migrated final plotters

[biopieces.git] / code_perl / Maasha / Plot.pm

diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm
index 88992c5e017c06b8f7d03e01ebc6b5e62bf327c7..cac8536aa5be44c479e5d3040bcf70d0b509b0c0 100644 (file)
--- a/code_perl/Maasha/Plot.pm
+++ b/code_perl/Maasha/Plot.pm
@@ -313,113 +313,6 @@ sub histogram_chrdist
 }
 
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DOTPLOT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub dotplot_matches
-{
-    # Martin A. Hansen, August 2007.
-
-    # Generates a dotplot from a list of matches using Gnuplot.
-
-    my ( $matches,   # list of hashrefs.
-         $options,   # options hash
-         $tmp_dir,   # temporary directory
-       ) = @_;
-
-    # Returns list.
-
-    my ( $forward_file, $backward_file, $pid, $fh_forward, $fh_backward,
-         $fh_in, $fh_out, $cmd, $match, $line, @lines, $q_max, $s_max );
-
-    $tmp_dir ||= $ENV{ 'BP_TMP' };
-
-    $forward_file  = "$tmp_dir/match_f.tab";
-    $backward_file = "$tmp_dir/match_r.tab";
-
-    $fh_forward  = Maasha::Filesys::file_write_open( $forward_file );
-    $fh_backward = Maasha::Filesys::file_write_open( $backward_file );
-
-    $q_max = 0;
-    $s_max = 0;
-
-    foreach $match ( @{ $matches } )
-    {
-        if ( $match->{ "DIR" } =~ /^f/ )
-        {
-            print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
-            print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";
-            print $fh_forward "\n\n";
-        }
-        else
-        {
-            print $fh_backward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_END" } + 1 ), "\n";
-            print $fh_backward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
-            print $fh_backward "\n\n";
-        }
-
-        $q_max = $match->{ "Q_END" } if $match->{ "Q_END" } > $q_max;
-        $s_max = $match->{ "S_END" } if $match->{ "S_END" } > $s_max;
-    }
-
-    $q_max++;
-    $s_max++;
-
-    close $fh_forward;
-    close $fh_backward;
-
-    $options->{ "terminal" } ||= "dumb";
-
-    $cmd  = "gnuplot";
-
-    $pid = open2( $fh_out, $fh_in, $cmd );
-    
-    print $fh_in "set terminal $options->{ 'terminal' }\n";
-    print $fh_in "set xrange [1:$q_max]\n";
-    print $fh_in "set yrange [1:$s_max]\n";
-    print $fh_in "set title \"$options->{ 'title' }\"\n"   if $options->{ "title" };
-    print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" };
-    print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" };
-    print $fh_in "unset key\n";
-
-    if ( $options->{ "terminal" } ne "dumb" )
-    {
-        print $fh_in "set style line 1 linetype 1 linecolor rgb \"green\" linewidth 2 pointtype 6 pointsize default\n";
-        print $fh_in "set style line 2 linetype 1 linecolor rgb \"red\" linewidth 2 pointtype 6 pointsize default\n";
-    }
-
-    print $fh_in "set xtics border out\n";
-    print $fh_in "set ytics border out\n";
-    print $fh_in "set grid\n";
-
-    if ( $options->{ "direction" } =~ /^b/ ) {
-        print $fh_in qq(plot "$forward_file" with lines ls 1, "$backward_file" with lines ls 2\n);
-    } elsif ( $options->{ "direction" } =~ /^f/ ) {
-        print $fh_in qq(plot "$forward_file" with lines ls 1\n);
-    } elsif ( $options->{ "direction" } =~ /^r/ ) {
-        print $fh_in qq(plot "$backward_file" with lines ls 2\n);
-    }
-
-    close $fh_in;
-
-    while ( $line = <$fh_out> )
-    {
-        chomp $line;
-
-        push @lines, $line;
-    }
-
-    close $fh_out;
-
-    waitpid $pid, 0;
-
-    unlink $forward_file;
-    unlink $backward_file;
-
-    return wantarray ? @lines : \@lines;
-}
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> KARYOGRAM <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<