added collapsable tracks to BGB

git-svn-id: http://biopieces.googlecode.com/svn/trunk@933 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/BGB/Draw.pm b/code_perl/Maasha/BGB/Draw.pm
index 3034974119e33ac45a5a02d819ca5cac9d4801d9..7cfe938ce3ac5f814ca2bd78c050ff91fedb2ff8 100644 (file)
--- a/code_perl/Maasha/BGB/Draw.pm
+++ b/code_perl/Maasha/BGB/Draw.pm
@@ -114,6 +114,12 @@ sub draw_feature
             $cr->set_font_size( $feature->{ 'font_size' } );
             $cr->show_text( $feature->{ 'txt' } );
         }
+        elsif ( $feature->{ 'type' } eq 'track_name' )
+        {
+            $cr->move_to( $feature->{ 'x1' }, $feature->{ 'y1' } );
+            $cr->set_font_size( $feature->{ 'font_size' } );
+            $cr->show_text( $feature->{ 'txt' } );
+        }
 
         #$cr->stroke;
     }

diff --git a/code_perl/Maasha/BGB/Track.pm b/code_perl/Maasha/BGB/Track.pm
index c43f1246ef2cb1b2733095d47e3a57967acde13e..e007f68c1d8a43f86d28199161a4a090743c0faf 100644 (file)
--- a/code_perl/Maasha/BGB/Track.pm
+++ b/code_perl/Maasha/BGB/Track.pm
@@ -173,38 +173,50 @@ sub track_feature
 
     # Returns a list.
 
-    my ( $data_wig, $data_kiss, $track_name, $features );
+    my ( $data_wig, $data_kiss, $track_pretty, $track_name, $features, $color );
 
     $track_name = ( split "/", $track )[ -1 ];
-    $track_name =~ s/^\d+_//;
-    $track_name =~ s/_/ /g;
+
+    $track_pretty = $track_name;
+    $track_pretty =~ s/^\d+_//;
+    $track_pretty =~ s/_/ /g;
+
+    if ( track_hide( $cookie, $track_name ) ) {
+        $color = [ 0.6, 0.6, 0.6 ];
+    } else {
+        $color = $cookie->{ 'SEQ_COLOR' };
+    }
 
     push @{ $features }, {
-        type      => 'text',
-        txt       => $track_name,
+        type      => 'track_name',
+        track     => $track_name,
+        txt       => $track_pretty,
         font_size => $cookie->{ 'SEQ_FONT_SIZE' },
-        color     => $cookie->{ 'SEQ_COLOR' },
+        color     => $color,
         x1        => 0,
         y1        => $cookie->{ 'TRACK_OFFSET' },
     };
 
     $cookie->{ 'TRACK_OFFSET' } += 10;
 
-    if ( -f "$track/track_data.wig" )
+    if ( not track_hide( $cookie, $track_name ) )
     {
-        $data_wig = Maasha::BGB::Wiggle::wiggle_retrieve( "$track/track_data.wig", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } ); 
+        if ( -f "$track/track_data.wig" )
+        {
+            $data_wig = Maasha::BGB::Wiggle::wiggle_retrieve( "$track/track_data.wig", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } ); 
 
-        push @{ $features }, track_wiggle( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_wig );
-    }
-    elsif ( -f "$track/track_data.kiss" )
-    {
-        $data_kiss = Maasha::KISS::kiss_retrieve( "$track/track_data.kiss", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
+            push @{ $features }, track_wiggle( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_wig );
+        }
+        elsif ( -f "$track/track_data.kiss" )
+        {
+            $data_kiss = Maasha::KISS::kiss_retrieve( "$track/track_data.kiss", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
 
-        push @{ $features }, track_linear( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_kiss );
-    }
-    else
-    {
-        Maasha::Common::error( "Unknown track data type" );
+            push @{ $features }, track_linear( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_kiss );
+        }
+        else
+        {
+            Maasha::Common::error( "Unknown track data type" );
+        }
     }
 
     return wantarray ? @{ $features } : $features;
@@ -991,6 +1003,35 @@ sub max_track
 }
 
 
+sub track_hide
+{
+    # Martin A. Hansen, March 2010.
+
+    # Check cookie information to see if a given track
+    # should be hidden or not.
+
+    my ( $cookie,   # cookie hash
+         $track,    # track name
+       ) = @_;
+
+    # Returns boolean.
+
+    my ( $clade, $genome, $assembly );
+
+    $clade    = $cookie->{ 'CLADE' };
+    $genome   = $cookie->{ 'GENOME' };
+    $assembly = $cookie->{ 'ASSEMBLY' };
+
+    if ( exists $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } and
+                $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } )
+    {
+        return 1;
+    }
+
+    return 0;
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 1;

diff --git a/www/index.cgi b/www/index.cgi
index fc1390f703e13f313a979f0bd595b519f259471a..85fed675115605e54c0fb8079670cc938fd8bfaf 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -103,13 +103,13 @@ sub cookie_default
         }
     }
 
-    $cookie->{ 'SCRIPT' }          = Maasha::Common::get_scriptname();
-    $cookie->{ 'DATA_DIR' }        = "Data";
-    $cookie->{ 'SESSION_DIR' }     = "Sessions";
-    $cookie->{ 'LIST_PAGES' }      = [ qw( clade genome assembly contig browse ) ];
-    $cookie->{ 'USER' }            = $cgi->param( 'user' );
-    $cookie->{ 'PASSWORD' }        = $cgi->param( 'password' );
-    $cookie->{ 'SESSION_ID' }      = $cgi->param( 'session_id' );
+    $cookie->{ 'SCRIPT' }      = Maasha::Common::get_scriptname();
+    $cookie->{ 'DATA_DIR' }    = "Data";
+    $cookie->{ 'SESSION_DIR' } = "Sessions";
+    $cookie->{ 'LIST_PAGES' }  = [ qw( clade genome assembly contig browse ) ];
+    $cookie->{ 'USER' }        = $cgi->param( 'user' );
+    $cookie->{ 'PASSWORD' }    = $cgi->param( 'password' );
+    $cookie->{ 'SESSION_ID' }  = $cgi->param( 'session_id' );
 
     $session = session_restore( $cookie );
 
@@ -138,17 +138,19 @@ sub cookie_default
          $cookie->{ 'PAGE' } = $cgi->param( 'page' ) || 'login';
     }
 
+    $cookie->{ 'TRACK_STATUS' }    = $session->{ 'TRACK_STATUS' };
     $cookie->{ 'CLADE' }           = $cgi->param( 'clade' )       || $session->{ 'CLADE' };
     $cookie->{ 'GENOME' }          = $cgi->param( 'genome' )      || $session->{ 'GENOME' };
     $cookie->{ 'ASSEMBLY' }        = $cgi->param( 'assembly' )    || $session->{ 'ASSEMBLY' };
     $cookie->{ 'CONTIG' }          = $cgi->param( 'contig' )      || $session->{ 'CONTIG' };
     $cookie->{ 'Q_ID' }            = $cgi->param( 'q_id' )        || $session->{ 'Q_ID' };
     $cookie->{ 'NAV_START' }     ||= defined $cgi->param( 'nav_start' ) ? $cgi->param( 'nav_start' ) : $session->{ 'NAV_START' };
-    $cookie->{ 'NAV_END' }       ||= $cgi->param( 'nav_end' )     || $session->{ 'NAV_END' };
+    $cookie->{ 'NAV_END' }       ||= defined $cgi->param( 'nav_end' )   ? $cgi->param( 'nav_end' )   : $session->{ 'NAV_END' };
     $cookie->{ 'NAV_CENTER' }      = $cgi->param( 'nav_center' );
     $cookie->{ 'S_BEG' }           = $cgi->param( 's_beg' )       || $session->{ 'S_BEG' };
     $cookie->{ 'S_END' }           = $cgi->param( 's_end' )       || $session->{ 'S_END' };
     $cookie->{ 'STRAND' }          = $cgi->param( 'strand' )      || $session->{ 'STRAND' };
+    $cookie->{ 'TRACK' }           = $cgi->param( 'track' );
     $cookie->{ 'ZOOM_IN1' }        = $cgi->param( 'zoom_in1' );
     $cookie->{ 'ZOOM_IN2' }        = $cgi->param( 'zoom_in2' );
     $cookie->{ 'ZOOM_IN3' }        = $cgi->param( 'zoom_in3' );
@@ -173,7 +175,7 @@ sub cookie_default
     $cookie->{ 'SEQ_COLOR' }       = [ 0, 0, 0, ];
     $cookie->{ 'FEAT_WIDTH' }      = 5;
     $cookie->{ 'FEAT_COLOR' }      = [ 0, 0, 0 ];
-    $cookie->{ 'FEAT_MAX' }        = 5000;   # TODO: Reduntant?
+#    $cookie->{ 'FEAT_MAX' }        = 5000;   # TODO: Reduntant?
 
 #    $cookie->{ 'LIST_USER' }       = Maasha::BGB::Track::list_users();  # TODO: Redundant?
 
@@ -191,6 +193,7 @@ sub cookie_default
             cookie_zoom( $cookie );
             cookie_move( $cookie );
             cookie_center( $cookie );
+            cookie_track_status( $cookie );
         }
     }
 
@@ -280,6 +283,8 @@ sub session_store
             $new_session->{ 'STRAND' }    = $cookie->{ 'STRAND' };
         }
 
+        $new_session->{ 'TRACK_STATUS' } = $cookie->{ 'TRACK_STATUS' };
+
         Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json", $new_session );
     }
 }
@@ -495,7 +500,7 @@ sub cookie_move
 
 sub cookie_center
 {
-    # Martin A. Hansen, March 2010
+    # Martin A. Hansen, March 2010.
    
     # Adjust the cookie values for NAV_START and NAV_END based
     # on cookie CENTER value if defined.
@@ -521,6 +526,35 @@ sub cookie_center
 }
 
 
+sub cookie_track_status
+{
+    # Martin A. Hansen, March 2010.
+
+    #
+    
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $clade, $genome, $assembly, $track );
+
+    $clade    = $cookie->{ 'CLADE' };
+    $genome   = $cookie->{ 'GENOME' };
+    $assembly = $cookie->{ 'ASSEMBLY' };
+    $track    = $cookie->{ 'TRACK' };
+
+    if ( $track )
+    {
+        if ( $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } ) {
+            $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 0;
+        } else {
+            $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
+        }
+    }
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PAGES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
@@ -1148,23 +1182,68 @@ sub section_browse
         {
             next if $elem->{ 'type' } =~ /text|wiggle/;
 
-            push @img, Maasha::XHTML::area(
-                href     => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
-                                       "session_id=$cookie->{ 'SESSION_ID' }",
-                                       "user=$cookie->{ 'USER' }",
-                                       "clade=$cookie->{ 'CLADE' }",
-                                       "genome=$cookie->{ 'GENOME' }",
-                                       "assembly=$cookie->{ 'ASSEMBLY' }",
-                                       "contig=$cookie->{ 'CONTIG' }",
-                                       "s_beg=$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 }, $elem->{ y2 }",
-                title  => "$elem->{ 'title' }",
-            );
+            if ( $elem->{ 'type' } eq 'track_name' )
+            {
+                $x1 = $elem->{ 'x1' };
+                $y1 = $elem->{ 'y1' } - 10;
+                $x2 = $elem->{ 'x1' } + 6 * length $elem->{ 'txt' };
+                $y2 = $elem->{ 'y1' };
+
+                if ( Maasha::BGB::Track::track_hide( $cookie, $elem->{ 'track' } ) )
+                {
+                    push @img, Maasha::XHTML::area(
+                        href   => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+                                             "session_id=$cookie->{ 'SESSION_ID' }",
+                                             "user=$cookie->{ 'USER' }",
+                                             "clade=$cookie->{ 'CLADE' }",
+                                             "genome=$cookie->{ 'GENOME' }",
+                                             "assembly=$cookie->{ 'ASSEMBLY' }",
+                                             "contig=$cookie->{ 'CONTIG' }",
+                                             "track=$elem->{ 'track' }",
+                                  ),
+                        shape  => 'rect',
+                        coords => "$x1, $y1, $x2, $y2",
+                        title  => qq(Show track: $elem->{ 'txt' }),
+                    );
+                }
+                else
+                {
+                    push @img, Maasha::XHTML::area(
+                        href   => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+                                             "session_id=$cookie->{ 'SESSION_ID' }",
+                                             "user=$cookie->{ 'USER' }",
+                                             "clade=$cookie->{ 'CLADE' }",
+                                             "genome=$cookie->{ 'GENOME' }",
+                                             "assembly=$cookie->{ 'ASSEMBLY' }",
+                                             "contig=$cookie->{ 'CONTIG' }",
+                                             "track=$elem->{ 'track' }",
+                                  ),
+                        shape  => 'rect',
+                        coords => "$x1, $y1, $x2, $y2",
+                        title  => qq(Hide track: $elem->{ 'txt' }),
+                    );
+                }
+            }
+            else
+            {
+                push @img, Maasha::XHTML::area(
+                    href     => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
+                                           "session_id=$cookie->{ 'SESSION_ID' }",
+                                           "user=$cookie->{ 'USER' }",
+                                           "clade=$cookie->{ 'CLADE' }",
+                                           "genome=$cookie->{ 'GENOME' }",
+                                           "assembly=$cookie->{ 'ASSEMBLY' }",
+                                           "contig=$cookie->{ 'CONTIG' }",
+                                           "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 }, $elem->{ y2 }",
+                    title  => "$elem->{ 'title' }",
+                );
+            }
         }
     }