implemented search function in bbrowser

git-svn-id: http://biopieces.googlecode.com/svn/trunk@792 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/BBrowser/Track.pm b/code_perl/Maasha/BBrowser/Track.pm
index e24bde81c14bd9076864bb3d4b1fd5d203d5bdbb..c43ca5f524eb5639b451940a61cd1ae8daf1b114 100644 (file)
--- a/code_perl/Maasha/BBrowser/Track.pm
+++ b/code_perl/Maasha/BBrowser/Track.pm
@@ -35,6 +35,7 @@ use Maasha::Common;
 use Maasha::Calc;
 use Maasha::Filesys;
 use Maasha::KISS;
+use Maasha::Biopieces;
 use Maasha::Seq;
 
 use vars qw( @ISA @EXPORT );
@@ -527,6 +528,56 @@ sub path_tracks
     }
 }
 
+
+sub search_tracks
+{
+    # Martin A. Hansen, December 2009.
+
+    # Uses grep to search all tracks in all contigs
+    # for a given pattern and return a list of KISS entries.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( $contig, @tracks, $track, $file, $line, $out_file, $fh, $entry, @entries );
+
+    foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
+    {
+        $cookie->{ 'CONTIG' } = $contig;
+
+        push @tracks, path_tracks( $cookie );
+    }
+
+    foreach $track ( @tracks )
+    {
+        $file = "$track/track_data.kiss";
+      
+        if ( -f $file )
+        {
+            $fh = Maasha::Filesys::file_read_open( $file );
+
+            while ( $line = <$fh> )
+            {
+                chomp $line;
+
+                if ( $line =~ /$cookie->{ 'SEARCH' }/i )
+                {
+                    $entry = Maasha::KISS::kiss_entry_parse( $line );
+
+                    push @entries, $entry;
+                }
+            }
+
+            close $fh;
+        }
+    }
+
+    return wantarray ? @entries : \@entries;
+}
+
+
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 1;

diff --git a/code_perl/Maasha/KISS.pm b/code_perl/Maasha/KISS.pm
index f15dc88cc55cce4207443ce7846ae57cb9f3c4fd..d0267675ddae568f772e783af21575a3b75d3211 100644 (file)
--- a/code_perl/Maasha/KISS.pm
+++ b/code_perl/Maasha/KISS.pm
@@ -103,6 +103,40 @@ sub kiss_entry_get
 }
 
 
+sub kiss_entry_parse
+{
+    # Martin A. Hansen, December 2009.
+
+    # Parses a line with a KISS entry.
+
+    my ( $line,   #  KISS line to parse
+       ) = @_;
+
+    # Returns a hash
+
+    my ( @fields, %entry );
+
+    @fields = split /\t/, $line;
+
+    Maasha::Common::error( qq(BAD kiss entry: $line) ) if not @fields == 12;
+    
+    $entry{ 'S_ID' }        = $fields[ S_ID ];
+    $entry{ 'S_BEG' }       = $fields[ S_BEG ];
+    $entry{ 'S_END' }       = $fields[ S_END ];
+    $entry{ 'Q_ID' }        = $fields[ Q_ID ];
+    $entry{ 'SCORE' }       = $fields[ SCORE ];
+    $entry{ 'STRAND' }      = $fields[ STRAND ];
+    $entry{ 'HITS' }        = $fields[ HITS ];
+    $entry{ 'ALIGN' }       = $fields[ ALIGN ];
+    $entry{ 'BLOCK_COUNT' } = $fields[ BLOCK_COUNT ];
+    $entry{ 'BLOCK_BEGS' }  = $fields[ BLOCK_BEGS ];
+    $entry{ 'BLOCK_LENS' }  = $fields[ BLOCK_LENS ];
+    $entry{ 'BLOCK_TYPE' }  = $fields[ BLOCK_TYPE ];
+
+    return wantarray ? %entry : \%entry;
+}
+
+
 sub kiss_entry_put
 {
     # Martin A. Hansen, November 2009.

diff --git a/www/bgb.css b/www/bgb.css
index c550c9f298bc5877b567cfed31ffaeddba61da2a..d0f5368522dcd15af1ab269d882a3a3bc09d7ed7 100644 (file)
--- a/www/bgb.css
+++ b/www/bgb.css
@@ -267,6 +267,10 @@ div.browse {
     display:            inline;
 }
 
+.monospace {
+    font-family:       courier;
+}
+
 
 /* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> IMAGE <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
 

diff --git a/www/index.cgi b/www/index.cgi
index 21d0f9ea7fcecaa73039b93243503d4ca9d62fdf..a8eabb311361c86350347b3b799ebc7195b37c58 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -86,6 +86,21 @@ sub cookie_default
 
     $cookie = {};
 
+    if ( $cgi->param( 'nav_search' ) )
+    {
+        if ( $cgi->param( 'nav_search' ) =~ /([0-9,]+)[ -]([0-9,]+)/ )
+        {
+            $cookie->{ 'NAV_START' } = $1;
+            $cookie->{ 'NAV_END' }   = $2;
+        }
+        else
+        {
+            $cookie->{ 'SEARCH' } = $cgi->param( 'nav_search' );
+
+            $cgi->param( 'page', 'search' );
+        }
+    }
+
     $cookie->{ 'SCRIPT' }          = Maasha::Common::get_scriptname();
     $cookie->{ 'DATA_DIR' }        = "Data";
     $cookie->{ 'LIST_PAGES' }      = [ qw( user clade genome assembly contig browse ) ];
@@ -99,8 +114,6 @@ sub cookie_default
     $cookie->{ 'S_BEG' }           = $cgi->param( 's_beg' );
     $cookie->{ 'S_END' }           = $cgi->param( 's_end' );
     $cookie->{ 'STRAND' }          = $cgi->param( 'strand' );
-    $cookie->{ 'NAV_START' }       = $cgi->param( 'nav_start' );
-    $cookie->{ 'NAV_END' }         = $cgi->param( 'nav_end' );
     $cookie->{ 'ZOOM_IN1' }        = $cgi->param( 'zoom_in1' );
     $cookie->{ 'ZOOM_IN2' }        = $cgi->param( 'zoom_in2' );
     $cookie->{ 'ZOOM_IN3' }        = $cgi->param( 'zoom_in3' );
@@ -154,7 +167,7 @@ sub cookie_default
         cookie_move( $cookie );
     }
 
-    $cookie->{ 'STRAND' } = '+' if $cookie->{ 'STRAND' } eq ' ';
+    $cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' ';   # FIXME ugly HTML fix
 
     return wantarray ? %{ $cookie } : $cookie;
 }
@@ -315,25 +328,39 @@ sub cookie_href
 
     # Returns a string.
 
-    my ( @href );
+    my ( @href_list, %href_hash, $href );
 
     while ( 1 )
     {
-        push @href, "$cookie->{ 'SCRIPT' }?page=$page";
-        push @href, "user=$cookie->{ 'USER' }"         if $cookie->{ 'USER' };
+        $href_hash{ "user" }  = $cookie->{ 'USER' }         if $cookie->{ 'USER' };
         last if $page eq 'user';
-        push @href, "clade=$cookie->{ 'CLADE' }"       if $cookie->{ 'CLADE' };
+        $href_hash{ "clade" } = $cookie->{ 'CLADE' }        if $cookie->{ 'CLADE' };
         last if $page eq 'clade';
-        push @href, "genome=$cookie->{ 'GENOME' }"     if $cookie->{ 'GENOME' };
+        $href_hash{ "genome" } = $cookie->{ 'GENOME' }      if $cookie->{ 'GENOME' };
         last if $page eq 'genome';
-        push @href, "assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
+        $href_hash{ "assembly" } = $cookie->{ 'ASSEMBLY' }  if $cookie->{ 'ASSEMBLY' };
         last if $page eq 'assembly';
-        push @href, "contig=$cookie->{ 'CONTIG' }"     if $cookie->{ 'CONTIG' };
+        $href_hash{ "contig" } = $cookie->{ 'CONTIG' }      if $cookie->{ 'CONTIG' };
         last if $page eq 'contig';
         last;
     }
 
-    return join "&", @href;
+    if ( defined $cookie->{ 'NAV_START' } and defined $cookie->{ 'NAV_END' } ) {
+        $href_hash{ "nav_search" } = "$cookie->{ 'NAV_START' }-$cookie->{ 'NAV_END' }";
+    }
+
+    $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{ "q_id" }   = $cookie->{ 'Q_ID' }   if defined $cookie->{ 'Q_ID' };
+    $href_hash{ "strand" } = $cookie->{ 'STRAND' } if defined $cookie->{ 'STRAND' };
+
+    push @href_list, "$cookie->{ 'SCRIPT' }?page=$page";
+
+    foreach $href ( keys %href_hash ) {
+        push @href_list, "$href=$href_hash{ $href }";
+    }
+
+    return join "&", @href_list;
 }
 
 
@@ -377,6 +404,8 @@ sub page
 
     if ( $cookie->{ 'PAGE' } eq 'export' ) {
         push @html, page_export( $cookie );
+    } elsif ( $cookie->{ 'PAGE' } eq 'search' ) {
+        push @html, page_search( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'browse' ) {
         push @html, page_browse( $cookie );
     } elsif ( $cookie->{ 'PAGE' } eq 'dna' ) {
@@ -409,6 +438,26 @@ sub page_export
 }
 
 
+sub page_search
+{
+    # Martin A. Hansen, December 2009.
+
+    # Renders the search page.
+
+    my ( $cookie,
+       ) = @_;
+
+    # Returns a list.
+
+    my ( @html );
+
+    push @html, section_taxonomy_table( $cookie );
+    push @html, section_search( $cookie );
+
+    return wantarray ? @html : \@html;
+}
+
+
 sub page_browse
 {
     # Martin A. Hansen, November 2009.
@@ -554,14 +603,14 @@ sub section_navigate
 
     # Returns a list.
 
-    my ( @html );
+    my ( @html, $nav_val );
+
+    $nav_val = Maasha::Calc::commify( $cookie->{ 'NAV_START' } ) . "-" . Maasha::Calc::commify( $cookie->{ 'NAV_END' } );
 
     push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
     push @html, Maasha::XHTML::table_row_simple( tr => [
-        "Start:",
-        Maasha::XHTML::text( name => "nav_start", value => Maasha::Calc::commify( $cookie->{ 'NAV_START' } ), size => 15 ),
-        "End:",
-        Maasha::XHTML::text( name => "nav_end",   value => Maasha::Calc::commify( $cookie->{ 'NAV_END' } ),   size => 15 ), 
+        "Position or search term:",
+        Maasha::XHTML::text( name => "nav_search", value => $nav_val, size => 30 ),
         Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
     ] );
     push @html, Maasha::XHTML::table_end;
@@ -652,8 +701,14 @@ sub section_browse
 
             #$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( $cookie, "export" ) . "&q_id=$elem->{ 'q_id' }&s_beg=$elem->{ 's_beg' }&s_end=$elem->{ 's_end' }&strand=$elem->{ 'strand' }",
+                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' }",
             );
@@ -708,6 +763,70 @@ sub section_export
 }
 
 
+sub section_search
+{
+    # Martin A. Hansen, November 2009.
+
+    # Returns a HTML section with export table.
+
+    my ( $cookie,   # cookie hash
+       ) = @_;
+
+    # Returns a list.
+
+    my ( $results, $result, $count, @html, $export, $browse );
+
+    $results = Maasha::BBrowser::Track::search_tracks( $cookie );
+
+    $count = scalar @{ $results };
+
+    push @html, Maasha::XHTML::h2( txt => "Search", class => 'center' );
+    push @html, Maasha::XHTML::p( txt => qq(Results for "$cookie->{ 'SEARCH' }": $count), class => 'center' );
+
+    if ( $count > 0 )
+    {
+        push @html, Maasha::XHTML::table_beg( summary => "Search table", align => 'center', cellpadding => '5px' );
+        push @html, Maasha::XHTML::table_row_simple( tr => [ qw( S_ID S_BEG S_END Q_ID SCORE STRAND HITS ALIGN BLOCK_COUNT BLOCK_BEGS BLOCK_LENS BLOCK_TYPE) ] );
+
+        foreach $result ( @{ $results } )
+        {
+            $cookie->{ 'CONTIG' }    = $result->{ 'S_ID' };
+            $cookie->{ 'NAV_START' } = $result->{ 'S_BEG' };
+            $cookie->{ 'NAV_END' }   = $result->{ 'S_END' };
+            $cookie->{ 'S_BEG' }     = $result->{ 'S_BEG' };
+            $cookie->{ 'S_END' }     = $result->{ 'S_END' };
+            $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" ) );
+
+            push @html, Maasha::XHTML::table_row_advanced(
+                tr => [ { td => $result->{ 'S_ID' } },
+                        { td => $result->{ 'S_BEG' }, align => 'right' },
+                        { td => $result->{ 'S_END' }, align => 'right' },
+                        { td => $result->{ 'Q_ID' } },
+                        { td => $result->{ 'SCORE' }, align => 'right' },
+                        { td => $result->{ 'STRAND' } },
+                        { td => $result->{ 'HITS' }, align => 'right' },
+                        { td => $result->{ 'ALIGN' } },
+                        { td => $result->{ 'BLOCK_COUNT' }, align => 'right' },
+                        { td => $result->{ 'BLOCK_BEGS' } },
+                        { td => $result->{ 'BLOCK_LENS' } },
+                        { td => $result->{ 'BLOCK_TYPE' } },
+                        { td => $browse },
+                        { td => $export },
+                ], class => "monospace"
+            );
+        }
+
+        push @html, Maasha::XHTML::table_end;
+    }
+
+    return wantarray ? @html : \@html;
+}
+
+
 sub section_dna
 {
     # Martin A. Hansen, November 2009.