BGB cleanup of hrefs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@881 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/www/index.cgi b/www/index.cgi
index 81d133c58d2c4f026aa4c88b8000668d47ece2f7..fb04e322a2da8233c588735094ab614ff2f39575 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -447,56 +447,6 @@ sub cookie_center
 }
 
 
-sub cookie_href
-{
-    # Martin A. Hansen, November 2009.
-
-    # Returns the href for a taxonomy path terminated at a given
-    # page using information stored in a cookie.
-
-    my ( $cookie,   # cookie hash
-         $page,     # page
-       ) = @_;
-
-    # Returns a string.
-
-    my ( @href_list, %href_hash, $href );
-
-    $href_hash{ "user" } = $cookie->{ 'USER' } if $cookie->{ 'USER' };
-
-    while ( 1 )
-    {
-        $href_hash{ "clade" } = $cookie->{ 'CLADE' }        if $cookie->{ 'CLADE' };
-        last if $page eq 'clade';
-        $href_hash{ "genome" } = $cookie->{ 'GENOME' }      if $cookie->{ 'GENOME' };
-        last if $page eq 'genome';
-        $href_hash{ "assembly" } = $cookie->{ 'ASSEMBLY' }  if $cookie->{ 'ASSEMBLY' };
-        last if $page eq 'assembly';
-        $href_hash{ "contig" } = $cookie->{ 'CONTIG' }      if $cookie->{ 'CONTIG' };
-        last if $page eq 'contig';
-        last;
-    }
-
-    if ( defined $cookie->{ 'NAV_START' } and defined $cookie->{ 'NAV_END' } and $page !~ /clade|genome|assembly|contig|browse/ ) {
-        $href_hash{ "nav_search" } = "$cookie->{ 'NAV_START' }-$cookie->{ 'NAV_END' }";
-    }
-
-    $href_hash{ "q_id" }       = URI::Escape::uri_escape( $cookie->{ 'Q_ID' } ) if defined $cookie->{ 'Q_ID' };
-    $href_hash{ "s_beg" }      = $cookie->{ 'S_BEG' }      if defined $cookie->{ 'S_BEG' };
-    $href_hash{ "s_end" }      = $cookie->{ 'S_END' }      if defined $cookie->{ 'S_END' };
-    $href_hash{ "strand" }     = $cookie->{ 'STRAND' }     if defined $cookie->{ 'STRAND' };
-    $href_hash{ "session_id" } = $cookie->{ 'SESSION_ID' } if defined $cookie->{ 'SESSION_ID' };
-
-    push @href_list, "$cookie->{ 'SCRIPT' }?page=$page";
-
-    foreach $href ( keys %href_hash ) {
-        push @href_list, "$href=$href_hash{ $href }";
-    }
-
-    return join "&", @href_list;
-}
-
-
 sub cookie_page_next
 {
     # Martin A. Hansen, November 2009.
@@ -732,7 +682,13 @@ sub section_taxonomy_table
     {
         last if $page eq $cookie->{ 'PAGE' } or $page eq 'browse';
 
-        $href = cookie_href( $cookie, $page );
+        $href  = "$cookie->{ 'SCRIPT' }?page=$page";
+        $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+        $href .= "&user=$cookie->{ 'USER' }";
+        $href .= "&clade=$cookie->{ 'CLADE' }"       if $page !~ /clade/;
+        $href .= "&genome=$cookie->{ 'GENOME' }"     if $page !~ /clade|genome/;
+        $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $page !~ /clade|genome|assembly/;
+        $href .= "&contig=$cookie->{ 'CONTIG' }"     if $page !~ /clade|genome|assembly|contig/;
 
         $txt = ": $cookie->{ uc $page }";
 
@@ -772,7 +728,13 @@ sub section_taxonomy_select
     {
         $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
 
-        $href = cookie_href( $cookie, cookie_page_next( $cookie ) );
+        $href  = "$cookie->{ 'SCRIPT' }?page=" . cookie_page_next( $cookie );
+        $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+        $href .= "&user=$cookie->{ 'USER' }";
+        $href .= "&clade=$cookie->{ 'CLADE' }";
+        $href .= "&genome=$cookie->{ 'GENOME' }"     if $cookie->{ 'GENOME' };
+        $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
+        $href .= "&contig=$cookie->{ 'CONTIG' }"     if $cookie->{ 'CONTIG' };
 
         push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
     }
@@ -882,31 +844,6 @@ sub section_browse
 
     push @img, Maasha::XHTML::map_beg( name => "browser_map", id => "browser_map" );
 
-    foreach $feat ( @features )
-    {
-        foreach $elem ( @{ $feat } )
-        {
-            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' };
-
-            push @img, Maasha::XHTML::area(
-                href   => cookie_href( $cookie, "export" ),
-                # href   => cookie_href( $cookie, "export" ) . "&q_id=$elem->{ 'q_id' }&s_beg=$elem->{ 's_beg' }&s_end=$elem->{ 's_end' }&strand=$elem->{ 'strand' }",
-                shape  => 'rect',
-                coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",
-                title  => "$elem->{ 'title' }",
-            );
-        }
-    }
-
-    $factor = $cookie->{ 'IMG_WIDTH' } / ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 );
     $factor = ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 ) / $cookie->{ 'IMG_WIDTH' };
 
     for ( $i = 0; $i < $cookie->{ 'IMG_WIDTH' }; $i += 5 )
@@ -919,7 +856,6 @@ sub section_browse
         $center = int( $cookie->{ 'NAV_START' } + $factor * $i );
 
         push @img, Maasha::XHTML::area(
-            # href   => cookie_href( $cookie, "browse" ) . "&nav_start=$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' }",
@@ -937,6 +873,39 @@ sub section_browse
         );
     }
 
+    foreach $feat ( @features )
+    {
+        foreach $elem ( @{ $feat } )
+        {
+            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' } = $elem->{ 'strand' };
+
+            push @img, Maasha::XHTML::area(
+                href     => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
+                                       "session_id=$cookie->{ 'SESSION_ID' }",
+                                       "user=$cookie->{ 'USER' }",
+                                       "clade=$cookie->{ 'CLADE' }",
+                                       "genome=$cookie->{ 'GENOME' }",
+                                       "contig=$cookie->{ 'CONTIG' }",
+                                       "assembly=$cookie->{ 'ASSEMBLY' }",
+                                       "s_beg=$cookie->{ 'S_BEG' }",
+                                       "s_end=$cookie->{ 'S_END' }",
+                                       "strand=$cookie->{ 'STRAND' }",
+                          ),
+                shape  => 'rect',
+                coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",
+                title  => "$elem->{ 'title' }",
+            );
+        }
+    }
+
     push @img, Maasha::XHTML::map_end();
 
     push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
@@ -1022,8 +991,35 @@ sub section_search
             $cookie->{ 'STRAND' }    = $result->{ 'STRAND' };
             $cookie->{ 'Q_ID' }      = $result->{ 'Q_ID' };
 
-            $browse = Maasha::XHTML::ln( txt => "browse", href => cookie_href( $cookie, "browse" ) );
-            $export = Maasha::XHTML::ln( txt => "export", href => cookie_href( $cookie, "export" ) );
+            $browse = Maasha::XHTML::ln(
+                txt  => "browse",
+                href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+                                   "session_id=$cookie->{ 'SESSION_ID' }",
+                                   "user=$cookie->{ 'USER' }",
+                                   "clade=$cookie->{ 'CLADE' }",
+                                   "genome=$cookie->{ 'GENOME' }",
+                                   "contig=$cookie->{ 'CONTIG' }",
+                                   "assembly=$cookie->{ 'ASSEMBLY' }",
+                                   "nav_start=$cookie->{ 'NAV_START' }",
+                                   "nav_end=$cookie->{ 'NAV_END' }",
+                ),
+            );
+
+
+            $export = Maasha::XHTML::ln(
+                txt  => "export",
+                href => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
+                                   "session_id=$cookie->{ 'SESSION_ID' }",
+                                   "user=$cookie->{ 'USER' }",
+                                   "clade=$cookie->{ 'CLADE' }",
+                                   "genome=$cookie->{ 'GENOME' }",
+                                   "contig=$cookie->{ 'CONTIG' }",
+                                   "assembly=$cookie->{ 'ASSEMBLY' }",
+                                   "s_beg=$cookie->{ 'S_BEG' }",
+                                   "s_end=$cookie->{ 'S_END' }",
+                                   "strand=$cookie->{ 'STRAND' }",
+                ),
+            );
 
             push @html, Maasha::XHTML::table_row_advanced(
                 tr => [ { td => $result->{ 'S_ID' } },