X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fviewmodel%2FAlignmentViewport.js;h=cdbd489de97790dcb70497d5836476d8eaaccdcb;hp=6f07731967e6f730d045b17dec15aa738e3e26b3;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/viewmodel/AlignmentViewport.js b/bin/jalview/viewmodel/AlignmentViewport.js
index 6f07731..cdbd489 100644
--- a/bin/jalview/viewmodel/AlignmentViewport.js
+++ b/bin/jalview/viewmodel/AlignmentViewport.js
@@ -1,1254 +1,1254 @@
-Clazz.declarePackage ("jalview.viewmodel");
-Clazz.load (["jalview.api.AlignViewportI", "jalview.structure.CommandListener", "$.VamsasSource", "jalview.datamodel.ColumnSelection", "jalview.viewmodel.styles.ViewStyle", "jalview.workers.AlignCalcManager", "java.beans.PropertyChangeSupport", "java.util.ArrayDeque", "$.HashMap"], "jalview.viewmodel.AlignmentViewport", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.AlignmentView", "$.CigarArray", "$.Sequence", "$.SequenceGroup", "jalview.schemes.Blosum62ColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "jalview.util.Comparison", "$.MappingUtils", "jalview.workers.ComplementConsensusThread", "$.ConsensusThread", "$.ConservationThread", "$.StrucConsensusThread", "java.awt.Color", "java.util.ArrayList", "$.BitSet", "$.Hashtable"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.viewStyle = null;
-this.codingComplement = null;
-this.featuresDisplayed = null;
-this.historyList = null;
-this.redoList = null;
-this.alignment = null;
-this.sequenceSetID = null;
-this.$isDataset = false;
-this.hiddenRepSequences = null;
-this.colSel = null;
-this.autoCalculateConsensus = true;
-this.autoCalculateStrucConsensus = true;
-this.ignoreGapsInConsensusCalculation = false;
-this.globalColourScheme = null;
-this.consensus = null;
-this.complementConsensus = null;
-this.strucConsensus = null;
-this.conservation = null;
-this.quality = null;
-this.groupConsensus = null;
-this.groupConservation = null;
-this.hconsensus = null;
-this.hcomplementConsensus = null;
-this.hStrucConsensus = null;
-this.hconservation = null;
-this.ConsPercGaps = 25;
-this.calculator = null;
-this.showGroupConservation = false;
-this.showGroupConsensus = false;
-this.showSequenceLogo = false;
-this.normaliseSequenceLogo = false;
-this.showConsensusHistogram = true;
-this.padGaps = false;
-this.sortByTree = false;
-this.selectionGroup = null;
-this.viewId = null;
-this.sgrouphash = -1;
-this.colselhash = -1;
-this.changeSupport = null;
-this.showConservation = true;
-this.showQuality = true;
-this.showConsensus = true;
-this.sequenceColours = null;
-this.sortAnnotationsBy = null;
-this.showAutocalculatedAbove = false;
-this.followHighlight = true;
-this.startRes = 0;
-this.endRes = 0;
-this.startSeq = 0;
-this.endSeq = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.viewmodel, "AlignmentViewport", null, [jalview.api.AlignViewportI, jalview.structure.CommandListener, jalview.structure.VamsasSource]);
-Clazz.prepareFields (c$, function () {
-this.viewStyle =  new jalview.viewmodel.styles.ViewStyle ();
-this.historyList =  new java.util.ArrayDeque ();
-this.redoList =  new java.util.ArrayDeque ();
-this.colSel =  new jalview.datamodel.ColumnSelection ();
-this.calculator =  new jalview.workers.AlignCalcManager ();
-this.changeSupport =  new java.beans.PropertyChangeSupport (this);
-this.sequenceColours =  new java.util.HashMap ();
-});
-Clazz.defineMethod (c$, "setFontName", 
-function (name) {
-this.viewStyle.setFontName (name);
-}, "~S");
-Clazz.defineMethod (c$, "setFontStyle", 
-function (style) {
-this.viewStyle.setFontStyle (style);
-}, "~N");
-Clazz.defineMethod (c$, "setFontSize", 
-function (size) {
-this.viewStyle.setFontSize (size);
-}, "~N");
-Clazz.defineMethod (c$, "getFontStyle", 
-function () {
-return this.viewStyle.getFontStyle ();
-});
-Clazz.defineMethod (c$, "getFontName", 
-function () {
-return this.viewStyle.getFontName ();
-});
-Clazz.defineMethod (c$, "getFontSize", 
-function () {
-return this.viewStyle.getFontSize ();
-});
-Clazz.defineMethod (c$, "setUpperCasebold", 
-function (upperCasebold) {
-this.viewStyle.setUpperCasebold (upperCasebold);
-}, "~B");
-Clazz.defineMethod (c$, "isUpperCasebold", 
-function () {
-return this.viewStyle.isUpperCasebold ();
-});
-Clazz.defineMethod (c$, "isSeqNameItalics", 
-function () {
-return this.viewStyle.isSeqNameItalics ();
-});
-Clazz.defineMethod (c$, "setColourByReferenceSeq", 
-function (colourByReferenceSeq) {
-this.viewStyle.setColourByReferenceSeq (colourByReferenceSeq);
-}, "~B");
-Clazz.defineMethod (c$, "setColourAppliesToAllGroups", 
-function (b) {
-this.viewStyle.setColourAppliesToAllGroups (b);
-}, "~B");
-Clazz.defineMethod (c$, "getColourAppliesToAllGroups", 
-function () {
-return this.viewStyle.getColourAppliesToAllGroups ();
-});
-Clazz.defineMethod (c$, "getAbovePIDThreshold", 
-function () {
-return this.viewStyle.getAbovePIDThreshold ();
-});
-Clazz.defineMethod (c$, "setIncrement", 
-function (inc) {
-this.viewStyle.setIncrement (inc);
-}, "~N");
-Clazz.defineMethod (c$, "getIncrement", 
-function () {
-return this.viewStyle.getIncrement ();
-});
-Clazz.defineMethod (c$, "setConservationSelected", 
-function (b) {
-this.viewStyle.setConservationSelected (b);
-}, "~B");
-Clazz.defineMethod (c$, "setShowHiddenMarkers", 
-function (show) {
-this.viewStyle.setShowHiddenMarkers (show);
-}, "~B");
-Clazz.defineMethod (c$, "getShowHiddenMarkers", 
-function () {
-return this.viewStyle.getShowHiddenMarkers ();
-});
-Clazz.defineMethod (c$, "setScaleRightWrapped", 
-function (b) {
-this.viewStyle.setScaleRightWrapped (b);
-}, "~B");
-Clazz.defineMethod (c$, "setScaleLeftWrapped", 
-function (b) {
-this.viewStyle.setScaleLeftWrapped (b);
-}, "~B");
-Clazz.defineMethod (c$, "setScaleAboveWrapped", 
-function (b) {
-this.viewStyle.setScaleAboveWrapped (b);
-}, "~B");
-Clazz.defineMethod (c$, "getScaleLeftWrapped", 
-function () {
-return this.viewStyle.getScaleLeftWrapped ();
-});
-Clazz.defineMethod (c$, "getScaleAboveWrapped", 
-function () {
-return this.viewStyle.getScaleAboveWrapped ();
-});
-Clazz.defineMethod (c$, "getScaleRightWrapped", 
-function () {
-return this.viewStyle.getScaleRightWrapped ();
-});
-Clazz.defineMethod (c$, "setAbovePIDThreshold", 
-function (b) {
-this.viewStyle.setAbovePIDThreshold (b);
-}, "~B");
-Clazz.defineMethod (c$, "setThreshold", 
-function (thresh) {
-this.viewStyle.setThreshold (thresh);
-}, "~N");
-Clazz.defineMethod (c$, "getThreshold", 
-function () {
-return this.viewStyle.getThreshold ();
-});
-Clazz.defineMethod (c$, "getShowJVSuffix", 
-function () {
-return this.viewStyle.getShowJVSuffix ();
-});
-Clazz.defineMethod (c$, "setShowJVSuffix", 
-function (b) {
-this.viewStyle.setShowJVSuffix (b);
-}, "~B");
-Clazz.defineMethod (c$, "setWrapAlignment", 
-function (state) {
-this.viewStyle.setWrapAlignment (state);
-}, "~B");
-Clazz.defineMethod (c$, "setShowText", 
-function (state) {
-this.viewStyle.setShowText (state);
-}, "~B");
-Clazz.defineMethod (c$, "setRenderGaps", 
-function (state) {
-this.viewStyle.setRenderGaps (state);
-}, "~B");
-Clazz.defineMethod (c$, "getColourText", 
-function () {
-return this.viewStyle.getColourText ();
-});
-Clazz.defineMethod (c$, "setColourText", 
-function (state) {
-this.viewStyle.setColourText (state);
-}, "~B");
-Clazz.defineMethod (c$, "getWrapAlignment", 
-function () {
-return this.viewStyle.getWrapAlignment ();
-});
-Clazz.defineMethod (c$, "getShowText", 
-function () {
-return this.viewStyle.getShowText ();
-});
-Clazz.defineMethod (c$, "getWrappedWidth", 
-function () {
-return this.viewStyle.getWrappedWidth ();
-});
-Clazz.defineMethod (c$, "setWrappedWidth", 
-function (w) {
-this.viewStyle.setWrappedWidth (w);
-}, "~N");
-Clazz.defineMethod (c$, "getCharHeight", 
-function () {
-return this.viewStyle.getCharHeight ();
-});
-Clazz.defineMethod (c$, "setCharHeight", 
-function (h) {
-this.viewStyle.setCharHeight (h);
-}, "~N");
-Clazz.defineMethod (c$, "getCharWidth", 
-function () {
-return this.viewStyle.getCharWidth ();
-});
-Clazz.defineMethod (c$, "setCharWidth", 
-function (w) {
-this.viewStyle.setCharWidth (w);
-}, "~N");
-Clazz.defineMethod (c$, "getShowBoxes", 
-function () {
-return this.viewStyle.getShowBoxes ();
-});
-Clazz.defineMethod (c$, "getShowUnconserved", 
-function () {
-return this.viewStyle.getShowUnconserved ();
-});
-Clazz.defineMethod (c$, "setShowUnconserved", 
-function (showunconserved) {
-this.viewStyle.setShowUnconserved (showunconserved);
-}, "~B");
-Clazz.defineMethod (c$, "setSeqNameItalics", 
-function (default1) {
-this.viewStyle.setSeqNameItalics (default1);
-}, "~B");
-Clazz.defineMethod (c$, "getAlignment", 
-function () {
-return this.alignment;
-});
-Clazz.overrideMethod (c$, "getGapCharacter", 
-function () {
-return this.alignment.getGapCharacter ();
-});
-Clazz.defineMethod (c$, "setDataset", 
-function (b) {
-this.$isDataset = b;
-}, "~B");
-Clazz.defineMethod (c$, "isDataset", 
-function () {
-return this.$isDataset;
-});
-Clazz.overrideMethod (c$, "setGlobalColourScheme", 
-function (cs) {
-this.globalColourScheme = cs;
-var recalc = false;
-if (cs != null) {
-cs.setConservationApplied (recalc = this.getConservationSelected ());
-if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
-recalc = true;
-cs.setThreshold (this.viewStyle.getThreshold (), this.ignoreGapsInConsensusCalculation);
-} else {
-cs.setThreshold (0, this.ignoreGapsInConsensusCalculation);
-}if (recalc) {
-cs.setConsensus (this.hconsensus);
-cs.setConservation (this.hconservation);
-}cs.alignmentChanged (this.alignment, this.hiddenRepSequences);
-}if (this.getColourAppliesToAllGroups ()) {
-for (var sg, $sg = this.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (cs == null) {
-sg.cs = null;
-continue;
-}sg.cs = cs.applyTo (sg, this.getHiddenRepSequences ());
-sg.setConsPercGaps (this.ConsPercGaps);
-if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
-sg.cs.setThreshold (this.viewStyle.getThreshold (), this.isIgnoreGapsConsensus ());
-recalc = true;
-} else {
-sg.cs.setThreshold (0, this.isIgnoreGapsConsensus ());
-}if (this.getConservationSelected ()) {
-sg.cs.setConservationApplied (true);
-recalc = true;
-} else {
-sg.cs.setConservation (null);
-}if (recalc) {
-sg.recalcConservation ();
-} else {
-sg.cs.alignmentChanged (sg, this.hiddenRepSequences);
-}}
-}}, "jalview.schemes.ColourSchemeI");
-Clazz.overrideMethod (c$, "getGlobalColourScheme", 
-function () {
-return this.globalColourScheme;
-});
-Clazz.overrideMethod (c$, "setConservation", 
-function (cons) {
-this.hconservation = cons;
-}, "jalview.analysis.Conservation");
-Clazz.overrideMethod (c$, "getConsPercGaps", 
-function () {
-return this.ConsPercGaps;
-});
-Clazz.overrideMethod (c$, "setSequenceConsensusHash", 
-function (hconsensus) {
-this.hconsensus = hconsensus;
-}, "~A");
-Clazz.overrideMethod (c$, "setComplementConsensusHash", 
-function (hconsensus) {
-this.hcomplementConsensus = hconsensus;
-}, "~A");
-Clazz.overrideMethod (c$, "getSequenceConsensusHash", 
-function () {
-return this.hconsensus;
-});
-Clazz.overrideMethod (c$, "getComplementConsensusHash", 
-function () {
-return this.hcomplementConsensus;
-});
-Clazz.overrideMethod (c$, "getRnaStructureConsensusHash", 
-function () {
-return this.hStrucConsensus;
-});
-Clazz.overrideMethod (c$, "setRnaStructureConsensusHash", 
-function (hStrucConsensus) {
-this.hStrucConsensus = hStrucConsensus;
-}, "~A");
-Clazz.overrideMethod (c$, "getAlignmentQualityAnnot", 
-function () {
-return this.quality;
-});
-Clazz.overrideMethod (c$, "getAlignmentConservationAnnotation", 
-function () {
-return this.conservation;
-});
-Clazz.overrideMethod (c$, "getAlignmentConsensusAnnotation", 
-function () {
-return this.consensus;
-});
-Clazz.overrideMethod (c$, "getComplementConsensusAnnotation", 
-function () {
-return this.complementConsensus;
-});
-Clazz.overrideMethod (c$, "getAlignmentStrucConsensusAnnotation", 
-function () {
-return this.strucConsensus;
-});
-Clazz.defineMethod (c$, "updateConservation", 
-function (ap) {
-if (this.alignment.isNucleotide () || this.conservation == null || !this.autoCalculateConsensus) {
-return;
-}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConservationThread) == null) {
-this.calculator.registerWorker ( new jalview.workers.ConservationThread (this, ap));
-}}, "jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "updateConsensus", 
-function (ap) {
-if (this.consensus == null || !this.autoCalculateConsensus) {
-return;
-}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConsensusThread) == null) {
-this.calculator.registerWorker ( new jalview.workers.ConsensusThread (this, ap));
-}var al = this.getAlignment ();
-if (!al.isNucleotide () && al.getCodonFrames () != null && !al.getCodonFrames ().isEmpty ()) {
-if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ComplementConsensusThread) == null) {
-this.calculator.registerWorker ( new jalview.workers.ComplementConsensusThread (this, ap));
-}}}, "jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "updateStrucConsensus", 
-function (ap) {
-if (this.autoCalculateStrucConsensus && this.strucConsensus == null && this.alignment.isNucleotide () && this.alignment.hasRNAStructure ()) {
-this.initRNAStructure ();
-}if (this.strucConsensus == null || !this.autoCalculateStrucConsensus) {
-return;
-}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.StrucConsensusThread) == null) {
-this.calculator.registerWorker ( new jalview.workers.StrucConsensusThread (this, ap));
-}}, "jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "isCalcInProgress", 
-function () {
-return this.calculator.isWorking ();
-});
-Clazz.overrideMethod (c$, "isCalculationInProgress", 
-function (alignmentAnnotation) {
-if (!alignmentAnnotation.autoCalculated) {
-return false;
-}if (this.calculator.workingInvolvedWith (alignmentAnnotation)) {
-return true;
-}return false;
-}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.overrideMethod (c$, "isClosed", 
-function () {
-return this.alignment == null;
-});
-Clazz.overrideMethod (c$, "getCalcManager", 
-function () {
-return this.calculator;
-});
-Clazz.overrideMethod (c$, "isShowSequenceLogo", 
-function () {
-return this.showSequenceLogo;
-});
-Clazz.defineMethod (c$, "setShowSequenceLogo", 
-function (showSequenceLogo) {
-if (showSequenceLogo != this.showSequenceLogo) {
-this.showSequenceLogo = showSequenceLogo;
-this.calculator.updateAnnotationFor (jalview.workers.ConsensusThread);
-this.calculator.updateAnnotationFor (jalview.workers.ComplementConsensusThread);
-this.calculator.updateAnnotationFor (jalview.workers.StrucConsensusThread);
-}this.showSequenceLogo = showSequenceLogo;
-}, "~B");
-Clazz.defineMethod (c$, "setShowConsensusHistogram", 
-function (showConsensusHistogram) {
-this.showConsensusHistogram = showConsensusHistogram;
-}, "~B");
-Clazz.defineMethod (c$, "isShowGroupConservation", 
-function () {
-return this.showGroupConservation;
-});
-Clazz.defineMethod (c$, "setShowGroupConservation", 
-function (showGroupConservation) {
-this.showGroupConservation = showGroupConservation;
-}, "~B");
-Clazz.defineMethod (c$, "isShowGroupConsensus", 
-function () {
-return this.showGroupConsensus;
-});
-Clazz.defineMethod (c$, "setShowGroupConsensus", 
-function (showGroupConsensus) {
-this.showGroupConsensus = showGroupConsensus;
-}, "~B");
-Clazz.overrideMethod (c$, "isShowConsensusHistogram", 
-function () {
-return this.showConsensusHistogram;
-});
-Clazz.overrideMethod (c$, "getSelectionGroup", 
-function () {
-return this.selectionGroup;
-});
-Clazz.overrideMethod (c$, "setSelectionGroup", 
-function (sg) {
-this.selectionGroup = sg;
-}, "jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "setHiddenColumns", 
-function (colsel) {
-this.colSel = colsel;
-}, "jalview.datamodel.ColumnSelection");
-Clazz.overrideMethod (c$, "getColumnSelection", 
-function () {
-return this.colSel;
-});
-Clazz.overrideMethod (c$, "setColumnSelection", 
-function (colSel) {
-this.colSel = colSel;
-if (colSel != null) {
-this.updateHiddenColumns ();
-}}, "jalview.datamodel.ColumnSelection");
-Clazz.overrideMethod (c$, "getHiddenRepSequences", 
-function () {
-return this.hiddenRepSequences;
-});
-Clazz.overrideMethod (c$, "setHiddenRepSequences", 
-function (hiddenRepSequences) {
-this.hiddenRepSequences = hiddenRepSequences;
-}, "java.util.Map");
-Clazz.overrideMethod (c$, "hasHiddenColumns", 
-function () {
-return this.colSel != null && this.colSel.hasHiddenColumns ();
-});
-Clazz.defineMethod (c$, "updateHiddenColumns", 
-function () {
-});
-Clazz.overrideMethod (c$, "hasHiddenRows", 
-function () {
-return this.alignment.getHiddenSequences ().getSize () > 0;
-});
-Clazz.defineMethod (c$, "setSequenceSetId", 
-function (newid) {
-if (this.sequenceSetID != null) {
-System.err.println ("Warning - overwriting a sequenceSetId for a viewport!");
-}this.sequenceSetID =  String.instantialize (newid);
-}, "~S");
-Clazz.overrideMethod (c$, "getSequenceSetId", 
-function () {
-if (this.sequenceSetID == null) {
-this.sequenceSetID = this.alignment.hashCode () + "";
-}return this.sequenceSetID;
-});
-Clazz.overrideMethod (c$, "getViewId", 
-function () {
-if (this.viewId == null) {
-this.viewId = this.getSequenceSetId () + "." + this.hashCode () + "";
-}return this.viewId;
-});
-Clazz.defineMethod (c$, "setIgnoreGapsConsensus", 
-function (b, ap) {
-this.ignoreGapsInConsensusCalculation = b;
-if (ap != null) {
-this.updateConsensus (ap);
-if (this.globalColourScheme != null) {
-this.globalColourScheme.setThreshold (this.globalColourScheme.getThreshold (), this.ignoreGapsInConsensusCalculation);
-}}}, "~B,jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "isSelectionGroupChanged", 
-function (b) {
-var hc = (this.selectionGroup == null || this.selectionGroup.getSize () == 0) ? -1 : this.selectionGroup.hashCode ();
-if (hc != -1 && hc != this.sgrouphash) {
-if (b) {
-this.sgrouphash = hc;
-}return true;
-}return false;
-}, "~B");
-Clazz.defineMethod (c$, "isColSelChanged", 
-function (b) {
-var hc = (this.colSel == null || this.colSel.size () == 0) ? -1 : this.colSel.hashCode ();
-if (hc != -1 && hc != this.colselhash) {
-if (b) {
-this.colselhash = hc;
-}return true;
-}return false;
-}, "~B");
-Clazz.overrideMethod (c$, "isIgnoreGapsConsensus", 
-function () {
-return this.ignoreGapsInConsensusCalculation;
-});
-Clazz.defineMethod (c$, "addPropertyChangeListener", 
-function (listener) {
-this.changeSupport.addPropertyChangeListener (listener);
-}, "java.beans.PropertyChangeListener");
-Clazz.defineMethod (c$, "removePropertyChangeListener", 
-function (listener) {
-this.changeSupport.removePropertyChangeListener (listener);
-}, "java.beans.PropertyChangeListener");
-Clazz.defineMethod (c$, "firePropertyChange", 
-function (prop, oldvalue, newvalue) {
-this.changeSupport.firePropertyChange (prop, oldvalue, newvalue);
-}, "~S,~O,~O");
-Clazz.defineMethod (c$, "hideSelectedColumns", 
-function () {
-if (this.colSel.size () < 1) {
-return;
-}this.colSel.hideSelectedColumns ();
-this.setSelectionGroup (null);
-});
-Clazz.defineMethod (c$, "hideColumns", 
-function (start, end) {
-if (start == end) {
-this.colSel.hideColumns (start);
-} else {
-this.colSel.hideColumns (start, end);
-}}, "~N,~N");
-Clazz.defineMethod (c$, "showColumn", 
-function (col) {
-this.colSel.revealHiddenColumns (col);
-}, "~N");
-Clazz.defineMethod (c$, "showAllHiddenColumns", 
-function () {
-this.colSel.revealAllHiddenColumns ();
-});
-Clazz.defineMethod (c$, "showAllHiddenSeqs", 
-function () {
-if (this.alignment.getHiddenSequences ().getSize () > 0) {
-if (this.selectionGroup == null) {
-this.selectionGroup =  new jalview.datamodel.SequenceGroup ();
-this.selectionGroup.setEndRes (this.alignment.getWidth () - 1);
-}var tmp = this.alignment.getHiddenSequences ().showAll (this.hiddenRepSequences);
-for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-this.selectionGroup.addSequence (seq, false);
-this.setSequenceAnnotationsVisible (seq, true);
-}
-this.hiddenRepSequences = null;
-this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
-this.sendSelection ();
-}});
-Clazz.defineMethod (c$, "showSequence", 
-function (index) {
-var tmp = this.alignment.getHiddenSequences ().showSequence (index, this.hiddenRepSequences);
-if (tmp.size () > 0) {
-if (this.selectionGroup == null) {
-this.selectionGroup =  new jalview.datamodel.SequenceGroup ();
-this.selectionGroup.setEndRes (this.alignment.getWidth () - 1);
-}for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
-this.selectionGroup.addSequence (seq, false);
-this.setSequenceAnnotationsVisible (seq, true);
-}
-this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
-this.sendSelection ();
-}}, "~N");
-Clazz.defineMethod (c$, "hideAllSelectedSeqs", 
-function () {
-if (this.selectionGroup == null || this.selectionGroup.getSize () < 1) {
-return;
-}var seqs = this.selectionGroup.getSequencesInOrder (this.alignment);
-this.hideSequence (seqs);
-this.setSelectionGroup (null);
-});
-Clazz.defineMethod (c$, "hideSequence", 
-function (seq) {
-if (seq != null) {
-for (var i = 0; i < seq.length; i++) {
-this.alignment.getHiddenSequences ().hideSequence (seq[i]);
-this.setSequenceAnnotationsVisible (seq[i], false);
-}
-this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
-}}, "~A");
-Clazz.defineMethod (c$, "setSequenceAnnotationsVisible", 
-function (sequenceI, visible) {
-for (var ann, $ann = 0, $$ann = this.alignment.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) {
-if (ann.sequenceRef === sequenceI) {
-ann.visible = visible;
-}}
-}, "jalview.datamodel.SequenceI,~B");
-Clazz.defineMethod (c$, "hideRepSequences", 
-function (repSequence, sg) {
-var sSize = sg.getSize ();
-if (sSize < 2) {
-return;
-}if (this.hiddenRepSequences == null) {
-this.hiddenRepSequences =  new java.util.Hashtable ();
-}this.hiddenRepSequences.put (repSequence, sg);
-var seqs =  new Array (sSize - 1);
-var index = 0;
-for (var i = 0; i < sSize; i++) {
-if (sg.getSequenceAt (i) !== repSequence) {
-if (index == sSize - 1) {
-return;
-}seqs[index++] = sg.getSequenceAt (i);
-}}
-sg.setSeqrep (repSequence);
-sg.setHidereps (true);
-this.hideSequence (seqs);
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup");
-Clazz.defineMethod (c$, "isHiddenRepSequence", 
-function (seq) {
-return this.alignment.getSeqrep () === seq || (this.hiddenRepSequences != null && this.hiddenRepSequences.containsKey (seq));
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "getRepresentedSequences", 
-function (seq) {
-return (this.hiddenRepSequences == null ? null : this.hiddenRepSequences.get (seq));
-}, "jalview.datamodel.SequenceI");
-Clazz.overrideMethod (c$, "adjustForHiddenSeqs", 
-function (alignmentIndex) {
-return this.alignment.getHiddenSequences ().adjustForHiddenSeqs (alignmentIndex);
-}, "~N");
-Clazz.overrideMethod (c$, "invertColumnSelection", 
-function () {
-this.colSel.invertColumnSelection (0, this.alignment.getWidth ());
-});
-Clazz.overrideMethod (c$, "getSelectionAsNewSequence", 
-function () {
-var sequences;
-if (this.selectionGroup == null || this.selectionGroup.getSize () == 0) {
-sequences = this.alignment.getSequencesArray ();
-var annots = this.alignment.getAlignmentAnnotation ();
-for (var i = 0; i < sequences.length; i++) {
-sequences[i] =  new jalview.datamodel.Sequence (sequences[i], annots);
-}
-} else {
-sequences = this.selectionGroup.getSelectionAsNewSequences (this.alignment);
-}return sequences;
-});
-Clazz.overrideMethod (c$, "getSequenceSelection", 
-function () {
-var sequences = null;
-if (this.selectionGroup != null) {
-sequences = this.selectionGroup.getSequencesInOrder (this.alignment);
-}if (sequences == null) {
-sequences = this.alignment.getSequencesArray ();
-}return sequences;
-});
-Clazz.overrideMethod (c$, "getViewAsCigars", 
-function (selectedRegionOnly) {
-return  new jalview.datamodel.CigarArray (this.alignment, this.colSel, (selectedRegionOnly ? this.selectionGroup : null));
-}, "~B");
-Clazz.defineMethod (c$, "getAlignmentView", 
-function (selectedOnly) {
-return this.getAlignmentView (selectedOnly, false);
-}, "~B");
-Clazz.defineMethod (c$, "getAlignmentView", 
-function (selectedOnly, markGroups) {
-return  new jalview.datamodel.AlignmentView (this.alignment, this.colSel, this.selectionGroup, this.colSel != null && this.colSel.hasHiddenColumns (), selectedOnly, markGroups);
-}, "~B,~B");
-Clazz.overrideMethod (c$, "getViewAsString", 
-function (selectedRegionOnly) {
-var selection = null;
-var seqs = null;
-var i;
-var iSize;
-var start = 0;
-var end = 0;
-if (selectedRegionOnly && this.selectionGroup != null) {
-iSize = this.selectionGroup.getSize ();
-seqs = this.selectionGroup.getSequencesInOrder (this.alignment);
-start = this.selectionGroup.getStartRes ();
-end = this.selectionGroup.getEndRes () + 1;
-} else {
-iSize = this.alignment.getHeight ();
-seqs = this.alignment.getSequencesArray ();
-end = this.alignment.getWidth ();
-}selection =  new Array (iSize);
-if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
-selection = this.colSel.getVisibleSequenceStrings (start, end, seqs);
-} else {
-for (i = 0; i < iSize; i++) {
-selection[i] = seqs[i].getSequenceAsString (start, end);
-}
-}return selection;
-}, "~B");
-Clazz.overrideMethod (c$, "getVisibleRegionBoundaries", 
-function (min, max) {
-var regions =  new java.util.ArrayList ();
-var start = min;
-var end = max;
-do {
-if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
-if (start == 0) {
-start = this.colSel.adjustForHiddenColumns (start);
-}end = this.colSel.getHiddenBoundaryRight (start);
-if (start == end) {
-end = max;
-}if (end > max) {
-end = max;
-}}regions.add ( Clazz.newIntArray (-1, [start, end]));
-if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
-start = this.colSel.adjustForHiddenColumns (end);
-start = this.colSel.getHiddenBoundaryLeft (start) + 1;
-}} while (end < max);
-var startEnd =  Clazz.newIntArray (regions.size (), 2, 0);
-return regions;
-}, "~N,~N");
-Clazz.overrideMethod (c$, "getVisibleAlignmentAnnotation", 
-function (selectedOnly) {
-var ala =  new java.util.ArrayList ();
-var aa;
-if ((aa = this.alignment.getAlignmentAnnotation ()) != null) {
-for (var annot, $annot = 0, $$annot = aa; $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) {
-var clone =  new jalview.datamodel.AlignmentAnnotation (annot);
-if (selectedOnly && this.selectionGroup != null) {
-this.colSel.makeVisibleAnnotation (this.selectionGroup.getStartRes (), this.selectionGroup.getEndRes (), clone);
-} else {
-this.colSel.makeVisibleAnnotation (clone);
-}ala.add (clone);
-}
-}return ala;
-}, "~B");
-Clazz.overrideMethod (c$, "isPadGaps", 
-function () {
-return this.padGaps;
-});
-Clazz.overrideMethod (c$, "setPadGaps", 
-function (padGaps) {
-this.padGaps = padGaps;
-}, "~B");
-Clazz.overrideMethod (c$, "alignmentChanged", 
-function (ap) {
-if (this.isPadGaps ()) {
-this.alignment.padGaps ();
-}if (this.autoCalculateConsensus) {
-this.updateConsensus (ap);
-}if (this.hconsensus != null && this.autoCalculateConsensus) {
-this.updateConservation (ap);
-}if (this.autoCalculateStrucConsensus) {
-this.updateStrucConsensus (ap);
-}var alWidth = this.alignment.getWidth ();
-var groups = this.alignment.getGroups ();
-if (groups != null) {
-for (var sg, $sg = groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.getEndRes () > alWidth) {
-sg.setEndRes (alWidth - 1);
-}}
-}if (this.selectionGroup != null && this.selectionGroup.getEndRes () > alWidth) {
-this.selectionGroup.setEndRes (alWidth - 1);
-}this.resetAllColourSchemes ();
-this.calculator.restartWorkers ();
-}, "jalview.api.AlignmentViewPanel");
-Clazz.defineMethod (c$, "resetAllColourSchemes", 
-function () {
-var cs = this.globalColourScheme;
-if (cs != null) {
-cs.alignmentChanged (this.alignment, this.hiddenRepSequences);
-cs.setConsensus (this.hconsensus);
-if (cs.conservationApplied ()) {
-cs.setConservation (jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.alignment.getWidth (), false, this.getConsPercGaps (), false));
-}}for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.cs != null) {
-sg.cs.alignmentChanged (sg, this.hiddenRepSequences);
-}sg.recalcConservation ();
-}
-});
-Clazz.defineMethod (c$, "initAutoAnnotation", 
-function () {
-if (this.hconsensus == null && !this.$isDataset) {
-if (!this.alignment.isNucleotide ()) {
-this.initConservation ();
-this.initQuality ();
-} else {
-this.initRNAStructure ();
-}this.consensus =  new jalview.datamodel.AlignmentAnnotation ("Consensus", "PID",  new Array (1), 0, 100, 1);
-this.initConsensus (this.consensus);
-this.initComplementConsensus ();
-}});
-Clazz.defineMethod (c$, "initComplementConsensus", 
-function () {
-if (!this.alignment.isNucleotide ()) {
-var codonMappings = this.alignment.getCodonFrames ();
-if (codonMappings != null && !codonMappings.isEmpty ()) {
-this.complementConsensus =  new jalview.datamodel.AlignmentAnnotation ("cDNA Consensus", "PID for cDNA",  new Array (1), 0, 100, 1);
-this.initConsensus (this.complementConsensus);
-}}});
-Clazz.defineMethod (c$, "initConsensus", 
-($fz = function (aa) {
-aa.hasText = true;
-aa.autoCalculated = true;
-if (this.showConsensus) {
-this.alignment.addAnnotation (aa);
-}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation");
-Clazz.defineMethod (c$, "initConservation", 
-($fz = function () {
-if (this.showConservation) {
-if (this.conservation == null) {
-this.conservation =  new jalview.datamodel.AlignmentAnnotation ("Conservation", "Conservation of total alignment less than " + this.getConsPercGaps () + "% gaps",  new Array (1), 0, 11, 1);
-this.conservation.hasText = true;
-this.conservation.autoCalculated = true;
-this.alignment.addAnnotation (this.conservation);
-}}}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "initQuality", 
-($fz = function () {
-if (this.showQuality) {
-if (this.quality == null) {
-this.quality =  new jalview.datamodel.AlignmentAnnotation ("Quality", "Alignment Quality based on Blosum62 scores",  new Array (1), 0, 11, 1);
-this.quality.hasText = true;
-this.quality.autoCalculated = true;
-this.alignment.addAnnotation (this.quality);
-}}}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "initRNAStructure", 
-($fz = function () {
-if (this.alignment.hasRNAStructure () && this.strucConsensus == null) {
-this.strucConsensus =  new jalview.datamodel.AlignmentAnnotation ("StrucConsensus", "PID",  new Array (1), 0, 100, 1);
-this.strucConsensus.hasText = true;
-this.strucConsensus.autoCalculated = true;
-if (this.showConsensus) {
-this.alignment.addAnnotation (this.strucConsensus);
-}}}, $fz.isPrivate = true, $fz));
-Clazz.overrideMethod (c$, "calcPanelHeight", 
-function () {
-var anns = this.getAlignment ().getAlignmentAnnotation ();
-var height = 0;
-var charHeight = this.getCharHeight ();
-if (anns != null) {
-var graphgrp =  new java.util.BitSet ();
-for (var aa, $aa = 0, $$aa = anns; $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) {
-if (aa == null) {
-System.err.println ("Null annotation row: ignoring.");
-continue;
-}if (!aa.visible) {
-continue;
-}if (aa.graphGroup > -1) {
-if (graphgrp.get (aa.graphGroup)) {
-continue;
-} else {
-graphgrp.set (aa.graphGroup);
-}}aa.height = 0;
-if (aa.hasText) {
-aa.height += charHeight;
-}if (aa.hasIcons) {
-aa.height += 16;
-}if (aa.graph > 0) {
-aa.height += aa.graphHeight;
-}if (aa.height == 0) {
-aa.height = 20;
-}height += aa.height;
-}
-}if (height == 0) {
-height = 20;
-}return height;
-});
-Clazz.overrideMethod (c$, "updateGroupAnnotationSettings", 
-function (applyGlobalSettings, preserveNewGroupSettings) {
-var updateCalcs = false;
-var conv = this.isShowGroupConservation ();
-var cons = this.isShowGroupConsensus ();
-var showprf = this.isShowSequenceLogo ();
-var showConsHist = this.isShowConsensusHistogram ();
-var normLogo = this.isNormaliseSequenceLogo ();
-var sortg = true;
-var aan = this.alignment.getAlignmentAnnotation ();
-var oldrfs =  new java.util.ArrayList ();
-if (aan != null) {
-for (var an = 0; an < aan.length; an++) {
-if (aan[an].autoCalculated && aan[an].groupRef != null) {
-oldrfs.add (aan[an].groupRef);
-this.alignment.deleteAnnotation (aan[an], false);
-}}
-}if (this.alignment.getGroups () != null) {
-for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-updateCalcs = false;
-if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.contains (sg))) {
-sg.setshowSequenceLogo (showprf);
-sg.setShowConsensusHistogram (showConsHist);
-sg.setNormaliseSequenceLogo (normLogo);
-}if (conv) {
-updateCalcs = true;
-this.alignment.addAnnotation (sg.getConservationRow (), 0);
-}if (cons) {
-updateCalcs = true;
-this.alignment.addAnnotation (sg.getConsensus (), 0);
-}if (updateCalcs) {
-sg.recalcConservation ();
-}}
-}oldrfs.clear ();
-}, "~B,~B");
-Clazz.defineMethod (c$, "isDisplayReferenceSeq", 
-function () {
-return this.alignment.hasSeqrep () && this.viewStyle.isDisplayReferenceSeq ();
-});
-Clazz.defineMethod (c$, "setDisplayReferenceSeq", 
-function (displayReferenceSeq) {
-this.viewStyle.setDisplayReferenceSeq (displayReferenceSeq);
-}, "~B");
-Clazz.defineMethod (c$, "isColourByReferenceSeq", 
-function () {
-return this.alignment.hasSeqrep () && this.viewStyle.isColourByReferenceSeq ();
-});
-Clazz.overrideMethod (c$, "getSequenceColour", 
-function (seq) {
-var sqc = this.sequenceColours.get (seq);
-return (sqc == null ? java.awt.Color.white : sqc);
-}, "jalview.datamodel.SequenceI");
-Clazz.overrideMethod (c$, "setSequenceColour", 
-function (seq, col) {
-if (col == null) {
-this.sequenceColours.remove (seq);
-} else {
-this.sequenceColours.put (seq, col);
-}}, "jalview.datamodel.SequenceI,java.awt.Color");
-Clazz.overrideMethod (c$, "updateSequenceIdColours", 
-function () {
-for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
-if (sg.idColour != null) {
-for (var s, $s = sg.getSequences (this.getHiddenRepSequences ()).iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
-this.sequenceColours.put (s, sg.idColour);
-}
-}}
-});
-Clazz.overrideMethod (c$, "clearSequenceColours", 
-function () {
-this.sequenceColours.clear ();
-});
-Clazz.defineMethod (c$, "getCodingComplement", 
-function () {
-return this.codingComplement;
-});
-Clazz.defineMethod (c$, "setCodingComplement", 
-function (av) {
-if (this === av) {
-System.err.println ("Ignoring recursive setCodingComplement request");
-} else {
-this.codingComplement = av;
-if (av.getCodingComplement () !== this) {
-av.setCodingComplement (this);
-}}}, "jalview.api.AlignViewportI");
-Clazz.overrideMethod (c$, "isNucleotide", 
-function () {
-return this.getAlignment () == null ? false : this.getAlignment ().isNucleotide ();
-});
-Clazz.overrideMethod (c$, "getFeaturesDisplayed", 
-function () {
-return this.featuresDisplayed;
-});
-Clazz.overrideMethod (c$, "setFeaturesDisplayed", 
-function (featuresDisplayedI) {
-this.featuresDisplayed = featuresDisplayedI;
-}, "jalview.api.FeaturesDisplayedI");
-Clazz.overrideMethod (c$, "areFeaturesDisplayed", 
-function () {
-return this.featuresDisplayed != null && this.featuresDisplayed.getRegisterdFeaturesCount () > 0;
-});
-Clazz.defineMethod (c$, "setShowSequenceFeatures", 
-function (b) {
-this.viewStyle.setShowSequenceFeatures (b);
-}, "~B");
-Clazz.defineMethod (c$, "isShowSequenceFeatures", 
-function () {
-return this.viewStyle.isShowSequenceFeatures ();
-});
-Clazz.defineMethod (c$, "setShowSequenceFeaturesHeight", 
-function (selected) {
-this.viewStyle.setShowSequenceFeaturesHeight (selected);
-}, "~B");
-Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", 
-function () {
-return this.viewStyle.isShowSequenceFeaturesHeight ();
-});
-Clazz.defineMethod (c$, "setShowAnnotation", 
-function (b) {
-this.viewStyle.setShowAnnotation (b);
-}, "~B");
-Clazz.defineMethod (c$, "isShowAnnotation", 
-function () {
-return this.viewStyle.isShowAnnotation ();
-});
-Clazz.defineMethod (c$, "isRightAlignIds", 
-function () {
-return this.viewStyle.isRightAlignIds ();
-});
-Clazz.defineMethod (c$, "setRightAlignIds", 
-function (rightAlignIds) {
-this.viewStyle.setRightAlignIds (rightAlignIds);
-}, "~B");
-Clazz.defineMethod (c$, "getConservationSelected", 
-function () {
-return this.viewStyle.getConservationSelected ();
-});
-Clazz.defineMethod (c$, "setShowBoxes", 
-function (state) {
-this.viewStyle.setShowBoxes (state);
-}, "~B");
-Clazz.defineMethod (c$, "getTextColour", 
-function () {
-return this.viewStyle.getTextColour ();
-});
-Clazz.defineMethod (c$, "getTextColour2", 
-function () {
-return this.viewStyle.getTextColour2 ();
-});
-Clazz.defineMethod (c$, "getThresholdTextColour", 
-function () {
-return this.viewStyle.getThresholdTextColour ();
-});
-Clazz.defineMethod (c$, "isConservationColourSelected", 
-function () {
-return this.viewStyle.isConservationColourSelected ();
-});
-Clazz.defineMethod (c$, "isRenderGaps", 
-function () {
-return this.viewStyle.isRenderGaps ();
-});
-Clazz.defineMethod (c$, "isShowColourText", 
-function () {
-return this.viewStyle.isShowColourText ();
-});
-Clazz.defineMethod (c$, "setConservationColourSelected", 
-function (conservationColourSelected) {
-this.viewStyle.setConservationColourSelected (conservationColourSelected);
-}, "~B");
-Clazz.defineMethod (c$, "setShowColourText", 
-function (showColourText) {
-this.viewStyle.setShowColourText (showColourText);
-}, "~B");
-Clazz.defineMethod (c$, "setTextColour", 
-function (textColour) {
-this.viewStyle.setTextColour (textColour);
-}, "java.awt.Color");
-Clazz.defineMethod (c$, "setThresholdTextColour", 
-function (thresholdTextColour) {
-this.viewStyle.setThresholdTextColour (thresholdTextColour);
-}, "~N");
-Clazz.defineMethod (c$, "setTextColour2", 
-function (textColour2) {
-this.viewStyle.setTextColour2 (textColour2);
-}, "java.awt.Color");
-Clazz.overrideMethod (c$, "getViewStyle", 
-function () {
-return  new jalview.viewmodel.styles.ViewStyle (this.viewStyle);
-});
-Clazz.overrideMethod (c$, "setViewStyle", 
-function (settingsForView) {
-this.viewStyle =  new jalview.viewmodel.styles.ViewStyle (settingsForView);
-}, "jalview.api.ViewStyleI");
-Clazz.defineMethod (c$, "sameStyle", 
-function (them) {
-return this.viewStyle.sameStyle (them);
-}, "jalview.api.ViewStyleI");
-Clazz.defineMethod (c$, "getIdWidth", 
-function () {
-return this.viewStyle.getIdWidth ();
-});
-Clazz.defineMethod (c$, "setIdWidth", 
-function (i) {
-this.viewStyle.setIdWidth (i);
-}, "~N");
-Clazz.defineMethod (c$, "isCentreColumnLabels", 
-function () {
-return this.viewStyle.isCentreColumnLabels ();
-});
-Clazz.defineMethod (c$, "setCentreColumnLabels", 
-function (centreColumnLabels) {
-this.viewStyle.setCentreColumnLabels (centreColumnLabels);
-}, "~B");
-Clazz.defineMethod (c$, "setShowDBRefs", 
-function (showdbrefs) {
-this.viewStyle.setShowDBRefs (showdbrefs);
-}, "~B");
-Clazz.defineMethod (c$, "isShowDBRefs", 
-function () {
-return this.viewStyle.isShowDBRefs ();
-});
-Clazz.defineMethod (c$, "isShowNPFeats", 
-function () {
-return this.viewStyle.isShowNPFeats ();
-});
-Clazz.defineMethod (c$, "setShowNPFeats", 
-function (shownpfeats) {
-this.viewStyle.setShowNPFeats (shownpfeats);
-}, "~B");
-Clazz.defineMethod (c$, "addToHistoryList", 
-function (command) {
-if (this.historyList != null) {
-this.historyList.push (command);
-this.broadcastCommand (command, false);
-}}, "jalview.commands.CommandI");
-Clazz.defineMethod (c$, "broadcastCommand", 
-function (command, undo) {
-this.getStructureSelectionManager ().commandPerformed (command, undo, this.getVamsasSource ());
-}, "jalview.commands.CommandI,~B");
-Clazz.defineMethod (c$, "addToRedoList", 
-function (command) {
-if (this.redoList != null) {
-this.redoList.push (command);
-}this.broadcastCommand (command, true);
-}, "jalview.commands.CommandI");
-Clazz.defineMethod (c$, "clearRedoList", 
-function () {
-if (this.redoList != null) {
-this.redoList.clear ();
-}});
-Clazz.defineMethod (c$, "setHistoryList", 
-function (list) {
-this.historyList = list;
-}, "java.util.Deque");
-Clazz.defineMethod (c$, "getHistoryList", 
-function () {
-return this.historyList;
-});
-Clazz.defineMethod (c$, "setRedoList", 
-function (list) {
-this.redoList = list;
-}, "java.util.Deque");
-Clazz.defineMethod (c$, "getRedoList", 
-function () {
-return this.redoList;
-});
-Clazz.overrideMethod (c$, "getVamsasSource", 
-function () {
-return this;
-});
-Clazz.defineMethod (c$, "getSortAnnotationsBy", 
-function () {
-return this.sortAnnotationsBy;
-});
-Clazz.defineMethod (c$, "setSortAnnotationsBy", 
-function (sortAnnotationsBy) {
-this.sortAnnotationsBy = sortAnnotationsBy;
-}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");
-Clazz.defineMethod (c$, "isShowAutocalculatedAbove", 
-function () {
-return this.showAutocalculatedAbove;
-});
-Clazz.defineMethod (c$, "setShowAutocalculatedAbove", 
-function (showAutocalculatedAbove) {
-this.showAutocalculatedAbove = showAutocalculatedAbove;
-}, "~B");
-Clazz.defineMethod (c$, "isScaleProteinAsCdna", 
-function () {
-return this.viewStyle.isScaleProteinAsCdna ();
-});
-Clazz.defineMethod (c$, "setScaleProteinAsCdna", 
-function (b) {
-this.viewStyle.setScaleProteinAsCdna (b);
-}, "~B");
-Clazz.defineMethod (c$, "isFollowHighlight", 
-function () {
-return this.followHighlight;
-});
-Clazz.overrideMethod (c$, "setFollowHighlight", 
-function (b) {
-this.followHighlight = b;
-}, "~B");
-Clazz.defineMethod (c$, "getStartRes", 
-function () {
-return this.startRes;
-});
-Clazz.overrideMethod (c$, "getEndRes", 
-function () {
-return this.endRes;
-});
-Clazz.defineMethod (c$, "getStartSeq", 
-function () {
-return this.startSeq;
-});
-Clazz.defineMethod (c$, "setStartRes", 
-function (res) {
-this.startRes = res;
-}, "~N");
-Clazz.defineMethod (c$, "setStartSeq", 
-function (seq) {
-this.startSeq = seq;
-}, "~N");
-Clazz.defineMethod (c$, "setEndRes", 
-function (res) {
-if (res > this.alignment.getWidth () - 1) {
-res = this.alignment.getWidth () - 1;
-}if (res < 0) {
-res = 0;
-}this.endRes = res;
-}, "~N");
-Clazz.defineMethod (c$, "setEndSeq", 
-function (seq) {
-if (seq > this.alignment.getHeight ()) {
-seq = this.alignment.getHeight ();
-}if (seq < 0) {
-seq = 0;
-}this.endSeq = seq;
-}, "~N");
-Clazz.defineMethod (c$, "getEndSeq", 
-function () {
-return this.endSeq;
-});
-Clazz.defineMethod (c$, "findComplementScrollTarget", 
-function (sr) {
-var complement = this.getCodingComplement ();
-if (complement == null || !complement.isFollowHighlight ()) {
-return 0;
-}var iAmProtein = !this.getAlignment ().isNucleotide ();
-var proteinAlignment = iAmProtein ? this.getAlignment () : complement.getAlignment ();
-if (proteinAlignment == null) {
-return 0;
-}var mappings = proteinAlignment.getCodonFrames ();
-var seqOffset = 0;
-var sequence = null;
-var middleColumn = this.getStartRes () + Clazz.doubleToInt ((this.getEndRes () - this.getStartRes ()) / 2);
-var hiddenSequences = this.getAlignment ().getHiddenSequences ();
-for (var seqNo = this.getStartSeq (); seqNo < this.getEndSeq (); seqNo++, seqOffset++) {
-sequence = this.getAlignment ().getSequenceAt (seqNo);
-if (hiddenSequences != null && hiddenSequences.isHidden (sequence)) {
-continue;
-}if (jalview.util.Comparison.isGap (sequence.getCharAt (middleColumn))) {
-continue;
-}var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (sequence, mappings);
-if (!seqMappings.isEmpty ()) {
-break;
-}}
-if (sequence == null) {
-return 0;
-}jalview.util.MappingUtils.addSearchResults (sr, sequence, sequence.findPosition (middleColumn), mappings);
-return seqOffset;
-}, "jalview.datamodel.SearchResults");
-});
+Clazz.declarePackage ("jalview.viewmodel");
+Clazz.load (["jalview.api.AlignViewportI", "jalview.structure.CommandListener", "$.VamsasSource", "jalview.datamodel.ColumnSelection", "jalview.viewmodel.styles.ViewStyle", "jalview.workers.AlignCalcManager", "java.beans.PropertyChangeSupport", "java.util.ArrayDeque", "$.HashMap"], "jalview.viewmodel.AlignmentViewport", ["jalview.analysis.Conservation", "jalview.datamodel.AlignmentAnnotation", "$.AlignmentView", "$.CigarArray", "$.Sequence", "$.SequenceGroup", "jalview.schemes.Blosum62ColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "jalview.util.Comparison", "$.MappingUtils", "jalview.workers.ComplementConsensusThread", "$.ConsensusThread", "$.ConservationThread", "$.StrucConsensusThread", "java.awt.Color", "java.util.ArrayList", "$.BitSet", "$.Hashtable"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.viewStyle = null;
+this.codingComplement = null;
+this.featuresDisplayed = null;
+this.historyList = null;
+this.redoList = null;
+this.alignment = null;
+this.sequenceSetID = null;
+this.$isDataset = false;
+this.hiddenRepSequences = null;
+this.colSel = null;
+this.autoCalculateConsensus = true;
+this.autoCalculateStrucConsensus = true;
+this.ignoreGapsInConsensusCalculation = false;
+this.globalColourScheme = null;
+this.consensus = null;
+this.complementConsensus = null;
+this.strucConsensus = null;
+this.conservation = null;
+this.quality = null;
+this.groupConsensus = null;
+this.groupConservation = null;
+this.hconsensus = null;
+this.hcomplementConsensus = null;
+this.hStrucConsensus = null;
+this.hconservation = null;
+this.ConsPercGaps = 25;
+this.calculator = null;
+this.showGroupConservation = false;
+this.showGroupConsensus = false;
+this.showSequenceLogo = false;
+this.normaliseSequenceLogo = false;
+this.showConsensusHistogram = true;
+this.padGaps = false;
+this.sortByTree = false;
+this.selectionGroup = null;
+this.viewId = null;
+this.sgrouphash = -1;
+this.colselhash = -1;
+this.changeSupport = null;
+this.showConservation = true;
+this.showQuality = true;
+this.showConsensus = true;
+this.sequenceColours = null;
+this.sortAnnotationsBy = null;
+this.showAutocalculatedAbove = false;
+this.followHighlight = true;
+this.startRes = 0;
+this.endRes = 0;
+this.startSeq = 0;
+this.endSeq = 0;
+Clazz.instantialize (this, arguments);
+}, jalview.viewmodel, "AlignmentViewport", null, [jalview.api.AlignViewportI, jalview.structure.CommandListener, jalview.structure.VamsasSource]);
+Clazz.prepareFields (c$, function () {
+this.viewStyle =  new jalview.viewmodel.styles.ViewStyle ();
+this.historyList =  new java.util.ArrayDeque ();
+this.redoList =  new java.util.ArrayDeque ();
+this.colSel =  new jalview.datamodel.ColumnSelection ();
+this.calculator =  new jalview.workers.AlignCalcManager ();
+this.changeSupport =  new java.beans.PropertyChangeSupport (this);
+this.sequenceColours =  new java.util.HashMap ();
+});
+Clazz.defineMethod (c$, "setFontName", 
+function (name) {
+this.viewStyle.setFontName (name);
+}, "~S");
+Clazz.defineMethod (c$, "setFontStyle", 
+function (style) {
+this.viewStyle.setFontStyle (style);
+}, "~N");
+Clazz.defineMethod (c$, "setFontSize", 
+function (size) {
+this.viewStyle.setFontSize (size);
+}, "~N");
+Clazz.defineMethod (c$, "getFontStyle", 
+function () {
+return this.viewStyle.getFontStyle ();
+});
+Clazz.defineMethod (c$, "getFontName", 
+function () {
+return this.viewStyle.getFontName ();
+});
+Clazz.defineMethod (c$, "getFontSize", 
+function () {
+return this.viewStyle.getFontSize ();
+});
+Clazz.defineMethod (c$, "setUpperCasebold", 
+function (upperCasebold) {
+this.viewStyle.setUpperCasebold (upperCasebold);
+}, "~B");
+Clazz.defineMethod (c$, "isUpperCasebold", 
+function () {
+return this.viewStyle.isUpperCasebold ();
+});
+Clazz.defineMethod (c$, "isSeqNameItalics", 
+function () {
+return this.viewStyle.isSeqNameItalics ();
+});
+Clazz.defineMethod (c$, "setColourByReferenceSeq", 
+function (colourByReferenceSeq) {
+this.viewStyle.setColourByReferenceSeq (colourByReferenceSeq);
+}, "~B");
+Clazz.defineMethod (c$, "setColourAppliesToAllGroups", 
+function (b) {
+this.viewStyle.setColourAppliesToAllGroups (b);
+}, "~B");
+Clazz.defineMethod (c$, "getColourAppliesToAllGroups", 
+function () {
+return this.viewStyle.getColourAppliesToAllGroups ();
+});
+Clazz.defineMethod (c$, "getAbovePIDThreshold", 
+function () {
+return this.viewStyle.getAbovePIDThreshold ();
+});
+Clazz.defineMethod (c$, "setIncrement", 
+function (inc) {
+this.viewStyle.setIncrement (inc);
+}, "~N");
+Clazz.defineMethod (c$, "getIncrement", 
+function () {
+return this.viewStyle.getIncrement ();
+});
+Clazz.defineMethod (c$, "setConservationSelected", 
+function (b) {
+this.viewStyle.setConservationSelected (b);
+}, "~B");
+Clazz.defineMethod (c$, "setShowHiddenMarkers", 
+function (show) {
+this.viewStyle.setShowHiddenMarkers (show);
+}, "~B");
+Clazz.defineMethod (c$, "getShowHiddenMarkers", 
+function () {
+return this.viewStyle.getShowHiddenMarkers ();
+});
+Clazz.defineMethod (c$, "setScaleRightWrapped", 
+function (b) {
+this.viewStyle.setScaleRightWrapped (b);
+}, "~B");
+Clazz.defineMethod (c$, "setScaleLeftWrapped", 
+function (b) {
+this.viewStyle.setScaleLeftWrapped (b);
+}, "~B");
+Clazz.defineMethod (c$, "setScaleAboveWrapped", 
+function (b) {
+this.viewStyle.setScaleAboveWrapped (b);
+}, "~B");
+Clazz.defineMethod (c$, "getScaleLeftWrapped", 
+function () {
+return this.viewStyle.getScaleLeftWrapped ();
+});
+Clazz.defineMethod (c$, "getScaleAboveWrapped", 
+function () {
+return this.viewStyle.getScaleAboveWrapped ();
+});
+Clazz.defineMethod (c$, "getScaleRightWrapped", 
+function () {
+return this.viewStyle.getScaleRightWrapped ();
+});
+Clazz.defineMethod (c$, "setAbovePIDThreshold", 
+function (b) {
+this.viewStyle.setAbovePIDThreshold (b);
+}, "~B");
+Clazz.defineMethod (c$, "setThreshold", 
+function (thresh) {
+this.viewStyle.setThreshold (thresh);
+}, "~N");
+Clazz.defineMethod (c$, "getThreshold", 
+function () {
+return this.viewStyle.getThreshold ();
+});
+Clazz.defineMethod (c$, "getShowJVSuffix", 
+function () {
+return this.viewStyle.getShowJVSuffix ();
+});
+Clazz.defineMethod (c$, "setShowJVSuffix", 
+function (b) {
+this.viewStyle.setShowJVSuffix (b);
+}, "~B");
+Clazz.defineMethod (c$, "setWrapAlignment", 
+function (state) {
+this.viewStyle.setWrapAlignment (state);
+}, "~B");
+Clazz.defineMethod (c$, "setShowText", 
+function (state) {
+this.viewStyle.setShowText (state);
+}, "~B");
+Clazz.defineMethod (c$, "setRenderGaps", 
+function (state) {
+this.viewStyle.setRenderGaps (state);
+}, "~B");
+Clazz.defineMethod (c$, "getColourText", 
+function () {
+return this.viewStyle.getColourText ();
+});
+Clazz.defineMethod (c$, "setColourText", 
+function (state) {
+this.viewStyle.setColourText (state);
+}, "~B");
+Clazz.defineMethod (c$, "getWrapAlignment", 
+function () {
+return this.viewStyle.getWrapAlignment ();
+});
+Clazz.defineMethod (c$, "getShowText", 
+function () {
+return this.viewStyle.getShowText ();
+});
+Clazz.defineMethod (c$, "getWrappedWidth", 
+function () {
+return this.viewStyle.getWrappedWidth ();
+});
+Clazz.defineMethod (c$, "setWrappedWidth", 
+function (w) {
+this.viewStyle.setWrappedWidth (w);
+}, "~N");
+Clazz.defineMethod (c$, "getCharHeight", 
+function () {
+return this.viewStyle.getCharHeight ();
+});
+Clazz.defineMethod (c$, "setCharHeight", 
+function (h) {
+this.viewStyle.setCharHeight (h);
+}, "~N");
+Clazz.defineMethod (c$, "getCharWidth", 
+function () {
+return this.viewStyle.getCharWidth ();
+});
+Clazz.defineMethod (c$, "setCharWidth", 
+function (w) {
+this.viewStyle.setCharWidth (w);
+}, "~N");
+Clazz.defineMethod (c$, "getShowBoxes", 
+function () {
+return this.viewStyle.getShowBoxes ();
+});
+Clazz.defineMethod (c$, "getShowUnconserved", 
+function () {
+return this.viewStyle.getShowUnconserved ();
+});
+Clazz.defineMethod (c$, "setShowUnconserved", 
+function (showunconserved) {
+this.viewStyle.setShowUnconserved (showunconserved);
+}, "~B");
+Clazz.defineMethod (c$, "setSeqNameItalics", 
+function (default1) {
+this.viewStyle.setSeqNameItalics (default1);
+}, "~B");
+Clazz.defineMethod (c$, "getAlignment", 
+function () {
+return this.alignment;
+});
+Clazz.overrideMethod (c$, "getGapCharacter", 
+function () {
+return this.alignment.getGapCharacter ();
+});
+Clazz.defineMethod (c$, "setDataset", 
+function (b) {
+this.$isDataset = b;
+}, "~B");
+Clazz.defineMethod (c$, "isDataset", 
+function () {
+return this.$isDataset;
+});
+Clazz.overrideMethod (c$, "setGlobalColourScheme", 
+function (cs) {
+this.globalColourScheme = cs;
+var recalc = false;
+if (cs != null) {
+cs.setConservationApplied (recalc = this.getConservationSelected ());
+if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
+recalc = true;
+cs.setThreshold (this.viewStyle.getThreshold (), this.ignoreGapsInConsensusCalculation);
+} else {
+cs.setThreshold (0, this.ignoreGapsInConsensusCalculation);
+}if (recalc) {
+cs.setConsensus (this.hconsensus);
+cs.setConservation (this.hconservation);
+}cs.alignmentChanged (this.alignment, this.hiddenRepSequences);
+}if (this.getColourAppliesToAllGroups ()) {
+for (var sg, $sg = this.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (cs == null) {
+sg.cs = null;
+continue;
+}sg.cs = cs.applyTo (sg, this.getHiddenRepSequences ());
+sg.setConsPercGaps (this.ConsPercGaps);
+if (this.getAbovePIDThreshold () || Clazz.instanceOf (cs, jalview.schemes.PIDColourScheme) || Clazz.instanceOf (cs, jalview.schemes.Blosum62ColourScheme)) {
+sg.cs.setThreshold (this.viewStyle.getThreshold (), this.isIgnoreGapsConsensus ());
+recalc = true;
+} else {
+sg.cs.setThreshold (0, this.isIgnoreGapsConsensus ());
+}if (this.getConservationSelected ()) {
+sg.cs.setConservationApplied (true);
+recalc = true;
+} else {
+sg.cs.setConservation (null);
+}if (recalc) {
+sg.recalcConservation ();
+} else {
+sg.cs.alignmentChanged (sg, this.hiddenRepSequences);
+}}
+}}, "jalview.schemes.ColourSchemeI");
+Clazz.overrideMethod (c$, "getGlobalColourScheme", 
+function () {
+return this.globalColourScheme;
+});
+Clazz.overrideMethod (c$, "setConservation", 
+function (cons) {
+this.hconservation = cons;
+}, "jalview.analysis.Conservation");
+Clazz.overrideMethod (c$, "getConsPercGaps", 
+function () {
+return this.ConsPercGaps;
+});
+Clazz.overrideMethod (c$, "setSequenceConsensusHash", 
+function (hconsensus) {
+this.hconsensus = hconsensus;
+}, "~A");
+Clazz.overrideMethod (c$, "setComplementConsensusHash", 
+function (hconsensus) {
+this.hcomplementConsensus = hconsensus;
+}, "~A");
+Clazz.overrideMethod (c$, "getSequenceConsensusHash", 
+function () {
+return this.hconsensus;
+});
+Clazz.overrideMethod (c$, "getComplementConsensusHash", 
+function () {
+return this.hcomplementConsensus;
+});
+Clazz.overrideMethod (c$, "getRnaStructureConsensusHash", 
+function () {
+return this.hStrucConsensus;
+});
+Clazz.overrideMethod (c$, "setRnaStructureConsensusHash", 
+function (hStrucConsensus) {
+this.hStrucConsensus = hStrucConsensus;
+}, "~A");
+Clazz.overrideMethod (c$, "getAlignmentQualityAnnot", 
+function () {
+return this.quality;
+});
+Clazz.overrideMethod (c$, "getAlignmentConservationAnnotation", 
+function () {
+return this.conservation;
+});
+Clazz.overrideMethod (c$, "getAlignmentConsensusAnnotation", 
+function () {
+return this.consensus;
+});
+Clazz.overrideMethod (c$, "getComplementConsensusAnnotation", 
+function () {
+return this.complementConsensus;
+});
+Clazz.overrideMethod (c$, "getAlignmentStrucConsensusAnnotation", 
+function () {
+return this.strucConsensus;
+});
+Clazz.defineMethod (c$, "updateConservation", 
+function (ap) {
+if (this.alignment.isNucleotide () || this.conservation == null || !this.autoCalculateConsensus) {
+return;
+}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConservationThread) == null) {
+this.calculator.registerWorker ( new jalview.workers.ConservationThread (this, ap));
+}}, "jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "updateConsensus", 
+function (ap) {
+if (this.consensus == null || !this.autoCalculateConsensus) {
+return;
+}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ConsensusThread) == null) {
+this.calculator.registerWorker ( new jalview.workers.ConsensusThread (this, ap));
+}var al = this.getAlignment ();
+if (!al.isNucleotide () && al.getCodonFrames () != null && !al.getCodonFrames ().isEmpty ()) {
+if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.ComplementConsensusThread) == null) {
+this.calculator.registerWorker ( new jalview.workers.ComplementConsensusThread (this, ap));
+}}}, "jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "updateStrucConsensus", 
+function (ap) {
+if (this.autoCalculateStrucConsensus && this.strucConsensus == null && this.alignment.isNucleotide () && this.alignment.hasRNAStructure ()) {
+this.initRNAStructure ();
+}if (this.strucConsensus == null || !this.autoCalculateStrucConsensus) {
+return;
+}if (this.calculator.getRegisteredWorkersOfClass (jalview.workers.StrucConsensusThread) == null) {
+this.calculator.registerWorker ( new jalview.workers.StrucConsensusThread (this, ap));
+}}, "jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "isCalcInProgress", 
+function () {
+return this.calculator.isWorking ();
+});
+Clazz.overrideMethod (c$, "isCalculationInProgress", 
+function (alignmentAnnotation) {
+if (!alignmentAnnotation.autoCalculated) {
+return false;
+}if (this.calculator.workingInvolvedWith (alignmentAnnotation)) {
+return true;
+}return false;
+}, "jalview.datamodel.AlignmentAnnotation");
+Clazz.overrideMethod (c$, "isClosed", 
+function () {
+return this.alignment == null;
+});
+Clazz.overrideMethod (c$, "getCalcManager", 
+function () {
+return this.calculator;
+});
+Clazz.overrideMethod (c$, "isShowSequenceLogo", 
+function () {
+return this.showSequenceLogo;
+});
+Clazz.defineMethod (c$, "setShowSequenceLogo", 
+function (showSequenceLogo) {
+if (showSequenceLogo != this.showSequenceLogo) {
+this.showSequenceLogo = showSequenceLogo;
+this.calculator.updateAnnotationFor (jalview.workers.ConsensusThread);
+this.calculator.updateAnnotationFor (jalview.workers.ComplementConsensusThread);
+this.calculator.updateAnnotationFor (jalview.workers.StrucConsensusThread);
+}this.showSequenceLogo = showSequenceLogo;
+}, "~B");
+Clazz.defineMethod (c$, "setShowConsensusHistogram", 
+function (showConsensusHistogram) {
+this.showConsensusHistogram = showConsensusHistogram;
+}, "~B");
+Clazz.defineMethod (c$, "isShowGroupConservation", 
+function () {
+return this.showGroupConservation;
+});
+Clazz.defineMethod (c$, "setShowGroupConservation", 
+function (showGroupConservation) {
+this.showGroupConservation = showGroupConservation;
+}, "~B");
+Clazz.defineMethod (c$, "isShowGroupConsensus", 
+function () {
+return this.showGroupConsensus;
+});
+Clazz.defineMethod (c$, "setShowGroupConsensus", 
+function (showGroupConsensus) {
+this.showGroupConsensus = showGroupConsensus;
+}, "~B");
+Clazz.overrideMethod (c$, "isShowConsensusHistogram", 
+function () {
+return this.showConsensusHistogram;
+});
+Clazz.overrideMethod (c$, "getSelectionGroup", 
+function () {
+return this.selectionGroup;
+});
+Clazz.overrideMethod (c$, "setSelectionGroup", 
+function (sg) {
+this.selectionGroup = sg;
+}, "jalview.datamodel.SequenceGroup");
+Clazz.defineMethod (c$, "setHiddenColumns", 
+function (colsel) {
+this.colSel = colsel;
+}, "jalview.datamodel.ColumnSelection");
+Clazz.overrideMethod (c$, "getColumnSelection", 
+function () {
+return this.colSel;
+});
+Clazz.overrideMethod (c$, "setColumnSelection", 
+function (colSel) {
+this.colSel = colSel;
+if (colSel != null) {
+this.updateHiddenColumns ();
+}}, "jalview.datamodel.ColumnSelection");
+Clazz.overrideMethod (c$, "getHiddenRepSequences", 
+function () {
+return this.hiddenRepSequences;
+});
+Clazz.overrideMethod (c$, "setHiddenRepSequences", 
+function (hiddenRepSequences) {
+this.hiddenRepSequences = hiddenRepSequences;
+}, "java.util.Map");
+Clazz.overrideMethod (c$, "hasHiddenColumns", 
+function () {
+return this.colSel != null && this.colSel.hasHiddenColumns ();
+});
+Clazz.defineMethod (c$, "updateHiddenColumns", 
+function () {
+});
+Clazz.overrideMethod (c$, "hasHiddenRows", 
+function () {
+return this.alignment.getHiddenSequences ().getSize () > 0;
+});
+Clazz.defineMethod (c$, "setSequenceSetId", 
+function (newid) {
+if (this.sequenceSetID != null) {
+System.err.println ("Warning - overwriting a sequenceSetId for a viewport!");
+}this.sequenceSetID =  String.instantialize (newid);
+}, "~S");
+Clazz.overrideMethod (c$, "getSequenceSetId", 
+function () {
+if (this.sequenceSetID == null) {
+this.sequenceSetID = this.alignment.hashCode () + "";
+}return this.sequenceSetID;
+});
+Clazz.overrideMethod (c$, "getViewId", 
+function () {
+if (this.viewId == null) {
+this.viewId = this.getSequenceSetId () + "." + this.hashCode () + "";
+}return this.viewId;
+});
+Clazz.defineMethod (c$, "setIgnoreGapsConsensus", 
+function (b, ap) {
+this.ignoreGapsInConsensusCalculation = b;
+if (ap != null) {
+this.updateConsensus (ap);
+if (this.globalColourScheme != null) {
+this.globalColourScheme.setThreshold (this.globalColourScheme.getThreshold (), this.ignoreGapsInConsensusCalculation);
+}}}, "~B,jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "isSelectionGroupChanged", 
+function (b) {
+var hc = (this.selectionGroup == null || this.selectionGroup.getSize () == 0) ? -1 : this.selectionGroup.hashCode ();
+if (hc != -1 && hc != this.sgrouphash) {
+if (b) {
+this.sgrouphash = hc;
+}return true;
+}return false;
+}, "~B");
+Clazz.defineMethod (c$, "isColSelChanged", 
+function (b) {
+var hc = (this.colSel == null || this.colSel.size () == 0) ? -1 : this.colSel.hashCode ();
+if (hc != -1 && hc != this.colselhash) {
+if (b) {
+this.colselhash = hc;
+}return true;
+}return false;
+}, "~B");
+Clazz.overrideMethod (c$, "isIgnoreGapsConsensus", 
+function () {
+return this.ignoreGapsInConsensusCalculation;
+});
+Clazz.defineMethod (c$, "addPropertyChangeListener", 
+function (listener) {
+this.changeSupport.addPropertyChangeListener (listener);
+}, "java.beans.PropertyChangeListener");
+Clazz.defineMethod (c$, "removePropertyChangeListener", 
+function (listener) {
+this.changeSupport.removePropertyChangeListener (listener);
+}, "java.beans.PropertyChangeListener");
+Clazz.defineMethod (c$, "firePropertyChange", 
+function (prop, oldvalue, newvalue) {
+this.changeSupport.firePropertyChange (prop, oldvalue, newvalue);
+}, "~S,~O,~O");
+Clazz.defineMethod (c$, "hideSelectedColumns", 
+function () {
+if (this.colSel.size () < 1) {
+return;
+}this.colSel.hideSelectedColumns ();
+this.setSelectionGroup (null);
+});
+Clazz.defineMethod (c$, "hideColumns", 
+function (start, end) {
+if (start == end) {
+this.colSel.hideColumns (start);
+} else {
+this.colSel.hideColumns (start, end);
+}}, "~N,~N");
+Clazz.defineMethod (c$, "showColumn", 
+function (col) {
+this.colSel.revealHiddenColumns (col);
+}, "~N");
+Clazz.defineMethod (c$, "showAllHiddenColumns", 
+function () {
+this.colSel.revealAllHiddenColumns ();
+});
+Clazz.defineMethod (c$, "showAllHiddenSeqs", 
+function () {
+if (this.alignment.getHiddenSequences ().getSize () > 0) {
+if (this.selectionGroup == null) {
+this.selectionGroup =  new jalview.datamodel.SequenceGroup ();
+this.selectionGroup.setEndRes (this.alignment.getWidth () - 1);
+}var tmp = this.alignment.getHiddenSequences ().showAll (this.hiddenRepSequences);
+for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
+this.selectionGroup.addSequence (seq, false);
+this.setSequenceAnnotationsVisible (seq, true);
+}
+this.hiddenRepSequences = null;
+this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
+this.sendSelection ();
+}});
+Clazz.defineMethod (c$, "showSequence", 
+function (index) {
+var tmp = this.alignment.getHiddenSequences ().showSequence (index, this.hiddenRepSequences);
+if (tmp.size () > 0) {
+if (this.selectionGroup == null) {
+this.selectionGroup =  new jalview.datamodel.SequenceGroup ();
+this.selectionGroup.setEndRes (this.alignment.getWidth () - 1);
+}for (var seq, $seq = tmp.iterator (); $seq.hasNext () && ((seq = $seq.next ()) || true);) {
+this.selectionGroup.addSequence (seq, false);
+this.setSequenceAnnotationsVisible (seq, true);
+}
+this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
+this.sendSelection ();
+}}, "~N");
+Clazz.defineMethod (c$, "hideAllSelectedSeqs", 
+function () {
+if (this.selectionGroup == null || this.selectionGroup.getSize () < 1) {
+return;
+}var seqs = this.selectionGroup.getSequencesInOrder (this.alignment);
+this.hideSequence (seqs);
+this.setSelectionGroup (null);
+});
+Clazz.defineMethod (c$, "hideSequence", 
+function (seq) {
+if (seq != null) {
+for (var i = 0; i < seq.length; i++) {
+this.alignment.getHiddenSequences ().hideSequence (seq[i]);
+this.setSequenceAnnotationsVisible (seq[i], false);
+}
+this.firePropertyChange ("alignment", null, this.alignment.getSequences ());
+}}, "~A");
+Clazz.defineMethod (c$, "setSequenceAnnotationsVisible", 
+function (sequenceI, visible) {
+for (var ann, $ann = 0, $$ann = this.alignment.getAlignmentAnnotation (); $ann < $$ann.length && ((ann = $$ann[$ann]) || true); $ann++) {
+if (ann.sequenceRef === sequenceI) {
+ann.visible = visible;
+}}
+}, "jalview.datamodel.SequenceI,~B");
+Clazz.defineMethod (c$, "hideRepSequences", 
+function (repSequence, sg) {
+var sSize = sg.getSize ();
+if (sSize < 2) {
+return;
+}if (this.hiddenRepSequences == null) {
+this.hiddenRepSequences =  new java.util.Hashtable ();
+}this.hiddenRepSequences.put (repSequence, sg);
+var seqs =  new Array (sSize - 1);
+var index = 0;
+for (var i = 0; i < sSize; i++) {
+if (sg.getSequenceAt (i) !== repSequence) {
+if (index == sSize - 1) {
+return;
+}seqs[index++] = sg.getSequenceAt (i);
+}}
+sg.setSeqrep (repSequence);
+sg.setHidereps (true);
+this.hideSequence (seqs);
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup");
+Clazz.defineMethod (c$, "isHiddenRepSequence", 
+function (seq) {
+return this.alignment.getSeqrep () === seq || (this.hiddenRepSequences != null && this.hiddenRepSequences.containsKey (seq));
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "getRepresentedSequences", 
+function (seq) {
+return (this.hiddenRepSequences == null ? null : this.hiddenRepSequences.get (seq));
+}, "jalview.datamodel.SequenceI");
+Clazz.overrideMethod (c$, "adjustForHiddenSeqs", 
+function (alignmentIndex) {
+return this.alignment.getHiddenSequences ().adjustForHiddenSeqs (alignmentIndex);
+}, "~N");
+Clazz.overrideMethod (c$, "invertColumnSelection", 
+function () {
+this.colSel.invertColumnSelection (0, this.alignment.getWidth ());
+});
+Clazz.overrideMethod (c$, "getSelectionAsNewSequence", 
+function () {
+var sequences;
+if (this.selectionGroup == null || this.selectionGroup.getSize () == 0) {
+sequences = this.alignment.getSequencesArray ();
+var annots = this.alignment.getAlignmentAnnotation ();
+for (var i = 0; i < sequences.length; i++) {
+sequences[i] =  new jalview.datamodel.Sequence (sequences[i], annots);
+}
+} else {
+sequences = this.selectionGroup.getSelectionAsNewSequences (this.alignment);
+}return sequences;
+});
+Clazz.overrideMethod (c$, "getSequenceSelection", 
+function () {
+var sequences = null;
+if (this.selectionGroup != null) {
+sequences = this.selectionGroup.getSequencesInOrder (this.alignment);
+}if (sequences == null) {
+sequences = this.alignment.getSequencesArray ();
+}return sequences;
+});
+Clazz.overrideMethod (c$, "getViewAsCigars", 
+function (selectedRegionOnly) {
+return  new jalview.datamodel.CigarArray (this.alignment, this.colSel, (selectedRegionOnly ? this.selectionGroup : null));
+}, "~B");
+Clazz.defineMethod (c$, "getAlignmentView", 
+function (selectedOnly) {
+return this.getAlignmentView (selectedOnly, false);
+}, "~B");
+Clazz.defineMethod (c$, "getAlignmentView", 
+function (selectedOnly, markGroups) {
+return  new jalview.datamodel.AlignmentView (this.alignment, this.colSel, this.selectionGroup, this.colSel != null && this.colSel.hasHiddenColumns (), selectedOnly, markGroups);
+}, "~B,~B");
+Clazz.overrideMethod (c$, "getViewAsString", 
+function (selectedRegionOnly) {
+var selection = null;
+var seqs = null;
+var i;
+var iSize;
+var start = 0;
+var end = 0;
+if (selectedRegionOnly && this.selectionGroup != null) {
+iSize = this.selectionGroup.getSize ();
+seqs = this.selectionGroup.getSequencesInOrder (this.alignment);
+start = this.selectionGroup.getStartRes ();
+end = this.selectionGroup.getEndRes () + 1;
+} else {
+iSize = this.alignment.getHeight ();
+seqs = this.alignment.getSequencesArray ();
+end = this.alignment.getWidth ();
+}selection =  new Array (iSize);
+if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
+selection = this.colSel.getVisibleSequenceStrings (start, end, seqs);
+} else {
+for (i = 0; i < iSize; i++) {
+selection[i] = seqs[i].getSequenceAsString (start, end);
+}
+}return selection;
+}, "~B");
+Clazz.overrideMethod (c$, "getVisibleRegionBoundaries", 
+function (min, max) {
+var regions =  new java.util.ArrayList ();
+var start = min;
+var end = max;
+do {
+if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
+if (start == 0) {
+start = this.colSel.adjustForHiddenColumns (start);
+}end = this.colSel.getHiddenBoundaryRight (start);
+if (start == end) {
+end = max;
+}if (end > max) {
+end = max;
+}}regions.add ( Clazz.newIntArray (-1, [start, end]));
+if (this.colSel != null && this.colSel.hasHiddenColumns ()) {
+start = this.colSel.adjustForHiddenColumns (end);
+start = this.colSel.getHiddenBoundaryLeft (start) + 1;
+}} while (end < max);
+var startEnd =  Clazz.newIntArray (regions.size (), 2, 0);
+return regions;
+}, "~N,~N");
+Clazz.overrideMethod (c$, "getVisibleAlignmentAnnotation", 
+function (selectedOnly) {
+var ala =  new java.util.ArrayList ();
+var aa;
+if ((aa = this.alignment.getAlignmentAnnotation ()) != null) {
+for (var annot, $annot = 0, $$annot = aa; $annot < $$annot.length && ((annot = $$annot[$annot]) || true); $annot++) {
+var clone =  new jalview.datamodel.AlignmentAnnotation (annot);
+if (selectedOnly && this.selectionGroup != null) {
+this.colSel.makeVisibleAnnotation (this.selectionGroup.getStartRes (), this.selectionGroup.getEndRes (), clone);
+} else {
+this.colSel.makeVisibleAnnotation (clone);
+}ala.add (clone);
+}
+}return ala;
+}, "~B");
+Clazz.overrideMethod (c$, "isPadGaps", 
+function () {
+return this.padGaps;
+});
+Clazz.overrideMethod (c$, "setPadGaps", 
+function (padGaps) {
+this.padGaps = padGaps;
+}, "~B");
+Clazz.overrideMethod (c$, "alignmentChanged", 
+function (ap) {
+if (this.isPadGaps ()) {
+this.alignment.padGaps ();
+}if (this.autoCalculateConsensus) {
+this.updateConsensus (ap);
+}if (this.hconsensus != null && this.autoCalculateConsensus) {
+this.updateConservation (ap);
+}if (this.autoCalculateStrucConsensus) {
+this.updateStrucConsensus (ap);
+}var alWidth = this.alignment.getWidth ();
+var groups = this.alignment.getGroups ();
+if (groups != null) {
+for (var sg, $sg = groups.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.getEndRes () > alWidth) {
+sg.setEndRes (alWidth - 1);
+}}
+}if (this.selectionGroup != null && this.selectionGroup.getEndRes () > alWidth) {
+this.selectionGroup.setEndRes (alWidth - 1);
+}this.resetAllColourSchemes ();
+this.calculator.restartWorkers ();
+}, "jalview.api.AlignmentViewPanel");
+Clazz.defineMethod (c$, "resetAllColourSchemes", 
+function () {
+var cs = this.globalColourScheme;
+if (cs != null) {
+cs.alignmentChanged (this.alignment, this.hiddenRepSequences);
+cs.setConsensus (this.hconsensus);
+if (cs.conservationApplied ()) {
+cs.setConservation (jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.alignment.getWidth (), false, this.getConsPercGaps (), false));
+}}for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.cs != null) {
+sg.cs.alignmentChanged (sg, this.hiddenRepSequences);
+}sg.recalcConservation ();
+}
+});
+Clazz.defineMethod (c$, "initAutoAnnotation", 
+function () {
+if (this.hconsensus == null && !this.$isDataset) {
+if (!this.alignment.isNucleotide ()) {
+this.initConservation ();
+this.initQuality ();
+} else {
+this.initRNAStructure ();
+}this.consensus =  new jalview.datamodel.AlignmentAnnotation ("Consensus", "PID",  new Array (1), 0, 100, 1);
+this.initConsensus (this.consensus);
+this.initComplementConsensus ();
+}});
+Clazz.defineMethod (c$, "initComplementConsensus", 
+function () {
+if (!this.alignment.isNucleotide ()) {
+var codonMappings = this.alignment.getCodonFrames ();
+if (codonMappings != null && !codonMappings.isEmpty ()) {
+this.complementConsensus =  new jalview.datamodel.AlignmentAnnotation ("cDNA Consensus", "PID for cDNA",  new Array (1), 0, 100, 1);
+this.initConsensus (this.complementConsensus);
+}}});
+Clazz.defineMethod (c$, "initConsensus", 
+($fz = function (aa) {
+aa.hasText = true;
+aa.autoCalculated = true;
+if (this.showConsensus) {
+this.alignment.addAnnotation (aa);
+}}, $fz.isPrivate = true, $fz), "jalview.datamodel.AlignmentAnnotation");
+Clazz.defineMethod (c$, "initConservation", 
+($fz = function () {
+if (this.showConservation) {
+if (this.conservation == null) {
+this.conservation =  new jalview.datamodel.AlignmentAnnotation ("Conservation", "Conservation of total alignment less than " + this.getConsPercGaps () + "% gaps",  new Array (1), 0, 11, 1);
+this.conservation.hasText = true;
+this.conservation.autoCalculated = true;
+this.alignment.addAnnotation (this.conservation);
+}}}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "initQuality", 
+($fz = function () {
+if (this.showQuality) {
+if (this.quality == null) {
+this.quality =  new jalview.datamodel.AlignmentAnnotation ("Quality", "Alignment Quality based on Blosum62 scores",  new Array (1), 0, 11, 1);
+this.quality.hasText = true;
+this.quality.autoCalculated = true;
+this.alignment.addAnnotation (this.quality);
+}}}, $fz.isPrivate = true, $fz));
+Clazz.defineMethod (c$, "initRNAStructure", 
+($fz = function () {
+if (this.alignment.hasRNAStructure () && this.strucConsensus == null) {
+this.strucConsensus =  new jalview.datamodel.AlignmentAnnotation ("StrucConsensus", "PID",  new Array (1), 0, 100, 1);
+this.strucConsensus.hasText = true;
+this.strucConsensus.autoCalculated = true;
+if (this.showConsensus) {
+this.alignment.addAnnotation (this.strucConsensus);
+}}}, $fz.isPrivate = true, $fz));
+Clazz.overrideMethod (c$, "calcPanelHeight", 
+function () {
+var anns = this.getAlignment ().getAlignmentAnnotation ();
+var height = 0;
+var charHeight = this.getCharHeight ();
+if (anns != null) {
+var graphgrp =  new java.util.BitSet ();
+for (var aa, $aa = 0, $$aa = anns; $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) {
+if (aa == null) {
+System.err.println ("Null annotation row: ignoring.");
+continue;
+}if (!aa.visible) {
+continue;
+}if (aa.graphGroup > -1) {
+if (graphgrp.get (aa.graphGroup)) {
+continue;
+} else {
+graphgrp.set (aa.graphGroup);
+}}aa.height = 0;
+if (aa.hasText) {
+aa.height += charHeight;
+}if (aa.hasIcons) {
+aa.height += 16;
+}if (aa.graph > 0) {
+aa.height += aa.graphHeight;
+}if (aa.height == 0) {
+aa.height = 20;
+}height += aa.height;
+}
+}if (height == 0) {
+height = 20;
+}return height;
+});
+Clazz.overrideMethod (c$, "updateGroupAnnotationSettings", 
+function (applyGlobalSettings, preserveNewGroupSettings) {
+var updateCalcs = false;
+var conv = this.isShowGroupConservation ();
+var cons = this.isShowGroupConsensus ();
+var showprf = this.isShowSequenceLogo ();
+var showConsHist = this.isShowConsensusHistogram ();
+var normLogo = this.isNormaliseSequenceLogo ();
+var sortg = true;
+var aan = this.alignment.getAlignmentAnnotation ();
+var oldrfs =  new java.util.ArrayList ();
+if (aan != null) {
+for (var an = 0; an < aan.length; an++) {
+if (aan[an].autoCalculated && aan[an].groupRef != null) {
+oldrfs.add (aan[an].groupRef);
+this.alignment.deleteAnnotation (aan[an], false);
+}}
+}if (this.alignment.getGroups () != null) {
+for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+updateCalcs = false;
+if (applyGlobalSettings || (!preserveNewGroupSettings && !oldrfs.contains (sg))) {
+sg.setshowSequenceLogo (showprf);
+sg.setShowConsensusHistogram (showConsHist);
+sg.setNormaliseSequenceLogo (normLogo);
+}if (conv) {
+updateCalcs = true;
+this.alignment.addAnnotation (sg.getConservationRow (), 0);
+}if (cons) {
+updateCalcs = true;
+this.alignment.addAnnotation (sg.getConsensus (), 0);
+}if (updateCalcs) {
+sg.recalcConservation ();
+}}
+}oldrfs.clear ();
+}, "~B,~B");
+Clazz.defineMethod (c$, "isDisplayReferenceSeq", 
+function () {
+return this.alignment.hasSeqrep () && this.viewStyle.isDisplayReferenceSeq ();
+});
+Clazz.defineMethod (c$, "setDisplayReferenceSeq", 
+function (displayReferenceSeq) {
+this.viewStyle.setDisplayReferenceSeq (displayReferenceSeq);
+}, "~B");
+Clazz.defineMethod (c$, "isColourByReferenceSeq", 
+function () {
+return this.alignment.hasSeqrep () && this.viewStyle.isColourByReferenceSeq ();
+});
+Clazz.overrideMethod (c$, "getSequenceColour", 
+function (seq) {
+var sqc = this.sequenceColours.get (seq);
+return (sqc == null ? java.awt.Color.white : sqc);
+}, "jalview.datamodel.SequenceI");
+Clazz.overrideMethod (c$, "setSequenceColour", 
+function (seq, col) {
+if (col == null) {
+this.sequenceColours.remove (seq);
+} else {
+this.sequenceColours.put (seq, col);
+}}, "jalview.datamodel.SequenceI,java.awt.Color");
+Clazz.overrideMethod (c$, "updateSequenceIdColours", 
+function () {
+for (var sg, $sg = this.alignment.getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+if (sg.idColour != null) {
+for (var s, $s = sg.getSequences (this.getHiddenRepSequences ()).iterator (); $s.hasNext () && ((s = $s.next ()) || true);) {
+this.sequenceColours.put (s, sg.idColour);
+}
+}}
+});
+Clazz.overrideMethod (c$, "clearSequenceColours", 
+function () {
+this.sequenceColours.clear ();
+});
+Clazz.defineMethod (c$, "getCodingComplement", 
+function () {
+return this.codingComplement;
+});
+Clazz.defineMethod (c$, "setCodingComplement", 
+function (av) {
+if (this === av) {
+System.err.println ("Ignoring recursive setCodingComplement request");
+} else {
+this.codingComplement = av;
+if (av.getCodingComplement () !== this) {
+av.setCodingComplement (this);
+}}}, "jalview.api.AlignViewportI");
+Clazz.overrideMethod (c$, "isNucleotide", 
+function () {
+return this.getAlignment () == null ? false : this.getAlignment ().isNucleotide ();
+});
+Clazz.overrideMethod (c$, "getFeaturesDisplayed", 
+function () {
+return this.featuresDisplayed;
+});
+Clazz.overrideMethod (c$, "setFeaturesDisplayed", 
+function (featuresDisplayedI) {
+this.featuresDisplayed = featuresDisplayedI;
+}, "jalview.api.FeaturesDisplayedI");
+Clazz.overrideMethod (c$, "areFeaturesDisplayed", 
+function () {
+return this.featuresDisplayed != null && this.featuresDisplayed.getRegisterdFeaturesCount () > 0;
+});
+Clazz.defineMethod (c$, "setShowSequenceFeatures", 
+function (b) {
+this.viewStyle.setShowSequenceFeatures (b);
+}, "~B");
+Clazz.defineMethod (c$, "isShowSequenceFeatures", 
+function () {
+return this.viewStyle.isShowSequenceFeatures ();
+});
+Clazz.defineMethod (c$, "setShowSequenceFeaturesHeight", 
+function (selected) {
+this.viewStyle.setShowSequenceFeaturesHeight (selected);
+}, "~B");
+Clazz.defineMethod (c$, "isShowSequenceFeaturesHeight", 
+function () {
+return this.viewStyle.isShowSequenceFeaturesHeight ();
+});
+Clazz.defineMethod (c$, "setShowAnnotation", 
+function (b) {
+this.viewStyle.setShowAnnotation (b);
+}, "~B");
+Clazz.defineMethod (c$, "isShowAnnotation", 
+function () {
+return this.viewStyle.isShowAnnotation ();
+});
+Clazz.defineMethod (c$, "isRightAlignIds", 
+function () {
+return this.viewStyle.isRightAlignIds ();
+});
+Clazz.defineMethod (c$, "setRightAlignIds", 
+function (rightAlignIds) {
+this.viewStyle.setRightAlignIds (rightAlignIds);
+}, "~B");
+Clazz.defineMethod (c$, "getConservationSelected", 
+function () {
+return this.viewStyle.getConservationSelected ();
+});
+Clazz.defineMethod (c$, "setShowBoxes", 
+function (state) {
+this.viewStyle.setShowBoxes (state);
+}, "~B");
+Clazz.defineMethod (c$, "getTextColour", 
+function () {
+return this.viewStyle.getTextColour ();
+});
+Clazz.defineMethod (c$, "getTextColour2", 
+function () {
+return this.viewStyle.getTextColour2 ();
+});
+Clazz.defineMethod (c$, "getThresholdTextColour", 
+function () {
+return this.viewStyle.getThresholdTextColour ();
+});
+Clazz.defineMethod (c$, "isConservationColourSelected", 
+function () {
+return this.viewStyle.isConservationColourSelected ();
+});
+Clazz.defineMethod (c$, "isRenderGaps", 
+function () {
+return this.viewStyle.isRenderGaps ();
+});
+Clazz.defineMethod (c$, "isShowColourText", 
+function () {
+return this.viewStyle.isShowColourText ();
+});
+Clazz.defineMethod (c$, "setConservationColourSelected", 
+function (conservationColourSelected) {
+this.viewStyle.setConservationColourSelected (conservationColourSelected);
+}, "~B");
+Clazz.defineMethod (c$, "setShowColourText", 
+function (showColourText) {
+this.viewStyle.setShowColourText (showColourText);
+}, "~B");
+Clazz.defineMethod (c$, "setTextColour", 
+function (textColour) {
+this.viewStyle.setTextColour (textColour);
+}, "java.awt.Color");
+Clazz.defineMethod (c$, "setThresholdTextColour", 
+function (thresholdTextColour) {
+this.viewStyle.setThresholdTextColour (thresholdTextColour);
+}, "~N");
+Clazz.defineMethod (c$, "setTextColour2", 
+function (textColour2) {
+this.viewStyle.setTextColour2 (textColour2);
+}, "java.awt.Color");
+Clazz.overrideMethod (c$, "getViewStyle", 
+function () {
+return  new jalview.viewmodel.styles.ViewStyle (this.viewStyle);
+});
+Clazz.overrideMethod (c$, "setViewStyle", 
+function (settingsForView) {
+this.viewStyle =  new jalview.viewmodel.styles.ViewStyle (settingsForView);
+}, "jalview.api.ViewStyleI");
+Clazz.defineMethod (c$, "sameStyle", 
+function (them) {
+return this.viewStyle.sameStyle (them);
+}, "jalview.api.ViewStyleI");
+Clazz.defineMethod (c$, "getIdWidth", 
+function () {
+return this.viewStyle.getIdWidth ();
+});
+Clazz.defineMethod (c$, "setIdWidth", 
+function (i) {
+this.viewStyle.setIdWidth (i);
+}, "~N");
+Clazz.defineMethod (c$, "isCentreColumnLabels", 
+function () {
+return this.viewStyle.isCentreColumnLabels ();
+});
+Clazz.defineMethod (c$, "setCentreColumnLabels", 
+function (centreColumnLabels) {
+this.viewStyle.setCentreColumnLabels (centreColumnLabels);
+}, "~B");
+Clazz.defineMethod (c$, "setShowDBRefs", 
+function (showdbrefs) {
+this.viewStyle.setShowDBRefs (showdbrefs);
+}, "~B");
+Clazz.defineMethod (c$, "isShowDBRefs", 
+function () {
+return this.viewStyle.isShowDBRefs ();
+});
+Clazz.defineMethod (c$, "isShowNPFeats", 
+function () {
+return this.viewStyle.isShowNPFeats ();
+});
+Clazz.defineMethod (c$, "setShowNPFeats", 
+function (shownpfeats) {
+this.viewStyle.setShowNPFeats (shownpfeats);
+}, "~B");
+Clazz.defineMethod (c$, "addToHistoryList", 
+function (command) {
+if (this.historyList != null) {
+this.historyList.push (command);
+this.broadcastCommand (command, false);
+}}, "jalview.commands.CommandI");
+Clazz.defineMethod (c$, "broadcastCommand", 
+function (command, undo) {
+this.getStructureSelectionManager ().commandPerformed (command, undo, this.getVamsasSource ());
+}, "jalview.commands.CommandI,~B");
+Clazz.defineMethod (c$, "addToRedoList", 
+function (command) {
+if (this.redoList != null) {
+this.redoList.push (command);
+}this.broadcastCommand (command, true);
+}, "jalview.commands.CommandI");
+Clazz.defineMethod (c$, "clearRedoList", 
+function () {
+if (this.redoList != null) {
+this.redoList.clear ();
+}});
+Clazz.defineMethod (c$, "setHistoryList", 
+function (list) {
+this.historyList = list;
+}, "java.util.Deque");
+Clazz.defineMethod (c$, "getHistoryList", 
+function () {
+return this.historyList;
+});
+Clazz.defineMethod (c$, "setRedoList", 
+function (list) {
+this.redoList = list;
+}, "java.util.Deque");
+Clazz.defineMethod (c$, "getRedoList", 
+function () {
+return this.redoList;
+});
+Clazz.overrideMethod (c$, "getVamsasSource", 
+function () {
+return this;
+});
+Clazz.defineMethod (c$, "getSortAnnotationsBy", 
+function () {
+return this.sortAnnotationsBy;
+});
+Clazz.defineMethod (c$, "setSortAnnotationsBy", 
+function (sortAnnotationsBy) {
+this.sortAnnotationsBy = sortAnnotationsBy;
+}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");
+Clazz.defineMethod (c$, "isShowAutocalculatedAbove", 
+function () {
+return this.showAutocalculatedAbove;
+});
+Clazz.defineMethod (c$, "setShowAutocalculatedAbove", 
+function (showAutocalculatedAbove) {
+this.showAutocalculatedAbove = showAutocalculatedAbove;
+}, "~B");
+Clazz.defineMethod (c$, "isScaleProteinAsCdna", 
+function () {
+return this.viewStyle.isScaleProteinAsCdna ();
+});
+Clazz.defineMethod (c$, "setScaleProteinAsCdna", 
+function (b) {
+this.viewStyle.setScaleProteinAsCdna (b);
+}, "~B");
+Clazz.defineMethod (c$, "isFollowHighlight", 
+function () {
+return this.followHighlight;
+});
+Clazz.overrideMethod (c$, "setFollowHighlight", 
+function (b) {
+this.followHighlight = b;
+}, "~B");
+Clazz.defineMethod (c$, "getStartRes", 
+function () {
+return this.startRes;
+});
+Clazz.overrideMethod (c$, "getEndRes", 
+function () {
+return this.endRes;
+});
+Clazz.defineMethod (c$, "getStartSeq", 
+function () {
+return this.startSeq;
+});
+Clazz.defineMethod (c$, "setStartRes", 
+function (res) {
+this.startRes = res;
+}, "~N");
+Clazz.defineMethod (c$, "setStartSeq", 
+function (seq) {
+this.startSeq = seq;
+}, "~N");
+Clazz.defineMethod (c$, "setEndRes", 
+function (res) {
+if (res > this.alignment.getWidth () - 1) {
+res = this.alignment.getWidth () - 1;
+}if (res < 0) {
+res = 0;
+}this.endRes = res;
+}, "~N");
+Clazz.defineMethod (c$, "setEndSeq", 
+function (seq) {
+if (seq > this.alignment.getHeight ()) {
+seq = this.alignment.getHeight ();
+}if (seq < 0) {
+seq = 0;
+}this.endSeq = seq;
+}, "~N");
+Clazz.defineMethod (c$, "getEndSeq", 
+function () {
+return this.endSeq;
+});
+Clazz.defineMethod (c$, "findComplementScrollTarget", 
+function (sr) {
+var complement = this.getCodingComplement ();
+if (complement == null || !complement.isFollowHighlight ()) {
+return 0;
+}var iAmProtein = !this.getAlignment ().isNucleotide ();
+var proteinAlignment = iAmProtein ? this.getAlignment () : complement.getAlignment ();
+if (proteinAlignment == null) {
+return 0;
+}var mappings = proteinAlignment.getCodonFrames ();
+var seqOffset = 0;
+var sequence = null;
+var middleColumn = this.getStartRes () + Clazz.doubleToInt ((this.getEndRes () - this.getStartRes ()) / 2);
+var hiddenSequences = this.getAlignment ().getHiddenSequences ();
+for (var seqNo = this.getStartSeq (); seqNo < this.getEndSeq (); seqNo++, seqOffset++) {
+sequence = this.getAlignment ().getSequenceAt (seqNo);
+if (hiddenSequences != null && hiddenSequences.isHidden (sequence)) {
+continue;
+}if (jalview.util.Comparison.isGap (sequence.getCharAt (middleColumn))) {
+continue;
+}var seqMappings = jalview.util.MappingUtils.findMappingsForSequence (sequence, mappings);
+if (!seqMappings.isEmpty ()) {
+break;
+}}
+if (sequence == null) {
+return 0;
+}jalview.util.MappingUtils.addSearchResults (sr, sequence, sequence.findPosition (middleColumn), mappings);
+return seqOffset;
+}, "jalview.datamodel.SearchResults");
+});