Merge pull request #108 in STRUC/icn3d from release260b to master

* commit '0daa6fb191a5f711f5444f17ca573c28fe362973': minor fix on color
ncbi · Mar 20, 2019 · d3c4ad2 · d3c4ad2
2 parents db1613f + 0daa6fb
commit d3c4ad2
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Showing 5 changed files with 26 additions and 16 deletions.
diff --git a/src/icn3d/display/display_common.js b/src/icn3d/display/display_common.js
@@ -18,8 +18,9 @@ iCn3D.prototype.updateChainsColor = function (atom) {
     }
 };
 
-iCn3D.prototype.setMmdbChainColor = function () {
-    this.applyOriginalColor(this.hash2Atoms(this.hAtoms));
+iCn3D.prototype.setMmdbChainColor = function (inAtoms) {
+    var atoms = (inAtoms === undefined) ? this.hAtoms : inAtoms;
+    this.applyOriginalColor(this.hash2Atoms(atoms));
 
     // atom color
     var atomHash = this.unionHash(this.chemicals, this.ions);
@@ -33,12 +34,15 @@ iCn3D.prototype.setMmdbChainColor = function () {
 };
 
 iCn3D.prototype.setConservationColor = function (atoms, bIdentity) {
+/*
     for (var i in atoms) {
         var atom = this.atoms[i];
         atom.color = this.defaultAtomColor;
 
         this.atomPrevColors[i] = atom.color;
     }
+*/
+    this.setMmdbChainColor(atoms);
 
     for(var chainid in this.alnChainsSeq) {
         var resObjectArray = this.alnChainsSeq[chainid];
@@ -261,6 +265,10 @@ iCn3D.prototype.setColorByOptions = function (options, atoms, bUseInputColor) {
             this.setConservationColor(atoms, true);
             break;
 
+        case 'conserved': // backward-compatible, "conserved" was changed to "identity"
+            this.setConservationColor(atoms, true);
+            break;
+
         case 'conservation':
             this.setConservationColor(atoms, false);
             break;
@@ -899,12 +907,12 @@ iCn3D.prototype.applyOriginalColor = function (atoms) {
 
         if(this.chainsColor.hasOwnProperty(chainid)) {
             atom.color = this.chainsColor[chainid];
-
-            this.atomPrevColors[i] = atom.color;
         }
         else {
-            //atom.color = this.atomColors[atom.elem];
-            break;
+            atom.color = this.atomColors[atom.elem];
+            //break;
         }
+
+        this.atomPrevColors[i] = atom.color;
     }
 };
diff --git a/src/icn3dui/annotations/annotations.js b/src/icn3dui/annotations/annotations.js
@@ -516,21 +516,20 @@ iCn3DUI.prototype.getAnnotationData = function() { var me = this;
                               me.fullpos2ConsTargetpos[i + nGap] = {'same': 1, 'pos': i+1, 'res': targetSeq[i], 'color': colorHexStr};
                               me.consrvResPosArray.push(i+1);
 
-                              me.icn3d.alnChainsSeq[chnid].push({'resi': i, 'color': '#FF0000', 'color2': '#' + colorHexStr});
+                              me.icn3d.alnChainsSeq[chnid].push({'resi': i+1, 'color': '#FF0000', 'color2': '#' + colorHexStr});
                           }
                           else if(me.conservativeReplacement(targetSeq[i], querySeq[target2queryHash[i]])) {
                               compText += '+';
                               me.fullpos2ConsTargetpos[i + nGap] = {'same': 0, 'pos': i+1, 'res': targetSeq[i], 'color': colorHexStr};
                               me.consrvResPosArray.push(i+1);
 
-                              //me.icn3d.alnChainsSeq[chnid].push({'resi': i, 'color': '#0000FF', 'color2': '#' + colorHexStr});
-                              me.icn3d.alnChainsSeq[chnid].push({'resi': i, 'color': '#00FF00', 'color2': '#' + colorHexStr});
+                              me.icn3d.alnChainsSeq[chnid].push({'resi': i+1, 'color': '#0000FF', 'color2': '#' + colorHexStr});
                           }
                           else {
                               compText += ' ';
                               me.fullpos2ConsTargetpos[i + nGap] = {'same': -1, 'pos': i+1, 'res': targetSeq[i], 'color': colorHexStr};
 
-                              me.icn3d.alnChainsSeq[chnid].push({'resi': i, 'color': me.GREYC, 'color2': '#' + colorHexStr});
+                              me.icn3d.alnChainsSeq[chnid].push({'resi': i+1, 'color': me.GREYC, 'color2': '#' + colorHexStr});
                           }
                       }
                       else {
@@ -999,8 +998,8 @@ iCn3DUI.prototype.showSeq = function(chnid, chnidBase, type, queryTitle, compTit
           //var color = (atom.color) ? atom.color.getHexString() : me.icn3d.defaultAtomColor;
 
           var color = '333333';
-          if(me.cfg.blast_rep_id == chnid) {
-              if(me.fullpos2ConsTargetpos !== undefined && me.fullpos2ConsTargetpos[i + nGap] !== undefined) color = me.fullpos2ConsTargetpos[i + nGap].color;
+          if(me.cfg.blast_rep_id == chnid && me.fullpos2ConsTargetpos !== undefined && me.fullpos2ConsTargetpos[i + nGap] !== undefined) {
+              color = me.fullpos2ConsTargetpos[i + nGap].color;
           }
           else {
               var atom = me.icn3d.getFirstCalphaAtomObj(me.icn3d.residues[chnid + '_' + pos]);

diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js
@@ -120,7 +120,7 @@ var iCn3DUI = function(cfg) {
     me.opts['pk']                 = 'residue';            //no, atom, residue, strand, chain
     me.opts['chemicalbinding']      = 'hide';               //show, hide
 
-    if(me.cfg.align !== undefined) me.opts['color'] = 'conservation';
+    if(me.cfg.align !== undefined) me.opts['color'] = 'identity';
     if(me.cfg.blast_rep_id !== undefined) me.opts['color'] = 'conservation';
     if(me.cfg.cid !== undefined) me.opts['color'] = 'atom';
 

diff --git a/src/icn3dui/html/set_html.js b/src/icn3dui/html/set_html.js
@@ -736,7 +736,11 @@ iCn3DUI.prototype.setMenu4 = function() { var me = this;
         html += me.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
         html += "    </ul>";
 
-        if(me.cfg.align !== undefined || me.cfg.blast_rep_id !== undefined) {
+        if(me.cfg.align !== undefined) {
+          html += me.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', true);
+          html += me.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation');
+        }
+        else if(me.cfg.blast_rep_id !== undefined) {
           html += me.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity');
           html += me.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', true);
         }

diff --git a/src/icn3dui/parsers/mmcif_mmdb_parser_align.js b/src/icn3dui/parsers/mmcif_mmdb_parser_align.js
@@ -398,8 +398,7 @@ iCn3DUI.prototype.setSeqAlign = function (seqalign, alignedStructures) { var me
                       me.consHash2[chainid2 + '_' + resi] = 1;
                   }
                   else {
-                      //color = '#0000FF';
-                      color = '#00FF00';
+                      color = '#0000FF';
                       classname = 'icn3d-ncons';
 
                       me.nconsHash1[chainid1 + '_' + id2aligninfo[j].resi] = 1;