X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fanalysis%2FAlignmentAnnotationUtils.js;h=9522f6eed2936cdb0f433608afdd711e8c963745;hp=f742aa97ea0692f90ed32eaf8d91d463999de1ae;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/analysis/AlignmentAnnotationUtils.js b/bin/jalview/analysis/AlignmentAnnotationUtils.js
index f742aa9..9522f6e 100644
--- a/bin/jalview/analysis/AlignmentAnnotationUtils.js
+++ b/bin/jalview/analysis/AlignmentAnnotationUtils.js
@@ -1,73 +1,73 @@
-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (null, "jalview.analysis.AlignmentAnnotationUtils", ["java.util.ArrayList", "$.Arrays", "$.BitSet", "$.Collections", "$.HashMap"], function () {
-c$ = Clazz.declareType (jalview.analysis, "AlignmentAnnotationUtils");
-c$.getShownHiddenTypes = Clazz.defineMethod (c$, "getShownHiddenTypes", 
-function (shownTypes, hiddenTypes, annotations, forSequences) {
-var visibleGraphGroups = jalview.analysis.AlignmentAnnotationUtils.getVisibleLineGraphGroups (annotations);
-var groupLabels =  new java.util.HashMap ();
-var addedToShown =  new java.util.ArrayList ();
-var addedToHidden =  new java.util.ArrayList ();
-for (var aa, $aa = annotations.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) {
-if (aa.annotations == null) {
-continue;
-}if (forSequences != null && (aa.sequenceRef != null && forSequences.contains (aa.sequenceRef))) {
-var calcId = aa.getCalcId ();
-var labelAsList =  new java.util.ArrayList ();
-var displayLabel = aa.label;
-labelAsList.add (displayLabel);
-if (aa.graph == 2 && aa.graphGroup > -1) {
-if (!groupLabels.containsKey (calcId)) {
-groupLabels.put (calcId,  new java.util.HashMap ());
-}var groupLabelsForCalcId = groupLabels.get (calcId);
-if (groupLabelsForCalcId.containsKey (new Integer (aa.graphGroup))) {
-if (!groupLabelsForCalcId.get (new Integer (aa.graphGroup)).contains (displayLabel)) {
-groupLabelsForCalcId.get (new Integer (aa.graphGroup)).add (displayLabel);
-}} else {
-groupLabelsForCalcId.put (new Integer (aa.graphGroup), labelAsList);
-}} else {
-var rememberAs = calcId + "!" + displayLabel;
-if (aa.visible && !addedToShown.contains (rememberAs)) {
-if (!shownTypes.containsKey (calcId)) {
-shownTypes.put (calcId,  new java.util.ArrayList ());
-}shownTypes.get (calcId).add (labelAsList);
-addedToShown.add (rememberAs);
-} else {
-if (!aa.visible && !addedToHidden.contains (rememberAs)) {
-if (!hiddenTypes.containsKey (calcId)) {
-hiddenTypes.put (calcId,  new java.util.ArrayList ());
-}hiddenTypes.get (calcId).add (labelAsList);
-addedToHidden.add (rememberAs);
-}}}}}
-for (var calcId, $calcId = groupLabels.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {
-for (var group, $group = groupLabels.get (calcId).keySet ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) {
-var groupLabel = groupLabels.get (calcId).get (new Integer (group));
-java.util.Collections.sort (groupLabel);
-if (visibleGraphGroups.get (group)) {
-if (!shownTypes.containsKey (calcId)) {
-shownTypes.put (calcId,  new java.util.ArrayList ());
-}if (!shownTypes.get (calcId).contains (groupLabel)) {
-shownTypes.get (calcId).add (groupLabel);
-}} else {
-if (!hiddenTypes.containsKey (calcId)) {
-hiddenTypes.put (calcId,  new java.util.ArrayList ());
-}if (!hiddenTypes.get (calcId).contains (groupLabel)) {
-hiddenTypes.get (calcId).add (groupLabel);
-}}}
-}
-}, "java.util.Map,java.util.Map,java.util.List,java.util.List");
-c$.getVisibleLineGraphGroups = Clazz.defineMethod (c$, "getVisibleLineGraphGroups", 
-function (annotations) {
-var result =  new java.util.BitSet ();
-for (var ann, $ann = annotations.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) {
-if (ann.graph == 2 && ann.visible) {
-var gg = ann.graphGroup;
-if (gg > -1) {
-result.set (gg);
-}}}
-return result;
-}, "java.util.List");
-c$.asList = Clazz.defineMethod (c$, "asList", 
-function (anns) {
-return (anns == null ? java.util.Collections.emptyList () : java.util.Arrays.asList (anns));
-}, "~A");
-});
+Clazz.declarePackage ("jalview.analysis");
+Clazz.load (null, "jalview.analysis.AlignmentAnnotationUtils", ["java.util.ArrayList", "$.Arrays", "$.BitSet", "$.Collections", "$.HashMap"], function () {
+c$ = Clazz.declareType (jalview.analysis, "AlignmentAnnotationUtils");
+c$.getShownHiddenTypes = Clazz.defineMethod (c$, "getShownHiddenTypes", 
+function (shownTypes, hiddenTypes, annotations, forSequences) {
+var visibleGraphGroups = jalview.analysis.AlignmentAnnotationUtils.getVisibleLineGraphGroups (annotations);
+var groupLabels =  new java.util.HashMap ();
+var addedToShown =  new java.util.ArrayList ();
+var addedToHidden =  new java.util.ArrayList ();
+for (var aa, $aa = annotations.iterator (); $aa.hasNext () && ((aa = $aa.next ()) || true);) {
+if (aa.annotations == null) {
+continue;
+}if (forSequences != null && (aa.sequenceRef != null && forSequences.contains (aa.sequenceRef))) {
+var calcId = aa.getCalcId ();
+var labelAsList =  new java.util.ArrayList ();
+var displayLabel = aa.label;
+labelAsList.add (displayLabel);
+if (aa.graph == 2 && aa.graphGroup > -1) {
+if (!groupLabels.containsKey (calcId)) {
+groupLabels.put (calcId,  new java.util.HashMap ());
+}var groupLabelsForCalcId = groupLabels.get (calcId);
+if (groupLabelsForCalcId.containsKey (new Integer (aa.graphGroup))) {
+if (!groupLabelsForCalcId.get (new Integer (aa.graphGroup)).contains (displayLabel)) {
+groupLabelsForCalcId.get (new Integer (aa.graphGroup)).add (displayLabel);
+}} else {
+groupLabelsForCalcId.put (new Integer (aa.graphGroup), labelAsList);
+}} else {
+var rememberAs = calcId + "!" + displayLabel;
+if (aa.visible && !addedToShown.contains (rememberAs)) {
+if (!shownTypes.containsKey (calcId)) {
+shownTypes.put (calcId,  new java.util.ArrayList ());
+}shownTypes.get (calcId).add (labelAsList);
+addedToShown.add (rememberAs);
+} else {
+if (!aa.visible && !addedToHidden.contains (rememberAs)) {
+if (!hiddenTypes.containsKey (calcId)) {
+hiddenTypes.put (calcId,  new java.util.ArrayList ());
+}hiddenTypes.get (calcId).add (labelAsList);
+addedToHidden.add (rememberAs);
+}}}}}
+for (var calcId, $calcId = groupLabels.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {
+for (var group, $group = groupLabels.get (calcId).keySet ().iterator (); $group.hasNext () && ((group = $group.next ()) || true);) {
+var groupLabel = groupLabels.get (calcId).get (new Integer (group));
+java.util.Collections.sort (groupLabel);
+if (visibleGraphGroups.get (group)) {
+if (!shownTypes.containsKey (calcId)) {
+shownTypes.put (calcId,  new java.util.ArrayList ());
+}if (!shownTypes.get (calcId).contains (groupLabel)) {
+shownTypes.get (calcId).add (groupLabel);
+}} else {
+if (!hiddenTypes.containsKey (calcId)) {
+hiddenTypes.put (calcId,  new java.util.ArrayList ());
+}if (!hiddenTypes.get (calcId).contains (groupLabel)) {
+hiddenTypes.get (calcId).add (groupLabel);
+}}}
+}
+}, "java.util.Map,java.util.Map,java.util.List,java.util.List");
+c$.getVisibleLineGraphGroups = Clazz.defineMethod (c$, "getVisibleLineGraphGroups", 
+function (annotations) {
+var result =  new java.util.BitSet ();
+for (var ann, $ann = annotations.iterator (); $ann.hasNext () && ((ann = $ann.next ()) || true);) {
+if (ann.graph == 2 && ann.visible) {
+var gg = ann.graphGroup;
+if (gg > -1) {
+result.set (gg);
+}}}
+return result;
+}, "java.util.List");
+c$.asList = Clazz.defineMethod (c$, "asList", 
+function (anns) {
+return (anns == null ? java.util.Collections.emptyList () : java.util.Arrays.asList (anns));
+}, "~A");
+});