added PDF/SVG export to BGB

git-svn-id: http://biopieces.googlecode.com/svn/trunk@935 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/BGB/Draw.pm b/code_perl/Maasha/BGB/Draw.pm
index 1a76cd5620c8a8f4a0d5dada62e7f8309dfa6466..2f0577a6ac639f95771aa263242f67f72193a09a 100644 (file)
--- a/code_perl/Maasha/BGB/Draw.pm
+++ b/code_perl/Maasha/BGB/Draw.pm
@@ -253,6 +253,100 @@ sub palette
 }   
 
 
+sub render_png
+{
+    # Martin A. Hansen, March 2010.
+
+    # Given a list of BGB tracks, render the
+    # PNG surface stream and return the base64
+    # encoded PNG data.
+
+    my ( $width,    # image width
+         $height,   # image height
+         $tracks,   # list of BGB tracks to render
+       ) = @_;
+
+    # Returns a string.
+
+    my ( $surface, $cr, $track, $png_data );
+
+    $surface = Cairo::ImageSurface->create( 'argb32', $width, $height );
+    $cr      = Cairo::Context->create( $surface );
+
+    $cr->rectangle( 0, 0, $width, $height );
+    $cr->set_source_rgb( 1, 1, 1 );
+    $cr->fill;
+
+    foreach $track ( @{ $tracks } ) {
+        draw_feature( $cr, $track ) if $track;
+    }
+
+    $png_data = base64_png( $surface );
+
+    return $png_data;
+}
+
+
+sub render_pdf_file
+{
+    # Martin A. Hansen, March 2010.
+
+    # Given a list of BGB tracks, render these and save
+    # to a PDF file.
+
+    my ( $file,     # path to PDF file
+         $width,    # image width
+         $height,   # image height
+         $tracks,   # list of BGB tracks to render
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $surface, $cr, $track );
+
+    $surface = Cairo::PdfSurface->create ( $file, $width, $height );
+    $cr      = Cairo::Context->create( $surface );
+
+    $cr->rectangle( 0, 0, $width, $height );
+    $cr->set_source_rgb( 1, 1, 1 );
+    $cr->fill;
+
+    foreach $track ( @{ $tracks } ) {
+        draw_feature( $cr, $track ) if $track;
+    }
+}
+
+
+sub render_svg_file
+{
+    # Martin A. Hansen, March 2010.
+
+    # Given a list of BGB tracks, render these and save
+    # to a SVG file.
+
+    my ( $file,     # path to PDF file
+         $width,    # image width
+         $height,   # image height
+         $tracks,   # list of BGB tracks to render
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $surface, $cr, $track );
+
+    $surface = Cairo::SvgSurface->create ( $file, $width, $height );
+    $cr      = Cairo::Context->create( $surface );
+
+    $cr->rectangle( 0, 0, $width, $height );
+    $cr->set_source_rgb( 1, 1, 1 );
+    $cr->fill;
+
+    foreach $track ( @{ $tracks } ) {
+        draw_feature( $cr, $track ) if $track;
+    }
+}
+
+
 sub file_png
 {
     # Martin A. Hansen, October 2009.

diff --git a/code_perl/Maasha/BGB/Track.pm b/code_perl/Maasha/BGB/Track.pm
index 75ba5526fcff1e0769e3d11a3783120117660654..ef99f42de27ebbca71deaaf30afa371b79d16775 100644 (file)
--- a/code_perl/Maasha/BGB/Track.pm
+++ b/code_perl/Maasha/BGB/Track.pm
@@ -78,8 +78,8 @@ sub track_grid
     {
         push @grid, {
             type       => 'grid',
-            line_width => 0.1,
-            color      => [ 0, 0, 0 ],
+            line_width => 1,
+            color      => [ 0.82, 0.89, 1 ],
             x1         => $i,
             y1         => 0,
             x2         => $i,
@@ -368,12 +368,17 @@ sub track_linear
         if ( $w >= 1 )
         {
             $x1 = sprintf( "%.0f", ( $entry->[ S_BEG ] - $beg ) * $factor );
+            $x2 = $x1 + $w;
+
+            $x1 = 0 if $x1 < 0;
+            $x2 = $cookie->{ 'IMG_WIDTH' } if $x2 > $cookie->{ 'IMG_WIDTH' };
 
             for ( $y_step = 0; $y_step < @ladder; $y_step++ ) {
                 last if $x1 >= $ladder[ $y_step ] + 1; 
             }
 
             $y1 = $cookie->{ 'TRACK_OFFSET' } + ( ( 1.1 + $cookie->{ 'FEAT_WIDTH' } ) * $y_step );
+            $y2 = $y1 + $cookie->{ 'FEAT_WIDTH' };
 
             $feature = {
                 line_width => $cookie->{ 'FEAT_WIDTH' },
@@ -385,8 +390,8 @@ sub track_linear
                 strand     => $entry->[ STRAND ],
                 x1         => $x1,
                 y1         => $y1,
-                x2         => $x1 + $w,
-                y2         => $y1 + $cookie->{ 'FEAT_WIDTH' },
+                x2         => $x2,
+                y2         => $y2,
             };
 
             if ( $entry->[ STRAND ] eq '+' or $entry->[ STRAND ] eq '-' ) {

diff --git a/code_perl/Maasha/KISS.pm b/code_perl/Maasha/KISS.pm
index be841089e82c147c78d620ee779a0d34b10dd99c..b304b025f601e1151b7774e99c3ec48bb9742028 100644 (file)
--- a/code_perl/Maasha/KISS.pm
+++ b/code_perl/Maasha/KISS.pm
@@ -108,8 +108,8 @@ sub kiss_retrieve
     # within an optional interval.
 
     my ( $file,   # path to KISS file
-         $beg,    # interval begin -  OPTIONAL
-         $end,    # interval end   -  OPTIONAL
+         $beg,    # interval begin  -  OPTIONAL
+         $end,    # interval end    -  OPTIONAL
        ) = @_;
 
     # Returns a list.
@@ -123,9 +123,8 @@ sub kiss_retrieve
 
     while ( $entry = kiss_entry_get( $fh ) )
     {
-        push @entries, $entry if $entry->[ S_END ] > $beg;
-        
         last if $entry->[ S_BEG ] > $end;
+        push @entries, $entry if $entry->[ S_END ] > $beg;
     }
 
     close $fh;

diff --git a/www/index.cgi b/www/index.cgi
index 38b1988af96addb41c9096f340b102c7874d6bc5..1dfeb539862cb92daf81e3f598a109b5366e6aab 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -247,7 +247,7 @@ sub session_store
         $new_session->{ 'TIME' }       = Maasha::Common::time_stamp();
         $new_session->{ 'PAGE' }       = $cookie->{ 'PAGE' };
 
-        if ( $cookie->{ 'PAGE' } eq 'browse' )
+        if ( $cookie->{ 'PAGE' } =~ /browse|export_pdf|export_svg/ )
         {
             $new_session->{ 'CLADE' }     = $cookie->{ 'CLADE' };
             $new_session->{ 'GENOME' }    = $cookie->{ 'GENOME' };
@@ -586,6 +586,10 @@ sub page
         push @html, page_dna( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
         push @html, page_export( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'export_pdf' ) {
+        push @html, page_export_pdf( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'export_svg' ) {
+        push @html, page_export_svg( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'clade' ) {
         push @html, page_clade( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'genome' ) {
@@ -701,6 +705,46 @@ sub page_export
 }
 
 
+sub page_export_pdf
+{
+    # Martin A. Hansen, March 2010.
+
+    # Renders the export PDF page.
+
+    my ( $cookie,
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_export_pdf( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub page_export_svg
+{
+    # Martin A. Hansen, March 2010.
+
+    # Renders the export SVG page.
+
+    my ( $cookie,
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_export_svg( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
 sub page_clade
 {
     # Martin A. Hansen, March 2010.
@@ -1081,9 +1125,9 @@ sub section_linkout
 
     # Returns a list.
 
-    my ( $link, @html );
+    my ( $link_out, $link_pdf, $link_svg, @html );
 
-    $link = Maasha::XHTML::ln(
+    $link_out = Maasha::XHTML::ln(
         txt  => 'link',
         href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
                            "clade=$cookie->{ 'CLADE' }",
@@ -1096,7 +1140,37 @@ sub section_linkout
         title  => "Static link to this view",
     );
 
-    push @html, Maasha::XHTML::p( txt => $link, class => 'center' );
+    $link_pdf = Maasha::XHTML::ln(
+        txt  => 'PDF',
+        href => join( "&", "$cookie->{ 'SCRIPT' }?page=export_pdf",
+                           "session_id=$cookie->{ 'SESSION_ID' }",
+                           "user=$cookie->{ 'USER' }",
+                           "clade=$cookie->{ 'CLADE' }",
+                           "genome=$cookie->{ 'GENOME' }",
+                           "assembly=$cookie->{ 'ASSEMBLY' }",
+                           "contig=$cookie->{ 'CONTIG' }",
+                           "nav_start=$cookie->{ 'NAV_START' }",
+                           "nav_end=$cookie->{ 'NAV_END' }",
+              ),
+        title  => "Export view in PDF",
+    );
+    
+    $link_svg = Maasha::XHTML::ln(
+        txt  => 'SVG',
+        href => join( "&", "$cookie->{ 'SCRIPT' }?page=export_svg",
+                           "session_id=$cookie->{ 'SESSION_ID' }",
+                           "user=$cookie->{ 'USER' }",
+                           "clade=$cookie->{ 'CLADE' }",
+                           "genome=$cookie->{ 'GENOME' }",
+                           "assembly=$cookie->{ 'ASSEMBLY' }",
+                           "contig=$cookie->{ 'CONTIG' }",
+                           "nav_start=$cookie->{ 'NAV_START' }",
+                           "nav_end=$cookie->{ 'NAV_END' }",
+              ),
+        title  => "Export view in SVG",
+    );
+
+    push @html, Maasha::XHTML::p( txt => "$link_out $link_pdf $link_svg", class => 'center' );
 
     return wantarray ? @html : \@html;
 }
@@ -1109,7 +1183,7 @@ sub section_browse
 
     # Returns a list.
 
-    my ( @track_list, $i, @tracks, $track, $elem, $surface, $cr, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
+    my ( @track_list, $i, @tracks, $track, $elem, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
 
     push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
     push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
@@ -1125,18 +1199,7 @@ sub section_browse
 
     unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
 
-    $surface = Cairo::ImageSurface->create( 'argb32', $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
-    $cr      = Cairo::Context->create( $surface );
-
-    $cr->rectangle( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
-    $cr->set_source_rgb( 1, 1, 1 );
-    $cr->fill;
-
-    foreach $track ( @tracks ) {
-        Maasha::BGB::Draw::draw_feature( $cr, $track ) if $track;
-    }
-
-    $png_data = Maasha::BGB::Draw::base64_png( $surface );
+    $png_data = Maasha::BGB::Draw::render_png( $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
 
     push @img, Maasha::XHTML::img(
         src    => "data:image/png;base64,$png_data",
@@ -1299,6 +1362,80 @@ sub section_export
 }
 
 
+sub section_export_pdf
+{
+    # Martin A. Hansen, March 2010.
+
+    # Returns a HTML section with export table.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @tracks, @track_list, $i, $file, @html );
+
+    push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+    push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+
+    @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
+
+    for ( $i = 0; $i < @track_list; $i++ )
+    {
+        $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
+
+        push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $cookie ) ];
+    }
+
+    unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
+
+    $file = "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/BGB_export.pdf";
+
+    Maasha::BGB::Draw::render_pdf_file( $file, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
+
+    push @html, Maasha::XHTML::p( txt => Maasha::XHTML::ln( txt => "BGB_export.pdf", href => $file ), class => 'center' );
+
+    return wantarray ? @html : \@html;
+}
+
+
+sub section_export_svg
+{
+    # Martin A. Hansen, March 2010.
+
+    # Export view in SVG format.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @tracks, @track_list, $i, $file, @html );
+
+    push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+    push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+
+    @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
+
+    for ( $i = 0; $i < @track_list; $i++ )
+    {
+        $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
+
+        push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $cookie ) ];
+    }
+
+    unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
+
+    $file = "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/BGB_export.svg";
+
+    Maasha::BGB::Draw::render_svg_file( $file, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
+
+    push @html, Maasha::XHTML::p( txt => Maasha::XHTML::ln( txt => "BGB_export.svg", href => $file ), class => 'center' );
+
+    return wantarray ? @html : \@html;
+}
+
+
 sub section_search
 {
     # Martin A. Hansen, November 2009.