1.1 --- a/.hgignore	Sat Jun 25 00:46:13 2011 +0400
     1.2 +++ b/.hgignore	Mon Jun 27 13:42:42 2011 +0400
     1.3 @@ -19,6 +19,7 @@
     1.4  
     1.5  # Temporary files from building
     1.6  allpy/data/components.cif
     1.7 +blocks3d/www/input/conservative_groups.js
     1.8  
     1.9  # Temporary files from sphinx
    1.10  docs/build

     2.1 --- a/NEWS	Sat Jun 25 00:46:13 2011 +0400
     2.2 +++ b/NEWS	Mon Jun 27 13:42:42 2011 +0400
     2.3 @@ -5,6 +5,7 @@
     2.4    * new: method allpy.base.Alignment.row_as_list(sequence)
     2.5    * new: method allpy.base.Alignment.row_as_string(sequence)
     2.6    * new: columns_as_lists() returns list of lists, each has 'column' attribute
     2.7 +  * new: javascript viewer marks conservative columns darker
     2.8  
     2.9  1.3.0 (2011-04-15)
    2.10  

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/blocks3d/www/Makefile	Mon Jun 27 13:42:42 2011 +0400
     3.3 @@ -0,0 +1,5 @@
     3.4 +
     3.5 +build:
     3.6 +	python ../../sequence_based_blocks_search/functional_groups_to_javascript.py > input/conservative_groups.js
     3.7 +	r2w
     3.8 +

     4.1 --- a/blocks3d/www/input/blocks.js	Sat Jun 25 00:46:13 2011 +0400
     4.2 +++ b/blocks3d/www/input/blocks.js	Mon Jun 27 13:42:42 2011 +0400
     4.3 @@ -41,12 +41,12 @@
     4.4  // alignment_strings[ID] = string with sequence for <pre>
     4.5  var alignment_strings = {};
     4.6  
     4.7 +var conservative_groups_dict = []; // list of dictsets of uppercased letters
     4.8  
     4.9  // useful_positions[ID][position] = block id
    4.10  // (if this element is a part of at least one block)
    4.11  var useful_positions = {};
    4.12  
    4.13 -
    4.14  var blocks_inited = false;
    4.15  
    4.16  // run application
    4.17 @@ -62,6 +62,18 @@
    4.18      var i, j, k;
    4.19      var t = '';
    4.20  
    4.21 +    for (i = 0; i < conservative_groups.length; i++)
    4.22 +    {
    4.23 +        var group = conservative_groups[i];
    4.24 +        var d = {};
    4.25 +        for (j = 0; j < group.length; j++)
    4.26 +        {
    4.27 +            var letter = group[j].toUpperCase();
    4.28 +            d[letter] = true;
    4.29 +        }
    4.30 +        conservative_groups_dict.push(d);
    4.31 +    }
    4.32 +
    4.33      var seq;
    4.34  
    4.35      // calculate max_ID_length
    4.36 @@ -81,12 +93,6 @@
    4.37      IDs_count = 0;
    4.38      $.each(fasta_dict, function(k,v) { IDs_count+=1});
    4.39  
    4.40 -    // calculate a color for each block
    4.41 -    for (i = 0; i < blocks.length; i++)
    4.42 -    {
    4.43 -        blocks[i].color = crc32_color(json(blocks[i]));
    4.44 -    }
    4.45 -
    4.46      // mark colorable positions
    4.47      useful_positions = {};
    4.48      for (ID in fasta_dict)
    4.49 @@ -106,6 +112,29 @@
    4.50          }
    4.51      }
    4.52  
    4.53 +    var is_conservative = [];
    4.54 +    for (j = 0; j < seq_length; j++)
    4.55 +    {
    4.56 +        for (i = 0; i < conservative_groups_dict.length; i++)
    4.57 +        {
    4.58 +            var inside_group = true;
    4.59 +            var group = conservative_groups_dict[i];
    4.60 +            for (ID in fasta_dict)
    4.61 +            {
    4.62 +                if (!group[fasta_dict[ID].charAt(j).toUpperCase()])
    4.63 +                {
    4.64 +                    inside_group = false;
    4.65 +                    break;
    4.66 +                }
    4.67 +            }
    4.68 +            if (inside_group)
    4.69 +            {
    4.70 +                is_conservative[j] = true;
    4.71 +                break;
    4.72 +            }
    4.73 +        }
    4.74 +    }
    4.75 +
    4.76      // pre-calculate strings for <pre>
    4.77      alignment_strings = {};
    4.78      var block_i;
    4.79 @@ -119,8 +148,10 @@
    4.80              if (block_i || block_i === 0)
    4.81              {
    4.82                  // current element is a part of block
    4.83 +                var dark = is_conservative[j] && seq.charAt(j) != '-';
    4.84 +                var color = crc32_color(json(blocks[block_i]), dark);
    4.85                  t += '<font ';
    4.86 -                t += ' style="background:' + blocks[block_i].color + '; cursor:pointer;" ' ;
    4.87 +                t += ' style="background:' + color + '; cursor:pointer;" ' ;
    4.88                  t += ' onclick=letter_click("' + ID + '",' + j + ') ' ;
    4.89                  t += '>';
    4.90              }
    4.91 @@ -146,11 +177,30 @@
    4.92          current_number = '' + current_number; // convert to string
    4.93          for (j = 0; j < legend_interval - current_number.length; j++)
    4.94          {
    4.95 -            t += '&nbsp;';
    4.96 +            t += ' ';
    4.97          }
    4.98          t += current_number;
    4.99      }
   4.100 -    t = '<pre><nobr>' + t + '</nobr></pre>';
   4.101 +    var conservative_t = '';
   4.102 +    for (i = 0; i < t.length; i++)
   4.103 +    {
   4.104 +        var dark = is_conservative[i];
   4.105 +        var bgcolor = dark ? 'black' : 'white';
   4.106 +        var fgcolor = dark ? 'white' : 'black';
   4.107 +        var l;
   4.108 +        if (t.charAt(i) == ' ')
   4.109 +        {
   4.110 +            l = '&nbsp;'
   4.111 +        }
   4.112 +        else
   4.113 +        {
   4.114 +            l = t.charAt(i);
   4.115 +        }
   4.116 +        conservative_t += '<font ';
   4.117 +        conservative_t += ' style="background:' + bgcolor + ';color:' + fgcolor + ';" ' ;
   4.118 +        conservative_t += '>' + l + '</font>';
   4.119 +    }
   4.120 +    t = '<pre><nobr>' + conservative_t + '</nobr></pre>';
   4.121      $('#legend').html(t);
   4.122  
   4.123      // run

     5.1 --- a/blocks3d/www/input/crc32_color.js	Sat Jun 25 00:46:13 2011 +0400
     5.2 +++ b/blocks3d/www/input/crc32_color.js	Mon Jun 27 13:42:42 2011 +0400
     5.3 @@ -2,9 +2,12 @@
     5.4  /**
     5.5   * returns color, corresponding to something (using crc32 value)
     5.6   *
     5.7 - * something -- string
     5.8 + * @param string something string
     5.9 + * @param bool dark Should color be dark
    5.10 + *      If dark is true, first bit of each byte from color is set to 0,
    5.11 + *      otherwise to 1
    5.12   */
    5.13 -function crc32_color(something)
    5.14 +function crc32_color(something, dark)
    5.15  {
    5.16      var crc = crc32(something);
    5.17      var rgb = []; // [r, g, b] (3 last bytes of crc32 are used)
    5.18 @@ -15,7 +18,14 @@
    5.19      // lighten
    5.20      for (j = 0; j < 3; j++)
    5.21      {
    5.22 -        rgb[j] |= 128;
    5.23 +        if (dark)
    5.24 +        {
    5.25 +            rgb[j] &= 0x7F;
    5.26 +        }
    5.27 +        else
    5.28 +        {
    5.29 +            rgb[j] |= 0x80;
    5.30 +        }
    5.31      }
    5.32      for (j = 0; j < 3; j++)
    5.33      {

     6.1 --- a/blocks3d/www/input/index.txt	Sat Jun 25 00:46:13 2011 +0400
     6.2 +++ b/blocks3d/www/input/index.txt	Mon Jun 27 13:42:42 2011 +0400
     6.3 @@ -16,7 +16,7 @@
     6.4              <div id="h1_header"><h1>Reliable blocks finding</h1></div>
     6.5          </td>
     6.6      </tr>
     6.7 -    
     6.8 +
     6.9      <tr align="left" valign="top">
    6.10          <td colspan="2">
    6.11              <div id="mainpanel">Enable Javascript!</div>
    6.12 @@ -54,6 +54,7 @@
    6.13  {include_minified;crc32_color.js}
    6.14  {include_minified;crc32.js}
    6.15  {include_minified;dechex.js}
    6.16 +{include_minified;conservative_groups.js}
    6.17  {include_minified;blocks.js}
    6.18  
    6.19  self_js_text

     7.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     7.2 +++ b/sequence_based_blocks_search/functional_groups_to_javascript.py	Mon Jun 27 13:42:42 2011 +0400
     7.3 @@ -0,0 +1,7 @@
     7.4 +import pprint
     7.5 +
     7.6 +from functional_groups import aminoacids2functional_groups
     7.7 +
     7.8 +print 'conservative_groups ='
     7.9 +pprint.pprint(list(aminoacids2functional_groups.values()))
    7.10 +