From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 18 Mar 2010 10:55:51 +0000 (+0000)
Subject: BGB cleanup
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e2400eb583950fccf90a76083026a2af3a625a48;p=biopieces.git

BGB cleanup

git-svn-id: http://biopieces.googlecode.com/svn/trunk@932 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_perl/Maasha/BGB/Track.pm b/code_perl/Maasha/BGB/Track.pm
index 2c08223..c43f124 100644
--- a/code_perl/Maasha/BGB/Track.pm
+++ b/code_perl/Maasha/BGB/Track.pm
@@ -591,52 +591,6 @@ sub path_seq
 }
 
 
-sub path_tracks
-{
-    # Martin A. Hansen, November 2009.
-    
-    # Returns a list of paths to all tracks for a specified
-    # contig as written in the cookie.
-
-    my ( $cookie,   # cookie path
-       ) = @_;
-
-    # Returns a list.
-
-    my ( $path, @tracks );
-
-    die qq(ERROR: no USER in cookie.\n)     if not $cookie->{ 'USER' };
-    die qq(ERROR: no CLADE in cookie.\n)    if not $cookie->{ 'CLADE' };
-    die qq(ERROR: no GENOME in cookie.\n)   if not $cookie->{ 'GENOME' };
-    die qq(ERROR: no ASSEMBLY in cookie.\n) if not $cookie->{ 'ASSEMBLY' };
-    die qq(ERROR: no CONTIG in cookie.\n)   if not $cookie->{ 'CONTIG' };
-
-    $path = join( "/",
-        $cookie->{ 'DATA_DIR' },
-        "Users",
-        $cookie->{ 'USER' },
-        $cookie->{ 'CLADE' },
-        $cookie->{ 'GENOME' },
-        $cookie->{ 'ASSEMBLY' },
-        $cookie->{ 'CONTIG' },
-        "Tracks",
-    );
-
-    if ( -d $path )
-    {
-        @tracks = Maasha::Filesys::ls_dirs( $path );
-
-        @tracks = grep { $_ !~ /\/\.\.?$/ } @tracks;
-
-        return wantarray ? @tracks : \@tracks;
-    }
-    else
-    {
-        return wantarray ? () : [];
-    }
-}
-
-
 sub search_tracks
 {
     # Martin A. Hansen, December 2009.
@@ -667,7 +621,7 @@ sub search_tracks
     {
         $cookie->{ 'CONTIG' } = $contig;
 
-        push @tracks, path_tracks( $cookie );
+        push @tracks, list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
     }
 
     foreach $track ( @tracks )
@@ -1074,7 +1028,7 @@ sub search_tracks_nc
     {
         $cookie->{ 'CONTIG' } = $contig;
 
-        push @tracks, path_tracks( $cookie );
+        push @tracks, list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
     }
 
     foreach $track ( @tracks )
diff --git a/www/index.cgi b/www/index.cgi
index 9d68897..fc1390f 100755
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -1075,29 +1075,29 @@ sub section_browse
 
     # Returns a list.
 
-    my ( @tracks, $i, @features, $feat, $elem, $surface, $cr, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
+    my ( @track_list, $i, @tracks, $track, $elem, $surface, $cr, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
 
-    push @features, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
-    push @features, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+    push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+    push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
 
-    @tracks = Maasha::BGB::Track::path_tracks( $cookie );
+    @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
 
-    for ( $i = 0; $i < @tracks; $i++ )
+    for ( $i = 0; $i < @track_list; $i++ )
     {
         $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
 
-        push @features, [ Maasha::BGB::Track::track_feature( $tracks[ $i ], $cookie ) ];
+        push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $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->rectangle( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
+    $cr->set_source_rgb( 1, 1, 1 );
     $cr->fill;
 
-    foreach $feat ( @features ) {
-        Maasha::BGB::Draw::draw_feature( $cr, $feat ) if $feat;
+    foreach $track ( @tracks ) {
+        Maasha::BGB::Draw::draw_feature( $cr, $track ) if $track;
     }
 
     $png_data = Maasha::BGB::Draw::base64_png( $surface );
@@ -1125,16 +1125,16 @@ sub section_browse
         $center = int( $cookie->{ 'NAV_START' } + $factor * $i );
 
         push @img, Maasha::XHTML::area(
-            href     => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
-                                   "session_id=$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=$cookie->{ 'NAV_END' }",
-                                   "nav_center=$center",
+            href   => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+                                 "session_id=$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=$cookie->{ 'NAV_END' }",
+                                 "nav_center=$center",
                       ),
             shape  => 'rect',
             coords => "$x1, $y1, $x2, $y2",
@@ -1142,19 +1142,11 @@ sub section_browse
         );
     }
 
-    foreach $feat ( @features )
+    foreach $track ( @tracks )
     {
-        foreach $elem ( @{ $feat } )
+        foreach $elem ( @{ $track } )
         {
-            next if $elem->{ 'type' } eq 'text';
-            next if $elem->{ 'type' } eq 'wiggle';
-
-            #$elem->{ 'strand' } = '&#43' if $elem->{ 'strand' } eq '+';
-
-            $cookie->{ 'Q_ID' }   = $elem->{ 'q_id' };
-            $cookie->{ 'S_BEG' }  = $elem->{ 's_beg' };
-            $cookie->{ 'S_END' }  = $elem->{ 's_end' };
-            $cookie->{ 'STRAND' } = $elem->{ 'strand' };
+            next if $elem->{ 'type' } =~ /text|wiggle/;
 
             push @img, Maasha::XHTML::area(
                 href     => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
@@ -1164,9 +1156,10 @@ sub section_browse
                                        "genome=$cookie->{ 'GENOME' }",
                                        "assembly=$cookie->{ 'ASSEMBLY' }",
                                        "contig=$cookie->{ 'CONTIG' }",
-                                       "s_beg=$cookie->{ 'S_BEG' }",
-                                       "s_end=$cookie->{ 'S_END' }",
-                                       "strand=$cookie->{ 'STRAND' }",
+                                       "s_beg=$elem->{ 's_beg' }",
+                                       "s_end=$elem->{ 's_end' }",
+                                       "strand=$elem->{ 'strand' }",
+                                       "q_id=$elem->{ 'q_id' }",
                           ),
                 shape  => 'rect',
                 coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",