misc changes

git-svn-id: http://biopieces.googlecode.com/svn/trunk@760 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 44d09ae14db52bef69c0578b11900ed1f4de0193..8ccd201499f8e8039be64eb3e08d3868aa5d450d 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -153,21 +153,9 @@ sub bowtie2biopiece
 
     my ( $record, $s_id, $s_len, $hits );
 
-    # S_ID: contig00005 length=75232   numreads=13115
-
-    if ( $entry->[ 2 ] =~ /^(.+) length=(\d+)\s+numreads=(\d+)$/ )
-    {
-        $record->{ 'S_ID' }  = $1;
-        # $record->{ 'S_LEN' } = $2;
-        $record->{ 'HITS' }  = $3;
-    }
-    else
-    {
-        Maasha::Common::error( qq(BAD S_ID: "$entry->[ 2 ]") );
-    }
-
     $record->{ 'Q_ID' }       = $entry->[ 0 ];
     $record->{ 'STRAND' }     = $entry->[ 1 ];
+    $record->{ 'S_ID' }       = $entry->[ 2 ];
     $record->{ 'S_BEG' }      = $entry->[ 3 ];
     $record->{ 'SEQ' }        = $entry->[ 4 ];
     $record->{ 'SCORES' }     = $entry->[ 5 ];
@@ -179,6 +167,7 @@ sub bowtie2biopiece
     $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
     $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
 
+    $record->{ 'HITS' }       = '.';
     $record->{ 'REC_TYPE' } = "BOWTIE";
 
     return wantarray ? %{ $record } : $record; 

diff --git a/www/cgi-bin/index.cgi b/www/cgi-bin/index.cgi
index 1b327bc46eeb479037eed886f00e8d06fb08b797..01a001138e1f08e4162a35d47e93c0f043171bf3 100755 (executable)
--- a/www/cgi-bin/index.cgi
+++ b/www/cgi-bin/index.cgi
@@ -218,7 +218,7 @@ sub sec_browse
 
     map { push @img, Maasha::XHTML::area( href => "www.dmi.dk", shape => "rect", coords => "$_->{ x1 }, $_->{ y1 }, $_->{ x2 }, $_->{ y2 }", title => "$_->{ title }" ) } @{ $features };
 
-    push @img, Maasha::XHTML::map_beg();
+    push @img, Maasha::XHTML::map_end();
 
     push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
 
@@ -230,11 +230,18 @@ sub sec_browse
 
 sub nav_list_clade
 {
-    my ( $list_clade );
+    my ( @dirs, $dir, @list_clade );
 
-    $list_clade = [ qw( Eukaryote Bacillus Fish ) ];
+    @dirs = Maasha::Filesys::ls_dirs( "Data" );
 
-    return wantarray ? @{ $list_clade } : $list_clade;
+    foreach $dir ( @dirs )
+    {
+        next if $dir eq "Data/." or $dir eq "Data/..";
+
+        push @list_clade, ( split "/", $dir )[ -1 ];
+    }
+
+    return wantarray ? @list_clade : \@list_clade;
 }
 
 

diff --git a/www/cgi-bin/kiss.css b/www/cgi-bin/kiss.css
new file mode 100644 (file)
index 0000000..af21647
--- /dev/null
+++ b/www/cgi-bin/kiss.css
@@ -0,0 +1,318 @@
+/* CSS test /*
+                                                      
+/* Martin A. Hansen, July 2005 /*
+/* email: mail@maasha.dk */
+                                                      
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUGGESTED READING <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* http://www.w3.org/TR/CSS21/
+/* http://www.w3.org/TR/CSS21/propidx.html
+/* http://www.w3schools.com/css/css_reference.asp
+/* http://htmldog.com/guides/cssbeginner/        
+/* http://htmldog.com/guides/cssintermediate/    
+/* http://htmldog.com/guides/cssadvanced/        
+/*
+/*
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UNITS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* Unit    Description
+/* %   a percentage of something
+/* in  inch
+/* cm  centimeter
+/* mm  millimeter
+/* em  one em is equal to the font size of the current element
+/* ex  one ex is the x-height of a font, the x-height is usually about half the font-size
+/* pt  point (1 pt is the same as 1/72 inch)
+/* pc  pica (1 pc is the same as 12 points)
+/* px  pixels (a dot on the computer screen)
+/*
+/*
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> COLORS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* Examples (all give the same result):
+/* red
+/* rgb(255,0,0)
+/* rgb(100%,0%,0%)
+/* #ff0000
+/* #f00
+/*
+/* There are 16 valid predefined colour names:
+/* aqua
+/* black
+/* blue
+/* fuchsia
+/* gray
+/* green
+/* lime
+/* maroon,
+/* navy
+/* olive
+/* purple
+/* red,
+/* silver
+/* teal
+/* white
+/* yellow
+/*
+/* transparent is also valid
+/*
+/*
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PROPERTIES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* background-attachment
+/* background-color
+/* background-image
+/* background-position
+/* background-repeat
+/* background
+/* border-collapse
+/* border-color
+/* border-spacing
+/* border-style
+/* border-top       border-right       border-bottom       border-left
+/* border-top-color border-right-color border-bottom-color border-left-color
+/* border-top-style border-right-style border-bottom-style border-left-style
+/* border-top-width border-right-width border-bottom-width border-left-width
+/* border-width
+/* border
+/* bottom
+/* caption-side
+/* clear
+/* clip
+/* color
+/* content
+/* counter-increment
+/* counter-reset
+/* cursor
+/* direction
+/* display
+/* empty-cells
+/* float
+/* font-family
+/* font-size
+/* font-style
+/* font-variant
+/* font-weight
+/* font
+/* height
+/* left
+/* letter-spacing
+/* line-height
+/* list-style-image
+/* list-style-position
+/* list-style-type
+/* list-style
+/* margin-right margin-left
+/* margin-top margin-bottom
+/* margin
+/* max-height
+/* max-width
+/* min-height
+/* min-width
+/* orphans
+/* outline-color
+/* outline-style
+/* outline-width
+/* outline
+/* overflow
+/* padding-top padding-right padding-bottom padding-left
+/* padding
+/* page-break-after
+/* page-break-before
+/* page-break-inside
+/* position
+/* quotes
+/* right
+/* table-layout
+/* text-align
+/* text-decoration
+/* text-indent
+/* text-transform
+/* top
+/* unicode-bidi
+/* vertical-align
+/* visibility
+/* white-space
+/* widows
+/* width
+/* word-spacing
+/* z-index
+/* 
+/* 
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+ 
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTORS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* Name            Values
+/* ----            ------
+/* ascent          <number>
+/* baseline        <number>
+/* bbox            <number>, <number>, <number>, <number>
+/* cap-height      <number>
+/* centerline      <number>
+/* definition-src  <uri>
+/* descent         <number>
+/* font-family     [ <family-name> | <generic-family> ] [, [<family-name> | <generic-family> ]]
+/* font-size       all | <length> [, <length>]
+/* font-stretch    all | [ normal | ultra-condensed | extra-condensed | condensed | semi-condensed | semi-expanded | expanded | extra-expanded | ultra-expanded ] [, [ normal |
+/*                 ultra-condensed | extra-condensed | condensed | semi-condensed | semi-expanded | expanded | extra-expanded | ultra-expanded] ]
+/* font-style      all | [ normal | italic | oblique ] [, [normal | italic | oblique] ]
+/* font-variant    [normal | small-caps] [,[normal | small-caps]]
+/* font-weight     all | [normal | bold | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900] [, [normal | bold | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900]]
+/* mathline        <number>
+/* panose-1        [<integer>]{10}
+/* slope           <number>
+/* src             [ <uri> [format(<string> [, <string>]*)] | <font-face-name> ] [, <uri> [format(<string> [, <string>]*)] | <font-face-name> ]
+/* stemh           <number>
+/* stemv           <number>
+/* topline         <number>
+/* unicode-range   <urange> [, <urange>]
+/* units-per-em    <number>
+/* widths          [<urange> ]? [<number> ]+ [,[<urange> ]? <number> ]+]
+/* x-height        <number>
+/* 
+/* 
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PROPERTY & VALUE EXAMPLES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+/*
+/*
+/* color: yellow;
+/* background-color: blue;
+/* font-family: "Times New Roman", arial, helvetica, serif;
+/* font-size: 0.8em;
+/* text-decoration: none;
+/* font-style: italic;
+/* text-transform: uppercase;
+/* letter-spacing: 0.5em;
+/* word-spacing: 2em;
+/* line-height: 1.5em;
+/* text-align: center;
+/* margin: 1em;
+/* padding: 3em;
+/* border-style: dashed;
+/* border-width: 3px;
+/* border-left-width: 10px;
+/* border-right-width: 10px;
+/* border-color: red;
+/*
+/*
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DIV <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+div.navigate {
+
+}
+
+div.browse {
+    text-align:         center;
+}
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GENERIC CLASSES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+
+.bold {
+    font-weight:        bold;
+}
+
+
+.italic {
+    font-style:        italic;
+}
+
+
+.oblique {
+    font-style:         oblique;
+}
+
+
+.align_right {
+    text-align:         right;
+}
+
+
+.align_center {
+    text-align:         center;
+}
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> HEADINGS AND PARAGRAPH <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */
+
+
+h1.right {
+    text-align:         right
+}
+
+h1.center {
+    text-align:         center
+}
+
+h2.right {
+    text-align:         right
+}
+
+h2.center {
+    text-align:         center
+}
+
+h3.right {
+    text-align:         right
+}
+
+h3.center {
+    text-align:         center
+}
+
+h4.right {
+    text-align:         right
+}
+
+h4.center {
+    text-align:         center
+}
+
+h5.right {
+    text-align:         right
+}
+
+h5.center {
+    text-align:         center
+}
+
+h6.right {
+    text-align:         right
+}
+
+h6.center {
+    text-align:         center
+}
+
+p.right {
+    text-align:         right
+}
+
+p.center {
+    text-align:         center
+}
+
+
+/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */