ];
-                       }
-               }
-               else {
-                       # 297-368
-                       if (/([[:alnum:]]+)-([[:alnum:]]+)/) {
-                               my @chains = $self->chains;
-                               if (@chains > 1) {
-                                       die "Don't know which chain to select"
-                               }
-                               my ($chain) = @chains;
-
-                               push @data, [ $self->select_positions($chain, $1, $2) ];
-                       }
-                       # -
-                       elsif (/^-$/) {
-                               for my $chain ($self->chains) {
-                                       push @data, [ $self->get_chain_defs($chain) ];
-                               }
-                       }
-                       # Otherwise we don't know what it is
-                       else {
-                               confess "Missed particular '$_'";
-                       }
-               }
-       }
-
-       return @data;
+  my ( $self, $defn ) = @_;
+
+  $defn =~ / / and croak "get_range('$defn') has a space in it, which isn't allowed";
+  my @ranges = split /,/, $defn;
+
+  my @data;
+  for (@ranges) {
+    my @range;
+
+    # A:1-200 or A:
+    if (/:/) {
+      my ( $chain, $range ) = split /:/, $_;
+
+      # A:1-200
+      if ( $range =~ /([[:alnum:]]+)-([[:alnum:]]+)/ ) {
+        push @data, [ $self->select_positions( $chain, $1, $2 ) ];
+      }
+
+      # Hmmmmm.
+      elsif ($range) {
+        confess "You shouldn't be here";
+      }
+
+      # A:
+      else {
+        push @data, [ $self->get_chain_defs($chain) ];
+      }
+    } else {
+
+      # 297-368
+      if (/([[:alnum:]]+)-([[:alnum:]]+)/) {
+        my @chains = $self->chains;
+        if ( @chains > 1 ) {
+          die "Don't know which chain to select";
+        }
+        my ($chain) = @chains;
+
+        push @data, [ $self->select_positions( $chain, $1, $2 ) ];
+      }
+
+      # -
+      elsif (/^-$/) {
+        for my $chain ( $self->chains ) {
+          push @data, [ $self->get_chain_defs($chain) ];
+        }
+      }
+
+      # Otherwise we don't know what it is
+      else {
+        confess "Missed particular '$_'";
+      }
+    }
+  }
+
+  return @data;
 }
 
 =head2 $self->select_positions($chain, $start, $end);
@@ -93,42 +98,42 @@ Passed a chain
 =cut
 
 sub select_positions {
-       my ($self, $chain, $start, $end) = @_;
-
-       confess "Not passed all arguments" if grep { not defined } $chain, $start, $end;
-       confess "Not passed a valid chain" unless grep { $_ eq $chain } $self->chains;
-       
-       my ($flag, @positions) = 0;
-       my $test = sub {
-               my ($off, $start, $end) = @_;
-               if (3 == grep { looks_like_number $_ } $off, $start, $end) {
-                       return 1 if $off >= $start and $off <= $end;
-               }
-               else {
-                       return undef;
-               }
-       };
-
-       for my $pos ($self->get_chain_defs($chain)) {
-               if ($pos->break) {
-                       push @positions, $pos if $flag;
-                       next;
-               }
-
-               my $off = $pos->off;
-               if (
-                       ($off eq $start or $test->($off, $start, $end))
-                       ..
-                       ($off eq $end or $test->($off, $start, $end))
-       #       $test($off, $start, $end) $off >= $start and $off <= $end)
-       #($off eq $start or )
-               ) {
-                       push @positions, $pos;
-                       $flag = 1;
-               }
-               else { $flag = 0 }
-       }
-       return @positions;
+  my ( $self, $chain, $start, $end ) = @_;
+
+  confess "Not passed all arguments" if grep { not defined } $chain, $start, $end;
+  confess "Not passed a valid chain" unless grep { $_ eq $chain } $self->chains;
+
+  my ( $flag, @positions ) = 0;
+  my $test = sub {
+    my ( $off, $start, $end ) = @_;
+    if ( 3 == grep { looks_like_number $_ } $off, $start, $end ) {
+      return 1 if $off >= $start and $off <= $end;
+    } else {
+      return undef;
+    }
+  };
+
+  for my $pos ( $self->get_chain_defs($chain) ) {
+    if ( $pos->break ) {
+      push @positions, $pos if $flag;
+      next;
+    }
+
+    my $off = $pos->off;
+    if (
+      ( $off eq $start or $test->( $off, $start, $end ) ) .. ( $off eq $end or $test->( $off, $start, $end ) )
+
+      #        $test($off, $start, $end) $off >= $start and $off <= $end)
+      #($off eq $start or )
+      )
+    {
+      push @positions, $pos;
+      $flag = 1;
+    } else {
+      $flag = 0;
+    }
+  }
+  return @positions;
 }
 
 1;