X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fcontroller%2FAlignViewController.js;fp=site%2Fj2s%2Fjalview%2Fcontroller%2FAlignViewController.js;h=c773729c4937fd5d0ee6f98ec9907f98638e2c8a;hp=966223d329df39608f717a2e0f4e36f2a15980c9;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/controller/AlignViewController.js b/site/j2s/jalview/controller/AlignViewController.js
index 966223d..c773729 100644
--- a/site/j2s/jalview/controller/AlignViewController.js
+++ b/site/j2s/jalview/controller/AlignViewController.js
@@ -1,219 +1,219 @@
-Clazz.declarePackage ("jalview.controller");
-Clazz.load (["jalview.api.AlignViewControllerI"], "jalview.controller.AlignViewController", ["jalview.analysis.AlignmentSorter", "$.Grouping", "jalview.commands.OrderCommand", "jalview.datamodel.ColumnSelection", "jalview.io.FeaturesFile", "jalview.util.MessageManager", "java.awt.Color", "java.util.ArrayList", "$.BitSet"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.viewport = null;
-this.alignPanel = null;
-this.avcg = null;
-Clazz.instantialize (this, arguments);
-}, jalview.controller, "AlignViewController", null, jalview.api.AlignViewControllerI);
-Clazz.overrideMethod (c$, "finalize", 
-function () {
-this.viewport = null;
-this.alignPanel = null;
-this.avcg = null;
-});
-Clazz.makeConstructor (c$, 
-function (alignFrame, viewport, alignPanel) {
-this.avcg = alignFrame;
-this.viewport = viewport;
-this.alignPanel = alignPanel;
-}, "jalview.api.AlignViewControllerGuiI,jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
-Clazz.overrideMethod (c$, "setViewportAndAlignmentPanel", 
-function (viewport, alignPanel) {
-this.alignPanel = alignPanel;
-this.viewport = viewport;
-}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
-Clazz.overrideMethod (c$, "makeGroupsFromSelection", 
-function () {
-var sg = this.viewport.getSelectionGroup ();
-var cs = this.viewport.getColumnSelection ();
-var gps = null;
-if (sg != null && (cs == null || cs.getSelected () == null || cs.size () == 0)) {
-gps = jalview.analysis.Grouping.makeGroupsFrom (this.viewport.getSequenceSelection (), this.viewport.getAlignmentView (true).getSequenceStrings (this.viewport.getGapCharacter ()), this.viewport.getAlignment ().getGroups ());
-} else {
-if (cs != null) {
-gps = jalview.analysis.Grouping.makeGroupsFromCols ((sg == null) ? this.viewport.getAlignment ().getSequencesArray () : sg.getSequences ().toArray ( new Array (0)), cs, this.viewport.getAlignment ().getGroups ());
-}}if (gps != null) {
-this.viewport.getAlignment ().deleteAllGroups ();
-this.viewport.clearSequenceColours ();
-this.viewport.setSelectionGroup (null);
-for (var g = 0; g < gps.length; g++) {
-gps[g].setshowSequenceLogo (this.viewport.isShowSequenceLogo ());
-this.viewport.getAlignment ().addGroup (gps[g]);
-var col =  new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255));
-col = col.brighter ();
-for (var sq, $sq = gps[g].getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
-this.viewport.setSequenceColour (sq, col);
-}
-}
-return true;
-}return false;
-});
-Clazz.overrideMethod (c$, "createGroup", 
-function () {
-var sg = this.viewport.getSelectionGroup ();
-if (sg != null) {
-this.viewport.getAlignment ().addGroup (sg);
-return true;
-}return false;
-});
-Clazz.overrideMethod (c$, "unGroup", 
-function () {
-var sg = this.viewport.getSelectionGroup ();
-if (sg != null) {
-this.viewport.getAlignment ().deleteGroup (sg);
-return true;
-}return false;
-});
-Clazz.overrideMethod (c$, "deleteGroups", 
-function () {
-if (this.viewport.getAlignment ().getGroups () != null && this.viewport.getAlignment ().getGroups ().size () > 0) {
-this.viewport.getAlignment ().deleteAllGroups ();
-this.viewport.clearSequenceColours ();
-this.viewport.setSelectionGroup (null);
-return true;
-}return false;
-});
-Clazz.overrideMethod (c$, "markColumnsContainingFeatures", 
-function (invert, extendCurrent, toggle, featureType) {
-var bs =  new java.util.BitSet ();
-var alw;
-var alStart;
-var sqcol = (this.viewport.getSelectionGroup () == null ? this.viewport.getAlignment () : this.viewport.getSelectionGroup ());
-alStart = sqcol.getStartRes ();
-alw = sqcol.getEndRes () + 1;
-var seqs = sqcol.getSequences ();
-var nseq = 0;
-for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
-var tfeat = 0;
-if (sq != null) {
-var sf = sq.getSequenceFeatures ();
-if (sf != null) {
-var ist = sq.findIndex (sq.getStart ());
-var iend = sq.findIndex (sq.getEnd ());
-if (iend < alStart || ist > alw) {
-continue;
-}for (var sfpos, $sfpos = 0, $$sfpos = sf; $sfpos < $$sfpos.length && ((sfpos = $$sfpos[$sfpos]) || true); $sfpos++) {
-if (sfpos != null && (featureType.equals (sfpos.getType ()))) {
-tfeat++;
-var i = sq.findIndex (sfpos.getBegin ());
-var j = sq.findIndex (sfpos.getEnd ());
-if (j < alStart || i > alw) {
-continue;
-}if (i < alStart) {
-i = alStart;
-}if (i < ist) {
-i = ist;
-}if (j > alw) {
-j = alw;
-}for (; i <= j; i++) {
-bs.set (i - 1);
-}
-}}
-}if (tfeat > 0) {
-nseq++;
-}}}
-var cs = this.viewport.getColumnSelection ();
-if (bs.cardinality () > 0 || invert) {
-if (cs == null) {
-cs =  new jalview.datamodel.ColumnSelection ();
-} else {
-if (!extendCurrent) {
-cs.clear ();
-}}if (invert) {
-for (var i = bs.nextClearBit (alStart), ibs = bs.nextSetBit (alStart); i >= alStart && i < (alw); ) {
-if (ibs < 0 || i < ibs) {
-if (toggle && cs.contains (i)) {
-cs.removeElement (i++);
-} else {
-cs.addElement (i++);
-}} else {
-i = bs.nextClearBit (ibs);
-ibs = bs.nextSetBit (i);
-}}
-} else {
-for (var i = bs.nextSetBit (alStart); i >= alStart; i = bs.nextSetBit (i + 1)) {
-if (toggle && cs.contains (i)) {
-cs.removeElement (i);
-} else {
-cs.addElement (i);
-}}
-}this.viewport.setColumnSelection (cs);
-this.alignPanel.paintAlignment (true);
-this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.view_controller_toggled_marked",  Clazz.newArray (-1, [(toggle ? jalview.util.MessageManager.getString ("label.toggled") : jalview.util.MessageManager.getString ("label.marked")), (invert ? (Integer.$valueOf ((alw - alStart) - bs.cardinality ()).toString ()) : (Integer.$valueOf (bs.cardinality ()).toString ())), featureType, Integer.$valueOf (nseq).toString ()])));
-return true;
-} else {
-this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.no_feature_of_type_found",  Clazz.newArray (-1, [featureType])));
-if (!extendCurrent && cs != null) {
-cs.clear ();
-this.alignPanel.paintAlignment (true);
-}return false;
-}}, "~B,~B,~B,~S");
-Clazz.overrideMethod (c$, "sortAlignmentByFeatureDensity", 
-function (typ) {
-this.sortBy (typ, "Sort by Density", jalview.analysis.AlignmentSorter.FEATURE_DENSITY);
-}, "~A");
-Clazz.defineMethod (c$, "sortBy", 
-function (typ, methodText, method) {
-var fr = this.alignPanel.getFeatureRenderer ();
-if (typ == null) {
-typ = fr == null ? null : fr.getDisplayedFeatureTypes ();
-}var gps = null;
-gps = fr == null ? null : fr.getDisplayedFeatureGroups ();
-if (typ != null) {
-var types =  new java.util.ArrayList ();
-for (var i = 0; i < typ.length; i++) {
-if (typ[i] != null) {
-types.add (typ[i]);
-}typ =  new Array (types.size ());
-types.toArray (typ);
-}
-}if (gps != null) {
-var grps =  new java.util.ArrayList ();
-for (var i = 0; i < gps.length; i++) {
-if (gps[i] != null) {
-grps.add (gps[i]);
-}}
-gps =  new Array (grps.size ());
-grps.toArray (gps);
-}var al = this.viewport.getAlignment ();
-var start;
-var stop;
-var sg = this.viewport.getSelectionGroup ();
-if (sg != null) {
-start = sg.getStartRes ();
-stop = sg.getEndRes ();
-} else {
-start = 0;
-stop = al.getWidth ();
-}var oldOrder = al.getSequencesArray ();
-jalview.analysis.AlignmentSorter.sortByFeature (typ, gps, start, stop, al, method);
-this.avcg.addHistoryItem ( new jalview.commands.OrderCommand (methodText, oldOrder, this.viewport.getAlignment ()));
-this.alignPanel.paintAlignment (true);
-}, "~A,~S,~S");
-Clazz.overrideMethod (c$, "sortAlignmentByFeatureScore", 
-function (typ) {
-this.sortBy (typ, "Sort by Feature Score", jalview.analysis.AlignmentSorter.FEATURE_SCORE);
-}, "~A");
-Clazz.overrideMethod (c$, "parseFeaturesFile", 
-function (file, protocol, relaxedIdMatching) {
-var featuresFile = false;
-try {
-featuresFile =  new jalview.io.FeaturesFile (file, protocol).parse (this.viewport.getAlignment ().getDataset (), this.alignPanel.getFeatureRenderer ().getFeatureColours (), false, relaxedIdMatching);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-if (featuresFile) {
-this.avcg.refreshFeatureUI (true);
-if (this.alignPanel.getFeatureRenderer () != null) {
-this.alignPanel.getFeatureRenderer ().findAllFeatures (true);
-}if (this.avcg.getFeatureSettingsUI () != null) {
-this.avcg.getFeatureSettingsUI ().discoverAllFeatureData ();
-}this.alignPanel.paintAlignment (true);
-}return featuresFile;
-}, "~S,~S,~B");
-});
+Clazz.declarePackage ("jalview.controller");
+Clazz.load (["jalview.api.AlignViewControllerI"], "jalview.controller.AlignViewController", ["jalview.analysis.AlignmentSorter", "$.Grouping", "jalview.commands.OrderCommand", "jalview.datamodel.ColumnSelection", "jalview.io.FeaturesFile", "jalview.util.MessageManager", "java.awt.Color", "java.util.ArrayList", "$.BitSet"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.viewport = null;
+this.alignPanel = null;
+this.avcg = null;
+Clazz.instantialize (this, arguments);
+}, jalview.controller, "AlignViewController", null, jalview.api.AlignViewControllerI);
+Clazz.overrideMethod (c$, "finalize", 
+function () {
+this.viewport = null;
+this.alignPanel = null;
+this.avcg = null;
+});
+Clazz.makeConstructor (c$, 
+function (alignFrame, viewport, alignPanel) {
+this.avcg = alignFrame;
+this.viewport = viewport;
+this.alignPanel = alignPanel;
+}, "jalview.api.AlignViewControllerGuiI,jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
+Clazz.overrideMethod (c$, "setViewportAndAlignmentPanel", 
+function (viewport, alignPanel) {
+this.alignPanel = alignPanel;
+this.viewport = viewport;
+}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
+Clazz.overrideMethod (c$, "makeGroupsFromSelection", 
+function () {
+var sg = this.viewport.getSelectionGroup ();
+var cs = this.viewport.getColumnSelection ();
+var gps = null;
+if (sg != null && (cs == null || cs.getSelected () == null || cs.size () == 0)) {
+gps = jalview.analysis.Grouping.makeGroupsFrom (this.viewport.getSequenceSelection (), this.viewport.getAlignmentView (true).getSequenceStrings (this.viewport.getGapCharacter ()), this.viewport.getAlignment ().getGroups ());
+} else {
+if (cs != null) {
+gps = jalview.analysis.Grouping.makeGroupsFromCols ((sg == null) ? this.viewport.getAlignment ().getSequencesArray () : sg.getSequences ().toArray ( new Array (0)), cs, this.viewport.getAlignment ().getGroups ());
+}}if (gps != null) {
+this.viewport.getAlignment ().deleteAllGroups ();
+this.viewport.clearSequenceColours ();
+this.viewport.setSelectionGroup (null);
+for (var g = 0; g < gps.length; g++) {
+gps[g].setshowSequenceLogo (this.viewport.isShowSequenceLogo ());
+this.viewport.getAlignment ().addGroup (gps[g]);
+var col =  new java.awt.Color (Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255), Clazz.doubleToInt (Math.random () * 255));
+col = col.brighter ();
+for (var sq, $sq = gps[g].getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
+this.viewport.setSequenceColour (sq, col);
+}
+}
+return true;
+}return false;
+});
+Clazz.overrideMethod (c$, "createGroup", 
+function () {
+var sg = this.viewport.getSelectionGroup ();
+if (sg != null) {
+this.viewport.getAlignment ().addGroup (sg);
+return true;
+}return false;
+});
+Clazz.overrideMethod (c$, "unGroup", 
+function () {
+var sg = this.viewport.getSelectionGroup ();
+if (sg != null) {
+this.viewport.getAlignment ().deleteGroup (sg);
+return true;
+}return false;
+});
+Clazz.overrideMethod (c$, "deleteGroups", 
+function () {
+if (this.viewport.getAlignment ().getGroups () != null && this.viewport.getAlignment ().getGroups ().size () > 0) {
+this.viewport.getAlignment ().deleteAllGroups ();
+this.viewport.clearSequenceColours ();
+this.viewport.setSelectionGroup (null);
+return true;
+}return false;
+});
+Clazz.overrideMethod (c$, "markColumnsContainingFeatures", 
+function (invert, extendCurrent, toggle, featureType) {
+var bs =  new java.util.BitSet ();
+var alw;
+var alStart;
+var sqcol = (this.viewport.getSelectionGroup () == null ? this.viewport.getAlignment () : this.viewport.getSelectionGroup ());
+alStart = sqcol.getStartRes ();
+alw = sqcol.getEndRes () + 1;
+var seqs = sqcol.getSequences ();
+var nseq = 0;
+for (var sq, $sq = seqs.iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
+var tfeat = 0;
+if (sq != null) {
+var sf = sq.getSequenceFeatures ();
+if (sf != null) {
+var ist = sq.findIndex (sq.getStart ());
+var iend = sq.findIndex (sq.getEnd ());
+if (iend < alStart || ist > alw) {
+continue;
+}for (var sfpos, $sfpos = 0, $$sfpos = sf; $sfpos < $$sfpos.length && ((sfpos = $$sfpos[$sfpos]) || true); $sfpos++) {
+if (sfpos != null && (featureType.equals (sfpos.getType ()))) {
+tfeat++;
+var i = sq.findIndex (sfpos.getBegin ());
+var j = sq.findIndex (sfpos.getEnd ());
+if (j < alStart || i > alw) {
+continue;
+}if (i < alStart) {
+i = alStart;
+}if (i < ist) {
+i = ist;
+}if (j > alw) {
+j = alw;
+}for (; i <= j; i++) {
+bs.set (i - 1);
+}
+}}
+}if (tfeat > 0) {
+nseq++;
+}}}
+var cs = this.viewport.getColumnSelection ();
+if (bs.cardinality () > 0 || invert) {
+if (cs == null) {
+cs =  new jalview.datamodel.ColumnSelection ();
+} else {
+if (!extendCurrent) {
+cs.clear ();
+}}if (invert) {
+for (var i = bs.nextClearBit (alStart), ibs = bs.nextSetBit (alStart); i >= alStart && i < (alw); ) {
+if (ibs < 0 || i < ibs) {
+if (toggle && cs.contains (i)) {
+cs.removeElement (i++);
+} else {
+cs.addElement (i++);
+}} else {
+i = bs.nextClearBit (ibs);
+ibs = bs.nextSetBit (i);
+}}
+} else {
+for (var i = bs.nextSetBit (alStart); i >= alStart; i = bs.nextSetBit (i + 1)) {
+if (toggle && cs.contains (i)) {
+cs.removeElement (i);
+} else {
+cs.addElement (i);
+}}
+}this.viewport.setColumnSelection (cs);
+this.alignPanel.paintAlignment (true);
+this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.view_controller_toggled_marked",  Clazz.newArray (-1, [(toggle ? jalview.util.MessageManager.getString ("label.toggled") : jalview.util.MessageManager.getString ("label.marked")), (invert ? (Integer.$valueOf ((alw - alStart) - bs.cardinality ()).toString ()) : (Integer.$valueOf (bs.cardinality ()).toString ())), featureType, Integer.$valueOf (nseq).toString ()])));
+return true;
+} else {
+this.avcg.setStatus (jalview.util.MessageManager.formatMessage ("label.no_feature_of_type_found",  Clazz.newArray (-1, [featureType])));
+if (!extendCurrent && cs != null) {
+cs.clear ();
+this.alignPanel.paintAlignment (true);
+}return false;
+}}, "~B,~B,~B,~S");
+Clazz.overrideMethod (c$, "sortAlignmentByFeatureDensity", 
+function (typ) {
+this.sortBy (typ, "Sort by Density", jalview.analysis.AlignmentSorter.FEATURE_DENSITY);
+}, "~A");
+Clazz.defineMethod (c$, "sortBy", 
+function (typ, methodText, method) {
+var fr = this.alignPanel.getFeatureRenderer ();
+if (typ == null) {
+typ = fr == null ? null : fr.getDisplayedFeatureTypes ();
+}var gps = null;
+gps = fr == null ? null : fr.getDisplayedFeatureGroups ();
+if (typ != null) {
+var types =  new java.util.ArrayList ();
+for (var i = 0; i < typ.length; i++) {
+if (typ[i] != null) {
+types.add (typ[i]);
+}typ =  new Array (types.size ());
+types.toArray (typ);
+}
+}if (gps != null) {
+var grps =  new java.util.ArrayList ();
+for (var i = 0; i < gps.length; i++) {
+if (gps[i] != null) {
+grps.add (gps[i]);
+}}
+gps =  new Array (grps.size ());
+grps.toArray (gps);
+}var al = this.viewport.getAlignment ();
+var start;
+var stop;
+var sg = this.viewport.getSelectionGroup ();
+if (sg != null) {
+start = sg.getStartRes ();
+stop = sg.getEndRes ();
+} else {
+start = 0;
+stop = al.getWidth ();
+}var oldOrder = al.getSequencesArray ();
+jalview.analysis.AlignmentSorter.sortByFeature (typ, gps, start, stop, al, method);
+this.avcg.addHistoryItem ( new jalview.commands.OrderCommand (methodText, oldOrder, this.viewport.getAlignment ()));
+this.alignPanel.paintAlignment (true);
+}, "~A,~S,~S");
+Clazz.overrideMethod (c$, "sortAlignmentByFeatureScore", 
+function (typ) {
+this.sortBy (typ, "Sort by Feature Score", jalview.analysis.AlignmentSorter.FEATURE_SCORE);
+}, "~A");
+Clazz.overrideMethod (c$, "parseFeaturesFile", 
+function (file, protocol, relaxedIdMatching) {
+var featuresFile = false;
+try {
+featuresFile =  new jalview.io.FeaturesFile (file, protocol).parse (this.viewport.getAlignment ().getDataset (), this.alignPanel.getFeatureRenderer ().getFeatureColours (), false, relaxedIdMatching);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+if (featuresFile) {
+this.avcg.refreshFeatureUI (true);
+if (this.alignPanel.getFeatureRenderer () != null) {
+this.alignPanel.getFeatureRenderer ().findAllFeatures (true);
+}if (this.avcg.getFeatureSettingsUI () != null) {
+this.avcg.getFeatureSettingsUI ().discoverAllFeatureData ();
+}this.alignPanel.paintAlignment (true);
+}return featuresFile;
+}, "~S,~S,~B");
+});