do a little cleaning and add usual doc

Changelog

@@ -0,0 +1 @@
+v0.1 :  12/11 Creation , Olivier Sallou <[email protected]>

LICENSE

@@ -0,0 +1 @@
+All the code hereby is licensed under the CeCILL license (http://www.cecill.info/licences/Licence_CeCILL_V2-en.html) which is a GNU GPL equivalent for the French law.

README

@@ -0,0 +1,16 @@
+
+* Requirements *
+
+This software needs a web server with PHP enabled for additional features loading and image save function.
+The rest of the software is pure web (HTML+Javascript).
+
+The img/tmp directory must be writable by the web server to create images when "save alignment image" is selected.
+Images in directory can be safely cleaned by a cron task to remove old images.
+
+* Configuration *
+
+If a seqcrawler server is available to extract additional features, then configuration must be updated
+in features.php, the URL need to be adapted to the seqcrawler server.
+
+In the other case, useFeatures must be set to 0 in js/uiseqblast.js
+

js/uiblast.js

@@ -1,3 +1,13 @@
+/**
+* Library for index.html, managing a blast alignement display
+*
+* Author: Olivier Sallou <[email protected]>
+*
+*/
+
+
+
+
 /**
 * Return a specific iteration from iterations
 */
@@ -52,19 +62,39 @@ function drawSequences(min,max) {
 
                 var from = sequence["from"];
                 var to = sequence["to"];
+		/*
+			min<------------------------------->max
+			            ----- case1
+
+						----------------- case2
+
+		  ------------- case3
+
+		   ----------------------------------------------- case4
+
+                  ---- case5
+								------- case6
+
+		*/
 
                 if((from>=min && from<=max)&&(to>=min && to<=max)) {
+			// case1 : complete sequence is between min and max
                 	context.fillText(sequence["seq"], xPos+Xseq+from-min, yPos);
                 }
                 else if(from>=min && from<=max) {
+			// case2
                         context.fillText(sequence["seq"].substring(0,max-from), xPos+Xseq+from-min, yPos);
                 }
                 else if(to>=min && to<=max) {
-                	context.fillText(sequence["seq"].substring(min-from,max-min), xPos+Xseq, yPos);
+			// case3
+                	//context.fillText(sequence["seq"].substring(min-from,max-min), xPos+Xseq, yPos);
+			context.fillText(sequence["seq"].substring(min-from), xPos+Xseq, yPos);
                 }
                 else if(from<=min && to>=max) {
+			// case 4
                         context.fillText(sequence["seq"].substring(min-from,max-from), xPos+Xseq, yPos);
                 }
+		// if none match, case 5 and 6, nothing to display for sequence
                 yPos+=step;                     
 	}
 	yPos=10;

js/uiseqblast.js

@@ -1,3 +1,19 @@
+/**
+* Library for sequence.html, managing a Hit alignement display and additional features extraction
+*
+* Author: Olivier Sallou <[email protected]>
+*
+*/
+
+/**
+* Configuration
+*/
+useFeatures = 1;
+
+
+/**
+* Clear the canvas
+*/
 function clearCanvas() {
 	context.save();
 	context.fillStyle = "white";
@@ -6,6 +22,9 @@ function clearCanvas() {
 }
 
 
+/**
+* Draw Hsps for the selected Hit between min and max position
+*/
 function drawSequences(min,max) {
 clearCanvas();
 max = parseInt(max);
@@ -92,12 +111,15 @@ for (var i=0;i<sequences.length;i++)
                 context.fillText(sequence["seq"].substring(min-from,max-from), xPos+Xseq, yPos);
         }
         yPos+=step;
-        addFeatures(sequence,max,min);
+        if(useFeatures==1) { addFeatures(sequence,max,min); }
 
 }
 yPos=20;
 }
 
+/**
+* Draw a filler (blank)
+*/
 function drawFiller(x) {
 	var empty="";
          for(var j=0;j<x;j++) {
@@ -107,6 +129,9 @@ function drawFiller(x) {
 	 return empty;
 }
 
+/**
+* Draw feature in canvas with input parameters
+*/
 function drawFeature(x,y,size,text,title) {
         var empty=drawFiller(x);
         var spaced="";
@@ -122,6 +147,9 @@ function drawFeature(x,y,size,text,title) {
         }
 }
 
+/**
+* Add features aligned with sequence alignment between min and max positions
+*/
 function addFeatures(sequence,max,min) {
         if(sequence["features"]!=null) {
         	for (var i=0;i<sequence["features"].length;i++) {
@@ -157,7 +185,9 @@ function addFeatures(sequence,max,min) {
         context.fillStyle="black";
 }
 
-
+/**
+* Load XML file from input URL, extract Hit from hitnum parameter and load additional features with a call to features.php
+*/
 function getXML(xmlUrl) {
 
 $.ajax( {
@@ -185,7 +215,7 @@ $.ajax( {
 
                         		if(hspnum==$.getURLParam("hspnum")) {
                         			$("#documentDetails" ).html('<p class="wait"><img title="loading" alt="loading" src="img/waiting.gif"/></p>');
-                                		$("#documentDetails" ).dialog({ title: 'Loading, please wait' , width : '200px'  });
+                                		$("#documentDetails" ).dialog({ title: 'Loading features, please wait' , width : '200px'  });
                                         	$.get("features.php?id="+accession+"&from="+$(this).find('Hsp_hit-from').text()+"&to="+$(this).find('Hsp_hit-to').text(),
                                            		function(jsonFeatures){
                             					$("#documentDetails" ).dialog( "close" );

savecanvas.php

@@ -16,10 +16,10 @@
 	// Save file.  This example uses a hard coded filename for testing, 
 	// but a real application can specify filename in POST variable
 	$name = "canvas".uniqid();
-	$fp = fopen( 'img/'.$name.'.png', 'wb' );
+	$fp = fopen( 'img/tmp/'.$name.'.png', 'wb' );
 	fwrite( $fp, $unencodedData);
 	fclose( $fp );
 
 	print $name.".png";
 }
-?>
+?>