From fad16e64d6c44ea41c16b0afa7b543bfad04f5f2 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 1 Dec 2009 13:38:12 +0000
Subject: [PATCH] set bbrowser and GFF to 0-base

git-svn-id: http://biopieces.googlecode.com/svn/trunk@789 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/BBrowser/Track.pm |  8 ++++----
 code_perl/Maasha/GFF.pm            |  6 +++---
 www/index.cgi                      | 10 +++++-----
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/code_perl/Maasha/BBrowser/Track.pm b/code_perl/Maasha/BBrowser/Track.pm
index d572854..e24bde8 100644
--- a/code_perl/Maasha/BBrowser/Track.pm
+++ b/code_perl/Maasha/BBrowser/Track.pm
@@ -61,7 +61,7 @@ sub track_ruler
 
     $beg    = $cookie->{ 'NAV_START' };
     $end    = $cookie->{ 'NAV_END' };
-    $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
+    $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg + 1 );
     
     $step = 10;
 
@@ -73,8 +73,8 @@ sub track_ruler
     {
         if ( ( $i % $step ) == 0 )
         {
-            $txt = Maasha::Calc::commify( $i ) . "|"; # TODO reverse this so |123 instead of 123|
-            $x   = sprintf( "%.0f", ( $i - $beg - length $txt ) * $factor );
+            $txt = "|" . Maasha::Calc::commify( $i );
+            $x   = sprintf( "%.0f", ( ( $i - $beg ) * $factor ) + 2 );
 
             if ( $x > 0 and $x + ( $cookie->{ 'RULER_FONT_SIZE' } * length $txt ) < $cookie->{ 'IMG_WIDTH' } )
             {
@@ -213,7 +213,7 @@ sub track_feature_linear
 
     @{ $entries } = sort { $a->{ 'S_BEG' } <=> $b->{ 'S_BEG' } or $a->{ 'S_END' } <=> $b->{ 'S_END' } } @{ $entries };
 
-    $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
+    $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg + 1 );
     $y_step = 0;
     $y_max  = 0;
 
diff --git a/code_perl/Maasha/GFF.pm b/code_perl/Maasha/GFF.pm
index 407a326..6201b09 100644
--- a/code_perl/Maasha/GFF.pm
+++ b/code_perl/Maasha/GFF.pm
@@ -145,9 +145,9 @@ sub gff2biopiece
         'S_ID'   => $entry->[ seqid ],
         'SOURCE' => $entry->[ source ],
         'TYPE'   => $entry->[ type ],
-        'S_BEG'  => $entry->[ start ],
-        'S_END'  => $entry->[ end ],
-        'S_LEN'  => $entry->[ end ] - $entry->[ start ] + 1,
+        'S_BEG'  => $entry->[ start ] - 1,
+        'S_END'  => $entry->[ end ]   - 1,
+        'S_LEN'  => $entry->[ end ]   - $entry->[ start ] + 1,
         'SCORE'  => $entry->[ score ],
         'STRAND' => $entry->[ strand ],
         'PHASE'  => $entry->[ phase ],
diff --git a/www/index.cgi b/www/index.cgi
index 038d311..21d0f9e 100755
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -175,11 +175,11 @@ sub cookie_start
     if ( defined $cookie->{ 'NAV_START' } )
     {
         $cookie->{ 'NAV_START' } =~ tr/,//d;
-        $cookie->{ 'NAV_START' } = 1 if $cookie->{ 'NAV_START' } <= 0;
+        $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
     }
     else
     {
-        $cookie->{ 'NAV_START' } = 1;
+        $cookie->{ 'NAV_START' } = 0;
     }
 }
 
@@ -252,7 +252,7 @@ sub cookie_zoom
         $cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
         $cookie->{ 'NAV_END' }   = int( $cookie->{ 'NAV_END' }   - ( $dist_diff / 2 ) );
 
-        $cookie->{ 'NAV_START' } = 1     if $cookie->{ 'NAV_START' } <= 0;
+        $cookie->{ 'NAV_START' } = 0    if $cookie->{ 'NAV_START' } < 0;
         $cookie->{ 'NAV_END' }   = $max if $cookie->{ 'NAV_END' } > $max;
     }
 }
@@ -623,8 +623,8 @@ sub section_browse
     $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 ) {
-- 
2.39.5