var alignment_strings = {};


 


+var conservative_groups_dict = []; // list of dictsets of uppercased letters


 


 // useful_positions[ID][position] = block id


 // (if this element is a part of at least one block)


 var useful_positions = {};


 


+var blocks_inited = false;


 


-var blocks_inited = false;


+function is_conservative_column(column, sequences)


+{


+    var result = false;


+    $.each(conservative_groups_dict, function(i, group) {


+        var inside_group = true;


+        $.each(sequences, function(j, ID) {


+            if (!group[fasta_dict[ID].charAt(column).toUpperCase()])


+            {


+                inside_group = false;


+            }


+        });


+        if (inside_group)


+        {


+            result = true;


+        }


+    });


+    return result;


+}


 


 // run application


 function blocks_init()


@@ -62,6 +82,18 @@

     var i, j, k;


     var t = '';


 


+    for (i = 0; i < conservative_groups.length; i++)


+    {


+        var group = conservative_groups[i];


+        var d = {};


+        for (j = 0; j < group.length; j++)


+        {


+            var letter = group[j].toUpperCase();


+            d[letter] = true;


+        }


+        conservative_groups_dict.push(d);


+    }


+


     var seq;


 


     // calculate max_ID_length


@@ -81,12 +113,6 @@

     IDs_count = 0;


     $.each(fasta_dict, function(k,v) { IDs_count+=1});


 


-    // calculate a color for each block


-    for (i = 0; i < blocks.length; i++)


-    {


-        blocks[i].color = crc32_color(json(blocks[i]));


-    }


-


     // mark colorable positions


     useful_positions = {};


     for (ID in fasta_dict)


@@ -106,6 +132,24 @@

         }


     }


 


+    var is_conservative = [];


+    var all_sequences = [];


+    $.each(fasta_dict, function(ID, seq) { all_sequences.push(ID); });


+    for (j = 0; j < seq_length; j++)


+    {


+        is_conservative[j] = is_conservative_column(j, all_sequences);


+    }


+


+    for (i = 0; i < blocks.length; i++)


+    {


+        block = blocks[i];


+        block.is_conservative = [];


+        for (j = block.start; j <= block.end; j++)


+        {


+            block.is_conservative[j] = is_conservative_column(j, block.IDs);


+        }


+    }


+


     // pre-calculate strings for 


     alignment_strings = {};


     var block_i;


@@ -116,12 +160,16 @@

         for (j = 0; j < seq_length; j++)


         {


             block_i = useful_positions[ID][j];


+            block = blocks[block_i];


             if (block_i || block_i === 0)


             {


                 // current element is a part of block


+                var dark = block.is_conservative[j] && seq.charAt(j) != '-';


+                var color = crc32_color(json(block), dark);


                 t += '
-                t += ' style="background:' + blocks[block_i].color + '; cursor:pointer;" ' ;


+                t += ' style="background:' + color + '; cursor:pointer;" ' ;


                 t += ' onclick=letter_click("' + ID + '",' + j + ') ' ;


+                t += ' class=block' + block_i + ' ';


                 t += '>';


             }


             t += seq.charAt(j);


@@ -146,11 +194,30 @@

         current_number = '' + current_number; // convert to string


         for (j = 0; j < legend_interval - current_number.length; j++)


         {


-            t += ' ';


+            t += ' ';


         }


         t += current_number;


     }


-    t = '
' + t + '
';


+    var conservative_t = '';


+    for (i = 0; i < t.length; i++)


+    {


+        var dark = is_conservative[i];


+        var bgcolor = dark ? 'black' : 'white';


+        var fgcolor = dark ? 'white' : 'black';


+        var l;


+        if (t.charAt(i) == ' ')


+        {


+            l = ' '


+        }


+        else


+        {


+            l = t.charAt(i);


+        }


+        conservative_t += '
+        conservative_t += ' style="background:' + bgcolor + ';color:' + fgcolor + ';" ' ;


+        conservative_t += '>' + l + '';


+    }


+    t = '
' + conservative_t + '
';


     $('#legend').html(t);


 


     // run


@@ -159,6 +226,19 @@

     blocks_show();


 }


 


+function blocks_bind_mouseover()


+{


+    for (var i = 0; i < blocks.length; i++)


+    {


+        var s = '.block' + i;


+        $(s).mouseover({s: s}, function(event) {


+            $(event.data.s).css('color', 'green');


+        });


+        $(s).mouseleave({s: s}, function(event) {


+            $(event.data.s).css('color', 'black');


+        });


+    }


+}


 // set width and height of main table


 function set_table_width_height()


 {


@@ -287,5 +367,6 @@

     }


     $('#mainpanel').html(t);


     blocks_make_pre();


+    blocks_bind_mouseover();


 }


 


diff -r 1a4a04829ba6 -r b0d3c9413cf9 blocks3d/www/input/crc32_color.js

--- a/blocks3d/www/input/crc32_color.js	Fri Jul 01 11:40:00 2011 +0400

+++ b/blocks3d/www/input/crc32_color.js	Fri Jul 01 11:42:26 2011 +0400

@@ -2,9 +2,12 @@

 /**


  * returns color, corresponding to something (using crc32 value)


  *


- * something -- string


+ * @param string something string


+ * @param bool dark Should color be dark


+ *      If dark is true, first bit of each byte from color is set to 0,


+ *      otherwise to 1


  */


-function crc32_color(something)


+function crc32_color(something, dark)


 {


     var crc = crc32(something);


     var rgb = []; // [r, g, b] (3 last bytes of crc32 are used)


@@ -15,12 +18,18 @@

     // lighten


     for (j = 0; j < 3; j++)


     {


-        rgb[j] |= 128;


+        rgb[j] |= 0x80;


+    }


+    for (j = 0; j < 3; j++)


+    {


+        if (dark)


+        {


+            rgb[j] *= 0.8;


+        }


     }


     for (j = 0; j < 3; j++)


     {


         rgb[j] = dechex(rgb[j]);


-        


         if (rgb[j].length == 1)


         {


             rgb[j] = '0' + rgb[j];


diff -r 1a4a04829ba6 -r b0d3c9413cf9 blocks3d/www/input/index.txt

--- a/blocks3d/www/input/index.txt	Fri Jul 01 11:40:00 2011 +0400

+++ b/blocks3d/www/input/index.txt	Fri Jul 01 11:42:26 2011 +0400

@@ -16,7 +16,7 @@

             
Reliable blocks finding


         


     


-    


+


     


         


             
Enable Javascript!


@@ -54,6 +54,7 @@

 {include_minified;crc32_color.js}


 {include_minified;crc32.js}


 {include_minified;dechex.js}


+{include_minified;conservative_groups.js}


 {include_minified;blocks.js}


 


 self_js_text


diff -r 1a4a04829ba6 -r b0d3c9413cf9 blocks3d/www/test.py

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000

+++ b/blocks3d/www/test.py	Fri Jul 01 11:42:26 2011 +0400

@@ -0,0 +1,10 @@

+

+print open('output/index.html').read().replace('self_js_text', """

+blocks = [{"start": 2, "end": 17, "IDs": ["B", "A"]},

+    {"start": 19, "end": 28, "IDs": ["B", "C"]},

+    {"start": 35, "end": 47, "IDs": ["B", "A", "C"]}];

+fasta_dict = {"A": "SNAKIDQLSSDVQTLNAK-DQLSNDVNAARSDAQAAKDDAARANQRLDNM",

+              "B": "SNAKIDQLSSDAQTANAK-DQASNDANAARSDAQAAKDDAARANQRLDNM",

+              "C": "SNAARANQRLDNMKIDQLSSDAQTANAKA-SDAQAAKDDAARANQRLDNM"};

+""")

+

diff -r 1a4a04829ba6 -r b0d3c9413cf9 sequence_based_blocks_search/functional_groups_to_javascript.py

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000

+++ b/sequence_based_blocks_search/functional_groups_to_javascript.py	Fri Jul 01 11:42:26 2011 +0400

@@ -0,0 +1,7 @@

+import pprint

+

+from functional_groups import aminoacids2functional_groups

+

+print 'conservative_groups ='

+pprint.pprint(list(aminoacids2functional_groups.values()))

+