merge -- refactor axis management

See !601. Great work by @duez. Streamline axis handling.
Will soon allow new features on displaying axes/color/...

.gitignore

@@ -32,3 +32,19 @@ node_modules/
 cypress/
 server/web2py/applications/vidjil/errors
 *.bak
+
+docker/vidjil-client/ssl/web2py.crt
+
+docker/vidjil-client/ssl/web2py.key
+
+tools/align.cgi
+
+tools/similarity.cgi
+
+germline/homo-sapiens/
+
+germline/germline-59.tar.gz
+
+germline/IMGT_RELEASE
+
+vidjil-algo

browser/css/segmenter_page.css

@@ -106,6 +106,7 @@ ul {
   -ms-user-select: none;
   user-select: none;
   overflow: hidden;
+  height : 100%;
 }
 #mid-container {
   position: fixed;
@@ -2377,6 +2378,7 @@ textarea {
   -moz-flex: 2 32%;
   -ms-flex: 2 32%;
   flex: 2 32%;
+  height : 100%;
 }
 #segmenter_panel {
   bottom: 0;

browser/js/app.js

@@ -50,8 +50,7 @@ function loadAfterConf() {
 
         require(["../germline"],
                 function() {
-                    require(["../generic_axis",
-                             "../closeable"],
+                    require(["../closeable"],
                             function() {
                                 require(["../compare",
                                          "../menu",
@@ -63,10 +62,11 @@ function loadAfterConf() {
                                          "../clone",
                                          "../dynprog",
                                          "../list",
-                                         "../germline_axis",
-                                         "../numerical_axis",
                                          "../axes",
+                                         "../axis",
                                          "../graph",
+                                         "../scatterPlot_menu",
+                                         "../scatterPlot_selector",
                                          "../scatterPlot",
                                          "../builder",
                                          "../info",

browser/js/clone.js

@@ -94,9 +94,6 @@ function Clone(data, model, index, attributes) {
     this.m.clusters[index]=[index]
     this.m.clones[index]=this
     this.tag = this.getTag();
-    this.computeGCContent()
-    this.computeCoverage()
-    this.computeEValue()
 
     // .warn, client computed warnings
     this.computeWarnings()
@@ -132,10 +129,10 @@ Clone.prototype = {
 
     computeWarnings: function() {
 
-        if (this.coverage < this.COVERAGE_WARN)
+        if (this.getCoverage() < this.COVERAGE_WARN)
             this.warn.push({'code': 'W51', 'level': warnLevels[WARN], 'msg': 'Low coverage (' + this.coverage.toFixed(3) + ')'}) ;
 
-        if (typeof(this.eValue) != 'undefined' && this.eValue > this.EVALUE_WARN)
+        if (typeof(this.getEValue()) != 'undefined' && this.eValue > this.EVALUE_WARN)
             this.warn.push({'code': 'Wxx', 'level': warnLevels[WARN], 'msg': 'Bad e-value (' + this.eValue + ')' });
     },
 
@@ -170,7 +167,7 @@ Clone.prototype = {
     REGEX_GENE_IGNORE_ALLELE: /(IGH|IGK|IGL|TRA|TRB|TRG|TRD|IKZF1-|ERG-)([\w-]*)([\w-*]*)$/,   // IGHV3-11*03  (ignore *03)
 
     getAverageReadLength: function(time) {
-        if (this._average_read_length == 'undefined')
+        if (typeof this._average_read_length == 'undefined')
             return 'undefined';
         time = this.m.getTime(time);
         var size = this._average_read_length[time];
@@ -402,6 +399,7 @@ Clone.prototype = {
         if (this.hasSizeDistrib()){
             // TODO: move this function into an update function and store result into an attribute of this clone
             var t = this.m.t
+            //if (this.current_clones == undefined) return "bob"
             var n = this.current_clones[t]
             var name = this.getDistributionsValues().toString() + " (" + n + " clone" + (n>1 ? "s" : "") + ")"
             return name
@@ -860,12 +858,16 @@ Clone.prototype = {
         return true
     },
 
-    computeEValue: function () {
+    getEValue: function () {
+        if (this.eValue) return this.eValue
+
         var e = this.seg.evalue;
         if (typeof(e) != 'undefined')
             this.eValue = parseFloat(e.val)
         else
             this.eValue = undefined
+
+        return this.eValue
     },
 
     getGene: function (type, withAllele) {
@@ -892,7 +894,7 @@ Clone.prototype = {
         if (this.hasSeg('3', '5')){
             return this.seg['3'].start-this.seg['5'].stop-1
         }else{
-            return 'undefined'
+            return '?'
         }
     },
     
@@ -943,8 +945,9 @@ Clone.prototype = {
     /*
      * Compute coverage as the average value of non-zero coverages
      */
+    getCoverage: function () {
+        if (this.coverage) return this.coverage
 
-    computeCoverage: function () {
         if (typeof (this._coverage) == 'undefined') {
             this.coverage = undefined
             return
@@ -960,9 +963,13 @@ Clone.prototype = {
             }
         }
         this.coverage = sum/nb
+
+        return this.coverage
     },
 
-    computeGCContent: function () {
+    getGCContent: function() {
+        if (this.GCContent) return this.GCContent
+
         if (this.getSequenceLength() === 0) {
             this.GCContent = undefined
             return
@@ -974,7 +981,9 @@ Clone.prototype = {
                 gc++ }
 
         this.GCContent = gc / this.sequence.length
-    },
+
+        return this.GCContent
+    },    
 
     getSequenceLength : function () {
         if (typeof (this.sequence) != 'undefined' &&
@@ -1102,51 +1111,86 @@ Clone.prototype = {
         var allele;
         if (!this.hasSizeConstant()){
             this.color = "rgba(150, 150, 150, 0.65)"
-        } else if (this.m.colorMethod == "abundance") {
-            var size = this.getSize()
-            if (this.getCluster().length===0){ size = this.getSequenceSize() }
-            if (size === 0){
-                this.color = "";
-            }else{
-                this.color = colorGenerator(this.m.scale_color(size * this.m.precision));
-            }
-        } else if (this.m.colorMethod == 'clone') {
-            this.color = colorGeneratorIndex(this.index)
-        } else if (this.m.colorMethod == 'cdr3') {
-            this.color = this.getCDR3Color();
-        }else if (this.m.colorMethod == "Tag"){
-            this.color =  this.m.tag[this.getTag()].color;
-        }else if (this.m.colorMethod == "dbscan"){
-            this.color =  this.colorDBSCAN;
-        }else if (this.m.colorMethod == "V" && this.getGene("5") != "undefined V"){
-            this.color = "";
-            allele = this.m.germlineV.allele[this.getGene("5")]
-            if (typeof allele != 'undefined' ) this.color = allele.color;
-        }else if (this.m.colorMethod == "D" && this.getGene("4") != "undefined D"){
-            this.color = "";
-            allele = this.m.germlineD.allele[this.getGene("4")]
-            if (typeof allele != 'undefined' ) this.color = allele.color;
-        }else if (this.m.colorMethod == "J" && this.getGene("3") != "undefined J"){
-            this.color = "";
-            allele = this.m.germlineJ.allele[this.getGene("3")]
-            if (typeof allele != 'undefined' ) this.color = allele.color;
-        }else if (this.m.colorMethod == "N"){
-            this.color =  this.colorN;
-        }else if (this.m.colorMethod == "system") {
-            this.color = this.m.germlineList.getColor(this.germline)
-        } else if (this.m.colorMethod == 'productive') {
-            if (this.hasSeg('junction') &&
-                typeof this.seg.junction.productive != 'undefined') {
-                this.color = colorProductivity(this.seg.junction.productive)
-            }
-        }else{
-            this.color = "";
+            return
         }
-        this.true_color = this.color
 
-        if (this.m.focus == this.index){
-            this.color = "";
+        switch (this.m.colorMethod){
+            
+            case "abundance":
+                var size = this.getSize()
+                if (this.getCluster().length===0)
+                    size = this.getSequenceSize()
+                if (size === 0)
+                    this.color = ""
+                else
+                    this.color = colorGenerator(this.m.scale_color(size * this.m.precision))
+
+                break;
+        
+            case "clone":
+                this.color = colorGeneratorIndex(this.index)
+                break;
+        
+            case "cdr3":
+                this.color = this.getCDR3Color()
+                break;
+        
+            case "Tag":
+                this.color =  this.m.tag[this.getTag()].color
+                if (this.color == "default") this.color = ""
+                break;
+
+            case "dbscan":
+                this.color =  this.colorDBSCAN
+                break;
+
+            case "system":
+                this.color = this.m.germlineList.getColor(this.germline)
+                break;
+
+            case "productive":
+                this.color = ""
+                if (this.hasSeg('junction') &&
+                    typeof this.seg.junction.productive != 'undefined') 
+                    this.color = colorProductivity(this.seg.junction.productive)
+                break;
+
+            case "N":
+                this.color =  this.colorN
+                break;
+
+            case "V":
+                this.color = ""
+                if (this.getGene("5") != "undefined V"){
+                    var alleleV = this.m.germlineV.allele[this.getGene("5")]
+                    if (typeof alleleV != 'undefined' ) this.color = alleleV.color
+                }
+                break;
+
+            case "D":
+                this.color = ""
+                if (this.getGene("4") != "undefined D"){
+                    var alleleD = this.m.germlineD.allele[this.getGene("4")]
+                    if (typeof alleleD != 'undefined' ) this.color = alleleD.color
+                }
+                break;
+
+            case "J":
+                this.color = ""
+                if (this.getGene("3") != "undefined J"){
+                    var alleleJ = this.m.germlineJ.allele[this.getGene("3")]
+                    if (typeof alleleJ != 'undefined' ) this.color = alleleJ.color
+                }
+                break;
+        
+            default:
+                this.color = ""
         }
+
+        this.true_color = this.color
+
+        if (this.m.focus == this.index)
+            this.color = ""
     },
     
     /**
@@ -1375,7 +1419,7 @@ Clone.prototype = {
         }
 
         //coverage info
-        if (typeof this.coverage != 'undefined') {
+        if (typeof this.getCoverage() != 'undefined') {
             html += row_1("average coverage",
                           "<span " +
                           (this.coverage < this.COVERAGE_WARN ? "class='warning'" : "") +
@@ -1384,7 +1428,7 @@ Clone.prototype = {
         }
 
         // e-value
-        if (typeof this.eValue != 'undefined') {
+        if (typeof this.getEValue() != 'undefined') {
             html += row_1("e-value",
                           "<span " +
                           (this.eValue > this.EVALUE_WARN ? "class='warning'" : "") +
@@ -1522,16 +1566,16 @@ Clone.prototype = {
         html += "</table></div>"
         return html
     },
-
+/*
     axisOptions: function() {
         return [
-            "consensusLength", "averageLength", "nLength", "lengthCDR3",
-            "productivity", "productivity-IMGT",
-            "VIdentity-IMGT",
-            "tag", "coverage", "locus", "size", "nbSamples"
+            "clone consensus length", "clone average read length", "GC content", "N length",
+            "CDR3 length (nt)", "productivity", "productivity-IMGT",
+            "VIdentity-IMGT", "clone consensus coverage",
+            "tag", "coverage", "size", "number of samples", "primers"
         ];
     },
-
+*/
     /**
       * start to fill a node with clone informations common between segmenter and list
       * @param {dom_object} div_elem - html element to complete
@@ -1784,8 +1828,7 @@ Clone.prototype = {
             round = true
         }
         var values = []
-        var axes_obj = this.m.axes
-        var available_axes = this.m.available_axes
+        var available_axes = Axis.prototype.available()
 
         for (var a = 0; a < axes.length; a++) {
             var axe  = axes[a]
@@ -1793,11 +1836,9 @@ Clone.prototype = {
             if (axe == undefined || naxe == undefined){
                 console.default.error("Getter: not axis " + axe + "; ("+naxe+")")
             }
-            if (available_axes[naxe] != undefined && available_axes[naxe].fct != undefined) {
-                var value = available_axes[naxe].fct(this, timepoint)
-                if (round && available_axes[naxe] != undefined && available_axes[naxe].round != undefined){ 
-                    value = available_axes[naxe].round(value)
-                }
+            if (available_axes.indexOf(naxe) != -1 ) {
+                var axis_p = Axis.prototype.getAxisProperties(naxe)
+                var value = axis_p.fct(this, timepoint)
                 values.push( value )
             } else {
                 console.default.error("Getter: not axis " + axe + "; ("+naxe+")")
@@ -1896,7 +1937,7 @@ Clone.prototype = {
             tmpValue.fill(value)
             value          = tmpValue
         }
-
+/*
         var naxe = this.m.distrib_convertion[axe]
         var available_axes = this.m.available_axes
         if (available_axes[naxe] != undefined) {
@@ -1907,12 +1948,16 @@ Clone.prototype = {
             }
         } else {
             console.default.error( "Axe not present in obj: " + axe + ";" + naxe)
-
+*/
             // Each content should be hardcoded. Not optimal
-            if (axe == "GCContent")            { this.GCContent            = value}
-            else if (axe == "lenSeqAverage")   { this._average_read_length = value}
-            else if (axe == "lenSeqConsensus") { this.consensusLength      = value}
-        }
+            if (axe == "GCContent")             { this.GCContent            = value}
+            else if (axe == "lenSeqAverage")    { this._average_read_length = value}
+            else if (axe == "lenSeqConsensus")  { this.consensusLength      = value}
+            else if (axe == "seg5")             { this.seg[5] =       { name: value}}
+            else if (axe == "seg4")             { this.seg[4] =       { name: value}}
+            else if (axe == "seg3")             { this.seg[3] =       { name: value}}
+            else if (axe == "lenCDR3")          { this.seg.cdr3 =     { start: 0, 
+                                                                        stop: value}} 
     },
 
     sameAxesAsScatter: function(scatterplot){
@@ -1930,15 +1975,7 @@ Clone.prototype = {
         }
 
         if (mode == "bar"){
-            // on doit retirer dans ce cas le "size"
-            var pos_size = axes.indexOf("size")
-            if (pos_size != -1){
-                axes.splice(pos_size, 1)
-                return x.equals(axes)
-            } else {
-                // In mode bar, each axes should be associated with size
-                // console.default.warn( "same_axes_as_scatter: Only one axe to test (size not present), "+ axes)
-            }
+            return (x.indexOf(axes[0]) != -1)
         } else {
             // console.default.warn("same_axes_as_scatter: The scatter mode is not correct; '"+mode+"'")
             return x.equals(axes)

browser/js/crossDomain.js

@@ -218,7 +218,7 @@ function imgtPostForSegmenter(species, data, system, segmenter, override_imgt_op
             // sai : segmenter axis inputs ; activate productivity-IMGT and VIdentity-IMGT
             var sai = document.getElementById('segmenter_axis_select').getElementsByTagName('input');
             for (var index in sai) {
-                if (!sai[index].checked && (sai[index].value == "productivity-IMGT" || sai[index].value == "VIdentity-IMGT"))
+                if (!sai[index].checked && (sai[index].value == "productivity IMGT" || sai[index].value == "VIdentity IMGT"))
                     sai[index].click();
             }
 

browser/js/database.js

@@ -39,6 +39,7 @@ function Database(model, address) {
         this.m = model
         this.uploader = new Uploader()
         this.build()
+        this.m.db = this
         
         window.onbeforeunload = function(e){
             if ( self.uploader.is_uploading() ){
@@ -1018,7 +1019,7 @@ Database.prototype = {
                         xhrFields: {withCredentials: true},
 		        timeout: DB_TIMEOUT_CALL,
 		        success: function (result) {
-		        	notification.parse_notification(result)
+		        	m.notification.parse_notification(result)
 		            
 		        }, 
 		        error: function (request, status, error) {

browser/js/generic_axis.js

-/*
- * This file is part of Vidjil <http://www.vidjil.org>,
- * High-throughput Analysis of V(D)J Immune Repertoire.
- * Copyright (C) 2013-2017 by Bonsai bioinformatics
- * at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
- * Contributors: 
- *     Marc Duez <marc.duez@vidjil.org>
- *     Antonin Carette <antonin.carette@etudiant.univ-lille1.fr>
- *     The Vidjil Team <contact@vidjil.org>
- * 
-* "Vidjil" is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* "Vidjil" is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
-*/
-
-
-/**
- * GenericAxis object contain labels and their position on an axis (from 0 to 1)
- * can provide the position of an element on it
- * @constructor
- * */
-function GenericAxis (reverse, can_undefined) {
-    this.labels = [];
-    this.label_mapping = {};
-    this.values = []
-    this.value_mapping = {};
-    this.can_undefined = true;
-    this.MAX_NB_STEPS_IN_AXIS = 14; // Number (max) of labels per numerical axis
-    this.MAX_NB_BARS_IN_AXIS = 200
-    this.NB_STEPS_BAR = 18; // Number (max) of labels per numerical axis in histograms
-    if(typeof can_undefined !== "undefined")
-        this.can_undefined = can_undefined;
-    this.reverse = false;
-    if(typeof reverse !== "undefined")
-        this.reverse = reverse
-    this.adapt = false
-}
-
-GenericAxis.prototype = {
-
-    init : function (values, key, labels, sort) {
-        this.reset();
-        this.values = values;
-        if (typeof sort === 'undefined') {sort = false;}
-
-        if (typeof key === 'function') {
-            this.converter = key;
-        } else {
-            this.converter = function(elem) {
-                return elem[key];
-            }
-        }
-
-        this.populateLabels(labels, sort);
-        this.populateValueMapping();
-
-
-        return this;
-    },
-
-    ignore: function(clone) {
-        return this.adapt && clone.isFiltered
-    },
-
-    compareLabels: function(a, b) {
-        if (typeof a === 'undefined') return (typeof b === 'undefined')  ? 0 :  -1;
-        if (typeof b === 'undefined') return (typeof a === 'undefined')  ? 0 :  1;
-  
-        if (a.constructor === String) {
-            if (b.constructor === String) return a.localeCompare(b);
-            if (b.constructor === Number ) return 1
-        }
- 
-        if (a.constructor === Number) return (b.constructor === Number ) ? (a-b) : -1;
-    },
-
-    populateLabels: function(labels, sort) {
-        var values = this.values;
-        var label_mapping = this.label_mapping;
-
-        if (typeof labels === 'undefined')
-            this.computeLabels(values, sort);
-        else {
-            for (var i=0; i < values.length; i++) {
-                var value = values[i];
-                if (this.ignore(value))
-                    continue;
-                var convert = this.applyConverter(value);
-                var pos;
-                if (labels.indexOf(convert) != -1) {
-                    if (typeof label_mapping[convert] === 'undefined') {
-                        pos = labels.indexOf(convert)/labels.length;
-                        if (this.reverse)
-                            pas = 1 - pos;
-                        this.addLabel("line", convert, pos, convert);
-                    }
-                } else {
-                    if (this.can_undefined) {
-                        pos = 1;
-                        if (this.reverse)
-                            pos = 0;
-                        this.addLabel("line", "?", pos, "?");
-                    }
-
-                }
-            }
-        }
-
-        var step = 1/(this.labels.length+1);
-        offset = step/2;
-        for (var idx in this.labels){
-            this.labels[idx].pos += offset;
-        }
-    },
-
-    populateValueMapping: function(round) {
-
-        for (var idx in this.values) {
-            var value = this.values[idx];
-
-            // if (value.isVirtual())
-            //    continue ;  // ? pas toujours ?
-
-            if (this.ignore(value))
-                continue;
-            var convert = this.applyConverter(value);
-
-            if (typeof round !== 'undefined')
-                convert = nice_ceil(convert - round/2, round)
-
-            if (typeof convert == "undefined" || convert == undefined || convert == "undefined" || Number.isNaN(convert)) {
-                if (this.can_undefined) {
-                    if (typeof this.value_mapping["?"] === 'undefined')
-                        this.value_mapping["?"] = [];
-                    this.value_mapping["?"].push(value);
-                }
-            }
-            else
-            {
-                this.value_mapping[convert] = this.value_mapping[convert] || []
-                this.value_mapping[convert].push(value);
-            }
-        }
-    },
-
-    sortValueMapping: function() {
-        var keys = Object.keys(this.value_mapping).sort()
-        var temp = {}
-        for (var key_pos in keys){
-            key = keys[key_pos]
-            temp[key] = this.value_mapping[key]