JAL-1807 update

[jalviewjs.git] / site / j2s / core / corejalview.z.js

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d=a.id.length;0<b.size();){var g=b.remove(0);this.names.put(C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,g.getName()),g);var h,j,e=g.getName().length;if((h=Math.abs(l-d))>(j=Math.abs(e-d))&&e>l)c.clear(),f=g,l=e,c.add(f);h==j&&e==l&&c.add(g)}return 0==c.size()?null:c},"jalview.analysis.SequenceIdMatcher.SeqIdName,java.util.List");d(c$,"findIdMatch",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a.getName());return this.findIdMatch(a)},"jalview.datamodel.SequenceI");
d(c$,"findIdMatch",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a);return this.findIdMatch(a)},"~S");d(c$,"findAllIdMatches",function(a){a=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a);a=this.findAllIdMatches(a);return null!=a?a.toArray(Array(a.size())):null},"~S");d(c$,"findIdMatch",function(a){var b=null,c=0,f;if(0<a.length){b=Array(a.length);do f=C(jalview.analysis.SequenceIdMatcher.SeqIdName,this,null,a[c].getName()),b[c]=this.names.containsKey(f)?this.findIdMatch(f):
null;while(++c<a.length)}return b},"~A");d(c$,"findIdMatch",function(a){for(var b=new java.util.Vector;this.names.containsKey(a);)b.addElement(this.names.remove(a));return this.pickbestMatch(a,b)},"jalview.analysis.SequenceIdMatcher.SeqIdName");d(c$,"findAllIdMatches",function(a){for(var b=new java.util.ArrayList;this.names.containsKey(a);)b.add(this.names.remove(a));return this.pickbestMatches(a,b)},"jalview.analysis.SequenceIdMatcher.SeqIdName");c$.$SequenceIdMatcher$SeqIdName$=function(){A(self.c$);
c$=s(function(){O(this,arguments);this.id=null;this.WORD_SEP="~. |#\\/<>!\"\u00a4$%^*)}[@',?_";r(this,arguments)},jalview.analysis.SequenceIdMatcher,"SeqIdName");m(c$,function(a){this.id=null!=a?String.instantialize(a):""},"~S");e(c$,"hashCode",function(){return 4<=this.id.length?this.id.substring(0,4).hashCode():this.id.hashCode()});d(c$,"equals",function(a){return null==a?!1:v(a,jalview.analysis.SequenceIdMatcher.SeqIdName)||v(a,String)?this.equals(a):!1},"~O");d(c$,"equals",function(a){return this.id.length>
a.id.length?this.id.startsWith(a.id)?-1<this.WORD_SEP.indexOf(this.id.charAt(a.id.length)):!1:a.id.startsWith(this.id)?a.id.equals(this.id)?!0:-1<this.WORD_SEP.indexOf(a.id.charAt(this.id.length)):!1},"jalview.analysis.SequenceIdMatcher.SeqIdName");d(c$,"equals",function(a){return this.id.length>a.length?this.id.startsWith(a)?-1<this.WORD_SEP.indexOf(this.id.charAt(a.length)):!1:a.startsWith(this.id)?a.equals(this.id)?!0:-1<this.WORD_SEP.indexOf(a.charAt(this.id.length)):!1},"~S");c$=z()}});p("jalview.appletgui");
q("awt2swing.Canvas jalview.api.AlignViewControllerGuiI jalview.appletgui.EmbmenuFrame java.awt.event.ActionListener $.ItemListener $.KeyListener awt2swing.CheckboxMenuItem $.Label $.Menu $.MenuBar $.MenuItem jalview.util.MessageManager java.awt.BorderLayout".split(" "),"jalview.appletgui.AlignFrame","awt2swing.Frame $.Util jalview.analysis.AlignmentSorter $.AnnotationSorter jalview.appletgui.AlignViewport $.AlignmentPanel $.AnnotationColourChooser $.AnnotationColumnChooser $.AppletJmol $.CutAndPasteTransfer $.FeatureSettings $.Finder $.FontChooser $.OverviewPanel $.PCAPanel $.PaintRefresher $.PairwiseAlignPanel $.RedundancyPanel $.SliderPanel $.TreePanel $.UserDefinedColours jalview.bin.JalviewLite jalview.commands.EditCommand $.OrderCommand $.RemoveGapColCommand $.RemoveGapsCommand $.SlideSequencesCommand $.TrimRegionCommand jalview.controller.AlignViewController jalview.datamodel.Alignment $.PDBEntry $.Sequence $.SequenceGroup jalview.io.AlignmentProperties $.AnnotationFile $.AppletFormatAdapter $.FeaturesFile jalview.jsdev.GenericFileAdapter jalview.schemes.Blosum62ColourScheme $.BuriedColourScheme $.ClustalxColourScheme $.HelixColourScheme $.HydrophobicColourScheme $.NucleotideColourScheme $.PIDColourScheme $.PurinePyrimidineColourScheme $.RNAHelicesColourChooser $.RNAInteractionColourScheme $.StrandColourScheme $.TCoffeeColourScheme $.TaylorColourScheme $.TurnColourScheme $.ZappoColourScheme jalview.structure.StructureSelectionManager jalview.util.Comparison $.MappingUtils java.awt.Color $.Font java.awt.event.FocusListener $.WindowAdapter java.lang.Character $.StringBuffer java.net.URL $.URLEncoder java.util.Arrays $.HashMap $.Hashtable $.StringTokenizer $.Vector".split(" "),
function(){c$=s(function(){this.viewport=this.alignPanel=this.avc=null;this.frameWidth=700;this.frameHeight=500;this.jalviewServletURL=null;this.showAutoCalculatedAbove=!1;this.splitFrame=this.showAutoLast=this.showAutoFirst=this.sortAnnByLabel=this.sortAnnBySequence=this.showSequenceAnnotations=this.showAlignmentAnnotations=this.$newView=this.showAllHidden=this.hideAllSelection=this.hideAllButSelection=this.hideSequences=this.hideColumns=this.showSeqs=this.showColumns=this.invertColSel=this.annotationColumnSelection=
this.annotationColour=this.sequenceFeatures=this.featureSettings=this.normSequenceLogo=this.showGroupConservation=this.showGroupConsensus=this.showConsensusHistogram=this.applyAutoAnnotationSettings=this.showSequenceLogo=this.followMouseOverFlag=this.centreColumnLabelFlag=this.seqLimits=this.about=this.documentation=this.inputText=this.sortByTreeMenu=this.$sortByTree=this.autoCalculate=this.modifyConservation=this.modifyPID=this.scaleRight=this.scaleLeft=this.scaleAbove=this.$font=this.applyToAllGroups=
this.pasteThis=this.pasteNew=this.pasteMenu=this.cut=this.copy=this.$delete=this.unGroup=this.createGroup=this.grpsFromSelection=this.deleteGroups=this.nucleotideColour=this.abovePIDThreshold=this.findMenuItem=this.renderGapsMenuItem=this.wrapMenuItem=this.noColourmenuItem=this.conservationMenuItem=this.redoMenuItem=this.undoMenuItem=this.overviewMenuItem=this.alProperties=this.displayNonconservedMenuItem=this.colourTextMenuItem=this.annotationPanelMenuItem=this.avDistanceTreeBlosumMenuItem=this.njTreeBlosumMenuItem=
this.tcoffeeColour=this.BLOSUM62Colour=this.PIDColour=this.userDefinedColour=this.RNAHelixColour=this.RNAInteractionColour=this.purinePyrimidineColour=this.buriedColour=this.turnColour=this.strandColour=this.helixColour=this.hydrophobicityColour=this.taylorColour=this.zappoColour=this.clustalColour=this.statusBar=this.borderLayout1=this.neighbourTreeMenuItem=this.averageDistanceTreeMenuItem=this.PCAMenuItem=this.pairwiseAlignmentMenuItem=this.removeRedundancyMenuItem=this.sortGroupMenuItem=this.sortLengthMenuItem=
this.sortIDMenuItem=this.sortPairwiseMenuItem=this.viewTextMenuItem=this.viewBoxesMenuItem=this.removeAllGapsMenuItem=this.removeGappedColumnMenuItem=this.remove2RightMenuItem=this.remove2LeftMenuItem=this.invertSequenceMenuItem=this.deselectAllSequenceMenuItem=this.selectAllSequenceMenuItem=this.closeMenuItem=this.$outputAnnotations=this.$outputFeatures=this.$loadAnnotations=this.$loadTree=this.loadApplication=this.fileMenu=this.alignFrameMenuBar=this.annotationSortOrder=null;r(this,arguments)},
jalview.appletgui,"AlignFrame",jalview.appletgui.EmbmenuFrame,[java.awt.event.ActionListener,java.awt.event.ItemListener,java.awt.event.KeyListener,jalview.api.AlignViewControllerGuiI]);J(c$,function(){this.alignFrameMenuBar=new awt2swing.MenuBar;this.fileMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("action.file"));this.loadApplication=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.view_full_application"));this.$loadTree=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.load_associated_tree"));
this.$loadAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.load_features_annotations"));this.$outputFeatures=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.export_features").concat("..."));this.$outputAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.export_annotations").concat("..."));this.closeMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.close"));this.selectAllSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.select_all"));
this.deselectAllSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.deselect_all"));this.invertSequenceMenuItem=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.invert_selection"));this.remove2LeftMenuItem=new awt2swing.MenuItem;this.remove2RightMenuItem=new awt2swing.MenuItem;this.removeGappedColumnMenuItem=new awt2swing.MenuItem;this.removeAllGapsMenuItem=new awt2swing.MenuItem;this.viewBoxesMenuItem=new awt2swing.CheckboxMenuItem;this.viewTextMenuItem=
new awt2swing.CheckboxMenuItem;this.sortPairwiseMenuItem=new awt2swing.MenuItem;this.sortIDMenuItem=new awt2swing.MenuItem;this.sortLengthMenuItem=new awt2swing.MenuItem;this.sortGroupMenuItem=new awt2swing.MenuItem;this.removeRedundancyMenuItem=new awt2swing.MenuItem;this.pairwiseAlignmentMenuItem=new awt2swing.MenuItem;this.PCAMenuItem=new awt2swing.MenuItem;this.averageDistanceTreeMenuItem=new awt2swing.MenuItem;this.neighbourTreeMenuItem=new awt2swing.MenuItem;this.borderLayout1=new java.awt.BorderLayout;
this.statusBar=new awt2swing.Label;this.clustalColour=new awt2swing.MenuItem;this.zappoColour=new awt2swing.MenuItem;this.taylorColour=new awt2swing.MenuItem;this.hydrophobicityColour=new awt2swing.MenuItem;this.helixColour=new awt2swing.MenuItem;this.strandColour=new awt2swing.MenuItem;this.turnColour=new awt2swing.MenuItem;this.buriedColour=new awt2swing.MenuItem;this.purinePyrimidineColour=new awt2swing.MenuItem;this.RNAInteractionColour=new awt2swing.MenuItem;this.RNAHelixColour=new awt2swing.MenuItem;
this.userDefinedColour=new awt2swing.MenuItem;this.PIDColour=new awt2swing.MenuItem;this.BLOSUM62Colour=new awt2swing.MenuItem;this.tcoffeeColour=new awt2swing.MenuItem;this.njTreeBlosumMenuItem=new awt2swing.MenuItem;this.avDistanceTreeBlosumMenuItem=new awt2swing.MenuItem;this.annotationPanelMenuItem=new awt2swing.CheckboxMenuItem;this.colourTextMenuItem=new awt2swing.CheckboxMenuItem;this.displayNonconservedMenuItem=new awt2swing.CheckboxMenuItem;this.alProperties=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.alignment_props"));
this.overviewMenuItem=new awt2swing.MenuItem;this.undoMenuItem=new awt2swing.MenuItem;this.redoMenuItem=new awt2swing.MenuItem;this.conservationMenuItem=new awt2swing.CheckboxMenuItem;this.noColourmenuItem=new awt2swing.MenuItem;this.wrapMenuItem=new awt2swing.CheckboxMenuItem;this.renderGapsMenuItem=new awt2swing.CheckboxMenuItem;this.findMenuItem=new awt2swing.MenuItem;this.abovePIDThreshold=new awt2swing.CheckboxMenuItem;this.nucleotideColour=new awt2swing.MenuItem;this.deleteGroups=new awt2swing.MenuItem;
this.grpsFromSelection=new awt2swing.MenuItem;this.createGroup=new awt2swing.MenuItem;this.unGroup=new awt2swing.MenuItem;this.$delete=new awt2swing.MenuItem;this.copy=new awt2swing.MenuItem;this.cut=new awt2swing.MenuItem;this.pasteMenu=new awt2swing.Menu;this.pasteNew=new awt2swing.MenuItem;this.pasteThis=new awt2swing.MenuItem;this.applyToAllGroups=new awt2swing.CheckboxMenuItem;this.$font=new awt2swing.MenuItem;this.scaleAbove=new awt2swing.CheckboxMenuItem;this.scaleLeft=new awt2swing.CheckboxMenuItem;
this.scaleRight=new awt2swing.CheckboxMenuItem;this.modifyPID=new awt2swing.MenuItem;this.modifyConservation=new awt2swing.MenuItem;this.$sortByTree=new awt2swing.CheckboxMenuItem("Sort Alignment With New Tree",!0);this.sortByTreeMenu=new awt2swing.Menu;this.inputText=new awt2swing.MenuItem;this.documentation=new awt2swing.MenuItem;this.about=new awt2swing.MenuItem;this.seqLimits=new awt2swing.CheckboxMenuItem;this.centreColumnLabelFlag=new awt2swing.CheckboxMenuItem;this.followMouseOverFlag=new awt2swing.CheckboxMenuItem;
this.showSequenceLogo=new awt2swing.CheckboxMenuItem;this.applyAutoAnnotationSettings=new awt2swing.CheckboxMenuItem;this.showConsensusHistogram=new awt2swing.CheckboxMenuItem;this.showGroupConsensus=new awt2swing.CheckboxMenuItem;this.showGroupConservation=new awt2swing.CheckboxMenuItem;this.normSequenceLogo=new awt2swing.CheckboxMenuItem;this.featureSettings=new awt2swing.MenuItem;this.sequenceFeatures=new awt2swing.CheckboxMenuItem;this.annotationColour=new awt2swing.MenuItem;this.annotationColumnSelection=
new awt2swing.MenuItem;this.invertColSel=new awt2swing.MenuItem;this.showColumns=new awt2swing.MenuItem;this.showSeqs=new awt2swing.MenuItem;this.hideColumns=new awt2swing.MenuItem;this.hideSequences=new awt2swing.MenuItem;this.hideAllButSelection=new awt2swing.MenuItem;this.hideAllSelection=new awt2swing.MenuItem;this.showAllHidden=new awt2swing.MenuItem;this.$newView=new awt2swing.MenuItem});m(c$,function(a,b,c,f){this.construct(a,b,c,f,!0)},"jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B");
m(c$,function(a,b,c,f,l){this.construct(a,null,null,b,c,f,l)},"jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B");m(c$,function(a,b,c,f,l,d){this.construct(a,b,c,f,l,d,!0)},"jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B");m(c$,function(a,b,c,f,l,d,g){t(this,jalview.appletgui.AlignFrame,[]);null!=f&&(this.jalviewServletURL=f.jalviewServletURL);try{this.jbInit()}catch(h){if(y(h,Exception))h.printStackTrace();else throw h;}if(null!=f){var j;
try{j=f.windowWidth,null!=j&&(this.frameWidth=Integer.parseInt(j)),j=f.windowHeight,null!=j&&(this.frameHeight=Integer.parseInt(j))}catch(e){if(!y(e,Exception))throw e;}}this.viewport=new jalview.appletgui.AlignViewport(a,f);null!=b&&0<b.length&&this.viewport.hideSequence(b);null!=c&&this.viewport.setColumnSelection(c);this.alignPanel=new jalview.appletgui.AlignmentPanel(this,this.viewport);this.avc=new jalview.controller.AlignViewController(this,this.viewport,this.alignPanel);this.viewport.updateConservation(this.alignPanel);
this.viewport.updateConsensus(this.alignPanel);this.displayNonconservedMenuItem.setState(this.viewport.getShowUnconserved());this.followMouseOverFlag.setState(this.viewport.isFollowHighlight());this.showGroupConsensus.setState(this.viewport.isShowGroupConsensus());this.showGroupConservation.setState(this.viewport.isShowGroupConservation());this.showConsensusHistogram.setState(this.viewport.isShowConsensusHistogram());this.showSequenceLogo.setState(this.viewport.isShowSequenceLogo());this.normSequenceLogo.setState(this.viewport.isNormaliseSequenceLogo());
this.applyToAllGroups.setState(this.viewport.getColourAppliesToAllGroups());this.annotationPanelMenuItem.setState(this.viewport.isShowAnnotation());this.showAlignmentAnnotations.setState(this.viewport.isShowAnnotation());this.showSequenceAnnotations.setState(this.viewport.isShowAnnotation());this.seqLimits.setState(this.viewport.getShowJVSuffix());null!=f&&(j=f.sortBy,null!=j&&(j.equalsIgnoreCase("Id")?this.sortIDMenuItem_actionPerformed():j.equalsIgnoreCase("Pairwise Identity")?this.sortPairwiseMenuItem_actionPerformed():
j.equalsIgnoreCase("Length")&&this.sortLengthMenuItem_actionPerformed()),j=f.wrap,null!=j&&j.equalsIgnoreCase("true")&&(this.wrapMenuItem.setState(!0),this.wrapMenuItem_actionPerformed()),j=f.centrecolumnlabels,null!=j&&(this.centreColumnLabelFlag.setState(!0),this.centreColumnLabelFlag_stateChanged()));this.viewport.getAlignment().isNucleotide()?(this.viewport.updateStrucConsensus(this.alignPanel),this.viewport.getAlignment().hasRNAStructure()?this.RNAHelixColour.setEnabled(!0):this.RNAHelixColour.setEnabled(!1)):
(this.RNAHelixColour.setEnabled(!1),this.purinePyrimidineColour.setEnabled(!1));this.addKeyListener(this);this.alignPanel.seqPanel.seqCanvas.addKeyListener(this);this.alignPanel.idPanel.idCanvas.addKeyListener(this);this.alignPanel.scalePanel.addKeyListener(this);this.alignPanel.annotationPanel.addKeyListener(this);this.alignPanel.annotationPanelHolder.addKeyListener(this);this.alignPanel.annotationSpaceFillerHolder.addKeyListener(this);this.alignPanel.alabels.addKeyListener(this);g&&this.addToDisplay(d)},
"jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B");d(c$,"addToDisplay",function(a){this.createAlignFrameWindow(a);this.validate();this.alignPanel.adjustAnnotationHeight();this.alignPanel.paintAlignment(!0)},"~B");d(c$,"getAlignViewport",function(){return this.viewport});d(c$,"getSeqcanvas",function(){return this.alignPanel.seqPanel.seqCanvas});d(c$,"parseFeaturesFile",function(a,b){return this.parseFeaturesFile(a,b,!0)},"~S,~S");d(c$,"parseFeaturesFile",
function(a,b,c){var f=new java.util.Hashtable,l=!1;try{l=(new jalview.io.FeaturesFile(a,b)).parse(this.viewport.getAlignment(),this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getFeatureColours(),f,!0,this.viewport.applet.getDefaultParameter("relaxedidmatch",!1))}catch(d){if(y(d,Exception))d.printStackTrace();else throw d;}l&&(0<f.size()&&(this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks=f),c&&(this.viewport.setShowSequenceFeatures(!0),this.sequenceFeatures.setState(!0)),
null!=this.alignPanel.seqPanel.seqCanvas.fr&&this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(!0),null!=this.viewport.featureSettings&&this.viewport.featureSettings.refreshTable(),this.alignPanel.paintAlignment(!0),this.setStatus(jalview.util.MessageManager.getString("label.successfully_added_features_alignment")));return l},"~S,~S,~B");e(c$,"keyPressed",function(a){this.viewport.cursorMode&&((48<=a.getKeyCode()&&57>=a.getKeyCode()||96<=a.getKeyCode()&&105>=a.getKeyCode())&&Character.isDigit(a.getKeyChar()))&&
this.alignPanel.seqPanel.numberPressed(a.getKeyChar());switch(a.getKeyCode()){case 27:this.deselectAllSequenceMenuItem_actionPerformed();this.alignPanel.alabels.cancelDrag();break;case 88:(a.isControlDown()||a.isMetaDown())&&this.cut_actionPerformed();break;case 67:this.viewport.cursorMode&&!a.isControlDown()&&this.alignPanel.seqPanel.setCursorColumn();(a.isControlDown()||a.isMetaDown())&&this.copy_actionPerformed();break;case 86:a.isControlDown()&&this.paste(a.isShiftDown());break;case 65:(a.isControlDown()||
a.isMetaDown())&&this.selectAllSequenceMenuItem_actionPerformed();break;case 40:this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(0,1):this.moveSelectedSequences(!1);break;case 38:this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(0,-1):this.moveSelectedSequences(!0);break;case 37:a.isAltDown()||!this.viewport.cursorMode?this.slideSequences(!1,this.alignPanel.seqPanel.getKeyboardNo1()):this.alignPanel.seqPanel.moveCursor(-1,0);break;case 39:a.isAltDown()||!this.viewport.cursorMode?
this.slideSequences(!0,this.alignPanel.seqPanel.getKeyboardNo1()):this.alignPanel.seqPanel.moveCursor(1,0);break;case 32:this.viewport.cursorMode&&this.alignPanel.seqPanel.insertGapAtCursor(a.isControlDown()||a.isShiftDown()||a.isAltDown());break;case 127:case 8:this.viewport.cursorMode?this.alignPanel.seqPanel.deleteGapAtCursor(a.isControlDown()||a.isShiftDown()||a.isAltDown()):(this.cut_actionPerformed(),this.alignPanel.seqPanel.seqCanvas.repaint());break;case 83:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorRow();
break;case 80:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorPosition();break;case 10:case 44:this.viewport.cursorMode&&this.alignPanel.seqPanel.setCursorRowAndColumn();break;case 81:this.viewport.cursorMode&&this.alignPanel.seqPanel.setSelectionAreaAtCursor(!0);break;case 77:this.viewport.cursorMode&&this.alignPanel.seqPanel.setSelectionAreaAtCursor(!1);break;case 113:this.viewport.cursorMode=!this.viewport.cursorMode;this.setStatus(jalview.util.MessageManager.formatMessage("label.keyboard_editing_mode",
E(-1,[this.viewport.cursorMode?"on":"off"])));this.viewport.cursorMode&&(this.alignPanel.seqPanel.seqCanvas.cursorX=this.viewport.startRes,this.alignPanel.seqPanel.seqCanvas.cursorY=this.viewport.startSeq);break;case 70:a.isControlDown()&&this.findMenuItem_actionPerformed();break;case 72:var b=!a.isControlDown();a=!a.isShiftDown();this.toggleHiddenRegions(b,a);break;case 33:this.viewport.getWrapAlignment()?this.alignPanel.scrollUp(!0):this.alignPanel.setScrollValues(this.viewport.startRes,this.viewport.startSeq-
this.viewport.endSeq+this.viewport.startSeq);break;case 34:this.viewport.getWrapAlignment()?this.alignPanel.scrollUp(!1):this.alignPanel.setScrollValues(this.viewport.startRes,this.viewport.startSeq+this.viewport.endSeq-this.viewport.startSeq);break;case 90:a.isControlDown()&&this.undoMenuItem_actionPerformed();break;case 89:a.isControlDown()&&this.redoMenuItem_actionPerformed();break;case 76:a.isControlDown()&&this.trimAlignment(!0);break;case 82:a.isControlDown()&&this.trimAlignment(!1);break;case 69:a.isControlDown()&&
(a.isShiftDown()?this.removeAllGapsMenuItem_actionPerformed():this.removeGappedColumnMenuItem_actionPerformed());break;case 73:a.isControlDown()&&(a.isAltDown()?this.invertColSel_actionPerformed():this.invertSequenceMenuItem_actionPerformed());break;case 71:a.isControlDown()&&(a.isShiftDown()?this.unGroup_actionPerformed():this.createGroup_actionPerformed());break;case 85:a.isControlDown()&&this.deleteGroups_actionPerformed();break;case 84:a.isControlDown()&&this.newView(null)}this.alignPanel.paintAlignment(!0)},
"java.awt.event.KeyEvent");d(c$,"toggleHiddenRegions",function(a,b){var c=!1,f=this.viewport.getSelectionGroup();if(!a&&!b&&(null!=this.viewport.getColumnSelection()&&null!=this.viewport.getColumnSelection().getSelected()&&0<this.viewport.getColumnSelection().getSelected().size()||null!=f&&0<f.getSize()&&f.getStartRes()<=f.getEndRes()))null!=f&&(this.invertSequenceMenuItem_actionPerformed(),f=this.viewport.getSelectionGroup(),a=!0),this.viewport.expandColSelection(f,!0),this.invertColSel_actionPerformed(),
b=!0;a&&(null!=f&&f.getSize()!=this.viewport.getAlignment().getHeight()?(c=!0,this.viewport.hideAllSelectedSeqs()):b&&0<this.viewport.getColumnSelection().getSelected().size()||this.viewport.showAllHiddenSeqs());b&&(0<this.viewport.getColumnSelection().getSelected().size()?(this.viewport.hideSelectedColumns(),a||this.viewport.setSelectionGroup(f)):c||this.viewport.showAllHiddenColumns())},"~B,~B");e(c$,"keyReleased",function(){},"java.awt.event.KeyEvent");e(c$,"keyTyped",function(){},"java.awt.event.KeyEvent");
e(c$,"itemStateChanged",function(a){a=a.getSource();a===this.displayNonconservedMenuItem?this.displayNonconservedMenuItem_actionPerformed():a===this.colourTextMenuItem?this.colourTextMenuItem_actionPerformed():a===this.wrapMenuItem?this.wrapMenuItem_actionPerformed():a===this.scaleAbove?this.viewport.setScaleAboveWrapped(this.scaleAbove.getState()):a===this.scaleLeft?this.viewport.setScaleLeftWrapped(this.scaleLeft.getState()):a===this.scaleRight?this.viewport.setScaleRightWrapped(this.scaleRight.getState()):
a===this.seqLimits?this.seqLimits_itemStateChanged():a===this.viewBoxesMenuItem?this.viewport.setShowBoxes(this.viewBoxesMenuItem.getState()):a===this.viewTextMenuItem?this.viewport.setShowText(this.viewTextMenuItem.getState()):a===this.renderGapsMenuItem?this.viewport.setRenderGaps(this.renderGapsMenuItem.getState()):a===this.annotationPanelMenuItem?(this.viewport.setShowAnnotation(this.annotationPanelMenuItem.getState()),this.alignPanel.setAnnotationVisible(this.annotationPanelMenuItem.getState())):
a===this.sequenceFeatures?(this.viewport.setShowSequenceFeatures(this.sequenceFeatures.getState()),this.alignPanel.seqPanel.seqCanvas.repaint()):a===this.showAlignmentAnnotations?this.setAnnotationsVisibility():a===this.showSequenceAnnotations?this.setAnnotationsVisibility():a===this.sortAnnBySequence?(a=this.sortAnnBySequence.getState(),this.sortAnnByLabel.setState(!1),this.setAnnotationSortOrder(a?jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL:jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE),
this.setViewportAnnotationOrder()):a===this.sortAnnByLabel?(a=this.sortAnnByLabel.getState(),this.sortAnnBySequence.setState(!1),this.setAnnotationSortOrder(a?jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE:jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE),this.setViewportAnnotationOrder()):a===this.showAutoFirst?(this.showAutoLast.setState(!this.showAutoFirst.getState()),this.setShowAutoCalculatedAbove(this.showAutoFirst.getState()),this.setViewportAnnotationOrder()):
a===this.showAutoLast?(this.showAutoFirst.setState(!this.showAutoLast.getState()),this.setShowAutoCalculatedAbove(this.showAutoFirst.getState()),this.setViewportAnnotationOrder()):a===this.conservationMenuItem?this.conservationMenuItem_actionPerformed():a===this.abovePIDThreshold?this.abovePIDThreshold_actionPerformed():a===this.applyToAllGroups?this.viewport.setColourAppliesToAllGroups(this.applyToAllGroups.getState()):a===this.autoCalculate?this.viewport.autoCalculateConsensus=this.autoCalculate.getState():
a===this.$sortByTree?this.viewport.sortByTree=this.$sortByTree.getState():a===this.centreColumnLabelFlag?this.centreColumnLabelFlag_stateChanged():a===this.followMouseOverFlag?this.mouseOverFlag_stateChanged():a===this.showGroupConsensus?this.showGroupConsensus_actionPerformed():a===this.showGroupConservation?this.showGroupConservation_actionPerformed():a===this.showSequenceLogo?this.showSequenceLogo_actionPerformed():a===this.normSequenceLogo?this.normSequenceLogo_actionPerformed():a===this.showConsensusHistogram?
this.showConsensusHistogram_actionPerformed():a===this.applyAutoAnnotationSettings&&this.applyAutoAnnotationSettings_actionPerformed();this.alignPanel.paintAlignment(!0)},"java.awt.event.ItemEvent");d(c$,"setAnnotationsVisibility",function(){for(var a=this.showAlignmentAnnotations.getState(),b=this.showSequenceAnnotations.getState(),c,f=0,l=this.alignPanel.getAlignment().getAlignmentAnnotation();f<l.length&&((c=l[f])||1);f++)c.visible=null==c.sequenceRef?a:b;this.alignPanel.validateAnnotationDimensions(!0);
this.validate();this.repaint()});d(c$,"setAnnotationSortOrder",function(a){this.annotationSortOrder=a},"jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");d(c$,"setViewportAnnotationOrder",function(){this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);this.alignPanel.av.setShowAutocalculatedAbove(this.showAutoCalculatedAbove)});d(c$,"setShowAutoCalculatedAbove",function(a){this.showAutoCalculatedAbove=a},"~B");d(c$,"mouseOverFlag_stateChanged",function(){this.viewport.setFollowHighlight(this.followMouseOverFlag.getState())});
d(c$,"centreColumnLabelFlag_stateChanged",function(){this.viewport.centreColumnLabels=this.centreColumnLabelFlag.getState();this.alignPanel.annotationPanel.repaint()});e(c$,"actionPerformed",function(a){a=a.getSource();if(a===this.inputText)this.inputText_actionPerformed();else if(a===this.$loadTree)this.loadTree_actionPerformed();else if(a===this.loadApplication)this.launchFullApplication();else if(a===this.$loadAnnotations)this.loadAnnotations();else if(a===this.$outputAnnotations)this.outputAnnotations(!0);
else if(a===this.$outputFeatures)this.outputFeatures(!0,"Jalview");else if(a===this.closeMenuItem)this.closeMenuItem_actionPerformed();else if(a===this.copy)this.copy_actionPerformed();else if(a===this.undoMenuItem)this.undoMenuItem_actionPerformed();else if(a===this.redoMenuItem)this.redoMenuItem_actionPerformed();else if(a===this.inputText)this.inputText_actionPerformed();else if(a===this.closeMenuItem)this.closeMenuItem_actionPerformed();else if(a===this.undoMenuItem)this.undoMenuItem_actionPerformed();
else if(a===this.redoMenuItem)this.redoMenuItem_actionPerformed();else if(a===this.copy)this.copy_actionPerformed();else if(a===this.pasteNew)this.pasteNew_actionPerformed();else if(a===this.pasteThis)this.pasteThis_actionPerformed();else if(a===this.cut)this.cut_actionPerformed();else if(a===this.$delete)this.delete_actionPerformed();else if(a===this.grpsFromSelection)this.makeGrpsFromSelection_actionPerformed();else if(a===this.deleteGroups)this.deleteGroups_actionPerformed();else if(a===this.selectAllSequenceMenuItem)this.selectAllSequenceMenuItem_actionPerformed();
else if(a===this.deselectAllSequenceMenuItem)this.deselectAllSequenceMenuItem_actionPerformed();else if(a===this.invertSequenceMenuItem)this.invertSequenceMenuItem_actionPerformed();else if(a===this.invertColSel)this.viewport.invertColumnSelection(),this.alignPanel.paintAlignment(!0);else if(a===this.remove2LeftMenuItem)this.trimAlignment(!0);else if(a===this.remove2RightMenuItem)this.trimAlignment(!1);else if(a===this.removeGappedColumnMenuItem)this.removeGappedColumnMenuItem_actionPerformed();else if(a===
this.removeAllGapsMenuItem)this.removeAllGapsMenuItem_actionPerformed();else if(a===this.findMenuItem)this.findMenuItem_actionPerformed();else if(a===this.$font)new jalview.appletgui.FontChooser(this.alignPanel);else if(a===this.$newView)this.newView(null);else if(a===this.showColumns)this.viewport.showAllHiddenColumns(),this.alignPanel.paintAlignment(!0);else if(a===this.showSeqs)this.viewport.showAllHiddenSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.hideColumns)this.viewport.hideSelectedColumns(),
this.alignPanel.paintAlignment(!0);else if(a===this.hideSequences&&null!=this.viewport.getSelectionGroup())this.viewport.hideAllSelectedSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.hideAllButSelection)this.toggleHiddenRegions(!1,!1),this.alignPanel.paintAlignment(!0);else if(a===this.hideAllSelection)a=this.viewport.getSelectionGroup(),this.viewport.expandColSelection(a,!1),this.viewport.hideAllSelectedSeqs(),this.viewport.hideSelectedColumns(),this.alignPanel.paintAlignment(!0);else if(a===
this.showAllHidden)this.viewport.showAllHiddenColumns(),this.viewport.showAllHiddenSeqs(),this.alignPanel.paintAlignment(!0);else if(a===this.showGroupConsensus)this.showGroupConsensus_actionPerformed();else if(a===this.showGroupConservation)this.showGroupConservation_actionPerformed();else if(a===this.showSequenceLogo)this.showSequenceLogo_actionPerformed();else if(a===this.normSequenceLogo)this.normSequenceLogo_actionPerformed();else if(a===this.showConsensusHistogram)this.showConsensusHistogram_actionPerformed();
else if(a===this.applyAutoAnnotationSettings)this.applyAutoAnnotationSettings_actionPerformed();else if(a===this.featureSettings)new jalview.appletgui.FeatureSettings(this.alignPanel);else if(a===this.alProperties){var b=(new jalview.io.AlignmentProperties(this.viewport.getAlignment())).formatAsString();a=new jalview.appletgui.CutAndPasteTransfer(!1,this);a.setText(b.toString());b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.formatMessage("label.alignment_properties",
E(-1,[this.getTitle()])),400,250)}else a===this.overviewMenuItem?this.overviewMenuItem_actionPerformed():a===this.noColourmenuItem?this.changeColour(null):a===this.clustalColour?(this.abovePIDThreshold.setState(!1),this.changeColour(new jalview.schemes.ClustalxColourScheme(this.viewport.getAlignment(),null))):a===this.zappoColour?this.changeColour(new jalview.schemes.ZappoColourScheme):a===this.taylorColour?this.changeColour(new jalview.schemes.TaylorColourScheme):a===this.hydrophobicityColour?this.changeColour(new jalview.schemes.HydrophobicColourScheme):
a===this.helixColour?this.changeColour(new jalview.schemes.HelixColourScheme):a===this.strandColour?this.changeColour(new jalview.schemes.StrandColourScheme):a===this.turnColour?this.changeColour(new jalview.schemes.TurnColourScheme):a===this.buriedColour?this.changeColour(new jalview.schemes.BuriedColourScheme):a===this.nucleotideColour?this.changeColour(new jalview.schemes.NucleotideColourScheme):a===this.purinePyrimidineColour?this.changeColour(new jalview.schemes.PurinePyrimidineColourScheme):
a===this.RNAInteractionColour?this.changeColour(new jalview.schemes.RNAInteractionColourScheme):a===this.RNAHelixColour?new jalview.schemes.RNAHelicesColourChooser(this.viewport,this.alignPanel):a===this.modifyPID?this.modifyPID_actionPerformed():a===this.modifyConservation?this.modifyConservation_actionPerformed():a===this.userDefinedColour?new jalview.appletgui.UserDefinedColours(this.alignPanel,null):a===this.PIDColour?this.changeColour(new jalview.schemes.PIDColourScheme):a===this.BLOSUM62Colour?
this.changeColour(new jalview.schemes.Blosum62ColourScheme):a===this.tcoffeeColour?this.changeColour(new jalview.schemes.TCoffeeColourScheme(this.alignPanel.getAlignment())):a===this.annotationColour?new jalview.appletgui.AnnotationColourChooser(this.viewport,this.alignPanel):a===this.annotationColumnSelection?new jalview.appletgui.AnnotationColumnChooser(this.viewport,this.alignPanel):a===this.sortPairwiseMenuItem?this.sortPairwiseMenuItem_actionPerformed():a===this.sortIDMenuItem?this.sortIDMenuItem_actionPerformed():
a===this.sortLengthMenuItem?this.sortLengthMenuItem_actionPerformed():a===this.sortGroupMenuItem?this.sortGroupMenuItem_actionPerformed():a===this.removeRedundancyMenuItem?this.removeRedundancyMenuItem_actionPerformed():a===this.pairwiseAlignmentMenuItem?this.pairwiseAlignmentMenuItem_actionPerformed():a===this.PCAMenuItem?this.PCAMenuItem_actionPerformed():a===this.averageDistanceTreeMenuItem?this.averageDistanceTreeMenuItem_actionPerformed():a===this.neighbourTreeMenuItem?this.neighbourTreeMenuItem_actionPerformed():
a===this.njTreeBlosumMenuItem?this.njTreeBlosumMenuItem_actionPerformed():a===this.avDistanceTreeBlosumMenuItem?this.avTreeBlosumMenuItem_actionPerformed():a===this.documentation?this.documentation_actionPerformed():a===this.about&&this.about_actionPerformed()},"java.awt.event.ActionEvent");d(c$,"inputText_actionPerformed",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this),b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("label.input_cut_paste"),
500,500)});d(c$,"outputText_actionPerformed",function(a){var b=new jalview.appletgui.CutAndPasteTransfer(!0,this),c=new awt2swing.Frame;c.add(b);jalview.bin.JalviewLite.addFrame(c,jalview.util.MessageManager.formatMessage("label.alignment_output_command",E(-1,[a.getActionCommand()])),600,500);this.alignPanel.cloneFeatureRenderer();b.setText((new jalview.io.AppletFormatAdapter(this.alignPanel)).formatSequences(a.getActionCommand(),this.viewport.getAlignment(),this.viewport.getShowJVSuffix()))},"java.awt.event.ActionEvent");
d(c$,"loadAnnotations",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this);a.setText(jalview.util.MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));a.setAnnotationImport();var b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("action.paste_annotations"),400,300)});d(c$,"outputAnnotations",function(a){var b=(new jalview.io.AnnotationFile).printAnnotationsForView(this.viewport);if(a){a=new jalview.appletgui.CutAndPasteTransfer(!1,
this);var c=new awt2swing.Frame;c.add(a);jalview.bin.JalviewLite.addFrame(c,jalview.util.MessageManager.getString("label.annotations"),600,500);a.setText(b)}return b},"~B");d(c$,"getDisplayedFeatureCols",function(){return null!=this.alignPanel.getFeatureRenderer()&&null!=this.viewport.getFeaturesDisplayed()?this.alignPanel.getFeatureRenderer().getDisplayedFeatureCols():null});d(c$,"outputFeatures",function(a,b){var c;c=b.equalsIgnoreCase("Jalview")?(new jalview.io.FeaturesFile).printJalviewFormat(this.viewport.getAlignment().getSequencesArray(),
this.getDisplayedFeatureCols()):(new jalview.io.FeaturesFile).printGFFFormat(this.viewport.getAlignment().getSequencesArray(),this.getDisplayedFeatureCols());if(a){var f=!1;if(null==c||c.equals("No Features Visible"))c="# No features visible - paste some and import them here.",f=!0;var l=new jalview.appletgui.CutAndPasteTransfer(f,this);f&&l.setAnnotationImport();f=new awt2swing.Frame;f.add(l);jalview.bin.JalviewLite.addFrame(f,jalview.util.MessageManager.getString("label.features"),600,500);l.setText(c)}else null==
c&&(c="");return c},"~B,~S");d(c$,"launchFullApplication",function(){var a=new StringBuffer(this.jalviewServletURL),b=a.lastIndexOf("?")>a.lastIndexOf("/")?"&":"?";a.append(b);b=this.viewport.applet;a.append("open="+this.appendProtocol(b.startupFile));null!=this.viewport.applet.features&&(a.append("&features="),a.append(this.appendProtocol(b.features)));null!=b.annotations&&(a.append("&annotations="),a.append(this.appendProtocol(b.annotations)));null!=b.jnetFile&&(a.append("&annotations="),a.append(this.appendProtocol(b.jnetFile)));
null!=b.defaultColour&&a.append("&colour="+this.removeWhiteSpace(b.defaultColour));null!=b.userDefinedColour&&a.append("&colour="+this.removeWhiteSpace(b.userDefinedColour));null!=b.treeFile&&a.append("&tree="+this.appendProtocol(b.treeFile));this.showURL(a.toString(),"FULL_APP")});d(c$,"removeWhiteSpace",function(a){for(var b=new StringBuffer,c=0;c<a.length;c++)Character.isWhitespace(a.charAt(c))?b.append("%20"):b.append(a.charAt(c));return b.toString()},"~S");d(c$,"appendProtocol",function(a){try{new java.net.URL(a),
a=java.net.URLEncoder.encode(a)}catch(b){if(y(b,java.net.MalformedURLException))a=this.viewport.applet.getCodeBase()+a;else throw b;}return a},"~S");d(c$,"closeMenuItem_actionPerformed",function(){jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel);null!=this.alignPanel.seqPanel&&null!=this.alignPanel.seqPanel.seqCanvas&&jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel.seqPanel.seqCanvas);null!=this.alignPanel.idPanel&&null!=this.alignPanel.idPanel.idCanvas&&jalview.appletgui.PaintRefresher.RemoveComponent(this.alignPanel.idPanel.idCanvas);
0==jalview.appletgui.PaintRefresher.components.size()&&null==this.viewport.applet&&System.exit(0);this.alignPanel=this.viewport=null;this.dispose()});d(c$,"updateEditMenuBar",function(){if(0<this.viewport.getHistoryList().size()){this.undoMenuItem.setEnabled(!0);var a=this.viewport.getHistoryList().peek();this.undoMenuItem.setLabel(jalview.util.MessageManager.formatMessage("label.undo_command",E(-1,[a.getDescription()])))}else this.undoMenuItem.setEnabled(!1),this.undoMenuItem.setLabel(jalview.util.MessageManager.getString("action.undo"));
0<this.viewport.getRedoList().size()?(this.redoMenuItem.setEnabled(!0),a=this.viewport.getRedoList().peek(),this.redoMenuItem.setLabel(jalview.util.MessageManager.formatMessage("label.redo_command",E(-1,[a.getDescription()])))):(this.redoMenuItem.setEnabled(!1),this.redoMenuItem.setLabel(jalview.util.MessageManager.getString("action.redo")))});e(c$,"addHistoryItem",function(a){0<a.getSize()&&(this.viewport.addToHistoryList(a),this.viewport.clearRedoList(),this.updateEditMenuBar(),this.viewport.updateHiddenColumns())},
"jalview.commands.CommandI");d(c$,"undoMenuItem_actionPerformed",function(){if(!this.viewport.getHistoryList().isEmpty()){var a=this.viewport.getHistoryList().pop();this.viewport.addToRedoList(a);a.undoCommand(null);a=this.getOriginatingSource(a);a!==this.viewport&&System.err.println("Warning: Viewport object mismatch whilst undoing");a.updateHiddenColumns();this.updateEditMenuBar();a.firePropertyChange("alignment",null,a.getAlignment().getSequences())}});d(c$,"redoMenuItem_actionPerformed",function(){if(!this.viewport.getRedoList().isEmpty()){var a=
this.viewport.getRedoList().pop();this.viewport.addToHistoryList(a);a.doCommand(null);a=this.getOriginatingSource(a);a!==this.viewport&&System.err.println("Warning: Viewport object mismatch whilst re-doing");a.updateHiddenColumns();this.updateEditMenuBar();a.firePropertyChange("alignment",null,a.getAlignment().getSequences())}});d(c$,"getOriginatingSource",function(a){var b=null,c=null;if(v(a,jalview.commands.EditCommand)){c=a.getAlignment();a=jalview.appletgui.PaintRefresher.components.get(this.viewport.getSequenceSetId());
for(var f=0;f<a.size();f++)if(v(a.elementAt(f),jalview.appletgui.AlignmentPanel)&&c===a.elementAt(f).av.getAlignment()){b=a.elementAt(f).av;break}}null==b&&(null!=c&&jalview.appletgui.PaintRefresher.validateSequences(c,this.viewport.getAlignment()),b=this.viewport);return b},"jalview.commands.CommandI");d(c$,"moveSelectedSequences",function(a){var b=this.viewport.getSelectionGroup();if(null!=b){this.viewport.getAlignment().moveSelectedSequencesByOne(b,a?null:this.viewport.getHiddenRepSequences(),
a);this.alignPanel.paintAlignment(!0);var c=this.viewport.getCodingComplement();null!=c&&(b=jalview.util.MappingUtils.mapSequenceGroup(b,this.viewport,c),c.getAlignment().moveSelectedSequencesByOne(b,a?null:c.getHiddenRepSequences(),a))}},"~B");d(c$,"slideSequences",function(a,b){var c=new java.util.Vector;this.viewport.cursorMode?c.add(this.viewport.getAlignment().getSequenceAt(this.alignPanel.seqPanel.seqCanvas.cursorY)):null!=this.viewport.getSelectionGroup()&&this.viewport.getSelectionGroup().getSize()!=
this.viewport.getAlignment().getHeight()&&(c=this.viewport.getSelectionGroup().getSequences(this.viewport.getHiddenRepSequences()));if(!(1>c.size())){for(var f=new java.util.Vector,l=0;l<this.viewport.getAlignment().getHeight();l++)c.contains(this.viewport.getAlignment().getSequenceAt(l))||f.addElement(this.viewport.getAlignment().getSequenceAt(l));for(var c=c.toArray(Array(c.size())),d=f.toArray(Array(f.size())),l=0;l<f.size();l++)d[l]=f.elementAt(l);f=a?new jalview.commands.SlideSequencesCommand("Slide Sequences",
d,c,b,this.viewport.getGapCharacter()):new jalview.commands.SlideSequencesCommand("Slide Sequences",c,d,b,this.viewport.getGapCharacter());l=0;f.getGapsInsertedBegin()&&a?this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(b,0):l=b:!f.getGapsInsertedBegin()&&!a&&(this.viewport.cursorMode?this.alignPanel.seqPanel.moveCursor(-b,0):l=-b);0!=l&&(this.viewport.getSelectionGroup().setStartRes(this.viewport.getSelectionGroup().getStartRes()+l),this.viewport.getSelectionGroup().setEndRes(this.viewport.getSelectionGroup().getEndRes()+
l));l=!1;c=this.viewport.getHistoryList();null!=c&&(0<c.size()&&v(c.peek(),jalview.commands.SlideSequencesCommand))&&(l=f.appendSlideCommand(c.peek()));l||this.addHistoryItem(f);this.repaint()}},"~B,~N");d(c$,"copy_actionPerformed",function(){if(null!=this.viewport.getSelectionGroup()){var a=this.viewport.getSelectionGroup();jalview.appletgui.AlignFrame.copiedSequences=new StringBuffer;for(var b=new java.util.HashMap,c=0;c<a.getSize();c++){var f=a.getSequenceAt(c),l=this.viewport.getAlignment().findIndex(f);
b.put(new Integer(l),f)}var l=0,d,g,h;if(this.viewport.hasHiddenColumns()&&null!=this.viewport.getSelectionGroup()){jalview.appletgui.AlignFrame.copiedHiddenColumns=new java.util.Vector;c=this.viewport.getSelectionGroup().getStartRes();for(f=this.viewport.getColumnSelection().getHiddenColumns().iterator();f.hasNext()&&((d=f.next())||1);)jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(w(-1,[d[0]-c,d[1]-c]))}else jalview.appletgui.AlignFrame.copiedHiddenColumns=null;for(c=0;c<a.getSize();c++){for(f=
null;null==f;)if(b.containsKey(new Integer(l))){f=b.get(new Integer(l));l++;break}else l++;d=f.findPosition(a.getStartRes());for(var j=g=0;j<a.getEndRes()+1&&j<f.getLength();j++)h=f.getCharAt(j),jalview.util.Comparison.isGap(h)||g++;0<g&&(g+=f.getStart()-1);jalview.appletgui.AlignFrame.copiedSequences.append(f.getName()+"\t"+d+"\t"+g+"\t"+f.getSequenceAsString(a.getStartRes(),a.getEndRes()+1)+"\n")}}});d(c$,"pasteNew_actionPerformed",function(){this.paste(!0)});d(c$,"pasteThis_actionPerformed",function(){this.paste(!1)});
d(c$,"paste",function(a){try{if(null!=jalview.appletgui.AlignFrame.copiedSequences){for(var b=new java.util.StringTokenizer(jalview.appletgui.AlignFrame.copiedSequences.toString()),c=new java.util.Vector;b.hasMoreElements();){var f=b.nextToken(),l=Integer.parseInt(b.nextToken()),d=Integer.parseInt(b.nextToken());c.addElement(new jalview.datamodel.Sequence(f,b.nextToken(),l,d))}for(var g=Array(c.size()),b=0;b<c.size();b++)g[b]=c.elementAt(b);if(a){var h=jalview.util.MessageManager.getString("label.copied_sequences"),
h=this.getTitle().startsWith(jalview.util.MessageManager.getString("label.copied_sequences"))?this.getTitle():h.concat(jalview.util.MessageManager.formatMessage("label.from_msname",E(-1,[this.getTitle()]))),j=new jalview.appletgui.AlignFrame(new jalview.datamodel.Alignment(g),this.viewport.applet,h,!1);if(null!=jalview.appletgui.AlignFrame.copiedHiddenColumns)for(b=0;b<jalview.appletgui.AlignFrame.copiedHiddenColumns.size();b++){var e=jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt(b);
j.viewport.hideColumns(e[0],e[1])}jalview.bin.JalviewLite.addFrame(j,h,this.frameWidth,this.frameHeight)}else this.addSequences(g)}}catch(x){if(!y(x,Exception))throw x;}},"~B");d(c$,"addSequences",function(a){for(var b=0;b<a.length;b++)this.viewport.getAlignment().addSequence(a[b]);this.addHistoryItem(new jalview.commands.EditCommand(jalview.util.MessageManager.getString("label.add_sequences"),jalview.commands.EditCommand.Action.PASTE,a,0,this.viewport.getAlignment().getWidth(),this.viewport.getAlignment()));
this.viewport.setEndSeq(this.viewport.getAlignment().getHeight());this.viewport.getAlignment().getWidth();this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences())},"~A");d(c$,"cut_actionPerformed",function(){this.copy_actionPerformed();this.delete_actionPerformed()});d(c$,"delete_actionPerformed",function(){var a=this.viewport.getSelectionGroup();if(null!=a){for(var b=new java.util.Vector,c,f=0;f<a.getSize();f++)c=a.getSequenceAt(f),b.addElement(c);a.getSize()==
this.viewport.getAlignment().getHeight()&&this.viewport.getColumnSelection().removeElements(a.getStartRes(),a.getEndRes()+1);c=Array(b.size());for(f=0;f<b.size();f++)c[f]=b.elementAt(f);this.addHistoryItem(new jalview.commands.EditCommand(jalview.util.MessageManager.getString("label.cut_sequences"),jalview.commands.EditCommand.Action.CUT,c,a.getStartRes(),a.getEndRes()-a.getStartRes()+1,this.viewport.getAlignment()));this.viewport.setSelectionGroup(null);this.viewport.getAlignment().deleteGroup(a);
this.viewport.firePropertyChange("alignment",null,this.viewport.getAlignment().getSequences());1>this.viewport.getAlignment().getHeight()&&this.setVisible(!1);this.viewport.sendSelection()}});d(c$,"showGroupConsensus_actionPerformed",function(){this.viewport.setShowGroupConsensus(this.showGroupConsensus.getState());this.alignPanel.updateAnnotation(this.applyAutoAnnotationSettings.getState())});d(c$,"showGroupConservation_actionPerformed",function(){this.viewport.setShowGroupConservation(this.showGroupConservation.getState());
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d(c$,"removeAllGapsMenuItem_actionPerformed",function(){var a=0,b=this.viewport.getAlignment().getWidth()-1,c;null!=this.viewport.getSelectionGroup()?(c=this.viewport.getSelectionGroup().getSequencesAsArray(this.viewport.getHiddenRepSequences()),a=this.viewport.getSelectionGroup().getStartRes(),b=this.viewport.getSelectionGroup().getEndRes()):c=this.viewport.getAlignment().getSequencesArray();var f=this.viewport.getAlignment().getSequenceAt(0),l=f.findPosition(this.viewport.startRes);this.addHistoryItem(new jalview.commands.RemoveGapsCommand("Remove Gaps",
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jalview.appletgui.PaintRefresher.Register(b.alignPanel,b.alignPanel.av.getSequenceSetId());jalview.appletgui.PaintRefresher.Register(b.alignPanel.idPanel.idCanvas,b.alignPanel.av.getSequenceSetId());jalview.appletgui.PaintRefresher.Register(b.alignPanel.seqPanel.seqCanvas,b.alignPanel.av.getSequenceSetId());for(var f=jalview.appletgui.PaintRefresher.components.get(this.viewport.getSequenceSetId()),l=-1,c=0;c<f.size();c++)v(f.elementAt(c),jalview.appletgui.AlignmentPanel)&&l++;c=String.instantialize(this.getTitle());
null!=a?c=a+" ( "+c+")":(-1<c.indexOf("(View")&&(c=c.substring(0,c.indexOf("(View"))),c+="(View "+l+")");b.setTitle(c.toString());b.viewport.setHistoryList(this.viewport.getHistoryList());b.viewport.setRedoList(this.viewport.getRedoList());return b},"~S");d(c$,"getFeatureGroups",function(){var a=null;return null!=this.alignPanel&&null!=(a=this.alignPanel.getFeatureRenderer())?(a=a.getFeatureGroups(),a.toArray(Array(a.size()))):null});d(c$,"getFeatureGroupsOfState",function(a){var b=null;return null!=
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"~A,~B");d(c$,"seqLimits_itemStateChanged",function(){this.viewport.setShowJVSuffix(this.seqLimits.getState());this.alignPanel.fontChanged();this.alignPanel.paintAlignment(!0)});d(c$,"colourTextMenuItem_actionPerformed",function(){this.viewport.setColourText(this.colourTextMenuItem.getState());this.alignPanel.paintAlignment(!0)});d(c$,"displayNonconservedMenuItem_actionPerformed",function(){this.viewport.setShowUnconserved(this.displayNonconservedMenuItem.getState());this.alignPanel.paintAlignment(!0)});
d(c$,"wrapMenuItem_actionPerformed",function(){this.viewport.setWrapAlignment(this.wrapMenuItem.getState());this.alignPanel.setWrapAlignment(this.wrapMenuItem.getState());this.scaleAbove.setEnabled(this.wrapMenuItem.getState());this.scaleLeft.setEnabled(this.wrapMenuItem.getState());this.scaleRight.setEnabled(this.wrapMenuItem.getState());this.alignPanel.paintAlignment(!0)});d(c$,"overviewMenuItem_actionPerformed",function(){if(null==this.alignPanel.overviewPanel){var a=new awt2swing.Frame,b=new jalview.appletgui.OverviewPanel(this.alignPanel);
a.add(b);jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.formatMessage("label.overview_params",E(-1,[this.getTitle()])),b.getPreferredSize().width,b.getPreferredSize().height+50);a.pack();var c=this.alignPanel;a.addWindowListener((H("jalview.appletgui.AlignFrame$1")?0:jalview.appletgui.AlignFrame.$AlignFrame$1$(),C(jalview.appletgui.AlignFrame$1,this,T("ap",c))));this.alignPanel.setOverviewPanel(b)}});e(c$,"changeColour",function(a){null!=a&&(this.viewport.getAbovePIDThreshold()&&this.viewport.setThreshold(jalview.appletgui.SliderPanel.setPIDSliderSource(this.alignPanel,
a,"Background")),this.viewport.getConservationSelected()?(a.setConservationApplied(!0),this.viewport.setIncrement(jalview.appletgui.SliderPanel.setConservationSlider(this.alignPanel,a,"Background"))):a.setConservationApplied(!1));this.viewport.setGlobalColourScheme(a);null!=this.alignPanel.getOverviewPanel()&&this.alignPanel.getOverviewPanel().updateOverviewImage();jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.viewport.applet).sequenceColoursChanged(this.alignPanel);
this.alignPanel.paintAlignment(!0)},"jalview.schemes.ColourSchemeI");d(c$,"modifyPID_actionPerformed",function(){this.viewport.getAbovePIDThreshold()&&null!=this.viewport.getGlobalColourScheme()&&(jalview.appletgui.SliderPanel.setPIDSliderSource(this.alignPanel,this.viewport.getGlobalColourScheme(),"Background"),jalview.appletgui.SliderPanel.showPIDSlider())});d(c$,"modifyConservation_actionPerformed",function(){this.viewport.getConservationSelected()&&null!=this.viewport.getGlobalColourScheme()&&
(jalview.appletgui.SliderPanel.setConservationSlider(this.alignPanel,this.viewport.getGlobalColourScheme(),"Background"),jalview.appletgui.SliderPanel.showConservationSlider())});d(c$,"conservationMenuItem_actionPerformed",function(){this.viewport.setConservationSelected(this.conservationMenuItem.getState());this.viewport.setAbovePIDThreshold(!1);this.abovePIDThreshold.setState(!1);this.changeColour(this.viewport.getGlobalColourScheme());this.modifyConservation_actionPerformed()});d(c$,"abovePIDThreshold_actionPerformed",
function(){this.viewport.setAbovePIDThreshold(this.abovePIDThreshold.getState());this.conservationMenuItem.setState(!1);this.viewport.setConservationSelected(!1);this.changeColour(this.viewport.getGlobalColourScheme());this.modifyPID_actionPerformed()});d(c$,"sortPairwiseMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByPID(this.viewport.getAlignment(),this.viewport.getAlignment().getSequenceAt(0),null);this.addHistoryItem(new jalview.commands.OrderCommand("Pairwise Sort",
a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortIDMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByID(this.viewport.getAlignment());this.addHistoryItem(new jalview.commands.OrderCommand("ID Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortLengthMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByLength(this.viewport.getAlignment());
this.addHistoryItem(new jalview.commands.OrderCommand("Length Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"sortGroupMenuItem_actionPerformed",function(){var a=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByGroup(this.viewport.getAlignment());this.addHistoryItem(new jalview.commands.OrderCommand("Group Sort",a,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0)});d(c$,"removeRedundancyMenuItem_actionPerformed",
function(){new jalview.appletgui.RedundancyPanel(this.alignPanel)});d(c$,"pairwiseAlignmentMenuItem_actionPerformed",function(){if(null!=this.viewport.getSelectionGroup()&&1<this.viewport.getSelectionGroup().getSize()){var a=new awt2swing.Frame;a.add(new jalview.appletgui.PairwiseAlignPanel(this.alignPanel));jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.getString("action.pairwise_alignment"),600,500)}});d(c$,"PCAMenuItem_actionPerformed",function(){if(!this.viewport.getAlignment().isAligned(!1)){for(var a,
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OutOfMemoryError))throw f;}});d(c$,"averageDistanceTreeMenuItem_actionPerformed",function(){this.NewTreePanel("AV","PID","Average distance tree using PID")});d(c$,"neighbourTreeMenuItem_actionPerformed",function(){this.NewTreePanel("NJ","PID","Neighbour joining tree using PID")});d(c$,"njTreeBlosumMenuItem_actionPerformed",function(){this.NewTreePanel("NJ","BL","Neighbour joining tree using BLOSUM62")});d(c$,"avTreeBlosumMenuItem_actionPerformed",function(){this.NewTreePanel("AV","BL","Average distance tree using BLOSUM62")});
d(c$,"NewTreePanel",function(a,b,c){if(!this.viewport.getAlignment().isAligned(!1)){for(var f,l=this.viewport.getAlignment().getWidth(),d=0;d<this.viewport.getAlignment().getSequences().size();d++)f=this.viewport.getAlignment().getSequenceAt(d),f.getLength()<l&&f.insertCharAt(l-1,this.viewport.getGapCharacter());this.alignPanel.paintAlignment(!0)}if(null!=this.viewport.getSelectionGroup()&&1<this.viewport.getSelectionGroup().getSize()||1<this.viewport.getAlignment().getHeight())a=new jalview.appletgui.TreePanel(this.alignPanel,
a,b),this.addTreeMenuItem(a,c),jalview.bin.JalviewLite.addFrame(a,c,600,500)},"~S,~S,~S");d(c$,"loadTree_actionPerformed",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!0,this);a.setText(jalview.util.MessageManager.getString("label.paste_newick_tree_file"));a.setTreeImport();var b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("label.paste_newick_file"),400,300)});d(c$,"loadTree",function(a,b){var c=new jalview.appletgui.TreePanel(this.alignPanel,
b,jalview.util.MessageManager.getString("label.load_tree_from_file"),a);jalview.bin.JalviewLite.addFrame(c,b,600,500);this.addTreeMenuItem(c,b)},"jalview.io.NewickFile,~S");d(c$,"sortByTree",function(a,b){var c=this.viewport.getAlignment().getSequencesArray();jalview.analysis.AlignmentSorter.sortByTree(this.viewport.getAlignment(),a.getTree());this.addHistoryItem(new jalview.commands.OrderCommand(jalview.util.MessageManager.formatMessage("label.order_by_params",E(-1,[b])),c,this.viewport.getAlignment()));
this.alignPanel.paintAlignment(!0)},"jalview.appletgui.TreePanel,~S");d(c$,"addTreeMenuItem",function(a,b){var c=new awt2swing.MenuItem(b);this.sortByTreeMenu.add(c);c.addActionListener((H("jalview.appletgui.AlignFrame$2")?0:jalview.appletgui.AlignFrame.$AlignFrame$2$(),C(jalview.appletgui.AlignFrame$2,this,T("treePanel",a,"title",b))));a.addWindowListener((H("jalview.appletgui.AlignFrame$3")?0:jalview.appletgui.AlignFrame.$AlignFrame$3$(),C(jalview.appletgui.AlignFrame$3,this,T("treePanel",a,"title",
b,"item",c))))},"jalview.appletgui.TreePanel,~S");d(c$,"sortBy",function(a,b){var c=this.viewport.getAlignment().getSequencesArray();(this.viewport.applet,jalview.bin.JalviewLite).debug&&System.err.println("Sorting "+a.getOrder().size()+" in alignment '"+this.getTitle()+"'");jalview.analysis.AlignmentSorter.sortBy(this.viewport.getAlignment(),a);null!=b&&this.addHistoryItem(new jalview.commands.OrderCommand(b,c,this.viewport.getAlignment()));this.alignPanel.paintAlignment(!0);return!0},"jalview.datamodel.AlignmentOrder,~S");
d(c$,"documentation_actionPerformed",function(){this.alignPanel.av.applet.openJalviewHelpUrl()});d(c$,"about_actionPerformed",function(){H("jalview.appletgui.AlignFrame$1AboutPanel")||jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$();var a=new awt2swing.Frame;a.add(C(jalview.appletgui.AlignFrame$1AboutPanel,this,null,jalview.bin.JalviewLite.getVersion(),jalview.bin.JalviewLite.getBuildDate()));jalview.bin.JalviewLite.addFrame(a,jalview.util.MessageManager.getString("label.jalview"),580,220)});
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new awt2swing.MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[b]);c.addActionListener((H("jalview.appletgui.AlignFrame$4")?0:jalview.appletgui.AlignFrame.$AlignFrame$4$(),C(jalview.appletgui.AlignFrame$4,this,null)));a.add(c)}this.closeMenuItem.addActionListener(this);this.loadApplication.addActionListener(this);this.$loadTree.addActionListener(this);this.$loadAnnotations.addActionListener(this);this.$outputFeatures.addActionListener(this);this.$outputAnnotations.addActionListener(this);
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this.remove2LeftMenuItem.addActionListener(this);this.remove2RightMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_right"));this.remove2RightMenuItem.addActionListener(this);this.removeGappedColumnMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_empty_columns"));this.removeGappedColumnMenuItem.addActionListener(this);this.removeAllGapsMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_all_gaps"));this.removeAllGapsMenuItem.addActionListener(this);
this.removeRedundancyMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_redundancy").concat("..."));this.removeRedundancyMenuItem.addActionListener(this);this.findMenuItem.setLabel(jalview.util.MessageManager.getString("action.find"));this.findMenuItem.addActionListener(this);this.selectAllSequenceMenuItem.addActionListener(this);this.deselectAllSequenceMenuItem.addActionListener(this);this.invertSequenceMenuItem.setLabel(jalview.util.MessageManager.getString("action.invert_sequence_selection"));
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c=new awt2swing.Menu(jalview.util.MessageManager.getString("action.hide"));this.hideColumns.setLabel(jalview.util.MessageManager.getString("label.selected_columns"));this.hideSequences.setLabel(jalview.util.MessageManager.getString("label.selected_sequences"));this.hideAllButSelection.setLabel(jalview.util.MessageManager.getString("label.all_but_selected_region"));this.hideAllSelection.setLabel(jalview.util.MessageManager.getString("label.selected_region"));this.showAllHidden.setLabel(jalview.util.MessageManager.getString("label.all_sequences_columns"));
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this.sequenceFeatures.addItemListener(this);this.sequenceFeatures.setState(!1);this.followMouseOverFlag.setLabel(jalview.util.MessageManager.getString("label.automatic_scrolling"));this.followMouseOverFlag.addItemListener(this);this.alProperties.addActionListener(this);this.overviewMenuItem.setLabel(jalview.util.MessageManager.getString("label.overview_window"));this.overviewMenuItem.addActionListener(this);this.annotationPanelMenuItem.setLabel(jalview.util.MessageManager.getString("label.show_annotations"));
this.annotationPanelMenuItem.addItemListener(this);this.showGroupConsensus.setLabel(jalview.util.MessageManager.getString("label.group_consensus"));this.showGroupConservation.setLabel(jalview.util.MessageManager.getString("label.group_conservation"));this.showConsensusHistogram.setLabel(jalview.util.MessageManager.getString("label.show_consensus_histogram"));this.showSequenceLogo.setLabel(jalview.util.MessageManager.getString("label.show_consensus_logo"));this.normSequenceLogo.setLabel(jalview.util.MessageManager.getString("label.norm_consensus_logo"));
this.applyAutoAnnotationSettings.setLabel(jalview.util.MessageManager.getString("label.apply_all_groups"));this.applyAutoAnnotationSettings.setState(!0);var f=new awt2swing.Menu(jalview.util.MessageManager.getString("label.autocalculated_annotation"));this.showGroupConsensus.addItemListener(this);this.showGroupConservation.addItemListener(this);this.showConsensusHistogram.addItemListener(this);this.showSequenceLogo.addItemListener(this);this.normSequenceLogo.addItemListener(this);this.applyAutoAnnotationSettings.addItemListener(this);
this.showAlignmentAnnotations=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_all_al_annotations"));this.showSequenceAnnotations=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_all_seq_annotations"));this.sortAnnBySequence=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.sort_annotations_by_sequence"));this.sortAnnByLabel=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.sort_annotations_by_label"));
this.showAutoFirst=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_first"));this.showAutoLast=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_last"));this.showAlignmentAnnotations.addItemListener(this);this.showSequenceAnnotations.addItemListener(this);this.sortAnnBySequence.addItemListener(this);this.sortAnnByLabel.addItemListener(this);this.showAutoFirst.addItemListener(this);this.showAutoLast.addItemListener(this);this.$font.setLabel(jalview.util.MessageManager.getString("action.font"));
this.$font.addActionListener(this);this.scaleAbove.setLabel(jalview.util.MessageManager.getString("action.scale_above"));this.scaleAbove.setState(!0);this.scaleAbove.setEnabled(!1);this.scaleAbove.addItemListener(this);this.scaleLeft.setEnabled(!1);this.scaleLeft.setState(!0);this.scaleLeft.setLabel(jalview.util.MessageManager.getString("action.scale_left"));this.scaleLeft.addItemListener(this);this.scaleRight.setEnabled(!1);this.scaleRight.setState(!0);this.scaleRight.setLabel(jalview.util.MessageManager.getString("action.scale_right"));
this.scaleRight.addItemListener(this);this.viewBoxesMenuItem.setLabel(jalview.util.MessageManager.getString("action.boxes"));this.viewBoxesMenuItem.setState(!0);this.viewBoxesMenuItem.addItemListener(this);this.viewTextMenuItem.setLabel(jalview.util.MessageManager.getString("action.text"));this.viewTextMenuItem.setState(!0);this.viewTextMenuItem.addItemListener(this);this.colourTextMenuItem.setLabel(jalview.util.MessageManager.getString("label.colour_text"));this.colourTextMenuItem.addItemListener(this);
this.displayNonconservedMenuItem.setLabel(jalview.util.MessageManager.getString("label.show_non_conversed"));this.displayNonconservedMenuItem.addItemListener(this);this.wrapMenuItem.setLabel(jalview.util.MessageManager.getString("action.wrap"));this.wrapMenuItem.addItemListener(this);this.renderGapsMenuItem.setLabel(jalview.util.MessageManager.getString("action.show_gaps"));this.renderGapsMenuItem.setState(!0);this.renderGapsMenuItem.addItemListener(this);this.centreColumnLabelFlag.setLabel(jalview.util.MessageManager.getString("label.centre_column_labels"));
this.centreColumnLabelFlag.addItemListener(this);this.seqLimits.setState(!0);this.seqLimits.setLabel(jalview.util.MessageManager.getString("label.show_sequence_limits"));this.seqLimits.addItemListener(this);this.applyToAllGroups.setLabel(jalview.util.MessageManager.getString("label.apply_colour_to_all_groups"));this.applyToAllGroups.setState(!0);this.applyToAllGroups.addItemListener(this);this.clustalColour.setLabel(jalview.util.MessageManager.getString("label.clustalx"));this.clustalColour.addActionListener(this);
this.zappoColour.setLabel(jalview.util.MessageManager.getString("label.zappo"));this.zappoColour.addActionListener(this);this.taylorColour.setLabel(jalview.util.MessageManager.getString("label.taylor"));this.taylorColour.addActionListener(this);this.hydrophobicityColour.setLabel(jalview.util.MessageManager.getString("label.hydrophobicity"));this.hydrophobicityColour.addActionListener(this);this.helixColour.setLabel(jalview.util.MessageManager.getString("label.helix_propensity"));this.helixColour.addActionListener(this);
this.strandColour.setLabel(jalview.util.MessageManager.getString("label.strand_propensity"));this.strandColour.addActionListener(this);this.turnColour.setLabel(jalview.util.MessageManager.getString("label.turn_propensity"));this.turnColour.addActionListener(this);this.buriedColour.setLabel(jalview.util.MessageManager.getString("label.buried_index"));this.buriedColour.addActionListener(this);this.purinePyrimidineColour.setLabel(jalview.util.MessageManager.getString("label.purine_pyrimidine"));this.purinePyrimidineColour.addActionListener(this);
this.RNAInteractionColour.setLabel(jalview.util.MessageManager.getString("label.rna_interaction"));this.RNAInteractionColour.addActionListener(this);this.RNAHelixColour.setLabel(jalview.util.MessageManager.getString("action.by_rna_helixes"));this.RNAHelixColour.addActionListener(this);this.userDefinedColour.setLabel(jalview.util.MessageManager.getString("action.user_defined"));this.userDefinedColour.addActionListener(this);this.PIDColour.setLabel(jalview.util.MessageManager.getString("label.percentage_identity"));
this.PIDColour.addActionListener(this);this.BLOSUM62Colour.setLabel(jalview.util.MessageManager.getString("label.blosum62_score"));this.BLOSUM62Colour.addActionListener(this);this.tcoffeeColour.setLabel(jalview.util.MessageManager.getString("label.tcoffee_scores"));this.tcoffeeColour.setEnabled(!1);this.tcoffeeColour.addActionListener(this);this.conservationMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_conservation"));this.conservationMenuItem.addItemListener(this);this.noColourmenuItem.setLabel(jalview.util.MessageManager.getString("label.none"));
this.noColourmenuItem.addActionListener(this);this.abovePIDThreshold.setLabel(jalview.util.MessageManager.getString("label.above_identity_threshold"));this.abovePIDThreshold.addItemListener(this);this.nucleotideColour.setLabel(jalview.util.MessageManager.getString("label.nucleotide"));this.nucleotideColour.addActionListener(this);this.modifyPID.setLabel(jalview.util.MessageManager.getString("label.modify_identity_thereshold"));this.modifyPID.addActionListener(this);this.modifyConservation.setLabel(jalview.util.MessageManager.getString("label.modify_conservation_thereshold"));
this.modifyConservation.addActionListener(this);this.annotationColour.setLabel(jalview.util.MessageManager.getString("action.by_annotation"));this.annotationColour.addActionListener(this);this.sortPairwiseMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_pairwise_id"));this.sortPairwiseMenuItem.addActionListener(this);this.sortIDMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_id"));this.sortIDMenuItem.addActionListener(this);this.sortLengthMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_length"));
this.sortLengthMenuItem.addActionListener(this);this.sortGroupMenuItem.setLabel(jalview.util.MessageManager.getString("action.by_group"));this.sortGroupMenuItem.addActionListener(this);this.pairwiseAlignmentMenuItem.setLabel(jalview.util.MessageManager.getString("action.pairwise_alignment"));this.pairwiseAlignmentMenuItem.addActionListener(this);this.PCAMenuItem.setLabel(jalview.util.MessageManager.getString("label.principal_component_analysis"));this.PCAMenuItem.addActionListener(this);this.autoCalculate=
new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.autocalculate_consensus"),!0);this.averageDistanceTreeMenuItem.setLabel(jalview.util.MessageManager.getString("label.average_distance_identity"));this.averageDistanceTreeMenuItem.addActionListener(this);this.neighbourTreeMenuItem.setLabel(jalview.util.MessageManager.getString("label.neighbour_joining_identity"));this.neighbourTreeMenuItem.addActionListener(this);this.avDistanceTreeBlosumMenuItem.setLabel(jalview.util.MessageManager.getString("label.average_distance_bloslum62"));
this.avDistanceTreeBlosumMenuItem.addActionListener(this);this.njTreeBlosumMenuItem.setLabel(jalview.util.MessageManager.getString("label.neighbour_blosum62"));this.njTreeBlosumMenuItem.addActionListener(this);this.sortByTreeMenu.setLabel(jalview.util.MessageManager.getString("action.by_tree_order"));var l=new awt2swing.Menu(jalview.util.MessageManager.getString("action.sort")),d=new awt2swing.Menu(jalview.util.MessageManager.getString("action.calculate_tree"));this.autoCalculate.addItemListener(this);
this.$sortByTree.addItemListener(this);var g=new awt2swing.Menu(jalview.util.MessageManager.getString("action.help"));this.documentation.setLabel(jalview.util.MessageManager.getString("label.documentation"));this.documentation.addActionListener(this);this.about.setLabel(jalview.util.MessageManager.getString("label.about"));this.about.addActionListener(this);this.alignFrameMenuBar.add(this.fileMenu);var h=new awt2swing.Menu(jalview.util.MessageManager.getString("action.edit"));this.alignFrameMenuBar.add(h);
var e=new awt2swing.Menu(jalview.util.MessageManager.getString("action.select"));this.alignFrameMenuBar.add(e);var n=new awt2swing.Menu(jalview.util.MessageManager.getString("action.view"));this.alignFrameMenuBar.add(n);var x=new awt2swing.Menu(jalview.util.MessageManager.getString("action.annotations"));this.alignFrameMenuBar.add(x);var u=new awt2swing.Menu(jalview.util.MessageManager.getString("action.format"));this.alignFrameMenuBar.add(u);var D=new awt2swing.Menu(jalview.util.MessageManager.getString("action.colour"));
this.alignFrameMenuBar.add(D);var m=new awt2swing.Menu(jalview.util.MessageManager.getString("action.calculate"));this.alignFrameMenuBar.add(m);this.alignFrameMenuBar.add(g);this.fileMenu.add(this.inputText);this.fileMenu.add(this.$loadTree);this.fileMenu.add(this.$loadAnnotations);this.fileMenu.addSeparator();this.fileMenu.add(a);this.fileMenu.add(this.$outputFeatures);this.fileMenu.add(this.$outputAnnotations);null!=this.jalviewServletURL&&this.fileMenu.add(this.loadApplication);this.fileMenu.addSeparator();
this.fileMenu.add(this.closeMenuItem);h.add(this.undoMenuItem);h.add(this.redoMenuItem);h.add(this.cut);h.add(this.copy);this.pasteMenu.add(this.pasteNew);this.pasteMenu.add(this.pasteThis);h.add(this.pasteMenu);h.add(this.$delete);h.addSeparator();h.add(this.remove2LeftMenuItem);h.add(this.remove2RightMenuItem);h.add(this.removeGappedColumnMenuItem);h.add(this.removeAllGapsMenuItem);h.add(this.removeRedundancyMenuItem);e.add(this.findMenuItem);e.addSeparator();e.add(this.selectAllSequenceMenuItem);
e.add(this.deselectAllSequenceMenuItem);e.add(this.invertSequenceMenuItem);e.add(this.invertColSel);e.add(this.createGroup);e.add(this.unGroup);e.add(this.grpsFromSelection);e.add(this.deleteGroups);e.add(this.annotationColumnSelection);n.add(this.$newView);n.addSeparator();b.add(this.showColumns);b.add(this.showSeqs);b.add(this.showAllHidden);n.add(b);c.add(this.hideColumns);c.add(this.hideSequences);c.add(this.hideAllSelection);c.add(this.hideAllButSelection);n.add(c);n.addSeparator();n.add(this.followMouseOverFlag);
n.addSeparator();n.add(this.sequenceFeatures);n.add(this.featureSettings);n.addSeparator();n.add(this.alProperties);n.addSeparator();n.add(this.overviewMenuItem);x.add(this.annotationPanelMenuItem);x.addSeparator();x.add(this.showAlignmentAnnotations);x.add(this.showSequenceAnnotations);x.add(this.sortAnnBySequence);x.add(this.sortAnnByLabel);x.addSeparator();f.add(this.showAutoFirst);f.add(this.showAutoLast);f.addSeparator();f.add(this.applyAutoAnnotationSettings);f.add(this.showConsensusHistogram);
f.add(this.showSequenceLogo);f.add(this.normSequenceLogo);f.addSeparator();f.add(this.showGroupConservation);f.add(this.showGroupConsensus);x.add(f);u.add(this.$font);u.add(this.seqLimits);u.add(this.wrapMenuItem);u.add(this.scaleAbove);u.add(this.scaleLeft);u.add(this.scaleRight);u.add(this.viewBoxesMenuItem);u.add(this.viewTextMenuItem);u.add(this.colourTextMenuItem);u.add(this.displayNonconservedMenuItem);u.add(this.renderGapsMenuItem);u.add(this.centreColumnLabelFlag);D.add(this.applyToAllGroups);
D.addSeparator();D.add(this.noColourmenuItem);D.add(this.clustalColour);D.add(this.BLOSUM62Colour);D.add(this.PIDColour);D.add(this.zappoColour);D.add(this.taylorColour);D.add(this.hydrophobicityColour);D.add(this.helixColour);D.add(this.strandColour);D.add(this.turnColour);D.add(this.buriedColour);D.add(this.nucleotideColour);D.add(this.purinePyrimidineColour);D.add(this.tcoffeeColour);D.add(this.userDefinedColour);D.addSeparator();D.add(this.conservationMenuItem);D.add(this.modifyConservation);
D.add(this.abovePIDThreshold);D.add(this.modifyPID);D.add(this.annotationColour);D.add(this.RNAHelixColour);l.add(this.sortIDMenuItem);l.add(this.sortLengthMenuItem);l.add(this.sortByTreeMenu);l.add(this.sortGroupMenuItem);l.add(this.sortPairwiseMenuItem);m.add(l);d.add(this.averageDistanceTreeMenuItem);d.add(this.neighbourTreeMenuItem);d.add(this.avDistanceTreeBlosumMenuItem);d.add(this.njTreeBlosumMenuItem);m.add(d);m.addSeparator();m.add(this.pairwiseAlignmentMenuItem);m.add(this.PCAMenuItem);
m.add(this.autoCalculate);m.add(this.$sortByTree);g.add(this.documentation);g.add(this.about);this.statusBar.setBackground(java.awt.Color.white);this.statusBar.setFont(new java.awt.Font("Verdana",0,11));this.setStatus(jalview.util.MessageManager.getString("label.status_bar"));this.add(this.statusBar,"South")});e(c$,"setStatus",function(a){this.statusBar.setText(a)},"~S");d(c$,"createAlignFrameWindow",function(a){a?this.embedAlignFrameInApplet(this.viewport.applet):(this.embedMenuIfNeeded(this.alignPanel)&&
this.alignPanel.setSize(this.getSize().width,this.getSize().height-this.statusBar.getHeight()),this.add(this.statusBar,"South"),this.add(this.alignPanel,"Center"),jalview.bin.JalviewLite.addFrame(this,this.getTitle(),this.frameWidth,this.frameHeight))},"~B");d(c$,"embedAlignFrameInApplet",function(a){this.fileMenu.remove(this.closeMenuItem);this.fileMenu.remove(3);this.embeddedMenu=this.makeEmbeddedPopupMenu(this.alignFrameMenuBar,!1,!1);a.setLayout(new java.awt.BorderLayout);a.add(this.embeddedMenu,
"North");a.add(this.statusBar,"South");this.alignPanel.setSize(a.getSize().width,a.getSize().height-this.embeddedMenu.getHeight()-this.statusBar.getHeight());a.add(this.alignPanel,"Center");a.addFocusListener((H("jalview.appletgui.AlignFrame$5")?0:jalview.appletgui.AlignFrame.$AlignFrame$5$(),C(jalview.appletgui.AlignFrame$5,this,T("theApplet",a,"me",this))));a.validate()},"jalview.bin.JalviewLite");d(c$,"addStructureViewInstance",function(){return null},"~O,~A");d(c$,"addPdbFile",function(a,b,c){a=
this.viewport.getAlignment().findName(a);var f=!1;if(null!=a){var l=a.getPDBId(),d=null;if(null!=l&&0<l.size())for(var g=0,h=l.size();g<h;g++)d=l.elementAt(g),!d.getId().equals(b)&&!d.getFile().equals(c)&&(d=null);null==d&&(d=new jalview.datamodel.PDBEntry,d.setId(b),d.setFile(c),f=!0);b=jalview.io.AppletFormatAdapter.resolveProtocol(c,"PDB");if(null==b)return!1;f&&(null==d.getProperty()&&d.setProperty(new java.util.Hashtable),d.getProperty().put("protocol",b),a.addPDBId(d),this.alignPanel.getStructureSelectionManager().registerPDBEntry(d))}return!0},
"~S,~S,~S");d(c$,"cleanSeqChainArrays",function(a,b){if(null!=a){for(var c=new java.util.Vector,f=0;f<a.length;f++)null!=a[f]&&c.addElement(E(-1,[a[f],null!=b?b[f]:null]));a=Array(c.size());b=Array(c.size());for(var f=0,l=c.size();f<l;f++){var d=c.elementAt(f);a[f]=d[0];b[f]=d[1]}}return E(-1,[a,b])},"~A,~A");d(c$,"newStructureView",function(a,b,c,f,l){f=this.cleanSeqChainArrays(c,f);c=f[0];f=f[1];(null==c||0==c.length)&&System.err.println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
if(null==l||0==l.trim().length||l.equals("null"))if(l=b.getProperty().get("protocol"),null==l){System.err.println("Couldn't work out protocol to open structure: "+b.getId());return}if(a.useXtrnalSviewer)null==jalview.structure.StructureSelectionManager.getStructureSelectionManager(a).setMapping(c,f,b.getFile(),l)&&System.err.println("Failed to map "+b.getFile()+" ("+l+") to any sequences");else{if(a.isAlignPdbStructures()&&a.jmolAvailable){for(var d=null,g=a.getAppletWindow(jalview.appletgui.AppletJmol),
h=0,e=g.size();h<e;h++)if(a=g.elementAt(h),a.ap.alignFrame===this){d=a;break}null!=d&&System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.")}new jalview.appletgui.AppletJmol(b,c,f,this.alignPanel,l);jalview.bin.JalviewLite.lastFrameX+=40;jalview.bin.JalviewLite.lastFrameY+=40}},"jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S");d(c$,"alignedStructureView",function(){System.err.println("Aligned Structure View: Not yet implemented.")},
"jalview.bin.JalviewLite,~A,~A,~A,~A");d(c$,"select",function(a,b){this.alignPanel.seqPanel.selection(a,b,null)},"jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection");d(c$,"scrollTo",function(a,b){this.alignPanel.seqPanel.scrollTo(a,b)},"~N,~N");d(c$,"scrollToRow",function(a){this.alignPanel.seqPanel.scrollToRow(a)},"~N");d(c$,"scrollToColumn",function(a){this.alignPanel.seqPanel.scrollToColumn(a)},"~N");d(c$,"getSequenceSetId",function(){return this.viewport.getSequenceSetId()});d(c$,
"loadScoreFile",function(a){var b=jalview.jsdev.GenericFileAdapter.getFile("TCoffeeScoreFile",[a,jalview.io.AppletFormatAdapter.checkProtocol(a)]);if(!b.isValid())return System.err.println("Problems parsing T-Coffee scores: "+b.getWarningMessage()),System.err.println("Origin was:\n"+a),!1;var c;null!=(c=this.viewport.getAlignment())&&(c.getHeight()!=b.getHeight()||c.getWidth()!=b.getWidth())&&System.err.println("The scores matrix does not match the alignment dimensions");if(b.annotateAlignment(this.alignPanel.getAlignment(),
!1))return this.alignPanel.fontChanged(),this.tcoffeeColour.setEnabled(!0),this.changeColour(new jalview.schemes.TCoffeeColourScheme(this.alignPanel.getAlignment())),!0;System.err.println("Problems resolving T-Coffee scores:");null!=b.getWarningMessage()&&System.err.println(b.getWarningMessage());return!1},"~S");d(c$,"getSplitFrame",function(){return this.splitFrame});d(c$,"setSplitFrame",function(a){this.splitFrame=a},"jalview.appletgui.SplitFrame");e(c$,"setShowSeqFeatures",function(a){this.viewport.setShowSequenceFeatures(a)},
"~B");e(c$,"setMenusForViewport",function(){});e(c$,"refreshFeatureUI",function(a){a&&(this.sequenceFeatures.setState(!0),this.alignPanel.av.setShowSequenceFeatures(!0))},"~B");e(c$,"getFeatureSettingsUI",function(){return this.alignPanel.av.featureSettings});c$.$AlignFrame$1$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$1",java.awt.event.WindowAdapter);e(c$,"windowClosing",function(){null!=this.f$.ap&&this.f$.ap.setOverviewPanel(null)},"java.awt.event.WindowEvent");c$=z()};c$.$AlignFrame$2$=
function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$2",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.AlignFrame"].sortByTree(this.f$.treePanel,this.f$.title)},"java.awt.event.ActionEvent");c$=z()};c$.$AlignFrame$3$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignFrame$3",java.awt.event.WindowAdapter);d(c$,"windowOpened",function(a){this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree&&this.b$["jalview.appletgui.AlignFrame"].sortByTree(this.f$.treePanel,
this.f$.title);K(this,jalview.appletgui.AlignFrame$3,"windowOpened",[a])},"java.awt.event.WindowEvent");e(c$,"windowClosing",function(){this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove(this.f$.item)},"java.awt.event.WindowEvent");c$=z()};c$.$AlignFrame$1AboutPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.builddate=this.version=null;r(this,arguments)},jalview.appletgui,"AlignFrame$1AboutPanel",awt2swing.Canvas);m(c$,function(a,b){t(this,jalview.appletgui.AlignFrame$1AboutPanel,
[]);this.version=a;this.builddate=b},"~S,~S");e(c$,"paintComponent",function(a){a.setColor(java.awt.Color.white);a.fillRect(0,0,this.getSize().width,this.getSize().height);a.setFont(new java.awt.Font("Helvetica",0,12));var b=a.getFontMetrics().getHeight(),c=5;a.setColor(java.awt.Color.black);a.setFont(new java.awt.Font("Helvetica",1,14));awt2swing.Util.drawString(a,jalview.util.MessageManager.formatMessage("label.jalviewLite_release",E(-1,[this.version])),7,c+=b);a.setFont(new java.awt.Font("Helvetica",
1,12));awt2swing.Util.drawString(a,jalview.util.MessageManager.formatMessage("label.jaview_build_date",E(-1,[this.builddate])),7,c+=b);a.setFont(new java.awt.Font("Helvetica",0,12));awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_authors_1"),7,c+=1.5*b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_authors_2"),57,c+=b+8);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_dev_managers"),7,c+=b);awt2swing.Util.drawString(a,
jalview.util.MessageManager.getString("label.jalview_distribution_lists"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_please_cite"),7,c+=b+8);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_authors"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_title"),7,c+=b);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.jalview_cite_1_ref"),7,c+b)},"java.awt.Graphics");
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1);)f.setSequence(c);f=0;for(var d,c=b.keySet().iterator();c.hasNext()&&((d=c.next())||1);){for(var g,l=b.get(d).entrySet().iterator();l.hasNext()&&((g=l.next())||1);)g.getKey().getSequence()[f]=g.getValue().charAt(0);f++}return 0},"jalview.datamodel.AlignmentI,java.util.Map");c$.addCodonPositions=d(c$,"addCodonPositions",function(a,b,c,f,l){for(a=f.getCodonIterator(a,c);a.hasNext();)c=a.next(),f=l.get(c),null==f&&(f=new java.util.HashMap,l.put(c,f)),f.put(b,c.product)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S,jalview.datamodel.Mapping,java.util.Map");
c$.isMappable=d(c$,"isMappable",function(a,b){if(a.isNucleotide()==b.isNucleotide())return!1;for(var c=a.isNucleotide()?a:b,f=c===a?b:a,l=f.getCodonFrames(),d,c=c.getSequences().iterator();c.hasNext()&&((d=c.next())||1);)for(var g,h=f.getSequences().iterator();h.hasNext()&&((g=h.next())||1);)if(jalview.analysis.AlignmentUtils.isMappable(d,g,l))return!0;return!1},"jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentI");c$.isMappable=d(c$,"isMappable",function(a,b,c){a=null==a.getDatasetSequence()?
a:a.getDatasetSequence();b=null==b.getDatasetSequence()?b:b.getDatasetSequence();var f;for(c=c.iterator();c.hasNext()&&((f=c.next())||1);)if(b===f.getAaForDnaSeq(a))return!0;return null!=jalview.analysis.AlignmentUtils.mapProteinToCdna(b,a)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,java.util.Set");c$.findAddableReferenceAnnotations=d(c$,"findAddableReferenceAnnotations",function(a,b,c,f){if(null!=a){var l;for(a=a.iterator();a.hasNext()&&((l=a.next())||1);){var d=l.getDatasetSequence();
if(null!=d){var g=d.getAnnotation();if(null!=g){for(var d=new java.util.ArrayList,h,e=0;e<g.length&&((h=g[e])||1);e++)f.findAnnotations(l,h.getCalcId(),h.label).iterator().hasNext()||(d.add(h),null!=b&&b.put(h.getCalcId(),h.label));d.isEmpty()||c.put(l,d)}}}}},"java.util.List,java.util.Map,java.util.Map,jalview.datamodel.AlignmentI");c$.addReferenceAnnotations=d(c$,"addReferenceAnnotations",function(a,b,c){for(var f,l=a.keySet().iterator();l.hasNext()&&((f=l.next())||1);)for(var d,g=a.get(f).iterator();g.hasNext()&&
((d=g.next())||1);){var h=new jalview.datamodel.AlignmentAnnotation(d),e=0,n=d.annotations.length;null!=c&&(e=c.getStartRes(),n=c.getEndRes());h.restrict(e,n);f.hasAnnotation(d)||f.addAlignmentAnnotation(h);h.adjustForAlignment();b.addAnnotation(h);h.visible=!0}},"java.util.Map,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");c$.showOrHideSequenceAnnotations=d(c$,"showOrHideSequenceAnnotations",function(a,b,c,f,l){var d,g=0;for(a=a.getAlignmentAnnotation();g<a.length&&((d=a[g])||1);g++)if(f||
b.contains(d.label))if(null!=d.sequenceRef&&(null==c||c.contains(d.sequenceRef)))d.visible=l},"jalview.datamodel.AlignmentI,java.util.Collection,java.util.List,~B,~B");c$.haveCrossRef=d(c$,"haveCrossRef",function(a,b){return jalview.analysis.AlignmentUtils.hasCrossRef(a,b)||jalview.analysis.AlignmentUtils.hasCrossRef(b,a)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.hasCrossRef=d(c$,"hasCrossRef",function(a,b){if(null==a||null==b)return!1;var c=b.getName(),f=a.getDBRef();if(null!=
f)for(var l,d=0;d<f.length&&((l=f[d])||1);d++)if((l.getSource()+"|"+l.getAccessionId()).equalsIgnoreCase(c))return!0;return!1},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");c$.makeExonAlignment=d(c$,"makeExonAlignment",function(a,b){for(var c=new java.util.LinkedHashSet,f=new java.util.ArrayList,l,d=0;d<a.length&&((l=a[d])||1);d++)for(var g=l.getDatasetSequence(),h,e=jalview.util.MappingUtils.findMappingsForSequence(g,b).iterator();e.hasNext()&&((h=e.next())||1);){var n=new jalview.datamodel.AlignedCodonFrame,
x=jalview.analysis.AlignmentUtils.makeExonSequences(g,h,n);x.isEmpty()||(f.addAll(x),c.add(n))}f=new jalview.datamodel.Alignment(f.toArray(Array(f.size())));f.setDataset(null);b.clear();b.addAll(c);return f},"~A,java.util.Set");c$.makeExonSequences=d(c$,"makeExonSequences",function(a,b,c){var f=new java.util.ArrayList,l=b.getMappingsForSequence(a);b=a.getSequence();for(var d,l=l.iterator();l.hasNext()&&((d=l.next())||1);){for(var g=new StringBuilder(a.getLength()),h=d.getMap().getFromRanges(),e,n=
h.iterator();n.hasNext()&&((e=n.next())||1);)for(var x=e[0];x<=e[1];x++)g.append(b[x-1]);var n=new jalview.datamodel.Sequence(a.getName(),g.toString()),x=jalview.datamodel.FeatureProperties.getCodingFeature(jalview.datamodel.DBRefSource.EMBL),u=jalview.util.DBRefUtils.selectRefs(d.getTo().getDBRef(),jalview.datamodel.DBRefSource.CODINGDBS);if(null!=u)for(var D,m=0;m<u.length&&((D=u[m])||1);m++)n.addDBRef(new jalview.datamodel.DBRefEntry(D)),x=D.getAccessionId();n.setName(n.getName()+"|"+x);n.createDatasetSequence();
x=new java.util.ArrayList;x.add(w(-1,[1,g.length()]));g=new jalview.util.MapList(x,d.getMap().getToRanges(),3,1);c.addMap(n.getDatasetSequence(),d.getTo(),g);h=new jalview.util.MapList(h,x,1,1);c.addMap(a,n.getDatasetSequence(),h);f.add(n)}return f},"jalview.datamodel.SequenceI,jalview.datamodel.AlignedCodonFrame,jalview.datamodel.AlignedCodonFrame")});p("jalview.analysis");c$=B(jalview.analysis,"CodonComparator",null,java.util.Comparator);e(c$,"compare",function(a,b){if(null==a||null==b||a.equals(b))return 0;
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"java.util.ArrayList"],function(){c$=s(function(){this.dnaToProt=this.dnaSeqs=null;r(this,arguments)},jalview.datamodel,"AlignedCodonFrame");m(c$,function(){});d(c$,"addMap",function(a,b,c){var f=1;null!=this.dnaSeqs&&(f=this.dnaSeqs.length+1);var l=Array(f),d=Array(f);null!=this.dnaSeqs&&(System.arraycopy(this.dnaSeqs,0,l,0,this.dnaSeqs.length),System.arraycopy(this.dnaToProt,0,d,0,this.dnaSeqs.length));this.dnaSeqs=l;this.dnaToProt=d;f--;this.dnaSeqs[f]=null==a.getDatasetSequence()?a:a.getDatasetSequence();
a=new jalview.datamodel.Mapping(c);a.to=null==b.getDatasetSequence()?b:b.getDatasetSequence();this.dnaToProt[f]=a},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList");d(c$,"getdnaSeqs",function(){return this.dnaSeqs});d(c$,"getAaSeqs",function(){if(null==this.dnaToProt)return null;for(var a=Array(this.dnaToProt.length),b=0;b<this.dnaToProt.length;b++)a[b]=this.dnaToProt[b].to;return a});d(c$,"getdnaToProt",function(){if(null==this.dnaToProt)return null;for(var a=Array(this.dnaToProt.length),
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"jalview.datamodel.SequenceI");d(c$,"markMappedRegion",function(a,b,c){if(null!=this.dnaToProt)for(var f,l=a.getDatasetSequence(),d=0;d<this.dnaToProt.length;d++)if(this.dnaSeqs[d]===a||this.dnaSeqs[d]===l){if(f=this.dnaToProt[d].map.locateInTo(b,b),null!=f)for(var g=0;g<f.length;g+=2)c.addResult(this.dnaToProt[d].to,f[g],f[g+1])}else if(this.dnaToProt[d].to===a||this.dnaToProt[d].to===l)if(f=this.dnaToProt[d].map.locateInFrom(b,b),null!=f)for(g=0;g<f.length;g+=2)c.addResult(this.dnaSeqs[d],f[g],
f[g+1])},"jalview.datamodel.SequenceI,~N,jalview.datamodel.SearchResults");d(c$,"getDnaPosition",function(a,b){for(var c=null,f=0;f<this.dnaToProt.length;f++)if(this.dnaSeqs[f]===a){c=this.getdnaToProt()[f];break}return null==c?null:c.locateInFrom(b,b)},"jalview.datamodel.SequenceI,~N");d(c$,"findAlignedSequence",function(a,b){if(null!=this.dnaToProt)for(var c=0;c<this.dnaToProt.length;c++)if(this.dnaSeqs[c]===a)for(var f,l=b.getSequences().iterator();l.hasNext()&&((f=l.next())||1);)if(this.dnaToProt[c].to===
f.getDatasetSequence())return f;if(null!=this.dnaToProt)for(c=0;c<this.dnaToProt.length;c++)if(this.dnaToProt[c].to===a)for(l=b.getSequences().iterator();l.hasNext()&&((f=l.next())||1);)if(this.dnaSeqs[c]===f.getDatasetSequence())return f;return null},"jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI");d(c$,"getMappedRegion",function(a,b,c){a=null==a.getDatasetSequence()?a:a.getDatasetSequence();b=null==b.getDatasetSequence()?b:b.getDatasetSequence();if(null==a||null==b||null==this.dnaToProt)return null;
for(var f=0;f<this.dnaToProt.length;f++)if(this.dnaSeqs[f]===a&&this.dnaToProt[f].to===b){var l=this.dnaToProt[f].map.locateInFrom(c,c);if(null!=l)return l}return null},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N");d(c$,"getMappedCodon",function(a,b){if(null==this.dnaToProt)return null;for(var c=null,f=null,l=0;l<this.dnaToProt.length;l++)if(this.dnaToProt[l].to===a){c=this.getdnaToProt()[l];f=this.dnaSeqs[l].getSequence();break}if(null==c)return null;c=c.locateInFrom(b,b);if(null==
c)return null;c=jalview.util.MappingUtils.flattenRanges(c);return N(-1,[f[c[0]-1],f[c[1]-1],f[c[2]-1]])},"jalview.datamodel.SequenceI,~N");d(c$,"getMappingsForSequence",function(a){var b=new java.util.ArrayList;if(null==this.dnaSeqs)return b;var c=new java.util.ArrayList,f=a.getDatasetSequence(),f=null!=f?f:a;for(a=0;a<this.dnaSeqs.length;a++){var l=this.dnaToProt[a];if((this.dnaSeqs[a]===f||l.to===f)&&!c.contains(l.to))b.add(l),c.add(l.to)}return b},"jalview.datamodel.SequenceI")});p("jalview.datamodel");
q(["java.util.Iterator"],"jalview.datamodel.Mapping","jalview.datamodel.AlignedCodon $.IncompleteCodonException $.SequenceFeature jalview.util.MapList java.util.NoSuchElementException $.Vector".split(" "),function(){c$=s(function(){H("jalview.datamodel.Mapping.AlignedCodonIterator")||jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$();this.to=this.map=null;r(this,arguments)},jalview.datamodel,"Mapping");m(c$,function(a){this.map=a},"jalview.util.MapList");m(c$,function(a,b){this.construct(b);
this.to=a},"jalview.datamodel.SequenceI,jalview.util.MapList");m(c$,function(a,b,c,f,l){this.construct(a,new jalview.util.MapList(b,c,f,l))},"jalview.datamodel.SequenceI,~A,~A,~N,~N");m(c$,function(a){a!==this&&null!=a&&(null!=a.map&&(this.map=new jalview.util.MapList(a.map)),this.to=a.to)},"jalview.datamodel.Mapping");d(c$,"getMap",function(){return this.map});d(c$,"setMap",function(a){this.map=a},"jalview.util.MapList");e(c$,"equals",function(a){return null==a||!v(a,jalview.datamodel.Mapping)?!1:
a===this?!0:a.to!==this.to||null!=this.map&&null==a.map||null==this.map&&null!=a.map?!1:null==this.map&&null==a.map||this.map.equals(a.map)?!0:!1},"~O");d(c$,"getPosition",function(a){if(null!=this.map){var b=this.map.shiftTo(a);if(null!=b)return b[0]}return a},"~N");d(c$,"getWord",function(a){return null!=this.map?this.map.getToWord(a):null},"~N");d(c$,"getWidth",function(){return null!=this.map?this.map.getFromRatio():1});d(c$,"getMappedWidth",function(){return null!=this.map?this.map.getToRatio():
1});d(c$,"getMappedPosition",function(a){if(null!=this.map){var b=this.map.shiftFrom(a);if(null!=b)return b[0]}return a},"~N");d(c$,"getMappedWord",function(a){return null!=this.map&&(a=this.map.shiftFrom(a),null!=a)?w(-1,[a[0],a[0]+a[2]*(this.map.getToRatio()-1)]):null},"~N");d(c$,"locateFeature",function(a){if(null!=this.map){var b=this.map.locateInFrom(a.getBegin(),a.getEnd());if(null==b)return null;for(var c=Array(F(b.length/2)),f=0,l=0;f<b.length;f+=2,l++)c[l]=new jalview.datamodel.SequenceFeature(a),
c[l].setBegin(b[f]),c[l].setEnd(b[f+1]),2<b.length&&c[l].setDescription(a.getDescription()+"\nPart "+(l+1));return c}return E(-1,[a])},"jalview.datamodel.SequenceFeature");d(c$,"locateRange",function(a,b){if(null!=this.map){if(a<=b){if(a=this.map.getToLowest()<a?a:this.map.getToLowest(),b=this.map.getToHighest()>b?b:this.map.getToHighest(),a>b)return null}else if(a=this.map.getToHighest()>a?a:this.map.getToHighest(),b=this.map.getToLowest()<b?b:this.map.getToLowest(),a<b)return null;return this.map.locateInFrom(a,
b)}return w(-1,[a,b])},"~N,~N");d(c$,"locateMappedRange",function(a,b){if(null!=this.map){if(a<=b){if(a=this.map.getFromLowest()<a?a:this.map.getFromLowest(),b=this.map.getFromHighest()>b?b:this.map.getFromHighest(),a>b)return null}else if(a=this.map.getFromHighest()>a?a:this.map.getFromHighest(),b=this.map.getFromLowest()<b?b:this.map.getFromLowest(),a<b)return null;return this.map.locateInTo(a,b)}return w(-1,[a,b])},"~N,~N");d(c$,"intersectVisContigs",function(a){var b=new jalview.datamodel.Mapping(this);
if(null!=this.map){for(var c=new java.util.Vector,f=new java.util.Vector,l=0;l<a.length;l+=2){var d=this.locateMappedRange(1+a[l],a[l+1]-1);if(null!=d)for(var g=0;g<d.length;g+=2){c.addElement(w(-1,[d[g],d[g+1]]));for(var h=this.locateRange(d[g],d[g+1]),e=0;e<h.length;e+=2)f.addElement(w(-1,[h[e],h[e+1]]))}}a=w(2*f.size(),0);l=w(2*c.size(),0);g=0;for(h=f.size();g<h;g++)d=f.elementAt(g),a[2*g]=d[0],a[2*g+1]=d[1];g=0;for(h=c.size();g<h;g++)d=c.elementAt(g),l[2*g]=d[0],l[2*g+1]=d[1];b.setMap(new jalview.util.MapList(a,
l,this.map.getFromRatio(),this.map.getToRatio()))}return b},"~A");d(c$,"getTo",function(){return this.to});d(c$,"setTo",function(a){this.to=a},"jalview.datamodel.SequenceI");d(c$,"finalize",function(){this.to=this.map=null;K(this,jalview.datamodel.Mapping,"finalize",[])});d(c$,"getCodonIterator",function(a,b){return C(jalview.datamodel.Mapping.AlignedCodonIterator,this,null,a.getSequence(),b)},"jalview.datamodel.SequenceI,~S");c$.$Mapping$AlignedCodonIterator$=function(){A(self.c$);c$=s(function(){O(this,
arguments);this.gap="\x00";this.alignedSeq=null;this.alignedBases=this.alignedColumn=0;this.currentToRange=this.currentFromRange=this.toRanges=this.fromRanges=null;this.toPosition=this.fromPosition=0;r(this,arguments)},jalview.datamodel.Mapping,"AlignedCodonIterator",null,java.util.Iterator);m(c$,function(a,b){this.alignedSeq=a;this.gap=b;this.fromRanges=this.b$["jalview.datamodel.Mapping"].map.getFromRanges().iterator();this.toRanges=this.b$["jalview.datamodel.Mapping"].map.getToRanges().iterator();
this.fromRanges.hasNext()&&(this.currentFromRange=this.fromRanges.next(),this.fromPosition=this.currentFromRange[0]);this.toRanges.hasNext()&&(this.currentToRange=this.toRanges.next(),this.toPosition=this.currentToRange[0])},"~A,~S");d(c$,"hasNext",function(){return this.fromRanges.hasNext()?!0:null==this.currentFromRange||this.fromPosition>=this.currentFromRange[1]?!1:!0});e(c$,"next",function(){if(!this.hasNext())throw new java.util.NoSuchElementException;var a=this.getNextCodon(),a=this.getAlignedCodon(a),
b=this.getPeptide();return new jalview.datamodel.AlignedCodon(a[0],a[1],a[2],b)});d(c$,"getPeptide",function(){if(this.toPosition<=this.currentToRange[1]){var a=this.b$["jalview.datamodel.Mapping"].to.getSequence()[this.toPosition-1];this.toPosition++;return String.valueOf(a)}if(!this.toRanges.hasNext())throw new java.util.NoSuchElementException("Ran out of peptide at position "+this.toPosition);this.currentToRange=this.toRanges.next();this.toPosition=this.currentToRange[0];return this.getPeptide()});
d(c$,"getNextCodon",function(){for(var a=w(3,0),b=0;3>b;)if(this.fromPosition<=this.currentFromRange[1])a[b++]=this.fromPosition++;else{if(!this.fromRanges.hasNext())throw new jalview.datamodel.IncompleteCodonException;this.currentFromRange=this.fromRanges.next();this.fromPosition=this.currentFromRange[0]}return a});d(c$,"getAlignedCodon",function(a){for(var b=w(a.length,0),c=0;c<a.length;c++)b[c]=this.getAlignedColumn(a[c]);return b},"~A");d(c$,"getAlignedColumn",function(a){for(;this.alignedBases<
a&&this.alignedColumn<this.alignedSeq.length;)this.alignedSeq[this.alignedColumn++]!=this.gap&&this.alignedBases++;return this.alignedColumn-1},"~N");e(c$,"remove",function(){});c$=z()}});p("jalview.datamodel");q(null,"jalview.datamodel.AlignedCodon",["java.lang.IllegalArgumentException","$.StringBuilder"],function(){c$=s(function(){this.pos3=this.pos2=this.pos1=0;this.product=null;r(this,arguments)},jalview.datamodel,"AlignedCodon");m(c$,function(a,b,c){this.construct(a,b,c,null)},"~N,~N,~N");m(c$,
function(a,b,c,f){this.pos1=a;this.pos2=b;this.pos3=c;this.product=f},"~N,~N,~N,~S");d(c$,"getBaseColumn",function(a){if(1>a||3<a)throw new IllegalArgumentException(Integer.toString(a));return 1==a?this.pos1:2==a?this.pos2:this.pos3},"~N");e(c$,"equals",function(a){return null==a?!0:!v(a,jalview.datamodel.AlignedCodon)?!1:this.pos1==a.pos1&&this.pos2==a.pos2&&this.pos3==a.pos3},"~O");e(c$,"toString",function(){var a=new StringBuilder;a.append("[").append(this.pos1).append(", ").append(this.pos2).append(", ").append(this.pos3).append("]");
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d(c$,"getFromRatio",function(){return this.fromRatio});d(c$,"getToRatio",function(){return this.toRatio});d(c$,"getFromLowest",function(){return this.fromLowest});d(c$,"getFromHighest",function(){return this.fromHighest});d(c$,"getToLowest",function(){return this.toLowest});d(c$,"getToHighest",function(){return this.toHighest});m(c$,function(a,b,c,f){this.fromRatio=c;this.toRatio=f;this.fromLowest=a[0];this.fromHighest=a[1];for(c=0;c<a.length;c+=2)this.fromLowest=Math.min(this.fromLowest,a[c]),this.fromHighest=
Math.max(this.fromHighest,a[c+1]),this.fromShifts.add(w(-1,[a[c],a[c+1]]));this.toLowest=b[0];this.toHighest=b[1];for(c=0;c<b.length;c+=2)this.toLowest=Math.min(this.toLowest,b[c]),this.toHighest=Math.max(this.toHighest,b[c+1]),this.toShifts.add(w(-1,[b[c],b[c+1]]))},"~A,~A,~N,~N");m(c$,function(a){this.fromLowest=a.fromLowest;this.fromHighest=a.fromHighest;this.toLowest=a.toLowest;this.toHighest=a.toHighest;this.fromRatio=a.fromRatio;this.toRatio=a.toRatio;if(null!=a.fromShifts)for(var b,c=a.fromShifts.iterator();c.hasNext()&&
((b=c.next())||1);)this.fromShifts.add(w(-1,[b[0],b[1]]));if(null!=a.toShifts)for(c=a.toShifts.iterator();c.hasNext()&&((b=c.next())||1);)this.toShifts.add(w(-1,[b[0],b[1]]))},"jalview.util.MapList");m(c$,function(a,b,c,f){this.fromShifts=a;this.toShifts=b;this.fromRatio=c;this.toRatio=f;this.fromLowest=2147483647;this.fromHighest=0;var l;for(a=a.iterator();a.hasNext()&&((l=a.next())||1);)this.fromLowest=Math.min(this.fromLowest,l[0]),this.fromHighest=Math.max(this.fromHighest,l[1]);this.toLowest=
2147483647;this.toHighest=0;for(a=b.iterator();a.hasNext()&&((l=a.next())||1);)this.toLowest=Math.min(this.toLowest,l[0]),this.toHighest=Math.max(this.toHighest,l[1])},"java.util.List,java.util.List,~N,~N");d(c$,"makeFromMap",function(){return this.posMap(this.fromShifts,this.fromRatio,this.toShifts,this.toRatio)});d(c$,"makeToMap",function(){return this.posMap(this.toShifts,this.toRatio,this.fromShifts,this.fromRatio)});d(c$,"posMap",function(a,b,c,f){var l=0,d=a.size();if(l>=d)return null;var g=
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b[0]:a},"~N");d(c$,"getMappedWord",function(a){a=this.shiftFrom(a);return null!=a?w(-1,[a[0],a[0]+a[2]*(this.getToRatio()-1)]):null},"~N");d(c$,"getInverse",function(){return new jalview.util.MapList(this.getToRanges(),this.getFromRanges(),this.getToRatio(),this.getFromRatio())});d(c$,"containsEither",function(a,b){return a?this.getFromLowest()>=b.getFromLowest()&&this.getFromHighest()<=b.getFromHighest()||this.getFromLowest()<=b.getFromLowest()&&this.getFromHighest()>=b.getFromHighest():this.getToLowest()>=
b.getToLowest()&&this.getToHighest()<=b.getToHighest()||this.getToLowest()<=b.getToLowest()&&this.getToHighest()>=b.getToHighest()},"~B,jalview.util.MapList");e(c$,"toString",function(){var a=new StringBuilder(64);a.append("From (").append(this.fromRatio).append(":").append(this.toRatio).append(") [");for(var b,c=this.fromShifts.iterator();c.hasNext()&&((b=c.next())||1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ] To [");for(c=this.toShifts.iterator();c.hasNext()&&((b=c.next())||
1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ]");return a.toString()})});p("jalview.util");q(null,"jalview.util.MappingUtils","jalview.analysis.AlignmentSorter jalview.commands.EditCommand $.OrderCommand jalview.datamodel.AlignmentOrder $.ColumnSelection $.SearchResults $.Sequence $.SequenceGroup jalview.util.Comparison $.StringUtils java.util.ArrayList $.Collections $.HashMap".split(" "),function(){c$=B(jalview.util,"MappingUtils");c$.mapCutOrPaste=d(c$,"mapCutOrPaste",function(a,
b){var c=a.getAction();b&&c.getUndoAction();System.err.println("MappingUtils.mapCutOrPaste not yet implemented")},"jalview.commands.EditCommand.Edit,~B,java.util.List,jalview.commands.EditCommand,java.util.Set");c$.mapEditCommand=d(c$,"mapEditCommand",function(a,b,c,f,l){if(!c.isNucleotide())return null;for(var d=new java.util.HashMap,g,h=c.getSequences().iterator();h.hasNext()&&((g=h.next())||1);){var e=g.getDatasetSequence();if(null!=e){var n=new jalview.datamodel.Sequence(g);n.setDatasetSequence(e);
d.put(e,n)}}g=a.priorState(b);h=new jalview.commands.EditCommand;for(a=a.getEditIterator(!b);a.hasNext();)e=a.next(),e.getAction()===jalview.commands.EditCommand.Action.CUT||e.getAction()===jalview.commands.EditCommand.Action.PASTE?jalview.util.MappingUtils.mapCutOrPaste(e,b,c.getSequences(),h,l):(e.getAction()===jalview.commands.EditCommand.Action.INSERT_GAP||e.getAction()===jalview.commands.EditCommand.Action.DELETE_GAP)&&jalview.util.MappingUtils.mapInsertOrDelete(e,b,g,c.getSequences(),d,f,h,
l);return 0<h.getSize()?h:null},"jalview.commands.EditCommand,~B,jalview.datamodel.AlignmentI,~S,java.util.Set");c$.mapInsertOrDelete=d(c$,"mapInsertOrDelete",function(a,b,c,f,l,d,g,h){var e=a.getAction();b&&(e=e.getUndoAction());b=a.getNumber();var n=a.getPosition(),x,u=0;for(a=a.getSequences();u<a.length&&((x=a[u])||1);u++){var D=x.getDatasetSequence();if(null!=D){var m=c.get(D),p=m.findPosition(n),p=jalview.util.MappingUtils.buildSearchResults(x,p,h);if(!p.isEmpty())for(var q,s=f.iterator();s.hasNext()&&
((q=s.next())||1);)if(D=q.getDatasetSequence(),null!=D){var D=l.get(D),r=p.getResults(D,0,D.getLength());if(null!=r){var t=3*b,r=e===jalview.commands.EditCommand.Action.DELETE_GAP?r[0]-t:r[0],v=resultClazz_innerTypeInstance(jalview.commands.EditCommand.Edit,this,null,e,E(-1,[q]),r,t,d);g.addEdit(v);e===jalview.commands.EditCommand.Action.INSERT_GAP?D.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(D.getSequence(),r,t,d))):e===jalview.commands.EditCommand.Action.DELETE_GAP&&
D.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(D.getSequence(),r,r+t)))}}e===jalview.commands.EditCommand.Action.INSERT_GAP?m.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(m.getSequence(),n,b,d))):e===jalview.commands.EditCommand.Action.DELETE_GAP&&m.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(m.getSequence(),n,n+b)))}}},"jalview.commands.EditCommand.Edit,~B,java.util.Map,java.util.List,java.util.Map,~S,jalview.commands.EditCommand,java.util.Set");
c$.buildSearchResults=d(c$,"buildSearchResults",function(a,b,c){var f=new jalview.datamodel.SearchResults;jalview.util.MappingUtils.addSearchResults(f,a,b,c);return f},"jalview.datamodel.SequenceI,~N,java.util.Set");c$.addSearchResults=d(c$,"addSearchResults",function(a,b,c,f){if(c>=b.getStart()&&c<=b.getEnd()){var l;for(f=f.iterator();f.hasNext()&&((l=f.next())||1);)l.markMappedRegion(b,c,a)}},"jalview.datamodel.SearchResults,jalview.datamodel.SequenceI,~N,java.util.Set");c$.mapSequenceGroup=d(c$,
"mapSequenceGroup",function(a,b,c){var f=c.isNucleotide();b=(f?b:c).getAlignment().getCodonFrames();var l=new jalview.datamodel.SequenceGroup(a);l.cs=c.getGlobalColourScheme();l.clear();var d=-1,g=-1,h=a.getStartRes(),e=a.getEndRes(),n;for(a=a.getSequences().iterator();a.hasNext()&&((n=a.next())||1);){for(var x=h;x<=e&&jalview.util.Comparison.isGap(n.getCharAt(x));)x++;if(!(x>e)){for(var u=e;u>=h&&jalview.util.Comparison.isGap(n.getCharAt(u));)u--;for(var x=n.findPosition(x),u=n.findPosition(u),D,
m=b.iterator();m.hasNext()&&((D=m.next())||1);){var p=f?D.getDnaForAaSeq(n):D.getAaForDnaSeq(n);if(null!=p)for(var q,s=c.getAlignment().getSequences().iterator();s.hasNext()&&((q=s.next())||1);){var r=0,t=0;if(q.getDatasetSequence()===p){for(var p=jalview.util.MappingUtils.buildSearchResults(n,x,java.util.Collections.singleton(D)),v,p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=v.getStart(),t=v.getEnd();p=jalview.util.MappingUtils.buildSearchResults(n,u,java.util.Collections.singleton(D));
for(p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=Math.min(r,v.getStart()),t=Math.max(t,v.getEnd());r=q.findIndex(r)-1;d=-1==d?r:Math.min(d,r);t=q.findIndex(t)-1;g=-1==g?t:Math.max(g,t);l.addSequence(q,!1);break}}}}}l.setStartRes(0>d?0:d);l.setEndRes(0>g?0:g);return l},"jalview.datamodel.SequenceGroup,jalview.api.AlignViewportI,jalview.api.AlignViewportI");c$.mapOrderCommand=d(c$,"mapOrderCommand",function(a,b,c,f){b=a.getSequenceOrder(b);for(var l=new java.util.ArrayList,d=0,g=c.isNucleotide(),
h,e=0;e<b.length&&((h=b[e])||1);e++)for(var n,x=f.iterator();x.hasNext()&&((n=x.next())||1);){var u=g?n.getDnaForAaSeq(h):n.getAaForDnaSeq(h);if(null!=u)for(var D,m=c.getSequences().iterator();m.hasNext()&&((D=m.next())||1);)if(D.getDatasetSequence()===u){l.add(D);d++;break}}if(0==d)return null;if(d<c.getHeight())for(e=c.getSequences().iterator();e.hasNext()&&((h=e.next())||1);)l.contains(h)||l.add(h);f=l.toArray(Array(l.size()));h=c.getSequencesArray();jalview.analysis.AlignmentSorter.sortBy(c,new jalview.datamodel.AlignmentOrder(f));
return new jalview.commands.OrderCommand(a.getDescription(),h,c)},"jalview.commands.OrderCommand,~B,jalview.datamodel.AlignmentI,java.util.Set");c$.mapColumnSelection=d(c$,"mapColumnSelection",function(a,b,c){var f=(c.isNucleotide()?b:c).getAlignment().getCodonFrames(),l=new jalview.datamodel.ColumnSelection;if(null==a)return l;var d=b.getAlignment().getGapCharacter(),g;for(a=a.getSelected().iterator();a.hasNext()&&((g=a.next())||1);){for(var h=g.intValue(),e=2147483647,n=-2147483648,x,u=b.getAlignment().getSequences().iterator();u.hasNext()&&
((x=u.next())||1);)if(x.getCharAt(h)!=d)for(var D=x.findPosition(h),m,D=jalview.util.MappingUtils.buildSearchResults(x,D,f).getResults().iterator();D.hasNext()&&((m=D.next())||1);)for(var p=m.getStart(),q=m.getEnd(),r=m.getSequence(),s,t=c.getAlignment().getSequences().iterator();t.hasNext()&&((s=t.next())||1);)if(s.getDatasetSequence()===r){p=s.findIndex(p);q=s.findIndex(q);e=Math.min(e,p);n=Math.max(n,q);break}for(h=e;h<=n;h++)l.addElement(h-1)}return l},"jalview.datamodel.ColumnSelection,jalview.api.AlignViewportI,jalview.api.AlignViewportI");
c$.findCodonFor=d(c$,"findCodonFor",function(a,b,c){b=a.findPosition(b);var f;for(c=c.iterator();c.hasNext()&&((f=c.next())||1);)if(f.involvesSequence(a))return f.getMappedCodon(a.getDatasetSequence(),b);return null},"jalview.datamodel.SequenceI,~N,java.util.Set");c$.flattenRanges=d(c$,"flattenRanges",function(a){for(var b=0,c=0;c<a.length-1;c+=2)b+=a[c+1]-a[c]+1;for(var b=w(b,0),f=0,c=0;c<a.length-1;c+=2)for(var l=a[c];l<=a[c+1];l++)b[f++]=l;return b},"~A");c$.findMappingsForSequence=d(c$,"findMappingsForSequence",
function(a,b){var c=new java.util.ArrayList;if(null==a||null==b)return c;for(var f,l=b.iterator();l.hasNext()&&((f=l.next())||1);)f.involvesSequence(a)&&c.add(f);return c},"jalview.datamodel.SequenceI,java.util.Set")});p("jalview.commands");q(["jalview.commands.CommandI","java.lang.Enum","java.util.ArrayList"],"jalview.commands.EditCommand","jalview.analysis.AlignSeq jalview.datamodel.AlignmentAnnotation $.Annotation $.Sequence $.SequenceFeature jalview.schemes.ResidueProperties jalview.util.Comparison $.ReverseListIterator $.StringUtils java.lang.StringBuffer java.util.HashMap $.Hashtable".split(" "),
function(){c$=s(function(){this.description=this.edits=null;H("jalview.commands.EditCommand.Edit")||jalview.commands.EditCommand.$EditCommand$Edit$();r(this,arguments)},jalview.commands,"EditCommand",null,jalview.commands.CommandI);J(c$,function(){this.edits=new java.util.ArrayList});m(c$,function(){});m(c$,function(a){this.description=a},"~S");m(c$,function(a,b,c,f,l,d){this.description=a;(b===jalview.commands.EditCommand.Action.CUT||b===jalview.commands.EditCommand.Action.PASTE)&&this.setEdit(C(jalview.commands.EditCommand.Edit,
this,null,b,c,f,l,d));this.performEdit(0,null)},"~S,jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");m(c$,function(a,b,c,f,l,d,g){this.description=a;b===jalview.commands.EditCommand.Action.REPLACE&&this.setEdit(C(jalview.commands.EditCommand.Edit,this,null,b,f,l,d,g,c));this.performEdit(0,null)},"~S,jalview.commands.EditCommand.Action,~S,~A,~N,~N,jalview.datamodel.AlignmentI");d(c$,"setEdit",function(a){this.edits.clear();this.edits.add(a)},"jalview.commands.EditCommand.Edit");
d(c$,"addEdit",function(a){jalview.commands.EditCommand.expandEdit(this.edits,a)||this.edits.add(a)},"jalview.commands.EditCommand.Edit");c$.expandEdit=d(c$,"expandEdit",function(a,b){if(null==a||a.isEmpty())return!1;var c=a.get(a.size()-1),f=b.command;if(c.command!==f||c.seqs.length!=b.seqs.length)return!1;for(var l=0;l<b.seqs.length;l++)if(c.seqs[l].getDatasetSequence()!==b.seqs[l].getDatasetSequence())return!1;return f===jalview.commands.EditCommand.Action.INSERT_GAP&&b.position==c.position+c.number||
f===jalview.commands.EditCommand.Action.DELETE_GAP&&b.position+b.number==c.position?(c.number+=b.number,c.seqs=b.seqs,f===jalview.commands.EditCommand.Action.DELETE_GAP&&c.position--,!0):!1},"java.util.List,jalview.commands.EditCommand.Edit");d(c$,"clearEdits",function(){this.edits.clear()});d(c$,"getEdit",function(a){return 0<=a&&a<this.edits.size()?this.edits.get(a):null},"~N");e(c$,"getDescription",function(){return this.description});e(c$,"getSize",function(){return this.edits.size()});d(c$,"getAlignment",
function(){return this.edits.isEmpty()?null:this.edits.get(0).al});d(c$,"appendEdit",function(a,b,c,f,l,d){this.appendEdit(a,b,c,f,l,d,null)},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B");d(c$,"appendEdit",function(a,b,c,f,l,d,g){a=C(jalview.commands.EditCommand.Edit,this,null,a,b,c,f,l.getGapCharacter());l.getHeight()==b.length&&(a.al=l,a.fullAlignmentHeight=!0);this.addEdit(a);d&&jalview.commands.EditCommand.performEdit(a,g)},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B,~A");
d(c$,"appendEdit",function(a,b,c,f){b.getHeight()==a.seqs.length&&(a.al=b,a.fullAlignmentHeight=!0);this.addEdit(a);c&&jalview.commands.EditCommand.performEdit(a,f)},"jalview.commands.EditCommand.Edit,jalview.datamodel.AlignmentI,~B,~A");d(c$,"performEdit",function(a,b){for(var c=this.edits.listIterator(a);c.hasNext();){var f=c.next();jalview.commands.EditCommand.performEdit(f,b)}},"~N,~A");c$.performEdit=d(c$,"performEdit",function(a,b){switch(a.command){case jalview.commands.EditCommand.Action.INSERT_GAP:jalview.commands.EditCommand.insertGap(a);
break;case jalview.commands.EditCommand.Action.DELETE_GAP:jalview.commands.EditCommand.deleteGap(a);break;case jalview.commands.EditCommand.Action.CUT:jalview.commands.EditCommand.cut(a,b);break;case jalview.commands.EditCommand.Action.PASTE:jalview.commands.EditCommand.paste(a,b);break;case jalview.commands.EditCommand.Action.REPLACE:jalview.commands.EditCommand.replace(a)}},"jalview.commands.EditCommand.Edit,~A");e(c$,"doCommand",function(a){this.performEdit(0,a)},"~A");e(c$,"undoCommand",function(a){for(var b=
this.edits.listIterator(this.edits.size());b.hasPrevious();){var c=b.previous();switch(c.command){case jalview.commands.EditCommand.Action.INSERT_GAP:jalview.commands.EditCommand.deleteGap(c);break;case jalview.commands.EditCommand.Action.DELETE_GAP:jalview.commands.EditCommand.insertGap(c);break;case jalview.commands.EditCommand.Action.CUT:jalview.commands.EditCommand.paste(c,a);break;case jalview.commands.EditCommand.Action.PASTE:jalview.commands.EditCommand.cut(c,a);break;case jalview.commands.EditCommand.Action.REPLACE:jalview.commands.EditCommand.replace(c)}}},
"~A");c$.insertGap=d(c$,"insertGap",function(a){for(var b=0;b<a.seqs.length;b++)a.seqs[b].insertCharAt(a.position,a.number,a.gapChar);jalview.commands.EditCommand.adjustAnnotations(a,!0,!1,null)},"jalview.commands.EditCommand.Edit");c$.deleteGap=d(c$,"deleteGap",function(a){for(var b=0;b<a.seqs.length;b++)a.seqs[b].deleteChars(a.position,a.position+a.number);jalview.commands.EditCommand.adjustAnnotations(a,!1,!1,null)},"jalview.commands.EditCommand.Edit");c$.cut=d(c$,"cut",function(a,b){var c=!1;
a.string=N(a.seqs.length,"\x00");for(var f=0;f<a.seqs.length;f++){var l=a.seqs[f];if(l.getLength()>a.position){a.string[f]=l.getSequence(a.position,a.position+a.number);var d=l.getDatasetSequence();null!=a.oldds&&null!=a.oldds[f]&&l.setDatasetSequence(null);l.deleteChars(a.position,a.position+a.number);if(null!=a.oldds&&null!=a.oldds[f])l.setDatasetSequence(a.oldds[f]),a.oldds[f]=d;else if(d!==l.getDatasetSequence()||null!=l.getSequenceFeatures())null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[f]=
d,jalview.commands.EditCommand.adjustFeatures(a,f,l.findPosition(a.position),l.findPosition(a.position+a.number),!1)}1>l.getLength()&&(a.al.deleteSequence(l),c=!0)}jalview.commands.EditCommand.adjustAnnotations(a,!1,c,b)},"jalview.commands.EditCommand.Edit,~A");c$.paste=d(c$,"paste",function(a,b){for(var c,f,l,d,g,h=!1,e=0,n=0,x=0;x<a.seqs.length;x++){f=!1;l=null!=a.oldds&&null!=a.oldds[x];1>a.seqs[x].getLength()&&(a.alIndex[x]<a.al.getHeight()?0>a.alIndex[x]||(void 0).add(a.alIndex[x],a.seqs[x]):
a.al.addSequence(a.seqs[x]),h=!0);d=a.seqs[x].getStart();g=a.seqs[x].getEnd();c=new StringBuffer;c.append(a.seqs[x].getSequence());if(null!=a.string&&null!=a.string[x]){if(a.position>=c.length())for(var u=a.position-c.length();0<u;)c.append(a.gapChar),u--;c.insert(a.position,a.string[x]);for(u=0;u<a.string[x].length;u++)23!=jalview.schemes.ResidueProperties.aaIndex[a.string[x][u].charCodeAt(0)]&&(f||(f=!0,e=a.seqs[x].findPosition(a.position),n=a.seqs[x].findPosition(a.position+a.number)),a.seqs[x].getStart()==
e?d--:g++);a.string[x]=null}a.seqs[x].setSequence(c.toString());a.seqs[x].setStart(d);a.seqs[x].setEnd(g);f&&(null!=a.seqs[x].getDatasetSequence()&&(l?c=a.oldds[x]:(c=new jalview.datamodel.Sequence(a.seqs[x].getName(),jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,a.seqs[x].getSequenceAsString()),a.seqs[x].getStart(),a.seqs[x].getEnd()),c.setDescription(a.seqs[x].getDescription())),null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[x]=a.seqs[x].getDatasetSequence(),a.seqs[x].setDatasetSequence(c)),
jalview.commands.EditCommand.adjustFeatures(a,x,e,n,!0))}jalview.commands.EditCommand.adjustAnnotations(a,!0,h,b);a.string=null},"jalview.commands.EditCommand.Edit,~A");c$.replace=d(c$,"replace",function(a){var b,c,f=a.position,l=a.number;a.number=f+a.string[0].length;for(var d=0;d<a.seqs.length;d++){var g=null!=a.oldds&&null!=a.oldds[d];c=a.seqs[d].getSequenceAsString();b=new StringBuffer(c.substring(0,f));b.append(a.string[d]);var h=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
String.instantialize(a.string[d])),e=a.seqs[d].findPosition(f)-a.seqs[d].getStart();b.append(c.substring(l));a.seqs[d].setSequence(b.toString());a.string[d]=c.substring(f,l).toCharArray();b=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(a.string[d]));h.toLowerCase().equals(b.toLowerCase())||(g?(h=a.seqs[d].getDatasetSequence(),a.seqs[d].setDatasetSequence(a.oldds[d]),a.oldds[d]=h):(null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[d]=a.seqs[d].getDatasetSequence(),
g=new jalview.datamodel.Sequence(a.seqs[d].getDatasetSequence()),b=g.getSequenceAsString(),h=b.substring(0,e)+h+b.substring(e+h.length),g.setSequence(h.toUpperCase()),a.seqs[d].setDatasetSequence(g)))}},"jalview.commands.EditCommand.Edit");c$.adjustAnnotations=d(c$,"adjustAnnotations",function(a,b,c,f){var l=null;c&&!b&&(a.deletedAnnotationRows=new java.util.Hashtable);if(a.fullAlignmentHeight)l=a.al.getAlignmentAnnotation();else for(var d=0,g,h=0;h<a.seqs.length;h++)if(c)if(b){if(null!=a.deletedAnnotationRows&&
a.deletedAnnotationRows.containsKey(a.seqs[h])){var e=a.deletedAnnotationRows.get(a.seqs[h]);a.seqs[h].setAlignmentAnnotation(e);if(null!=e){for(u=0;u<e.length;u++)a.al.addAnnotation(e[u]);for(u=0;u<e.length;u++)a.al.setAnnotationIndex(e[u],u);for(u=0;null!=f&&u<f.length;u++)if(f[u]!==a.al){var n=f[u].getWidth()+1;for(g=0;g<e.length;g++){var x=new jalview.datamodel.AlignmentAnnotation(e[g]);a.seqs[h].addAlignmentAnnotation(x);x.padAnnotation(n);f[u].addAnnotation(x);f[u].setAnnotationIndex(x,g)}}}}}else{if(g=
a.seqs[h].getAnnotation(),null!=g){for(var e=g.length,u=0;u<g.length;u++)a.al.deleteAnnotation(g[u])||(g[u]=null,e--);a.seqs[h].setAlignmentAnnotation(null);if(e!=g.length){e=Array(e);for(n=u=0;u<g.length;u++)null!=g[u]&&(e[n++]=g[u],g[u]=null);a.deletedAnnotationRows.put(a.seqs[h],e);for(g=0;null!=f&&g<f.length;g++)if(f[g]!==a.al&&(e=f[g].getAlignmentAnnotation(),!(null==e||0==e.length)))for(u=0;u<e.length;u++)e[u].sequenceRef===a.seqs[h]&&f[g].deleteAnnotation(e[u])}else a.deletedAnnotationRows.put(a.seqs[h],
g)}}else null!=a.seqs[h].getAnnotation()&&(0==d?l=a.seqs[h].getAnnotation():(g=Array(d+a.seqs[h].getAnnotation().length),System.arraycopy(l,0,g,0,d),System.arraycopy(a.seqs[h].getAnnotation(),0,g,d,a.seqs[h].getAnnotation().length),l=g),d=l.length);if(null!=l){b||(a.deletedAnnotations=new java.util.Hashtable);for(g=0;g<l.length;g++)if(!(l[g].autoCalculated||null==l[g].annotations)){f=0;d=l[g].annotations.length;if(b){if(c=Array(d+a.number),l[g].padGaps)for(u=0;u<c.length;u++)c[u]=new jalview.datamodel.Annotation(a.gapChar+
"",null," ",0)}else f=a.position<d?a.position+a.number>=d?d:d-a.number:d,0>f&&(f=d),c=Array(f);b?a.position<l[g].annotations.length?(System.arraycopy(l[g].annotations,0,c,0,a.position),null!=a.deletedAnnotations&&a.deletedAnnotations.containsKey(l[g].annotationId)&&(f=a.deletedAnnotations.get(l[g].annotationId),System.arraycopy(f,0,c,a.position,a.number)),System.arraycopy(l[g].annotations,a.position,c,a.position+a.number,d-a.position)):null!=a.deletedAnnotations&&a.deletedAnnotations.containsKey(l[g].annotationId)?
(f=a.deletedAnnotations.get(l[g].annotationId),c=Array(l[g].annotations.length+f.length),System.arraycopy(l[g].annotations,0,c,0,l[g].annotations.length),System.arraycopy(f,0,c,l[g].annotations.length,f.length)):c=l[g].annotations:f!=d||2>a.position?(f=Math.min(a.position,l[g].annotations.length),0<f&&System.arraycopy(l[g].annotations,0,c,0,f),d=Array(a.number),f>=a.position&&(f=Math.min(a.number,l[g].annotations.length-a.position),0<f&&System.arraycopy(l[g].annotations,a.position,d,0,f)),a.deletedAnnotations.put(l[g].annotationId,
d),l[g].annotations.length>a.position+a.number&&System.arraycopy(l[g].annotations,a.position+a.number,c,a.position,l[g].annotations.length-a.position-a.number)):(c=d-a.position,0<c?(d=Array(a.number),System.arraycopy(l[g].annotations,a.position,d,0,c),a.deletedAnnotations.put(l[g].annotationId,d),f=Math.min(l[g].annotations.length,a.position),c=Array(f),System.arraycopy(l[g].annotations,0,c,0,f)):c=l[g].annotations);l[g].annotations=c}}},"jalview.commands.EditCommand.Edit,~B,~B,~A");c$.adjustFeatures=
d(c$,"adjustFeatures",function(a,b,c,f,l){b=a.seqs[b];var d=b.getDatasetSequence();null==d&&(d=b);if(l)null!=a.editedFeatures&&a.editedFeatures.containsKey(b)&&d.setSequenceFeatures(a.editedFeatures.get(b));else if(l=d.getSequenceFeatures(),null!=l){for(var g=Array(l.length),h=f-c,e=0;e<l.length;e++){var n=new jalview.datamodel.SequenceFeature(l[e]);g[e]=n;l[e].getEnd()<c||(l[e].getBegin()>f?(l[e].setBegin(n.getBegin()-h),l[e].setEnd(n.getEnd()-h)):(l[e].getBegin()>=c&&l[e].setBegin(c),l[e].getEnd()<
f&&l[e].setEnd(f-1),l[e].setEnd(l[e].getEnd()-h),l[e].getBegin()>l[e].getEnd()&&d.deleteFeature(l[e])))}null==a.editedFeatures&&(a.editedFeatures=new java.util.Hashtable);a.editedFeatures.put(b,g)}},"jalview.commands.EditCommand.Edit,~N,~N,~N,~B");d(c$,"getEdits",function(){return this.edits});d(c$,"priorState",function(a){var b=new java.util.HashMap;if(null==this.getEdits())return b;if(a){for(var c,f=this.getEdits().iterator();f.hasNext()&&((c=f.next())||1);){var l;a=0;for(var d=c.getSequences();a<
d.length&&((l=d[a])||1);a++){var g=l.getDatasetSequence(),e=b.get(g);null==e&&(e=new jalview.datamodel.Sequence("",l.getSequenceAsString()),e.setDatasetSequence(g),b.put(g,e))}}return b}for(c=new jalview.util.ReverseListIterator(this.getEdits());c.hasNext();){var d=c.next(),f=d.getAction(),j=d.getPosition(),n=d.getNumber(),x=d.getGapCharacter();a=0;for(d=d.getSequences();a<d.length&&((l=d[a])||1);a++)g=l.getDatasetSequence(),e=b.get(g),null==e&&(e=new jalview.datamodel.Sequence("",l.getSequenceAsString()),
e.setDatasetSequence(g),b.put(g,e)),null!=g&&(f===jalview.commands.EditCommand.Action.DELETE_GAP?e.setSequence(String.instantialize(jalview.util.StringUtils.insertCharAt(e.getSequence(),j,n,x))):f===jalview.commands.EditCommand.Action.INSERT_GAP?e.setSequence(String.instantialize(jalview.util.StringUtils.deleteChars(e.getSequence(),j,j+n))):System.err.println("Can't undo edit action "+f))}return b},"~B");d(c$,"getEditIterator",function(a){return a?this.getEdits().iterator():new jalview.util.ReverseListIterator(this.getEdits())},
"~B");c$.$EditCommand$Edit$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.oldds=null;this.fullAlignmentHeight=!1;this.alIndex=this.seqs=this.string=this.command=this.al=this.editedFeatures=this.deletedAnnotations=this.deletedAnnotationRows=null;this.number=this.position=0;this.gapChar="\x00";r(this,arguments)},jalview.commands.EditCommand,"Edit");m(c$,function(a,b,c,f,l){this.command=a;this.seqs=b;this.position=c;this.number=f;this.gapChar=l},"jalview.commands.EditCommand.Action,~A,~N,~N,~S");
m(c$,function(a,b,c,f,l){this.gapChar=l.getGapCharacter();this.command=a;this.seqs=b;this.position=c;this.number=f;this.al=l;this.alIndex=w(b.length,0);for(a=0;a<b.length;a++)this.alIndex[a]=l.findIndex(b[a]);this.fullAlignmentHeight=l.getHeight()==b.length},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");m(c$,function(a,b,c,f,l,d){this.command=a;this.seqs=b;this.position=c;this.number=f;this.al=l;this.gapChar=l.getGapCharacter();this.string=N(b.length,"\x00");for(a=0;a<
b.length;a++)this.string[a]=d.toCharArray();this.fullAlignmentHeight=l.getHeight()==b.length},"jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~S");d(c$,"getSequences",function(){return this.seqs});d(c$,"getPosition",function(){return this.position});d(c$,"getAction",function(){return this.command});d(c$,"getNumber",function(){return this.number});d(c$,"getGapCharacter",function(){return this.gapChar});c$=z()};A(self.c$);c$=B(jalview.commands.EditCommand,"Action",Enum);d(c$,
"getUndoAction",function(){switch(this){case jalview.commands.EditCommand.Action.INSERT_GAP:return jalview.commands.EditCommand.Action.DELETE_GAP;case jalview.commands.EditCommand.Action.CUT:return jalview.commands.EditCommand.Action.PASTE;case jalview.commands.EditCommand.Action.DELETE_GAP:return jalview.commands.EditCommand.Action.INSERT_GAP;case jalview.commands.EditCommand.Action.PASTE:return jalview.commands.EditCommand.Action.CUT;case jalview.commands.EditCommand.Action.REPLACE:return jalview.commands.EditCommand.Action.REPLACE}return null});
R(c$,"INSERT_GAP",0,[]);R(c$,"DELETE_GAP",1,[]);R(c$,"CUT",2,[]);R(c$,"PASTE",3,[]);R(c$,"REPLACE",4,[]);R(c$,"INSERT_NUC",5,[]);c$=z()});p("jalview.commands");M(jalview.commands,"CommandI");p("jalview.analysis");q(["jalview.schemes.ResidueProperties","java.lang.StringBuffer"],"jalview.analysis.AlignSeq","jalview.datamodel.Mapping $.Sequence jalview.util.Comparison $.Format $.MapList $.MessageManager java.awt.Color java.lang.Error $.StringBuilder java.util.ArrayList $.Arrays $.StringTokenizer".split(" "),
function(){c$=s(function(){this.s2str=this.s1str=this.s2=this.s1=this.seq2=this.seq1=this.traceback=this.F=this.E=this.score=null;this.maxj=this.maxi=0;this.aseq2=this.aseq1=null;this.astr2=this.astr1="";this.prev=this.pid=this.maxscore=this.count=this.seq2end=this.seq2start=this.seq1end=this.seq1start=0;this.gapOpen=120;this.gapExtend=20;this.intToStr=this.lookup=null;this.defInt=23;this.charToInt=this.type=this.output=null;r(this,arguments)},jalview.analysis,"AlignSeq");J(c$,function(){this.lookup=
jalview.schemes.ResidueProperties.getBLOSUM62();this.intToStr=jalview.analysis.AlignSeq.pep;this.output=new StringBuffer});m(c$,function(a,b,c){this.SeqInit(a,a.getSequenceAsString(),b,b.getSequenceAsString(),c)},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S");m(c$,function(a,b,c,f,l){this.SeqInit(a,b.toUpperCase(),c,f.toUpperCase(),l)},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S");d(c$,"getMaxScore",function(){return this.maxscore});d(c$,"getSeq2Start",function(){return this.seq2start});
d(c$,"getSeq2End",function(){return this.seq2end});d(c$,"getSeq1Start",function(){return this.seq1start});d(c$,"getSeq1End",function(){return this.seq1end});d(c$,"getOutput",function(){return this.output.toString()});d(c$,"getAStr1",function(){return this.astr1});d(c$,"getAStr2",function(){return this.astr2});d(c$,"getASeq1",function(){return this.aseq1});d(c$,"getASeq2",function(){return this.aseq2});d(c$,"getS1",function(){return this.s1});d(c$,"getS2",function(){return this.s2});d(c$,"getAlignedSeq1",
function(){var a=new jalview.datamodel.Sequence(this.s1.getName(),this.getAStr1());a.setStart(this.s1.getStart()+this.getSeq1Start()-1);a.setEnd(this.s1.getStart()+this.getSeq1End()-1);a.setDatasetSequence(null==this.s1.getDatasetSequence()?this.s1:this.s1.getDatasetSequence());return a});d(c$,"getAlignedSeq2",function(){var a=new jalview.datamodel.Sequence(this.s2.getName(),this.getAStr2());a.setStart(this.s2.getStart()+this.getSeq2Start()-1);a.setEnd(this.s2.getStart()+this.getSeq2End()-1);a.setDatasetSequence(null==
this.s2.getDatasetSequence()?this.s2:this.s2.getDatasetSequence());return a});d(c$,"SeqInit",function(a,b,c,f,l){this.s1=a;this.s2=c;this.setDefaultParams(l);this.SeqInit(b,f)},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,~S");d(c$,"SeqInit",function(a,b,c,f,l){this.s1=a;this.s2=c;this.setType(l.isDNA()?"dna":"pep");this.lookup=l.getMatrix()},"jalview.datamodel.SequenceI,~S,jalview.datamodel.SequenceI,~S,jalview.schemes.ScoreMatrix");d(c$,"SeqInit",function(a,b){this.s1str=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
a);this.s2str=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,b);0==this.s1str.length||0==this.s2str.length?this.output.append("ALL GAPS: "+(0==this.s1str.length?this.s1.getName():" ")+(0==this.s2str.length?this.s2.getName():"")):(this.seq1=w(this.s1str.length,0),this.seq2=w(this.s2str.length,0),this.score=w(this.s1str.length,this.s2str.length,0),this.E=w(this.s1str.length,this.s2str.length,0),this.F=w(this.s1str.length,this.s2str.length,0),this.traceback=w(this.s1str.length,
this.s2str.length,0),this.seq1=this.stringToInt(this.s1str,this.type),this.seq2=this.stringToInt(this.s2str,this.type))},"~S,~S");d(c$,"setDefaultParams",function(a){this.setType(a);a.equals("pep")?this.lookup=jalview.schemes.ResidueProperties.getDefaultPeptideMatrix():a.equals("dna")&&(this.lookup=jalview.schemes.ResidueProperties.getDefaultDnaMatrix())},"~S");d(c$,"setType",function(a){this.type=a;if(this.type.equals("pep"))this.intToStr=jalview.analysis.AlignSeq.pep,this.charToInt=jalview.schemes.ResidueProperties.aaIndex,
this.defInt=23;else if(this.type.equals("dna"))this.intToStr=jalview.analysis.AlignSeq.dna,this.charToInt=jalview.schemes.ResidueProperties.nucleotideIndex,this.defInt=10;else throw this.output.append("Wrong type = dna or pep only"),Error(jalview.util.MessageManager.formatMessage("error.unknown_type_dna_or_pep",E(-1,[a])));},"~S");d(c$,"traceAlignment",function(){for(var a=-9999,b=0;b<this.seq1.length;b++)this.score[b][this.seq2.length-1]>a&&(a=this.score[b][this.seq2.length-1],this.maxi=b,this.maxj=
this.seq2.length-1);for(var c=0;c<this.seq2.length;c++)this.score[this.seq1.length-1][c]>a&&(a=this.score[this.seq1.length-1][c],this.maxi=this.seq1.length-1,this.maxj=c);b=this.maxi;c=this.maxj;this.maxscore=F(this.score[b][c]/10);this.seq1end=this.maxi+1;this.seq2end=this.maxj+1;this.aseq1=w(this.seq1.length+this.seq2.length,0);this.aseq2=w(this.seq1.length+this.seq2.length,0);for(this.count=this.seq1.length+this.seq2.length-1;0<b&&0<c;)this.aseq1[this.count]!=this.defInt&&0<=b&&(this.aseq1[this.count]=
this.seq1[b],this.astr1=this.s1str.charAt(b)+this.astr1),this.aseq2[this.count]!=this.defInt&&0<c&&(this.aseq2[this.count]=this.seq2[c],this.astr2=this.s2str.charAt(c)+this.astr2),a=this.findTrace(b,c),0==a?(b--,c--):1==a?(c--,this.aseq1[this.count]=this.defInt,this.astr1="-"+this.astr1.substring(1)):-1==a&&(b--,this.aseq2[this.count]=this.defInt,this.astr2="-"+this.astr2.substring(1)),this.count--;this.seq1start=b+1;this.seq2start=c+1;this.aseq1[this.count]!=this.defInt&&(this.aseq1[this.count]=
this.seq1[b],this.astr1=this.s1str.charAt(b)+this.astr1);this.aseq2[this.count]!=this.defInt&&(this.aseq2[this.count]=this.seq2[c],this.astr2=this.s2str.charAt(c)+this.astr2)});d(c$,"printAlignment",function(a){var b=this.s1.getName(),c=this.s2.getName(),f=this.s1.getName().length;this.s2.getName().length>f&&(f=this.s2.getName().length);30<f&&(f=30,this.s1.getName().length>f&&(b=this.s1.getName().substring(0,30)),this.s2.getName().length>f&&(c=this.s2.getName().substring(0,30)));var l=72-f-1,d=F((this.aseq1.length-
this.count)/l)+1;this.pid=0;this.output.append("Score = ").append(""+this.score[this.maxi][this.maxj]).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Length of alignment = ").append(String.valueOf(this.aseq1.length-this.count)).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s1.getName()));this.output.append(" :  ").append(String.valueOf(this.s1.getStart())).append(" - ").append(String.valueOf(this.s1.getEnd()));
this.output.append(" (Sequence length = ").append(String.valueOf(this.s1str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s2.getName()));this.output.append(" :  ").append(String.valueOf(this.s2.getStart())).append(" - ").append(String.valueOf(this.s2.getEnd()));this.output.append(" (Sequence length = ").append(String.valueOf(this.s2str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE).append(jalview.analysis.AlignSeq.NEWLINE);
for(var g=0;g<d;g++){this.output.append((new jalview.util.Format("%"+f+"s")).form(b)).append(" ");for(var e=0;e<l;e++)e+g*l<this.astr1.length&&this.output.append(this.astr1.charAt(e+g*l));this.output.append(jalview.analysis.AlignSeq.NEWLINE);this.output.append((new jalview.util.Format("%"+f+"s")).form(" ")).append(" ");for(e=0;e<l;e++)e+g*l<this.astr1.length&&(this.astr1.charAt(e+g*l)==this.astr2.charAt(e+g*l)&&!jalview.util.Comparison.isGap(this.astr1.charAt(e+g*l))?(this.pid++,this.output.append("|")):
this.type.equals("pep")?0<jalview.schemes.ResidueProperties.getPAM250(this.astr1.charAt(e+g*l),this.astr2.charAt(e+g*l))?this.output.append("."):this.output.append(" "):this.output.append(" "));this.output=this.output.append(jalview.analysis.AlignSeq.NEWLINE);this.output=this.output.append((new jalview.util.Format("%"+f+"s")).form(c)).append(" ");for(e=0;e<l;e++)e+g*l<this.astr2.length&&this.output.append(this.astr2.charAt(e+g*l));this.output.append(jalview.analysis.AlignSeq.NEWLINE).append(jalview.analysis.AlignSeq.NEWLINE)}this.pid=
100*(this.pid/(this.aseq1.length-this.count));this.output=this.output.append((new jalview.util.Format("Percentage ID = %2.2f\n\n")).formDouble(this.pid));try{a.print(this.output.toString())}catch(j){if(!y(j,Exception))throw j;}},"java.io.PrintStream");d(c$,"printScoreMatrix",function(a){for(var b=this.seq1.length,c=this.seq2.length,f=0;f<b;f++){if(0==f){jalview.util.Format.print(System.out,"%8s",this.s2str.substring(0,1));for(var l=1;l<c;l++)jalview.util.Format.print(System.out,"%5s",this.s2str.substring(l,
l+1));System.out.println()}for(l=0;l<c;l++)0==l&&jalview.util.Format.print(System.out,"%3s",this.s1str.substring(f,f+1)),jalview.util.Format.printLong(System.out,"%3d ",F(a[f][l]/10));System.out.println()}},"~A");d(c$,"findTrace",function(a,b){var c=0,f=this.score[a-1][b-1]+10*this.lookup[this.seq1[a]][this.seq2[b]];this.F[a][b]>f?(f=this.F[a][b],c=-1):this.F[a][b]==f&&-1==this.prev&&(f=this.F[a][b],c=-1);this.E[a][b]>=f?c=1:this.E[a][b]==f&&1==this.prev&&(c=1);return this.prev=c},"~N,~N");d(c$,"calcScoreMatrix",
function(){var a=this.seq1.length,b=this.seq2.length;this.score[0][0]=10*this.lookup[this.seq1[0]][this.seq2[0]];this.E[0][0]=-this.gapExtend;this.F[0][0]=0;for(var c=1;c<b;c++)this.E[0][c]=this.max(this.score[0][c-1]-this.gapOpen,this.E[0][c-1]-this.gapExtend),this.F[0][c]=-this.gapExtend,this.score[0][c]=this.max(10*this.lookup[this.seq1[0]][this.seq2[c]],-this.gapOpen,-this.gapExtend),this.traceback[0][c]=1;for(var f=1;f<a;f++)this.E[f][0]=-this.gapOpen,this.F[f][0]=this.max(this.score[f-1][0]-
this.gapOpen,this.F[f-1][0]-this.gapExtend),this.score[f][0]=this.max(10*this.lookup[this.seq1[f]][this.seq2[0]],this.E[f][0],this.F[f][0]),this.traceback[f][0]=-1;for(f=1;f<a;f++)for(c=1;c<b;c++)this.E[f][c]=this.max(this.score[f][c-1]-this.gapOpen,this.E[f][c-1]-this.gapExtend),this.F[f][c]=this.max(this.score[f-1][c]-this.gapOpen,this.F[f-1][c]-this.gapExtend),this.score[f][c]=this.max(this.score[f-1][c-1]+10*this.lookup[this.seq1[f]][this.seq2[c]],this.E[f][c],this.F[f][c]),this.traceback[f][c]=
this.findTrace(f,c)});c$.extractGaps=d(c$,"extractGaps",function(a,b){if(null==a||null==b)return null;for(var c=new java.util.StringTokenizer(b,a),f=new StringBuilder(b.length);c.hasMoreTokens();)f.append(c.nextToken());return f.toString()},"~S,~S");d(c$,"max",function(a,b,c){var f=a;b>a&&(f=b);c>f&&(f=c);return f},"~N,~N,~N");d(c$,"max",function(a,b){var c=a;b>a&&(c=b);return c},"~N,~N");d(c$,"stringToInt",function(a){for(var b=w(a.length,0),c=0;c<a.length;c++){var f=a.charAt(c);"a"<=f&&"z">=f&&
(f=String.fromCharCode(f.charCodeAt(0)-32));try{if(b[c]=this.charToInt[f.charCodeAt(0)],0>b[c]||b[c]>this.defInt)b[c]=this.defInt}catch(l){if(y(l,Exception))b[c]=this.defInt;else throw l;}}return b},"~S,~S");c$.displayMatrix=d(c$,"displayMatrix",function(a,b,c,f,l){for(var d=-1E3,g=1E3,e=0;e<c;e++)for(var j=0;j<f;j++)b[e][j]>=d&&(d=b[e][j]),b[e][j]<=g&&(g=b[e][j]);System.out.println(d+" "+g);for(e=0;e<c;e++)for(j=0;j<f;j++){var n=l*e,x=l*j;a.setColor(new java.awt.Color((b[e][j]-g)/(d-g),0,0));a.fillRect(n,
x,l,l)}},"java.awt.Graphics,~A,~N,~N,~N");c$.doGlobalNWAlignment=d(c$,"doGlobalNWAlignment",function(a,b,c){a=new jalview.analysis.AlignSeq(a,b,c);a.calcScoreMatrix();a.traceAlignment();return a},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~S");d(c$,"getMappingFromS1",function(a){for(var b=new java.util.ArrayList,c=new java.util.ArrayList,f=this.s2.getStart()+this.getSeq2Start()-2,l=this.s1.getStart()+this.getSeq1Start()-2,d=f-3,g=l-3,e=!1,j=0;j<this.astr1.length;j++){var n=this.astr1.charAt(j),
x=this.astr2.charAt(j);"-"!=n&&l++;"-"!=x&&f++;if(a||n==x){if(g+1!=l||d+1!=f)b.add(Integer.$valueOf(l)),c.add(Integer.$valueOf(f));e=!0;g=l;d=f}else e&&(b.add(Integer.$valueOf(g)),c.add(Integer.$valueOf(d))),e=!1}a=w(b.size()+(e?1:0),0);for(var d=w(c.size()+(e?1:0),0),j=0,u,b=b.iterator();b.hasNext()&&((u=b.next())||1);)a[j++]=u.intValue();j=0;for(b=c.iterator();b.hasNext()&&((u=b.next())||1);)d[j++]=u.intValue();e&&(a[a.length-1]=l,d[d.length-1]=f);c=new jalview.util.MapList(a,d,1,1);c=new jalview.datamodel.Mapping(c);
c.setTo(this.s2);return c},"~B");c$.replaceMatchingSeqsWith=d(c$,"replaceMatchingSeqsWith",function(a,b,c,f,l,d){var g=new java.util.ArrayList,e=new java.util.ArrayList,j=new java.util.ArrayList;if(null!=f&&0<f.getHeight()){for(var n=new java.util.ArrayList,x=new java.util.ArrayList,u,D=c.iterator();D.hasNext()&&((u=D.next())||1);){for(var m=null,p=null,q=0,s,r=f.getSequences().iterator();r.hasNext()&&((s=r.next())||1);){var t=jalview.analysis.AlignSeq.doGlobalNWAlignment(s,u,l);if(null==m||t.getMaxScore()>
q)q=t.getMaxScore(),p=t,m=s}System.out.println("Best Score for "+(n.size()+1)+" :"+q);n.add(m);x.add(p);f.deleteSequence(m)}f=0;for(l=a.size();f<l;f++)if(D=a.get(f),-1<(p=c.indexOf(D))){a.set(f,u=n.get(p));g.add(D);e.add(u);u.setName(D.getName());u.setDescription(D.getDescription());u.transferAnnotation(D,m=x.get(p).getMappingFromS1(!1));j.add(x.get(p));p=-1;for(q=0;q<b.size();)b.get(q).sequenceRef===D?(-1==p&&(p=q),d?b.remove(q):(s=b.remove(q),s.liftOver(u,m),s.setSequenceRef(u),u.addAlignmentAnnotation(s))):
q++;null!=u.getAnnotation()&&0<u.getAnnotation().length&&b.addAll(-1==p?b.size():p,java.util.Arrays.asList(u.getAnnotation()))}}return java.util.Arrays.asList([g,e,j])},"java.util.List,java.util.List,java.util.List,jalview.datamodel.AlignmentI,~S,~B");c$.computeRedundancyMatrix=d(c$,"computeRedundancyMatrix",function(a,b,c,f,l){for(var d=a.length,g=Q(d,0),e=w(d,0),j=0;j<d;j++)g[j]=0,e[j]=-1;for(var n,x,j=0;j<d;j++)for(var u=0;u<j;u++)if(j!=u){null==b?(n=a[j].getSequenceAsString(c,f),x=a[u].getSequenceAsString(c,
f)):(n=b[j],x=b[u]);if(-1==e[j]){var D=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,n);e[j]=D.length;l&&(n=D)}-1==e[u]&&(D=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,x),e[u]=D.length,l&&(x=D));n=jalview.util.Comparison.PID(n,x);e[u]<e[j]?g[u]=Math.max(n,g[u]):g[j]=Math.max(n,g[j])}return g},"~A,~A,~N,~N,~B");G(c$,"PEP","pep","DNA","dna");c$.NEWLINE=c$.prototype.NEWLINE=System.lineSeparator();G(c$,"dna",E(-1,["A","C","G","T","-"]),"pep",E(-1,"ARNDCQEGHILKMFPSTWYVBZX-".split("")))});
p("jalview.schemes");q("jalview.analysis.scoremodels.FeatureScoreModel $.PIDScoreModel jalview.schemes.ScoreMatrix java.awt.Color java.util.ArrayList $.HashMap $.Hashtable $.Vector".split(" "),"jalview.schemes.ResidueProperties",["java.lang.StringBuffer"],function(){c$=B(jalview.schemes,"ResidueProperties");c$.buildAmbiguityCodonSet=d(c$,"buildAmbiguityCodonSet",function(){if(0<jalview.schemes.ResidueProperties._ambiguityCodes.size())System.err.println("Ignoring multiple calls to buildAmbiguityCodonSet");
else{for(var a,b=jalview.schemes.ResidueProperties.ambiguityCodes.entrySet().iterator();b.hasNext()&&((a=b.next())||1);)for(var c,f=0,l=a.getValue();f<l.length&&((c=l[f])||1);f++){var d=jalview.schemes.ResidueProperties._ambiguityCodes.get(c);null==d&&jalview.schemes.ResidueProperties._ambiguityCodes.put(c,d=new java.util.ArrayList);d.contains(a.getKey())?System.err.println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for "+a.getKey()+" in residue "+c):d.add(a.getKey())}var g;
a=0;for(b=jalview.schemes.ResidueProperties.codonHash2.keySet().toArray(Array(jalview.schemes.ResidueProperties.codonHash2.size()));a<b.length&&((g=b[a])||1);a++){c=jalview.schemes.ResidueProperties.codonHash2.get(g);for(var f=Array(g.length),k=0,l=g.length;k<l;k++)d=""+g.charAt(k),d=jalview.schemes.ResidueProperties._ambiguityCodes.get(d),f[k]=null!=d?d.toArray(Array(d.size())):E(-1,[]);l=w(g.length,0);d=w(g.length,0);for(k=0;k<l.length;k++)l[k]=-1;l[f.length-1]=0;for(var e,h;l[0]<f[0].length;){var k=
N(l.length,"\x00"),j="";for(e=0;e<l.length;e++)if(0==f[e].length||0>l[e])j+=g.charAt(e),k[e]=N(-1,[g.charAt(e)]);else{var j=j+f[e][l[e]],n=jalview.schemes.ResidueProperties.ambiguityCodes.get(f[e][l[e]]);k[e]=N(n.length,"\x00");h=0;for(var x,u=0;u<n.length&&((x=n[u])||1);u++)k[e][h++]=x.charAt(0)}for(e=0;e<d.length;e++)d[e]=0;h=!0;do{e="";for(h=0;h<d.length;h++)e+=k[h][d[h]];e=jalview.schemes.ResidueProperties.codonHash2.get(e);if(h=null!=e&&e.equals(c))for(e=f.length-1;++d[e]>=k[e].length&&0<e;)d[e]=
0,e--}while(h&&d[0]<k[0].length);h&&jalview.schemes.ResidueProperties.codonHash2.put(j,c);for(e=f.length-1;++l[e]>=f[e].length&&0<e;)l[e]=-1,e--}}}});c$.getHydmax=d(c$,"getHydmax",function(){return 4.5});c$.getHydmin=d(c$,"getHydmin",function(){return-3.9});c$.getHyd=d(c$,"getHyd",function(){return jalview.schemes.ResidueProperties.hyd});c$.getAA3Hash=d(c$,"getAA3Hash",function(){return jalview.schemes.ResidueProperties.aa3Hash});c$.getDNA=d(c$,"getDNA",function(){return jalview.schemes.ResidueProperties.DNA});
c$.getBLOSUM62=d(c$,"getBLOSUM62",function(){return jalview.schemes.ResidueProperties.BLOSUM62});c$.getPAM250=d(c$,"getPAM250",function(a,b){return jalview.schemes.ResidueProperties.getPAM250(a.charAt(0),b.charAt(0))},"~S,~S");c$.getBLOSUM62=d(c$,"getBLOSUM62",function(a,b){var c=0;try{var f=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)],l=jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)],c=jalview.schemes.ResidueProperties.BLOSUM62[f][l]}catch(d){if(!y(d,Exception))throw d;}return c},
"~S,~S");c$.getCodons=d(c$,"getCodons",function(a){return jalview.schemes.ResidueProperties.codonHash.containsKey(a)?jalview.schemes.ResidueProperties.codonHash.get(a):null},"~S");c$.codonTranslate=d(c$,"codonTranslate",function(a){a=jalview.schemes.ResidueProperties.codonHash2.get(a.toUpperCase());return null!=a&&a.equals("*")?"STOP":a},"~S");c$._codonTranslate=d(c$,"_codonTranslate",function(a){a=a.toUpperCase();if(-1<a.indexOf("X")||-1<a.indexOf("N"))return"X";for(var b,c=jalview.schemes.ResidueProperties.codonHash.keySet().iterator();c.hasNext()&&
((b=c.next())||1);)if(jalview.schemes.ResidueProperties.codonHash.get(b).contains(a))return b;return null},"~S");c$.getDefaultPeptideMatrix=d(c$,"getDefaultPeptideMatrix",function(){return jalview.schemes.ResidueProperties.getBLOSUM62()});c$.getDefaultDnaMatrix=d(c$,"getDefaultDnaMatrix",function(){return jalview.schemes.ResidueProperties.getDNA()});c$.getScoreMatrix=d(c$,"getScoreMatrix",function(a){a=jalview.schemes.ResidueProperties.scoreMatrices.get(a);return null!=a&&v(a,jalview.schemes.ScoreMatrix)?
a:null},"~S");c$.getScoreModel=d(c$,"getScoreModel",function(a){return jalview.schemes.ResidueProperties.scoreMatrices.get(a)},"~S");c$.getPAM250=d(c$,"getPAM250",function(a,b){var c=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)],f=jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)];return jalview.schemes.ResidueProperties.PAM250[c][f]},"~S,~S");c$.getDssp3state=d(c$,"getDssp3state",function(a){if(null==a)return null;for(var b=new StringBuffer,c=0;c<a.length;c++){var f=a.substring(c,
c+1);jalview.schemes.ResidueProperties.toDssp3State.containsKey(f)?b.append(jalview.schemes.ResidueProperties.toDssp3State.get(f)):b.append(" ")}return b.toString()},"~S");c$.getRNASecStrucState=d(c$,"getRNASecStrucState",function(a){if(null==a)return null;for(var b=new StringBuffer,c=0;c<a.length;c++){var f=a.substring(c,c+1);jalview.schemes.ResidueProperties.toRNAssState.containsKey(f)?b.append(f):b.append(" ")}return b.toString()},"~S");c$.isCloseParenRNA=d(c$,"isCloseParenRNA",function(a){return jalview.schemes.ResidueProperties.RNAcloseParen[a.charCodeAt(0)]},
"~S");c$.getResidues=d(c$,"getResidues",function(a,b){var c=new java.util.ArrayList;if(a)for(var f,l=jalview.schemes.ResidueProperties.nucleotideName.keySet().iterator();l.hasNext()&&((f=l.next())||1);){var d=jalview.schemes.ResidueProperties.nucleotideIndex[f.charCodeAt(0)];!b&&4<d||10<=d||(f=f.toUpperCase(),c.contains(f)||c.add(f))}else for(f=jalview.schemes.ResidueProperties.aa3Hash.keySet().iterator();f.hasNext()&&((l=f.next())||1);)d=jalview.schemes.ResidueProperties.aa3Hash.get(l).intValue(),
!b&&20<=d||23<=d||(l=l.toUpperCase(),c.contains(l)||c.add(l));return c},"~B,~B");c$.scoreMatrices=c$.prototype.scoreMatrices=new java.util.Hashtable;G(c$,"aaIndex",null,"nucleotideIndex",null,"purinepyrimidineIndex",null);c$.aa3Hash=c$.prototype.aa3Hash=new java.util.HashMap;c$.aa2Triplet=c$.prototype.aa2Triplet=new java.util.HashMap;c$.nucleotideName=c$.prototype.nucleotideName=new java.util.HashMap;jalview.schemes.ResidueProperties.aaIndex=w(255,0);for(var a=0;255>a;a++)jalview.schemes.ResidueProperties.aaIndex[a]=
23;jalview.schemes.ResidueProperties.aaIndex[65]=0;jalview.schemes.ResidueProperties.aaIndex[82]=1;jalview.schemes.ResidueProperties.aaIndex[78]=2;jalview.schemes.ResidueProperties.aaIndex[68]=3;jalview.schemes.ResidueProperties.aaIndex[67]=4;jalview.schemes.ResidueProperties.aaIndex[81]=5;jalview.schemes.ResidueProperties.aaIndex[69]=6;jalview.schemes.ResidueProperties.aaIndex[71]=7;jalview.schemes.ResidueProperties.aaIndex[72]=8;jalview.schemes.ResidueProperties.aaIndex[73]=9;jalview.schemes.ResidueProperties.aaIndex[76]=
10;jalview.schemes.ResidueProperties.aaIndex[75]=11;jalview.schemes.ResidueProperties.aaIndex[77]=12;jalview.schemes.ResidueProperties.aaIndex[70]=13;jalview.schemes.ResidueProperties.aaIndex[80]=14;jalview.schemes.ResidueProperties.aaIndex[83]=15;jalview.schemes.ResidueProperties.aaIndex[84]=16;jalview.schemes.ResidueProperties.aaIndex[87]=17;jalview.schemes.ResidueProperties.aaIndex[89]=18;jalview.schemes.ResidueProperties.aaIndex[86]=19;jalview.schemes.ResidueProperties.aaIndex[66]=20;jalview.schemes.ResidueProperties.aaIndex[90]=
21;jalview.schemes.ResidueProperties.aaIndex[88]=22;jalview.schemes.ResidueProperties.aaIndex[85]=22;jalview.schemes.ResidueProperties.aaIndex[97]=0;jalview.schemes.ResidueProperties.aaIndex[114]=1;jalview.schemes.ResidueProperties.aaIndex[110]=2;jalview.schemes.ResidueProperties.aaIndex[100]=3;jalview.schemes.ResidueProperties.aaIndex[99]=4;jalview.schemes.ResidueProperties.aaIndex[113]=5;jalview.schemes.ResidueProperties.aaIndex[101]=6;jalview.schemes.ResidueProperties.aaIndex[103]=7;jalview.schemes.ResidueProperties.aaIndex[104]=
8;jalview.schemes.ResidueProperties.aaIndex[105]=9;jalview.schemes.ResidueProperties.aaIndex[108]=10;jalview.schemes.ResidueProperties.aaIndex[107]=11;jalview.schemes.ResidueProperties.aaIndex[109]=12;jalview.schemes.ResidueProperties.aaIndex[102]=13;jalview.schemes.ResidueProperties.aaIndex[112]=14;jalview.schemes.ResidueProperties.aaIndex[115]=15;jalview.schemes.ResidueProperties.aaIndex[116]=16;jalview.schemes.ResidueProperties.aaIndex[119]=17;jalview.schemes.ResidueProperties.aaIndex[121]=18;
jalview.schemes.ResidueProperties.aaIndex[118]=19;jalview.schemes.ResidueProperties.aaIndex[98]=20;jalview.schemes.ResidueProperties.aaIndex[122]=21;jalview.schemes.ResidueProperties.aaIndex[120]=22;jalview.schemes.ResidueProperties.aaIndex[117]=22;G(c$,"maxProteinIndex",23,"maxNucleotideIndex",10);jalview.schemes.ResidueProperties.nucleotideIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.nucleotideIndex[a]=10;jalview.schemes.ResidueProperties.nucleotideIndex[65]=0;jalview.schemes.ResidueProperties.nucleotideIndex[97]=
0;jalview.schemes.ResidueProperties.nucleotideIndex[67]=1;jalview.schemes.ResidueProperties.nucleotideIndex[99]=1;jalview.schemes.ResidueProperties.nucleotideIndex[71]=2;jalview.schemes.ResidueProperties.nucleotideIndex[103]=2;jalview.schemes.ResidueProperties.nucleotideIndex[84]=3;jalview.schemes.ResidueProperties.nucleotideIndex[116]=3;jalview.schemes.ResidueProperties.nucleotideIndex[85]=4;jalview.schemes.ResidueProperties.nucleotideIndex[117]=4;jalview.schemes.ResidueProperties.nucleotideIndex[73]=
5;jalview.schemes.ResidueProperties.nucleotideIndex[105]=5;jalview.schemes.ResidueProperties.nucleotideIndex[88]=6;jalview.schemes.ResidueProperties.nucleotideIndex[120]=6;jalview.schemes.ResidueProperties.nucleotideIndex[82]=7;jalview.schemes.ResidueProperties.nucleotideIndex[114]=7;jalview.schemes.ResidueProperties.nucleotideIndex[89]=8;jalview.schemes.ResidueProperties.nucleotideIndex[121]=8;jalview.schemes.ResidueProperties.nucleotideIndex[78]=9;jalview.schemes.ResidueProperties.nucleotideIndex[110]=
9;jalview.schemes.ResidueProperties.nucleotideName.put("A","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("a","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("G","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("g","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("C","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("c","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("T","Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("t",
"Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("U","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("u","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("I","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("i","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("X","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("x","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("R","Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("r",
"Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("Y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("N","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("n","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("W","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("w","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("S",
"Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("s","Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("M","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("m","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("K","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("k","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("B","Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("b",
"Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("H","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("h","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("D","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("d","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("V","Not T (A or G or C");jalview.schemes.ResidueProperties.nucleotideName.put("v","Not T (A or G or C");
jalview.schemes.ResidueProperties.purinepyrimidineIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.purinepyrimidineIndex[a]=3;jalview.schemes.ResidueProperties.purinepyrimidineIndex[65]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[97]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[67]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[99]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[71]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[103]=
0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[84]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[116]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[85]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[117]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[73]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[105]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[88]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[120]=2;
jalview.schemes.ResidueProperties.purinepyrimidineIndex[82]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[114]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[89]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[121]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[78]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[110]=2;jalview.schemes.ResidueProperties.aa3Hash.put("ALA",new Integer(0));jalview.schemes.ResidueProperties.aa3Hash.put("ARG",new Integer(1));
jalview.schemes.ResidueProperties.aa3Hash.put("ASN",new Integer(2));jalview.schemes.ResidueProperties.aa3Hash.put("ASP",new Integer(3));jalview.schemes.ResidueProperties.aa3Hash.put("CYS",new Integer(4));jalview.schemes.ResidueProperties.aa3Hash.put("GLN",new Integer(5));jalview.schemes.ResidueProperties.aa3Hash.put("GLU",new Integer(6));jalview.schemes.ResidueProperties.aa3Hash.put("GLY",new Integer(7));jalview.schemes.ResidueProperties.aa3Hash.put("HIS",new Integer(8));jalview.schemes.ResidueProperties.aa3Hash.put("ILE",
new Integer(9));jalview.schemes.ResidueProperties.aa3Hash.put("LEU",new Integer(10));jalview.schemes.ResidueProperties.aa3Hash.put("LYS",new Integer(11));jalview.schemes.ResidueProperties.aa3Hash.put("MET",new Integer(12));jalview.schemes.ResidueProperties.aa3Hash.put("PHE",new Integer(13));jalview.schemes.ResidueProperties.aa3Hash.put("PRO",new Integer(14));jalview.schemes.ResidueProperties.aa3Hash.put("SER",new Integer(15));jalview.schemes.ResidueProperties.aa3Hash.put("THR",new Integer(16));jalview.schemes.ResidueProperties.aa3Hash.put("TRP",
new Integer(17));jalview.schemes.ResidueProperties.aa3Hash.put("TYR",new Integer(18));jalview.schemes.ResidueProperties.aa3Hash.put("VAL",new Integer(19));jalview.schemes.ResidueProperties.aa3Hash.put("ASX",new Integer(20));jalview.schemes.ResidueProperties.aa3Hash.put("GLX",new Integer(21));jalview.schemes.ResidueProperties.aa3Hash.put("XAA",new Integer(22));jalview.schemes.ResidueProperties.aa3Hash.put("-",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("*",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(".",
new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(" ",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("Gap",new Integer(23));jalview.schemes.ResidueProperties.aa2Triplet.put("A","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("a","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("R","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("r","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("N","ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("n",
"ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("D","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("d","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("C","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("c","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("Q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("E","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("e","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("G",
"GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("g","GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("H","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("h","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("I","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("i","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("L","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("l","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("K","LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("k",
"LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("M","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("m","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("F","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("f","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("P","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("p","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("S","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("s","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("T",
"THR");jalview.schemes.ResidueProperties.aa2Triplet.put("t","THR");jalview.schemes.ResidueProperties.aa2Triplet.put("W","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("w","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("Y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("V","VAL");jalview.schemes.ResidueProperties.aa2Triplet.put("v","VAL");G(c$,"aa",E(-1,"ARNDCQEGHILKMFPSTWYVBZX_*. ".split("")));c$.midBlue=c$.prototype.midBlue=
new java.awt.Color(100,100,255);c$.scaleColours=c$.prototype.scaleColours=new java.util.Vector;jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(114,0,147));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(156,0,98));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(190,0,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.red);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,
125,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.orange);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,194,85));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.yellow);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,255,181));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.white);c$.taylor=c$.prototype.taylor=E(-1,[new java.awt.Color(204,255,0),new java.awt.Color(0,
0,255),new java.awt.Color(204,0,255),new java.awt.Color(255,0,0),new java.awt.Color(255,255,0),new java.awt.Color(255,0,204),new java.awt.Color(255,0,102),new java.awt.Color(255,153,0),new java.awt.Color(0,102,255),new java.awt.Color(102,255,0),new java.awt.Color(51,255,0),new java.awt.Color(102,0,255),new java.awt.Color(0,255,0),new java.awt.Color(0,255,102),new java.awt.Color(255,204,0),new java.awt.Color(255,51,0),new java.awt.Color(255,102,0),new java.awt.Color(0,204,255),new java.awt.Color(0,
255,204),new java.awt.Color(153,255,0),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.nucleotide=c$.prototype.nucleotide=E(-1,[new java.awt.Color(100,247,63),new java.awt.Color(255,179,64),new java.awt.Color(235,65,60),new java.awt.Color(60,136,238),new java.awt.Color(60,136,238),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.purinepyrimidine=
c$.prototype.purinepyrimidine=E(-1,[new java.awt.Color(255,131,250),new java.awt.Color(64,224,208),java.awt.Color.white,java.awt.Color.white]);c$.zappo=c$.prototype.zappo=E(-1,[java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.green,java.awt.Color.red,java.awt.Color.yellow,java.awt.Color.green,java.awt.Color.red,java.awt.Color.magenta,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink,java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink,
java.awt.Color.orange,java.awt.Color.magenta,java.awt.Color.green,java.awt.Color.green,java.awt.Color.orange,java.awt.Color.orange,java.awt.Color.pink,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);G(c$,"hyd2",U(-1,[0.62,0.29,-0.9,-0.74,1.19,0.48,-0.4,1.38,-1.5,1.06,0.64,-0.78,0.12,-0.85,-2.53,-0.18,-0.05,1.08,0.81,0,0.26,0,0]),"helix",U(-1,[1.42,0.98,0.67,1.01,0.7,1.11,1.51,0.57,1,1.08,1.21,1.16,
1.45,1.13,0.57,0.77,0.83,1.08,0.69,1.06,0.84,1.31,1,0]),"helixmin",0.57,"helixmax",1.51,"strand",U(-1,[0.83,0.93,0.89,0.54,1.19,1.1,0.37,0.75,0.87,1.6,1.3,0.74,1.05,1.38,0.55,0.75,1.19,1.37,1.47,1.7,0.72,0.74,1,0]),"strandmin",0.37,"strandmax",1.7,"turn",U(-1,[0.66,0.95,1.56,1.46,1.19,0.98,0.74,1.56,0.95,0.47,0.59,1.01,0.6,0.6,1.52,1.43,0.96,0.96,1.14,0.5,1.51,0.86,1,0,0]),"turnmin",0.47,"turnmax",1.56,"buried",U(-1,[1.7,0.1,0.4,0.4,4.6,0.3,0.3,1.8,0.8,3.1,2.4,0.05,1.9,2.2,0.6,0.8,0.7,1.6,0.5,2.9,
0.4,0.3,1.358,0]),"buriedmin",0.05,"buriedmax",4.6,"hyd",U(-1,[1.8,-4.5,-3.5,-3.5,2.5,-3.5,-3.5,-0.4,-3.2,4.5,3.8,-3.9,1.9,2.8,-1.6,-0.8,-0.7,-0.9,-1.3,4.2,-3.5,-3.5,-0.49,0]),"hydmax",4.5,"hydmin",-3.9,"BLOSUM62",E(-1,[w(-1,[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4]),w(-1,[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4]),w(-1,[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4]),w(-1,[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,
-4]),w(-1,[0,3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4]),w(-1,[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4]),w(-1,[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4]),w(-1,[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4]),w(-1,[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4]),w(-1,[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,
1,-4,-3,-1,-4]),w(-1,[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4]),w(-1,[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4]),w(-1,[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4]),w(-1,[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4]),w(-1,[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4]),w(-1,[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4]),w(-1,[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,
1,-4,-3,-2,11,2,-3,-4,-3,-2,-4]),w(-1,[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4]),w(-1,[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4]),w(-1,[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4]),w(-1,[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4]),w(-1,[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1])]),"PAM250",E(-1,[w(-1,
[2,-2,0,0,-2,0,0,1,-1,-1,-2,-1,-1,-3,1,1,1,-6,-3,0,0,0,0,-8]),w(-1,[-2,6,0,-1,-4,1,-1,-3,2,-2,-3,3,0,-4,0,0,-1,2,-4,-2,-1,0,-1,-8]),w(-1,[0,0,2,2,-4,1,1,0,2,-2,-3,1,-2,-3,0,1,0,-4,-2,-2,2,1,0,-8]),w(-1,[0,-1,2,4,-5,2,3,1,1,-2,-4,0,-3,-6,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[-2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3,0,-2,-8,0,-2,-4,-5,-3,-8]),w(-1,[0,1,1,2,-5,4,2,-1,3,-2,-2,1,-1,-5,0,-1,-1,-5,-4,-2,1,3,-1,-8]),w(-1,[0,-1,1,3,-5,2,4,0,1,-2,-3,0,-2,-5,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[1,-3,0,1,-3,-1,
0,5,-2,-3,-4,-2,-3,-5,0,1,0,-7,-5,-1,0,0,-1,-8]),w(-1,[-1,2,2,1,-3,3,1,-2,6,-2,-2,0,-2,-2,0,-1,-1,-3,0,-2,1,2,-1,-8]),w(-1,[-1,-2,-2,-2,-2,-2,-2,-3,-2,5,2,-2,2,1,-2,-1,0,-5,-1,4,-2,-2,-1,-8]),w(-1,[-2,-3,-3,-4,-6,-2,-3,-4,-2,2,6,-3,4,2,-3,-3,-2,-2,-1,2,-3,-3,-1,-8]),w(-1,[-1,3,1,0,-5,1,0,-2,0,-2,-3,5,0,-5,-1,0,0,-3,-4,-2,1,0,-1,-8]),w(-1,[-1,0,-2,-3,-5,-1,-2,-3,-2,2,4,0,6,0,-2,-2,-1,-4,-2,2,-2,-2,-1,-8]),w(-1,[-3,-4,-3,-6,-4,-5,-5,-5,-2,1,2,-5,0,9,-5,-3,-3,0,7,-1,-4,-5,-2,-8]),w(-1,[1,0,0,-1,-3,0,
-1,0,0,-2,-3,-1,-2,-5,6,1,0,-6,-5,-1,-1,0,-1,-8]),w(-1,[1,0,1,0,0,-1,0,1,-1,-1,-3,0,-2,-3,1,2,1,-2,-3,-1,0,0,0,-8]),w(-1,[1,-1,0,0,-2,-1,0,0,-1,0,-2,0,-1,-3,0,1,3,-5,-3,0,0,-1,0,-8]),w(-1,[-6,2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4,0,-6,-2,-5,17,0,-6,-5,-6,-4,-8]),w(-1,[-3,-4,-2,-4,0,-4,-4,-5,0,-1,-1,-4,-2,7,-5,-3,-3,0,10,-2,-3,-4,-2,-8]),w(-1,[0,-2,-2,-2,-2,-2,-2,-1,-2,4,2,-2,2,-1,-1,-1,0,-6,-2,4,-2,-2,-1,-8]),w(-1,[0,-1,2,3,-4,1,3,0,1,-2,-3,1,-2,-4,-1,0,0,-5,-3,-2,3,2,-1,-8]),w(-1,[0,0,1,3,-5,3,3,0,
2,-2,-3,0,-2,-5,0,0,-1,-6,-4,-2,2,3,-1,-8]),w(-1,[0,-1,0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1,0,0,-4,-2,-1,-1,-1,-1,-8]),w(-1,[-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,1])]));c$.ssHash=c$.prototype.ssHash=new java.util.Hashtable;jalview.schemes.ResidueProperties.ssHash.put("H",java.awt.Color.magenta);jalview.schemes.ResidueProperties.ssHash.put("E",java.awt.Color.yellow);jalview.schemes.ResidueProperties.ssHash.put("-",java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put(".",
java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put("S",java.awt.Color.cyan);jalview.schemes.ResidueProperties.ssHash.put("T",java.awt.Color.blue);jalview.schemes.ResidueProperties.ssHash.put("G",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("I",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("B",java.awt.Color.yellow);G(c$,"DNA",E(-1,[w(-1,[10,-8,-8,-8,-8,1,1,1,-8,1,1]),w(-1,[-8,10,-8,-8,-8,1,1,-8,1,1,1]),w(-1,[-8,-8,10,-8,-8,1,1,1,-8,1,1]),w(-1,
[-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[1,1,1,1,1,10,0,0,0,1,1]),w(-1,[1,1,1,1,1,0,10,0,0,1,1]),w(-1,[1,-8,1,-8,-8,0,0,10,-8,1,1]),w(-1,[-8,1,-8,1,1,0,0,-8,10,1,1]),w(-1,[1,1,1,1,1,1,1,1,1,10,1]),w(-1,[1,1,1,1,1,1,1,1,1,1,1])]));jalview.schemes.ResidueProperties.scoreMatrices.put("BLOSUM62",new jalview.schemes.ScoreMatrix("BLOSUM62",jalview.schemes.ResidueProperties.BLOSUM62,0));jalview.schemes.ResidueProperties.scoreMatrices.put("PAM250",new jalview.schemes.ScoreMatrix("PAM250",
jalview.schemes.ResidueProperties.PAM250,0));jalview.schemes.ResidueProperties.scoreMatrices.put("DNA",new jalview.schemes.ScoreMatrix("DNA",jalview.schemes.ResidueProperties.DNA,1));c$.pidColours=c$.prototype.pidColours=E(-1,[jalview.schemes.ResidueProperties.midBlue,new java.awt.Color(153,153,255),new java.awt.Color(204,204,255)]);G(c$,"pidThresholds",Q(-1,[80,60,40]));c$.codonHash=c$.prototype.codonHash=new java.util.HashMap;c$.Lys=c$.prototype.Lys=new java.util.ArrayList;c$.Asn=c$.prototype.Asn=
new java.util.ArrayList;c$.Gln=c$.prototype.Gln=new java.util.ArrayList;c$.His=c$.prototype.His=new java.util.ArrayList;c$.Glu=c$.prototype.Glu=new java.util.ArrayList;c$.Asp=c$.prototype.Asp=new java.util.ArrayList;c$.Tyr=c$.prototype.Tyr=new java.util.ArrayList;c$.Thr=c$.prototype.Thr=new java.util.ArrayList;c$.Pro=c$.prototype.Pro=new java.util.ArrayList;c$.Ala=c$.prototype.Ala=new java.util.ArrayList;c$.Ser=c$.prototype.Ser=new java.util.ArrayList;c$.Arg=c$.prototype.Arg=new java.util.ArrayList;
c$.Gly=c$.prototype.Gly=new java.util.ArrayList;c$.Trp=c$.prototype.Trp=new java.util.ArrayList;c$.Cys=c$.prototype.Cys=new java.util.ArrayList;c$.Ile=c$.prototype.Ile=new java.util.ArrayList;c$.Met=c$.prototype.Met=new java.util.ArrayList;c$.Leu=c$.prototype.Leu=new java.util.ArrayList;c$.Val=c$.prototype.Val=new java.util.ArrayList;c$.Phe=c$.prototype.Phe=new java.util.ArrayList;c$.STOP=c$.prototype.STOP=new java.util.ArrayList;G(c$,"START","ATG");jalview.schemes.ResidueProperties.codonHash.put("K",
jalview.schemes.ResidueProperties.Lys);jalview.schemes.ResidueProperties.codonHash.put("N",jalview.schemes.ResidueProperties.Asn);jalview.schemes.ResidueProperties.codonHash.put("Q",jalview.schemes.ResidueProperties.Gln);jalview.schemes.ResidueProperties.codonHash.put("H",jalview.schemes.ResidueProperties.His);jalview.schemes.ResidueProperties.codonHash.put("E",jalview.schemes.ResidueProperties.Glu);jalview.schemes.ResidueProperties.codonHash.put("D",jalview.schemes.ResidueProperties.Asp);jalview.schemes.ResidueProperties.codonHash.put("Y",
jalview.schemes.ResidueProperties.Tyr);jalview.schemes.ResidueProperties.codonHash.put("T",jalview.schemes.ResidueProperties.Thr);jalview.schemes.ResidueProperties.codonHash.put("P",jalview.schemes.ResidueProperties.Pro);jalview.schemes.ResidueProperties.codonHash.put("A",jalview.schemes.ResidueProperties.Ala);jalview.schemes.ResidueProperties.codonHash.put("S",jalview.schemes.ResidueProperties.Ser);jalview.schemes.ResidueProperties.codonHash.put("R",jalview.schemes.ResidueProperties.Arg);jalview.schemes.ResidueProperties.codonHash.put("G",
jalview.schemes.ResidueProperties.Gly);jalview.schemes.ResidueProperties.codonHash.put("W",jalview.schemes.ResidueProperties.Trp);jalview.schemes.ResidueProperties.codonHash.put("C",jalview.schemes.ResidueProperties.Cys);jalview.schemes.ResidueProperties.codonHash.put("I",jalview.schemes.ResidueProperties.Ile);jalview.schemes.ResidueProperties.codonHash.put("M",jalview.schemes.ResidueProperties.Met);jalview.schemes.ResidueProperties.codonHash.put("L",jalview.schemes.ResidueProperties.Leu);jalview.schemes.ResidueProperties.codonHash.put("V",
jalview.schemes.ResidueProperties.Val);jalview.schemes.ResidueProperties.codonHash.put("F",jalview.schemes.ResidueProperties.Phe);jalview.schemes.ResidueProperties.codonHash.put("STOP",jalview.schemes.ResidueProperties.STOP);c$.ambiguityCodes=c$.prototype.ambiguityCodes=new java.util.Hashtable;c$.codonHash2=c$.prototype.codonHash2=new java.util.Hashtable;c$._ambiguityCodes=c$.prototype._ambiguityCodes=new java.util.Hashtable;jalview.schemes.ResidueProperties.ambiguityCodes.put("R",E(-1,["A","G"]));
jalview.schemes.ResidueProperties.ambiguityCodes.put("Y",E(-1,["T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("W",E(-1,["A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("S",E(-1,["G","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("M",E(-1,["A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("K",E(-1,["G","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("H",E(-1,["A","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("B",
E(-1,["G","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("V",E(-1,["G","A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("D",E(-1,["G","A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("N",E(-1,["G","A","T","C"]));jalview.schemes.ResidueProperties.codonHash2.put("AAA","K");jalview.schemes.ResidueProperties.codonHash2.put("AAG","K");jalview.schemes.ResidueProperties.codonHash2.put("AAC","N");jalview.schemes.ResidueProperties.codonHash2.put("AAT","N");jalview.schemes.ResidueProperties.codonHash2.put("CAA",
"Q");jalview.schemes.ResidueProperties.codonHash2.put("CAG","Q");jalview.schemes.ResidueProperties.codonHash2.put("CAC","H");jalview.schemes.ResidueProperties.codonHash2.put("CAT","H");jalview.schemes.ResidueProperties.codonHash2.put("GAA","E");jalview.schemes.ResidueProperties.codonHash2.put("GAG","E");jalview.schemes.ResidueProperties.codonHash2.put("GAC","D");jalview.schemes.ResidueProperties.codonHash2.put("GAT","D");jalview.schemes.ResidueProperties.codonHash2.put("TAC","Y");jalview.schemes.ResidueProperties.codonHash2.put("TAT",
"Y");jalview.schemes.ResidueProperties.codonHash2.put("ACA","T");jalview.schemes.ResidueProperties.codonHash2.put("ACC","T");jalview.schemes.ResidueProperties.codonHash2.put("ACT","T");jalview.schemes.ResidueProperties.codonHash2.put("ACG","T");jalview.schemes.ResidueProperties.codonHash2.put("CCA","P");jalview.schemes.ResidueProperties.codonHash2.put("CCG","P");jalview.schemes.ResidueProperties.codonHash2.put("CCC","P");jalview.schemes.ResidueProperties.codonHash2.put("CCT","P");jalview.schemes.ResidueProperties.codonHash2.put("GCA",
"A");jalview.schemes.ResidueProperties.codonHash2.put("GCG","A");jalview.schemes.ResidueProperties.codonHash2.put("GCC","A");jalview.schemes.ResidueProperties.codonHash2.put("GCT","A");jalview.schemes.ResidueProperties.codonHash2.put("TCA","S");jalview.schemes.ResidueProperties.codonHash2.put("TCG","S");jalview.schemes.ResidueProperties.codonHash2.put("TCC","S");jalview.schemes.ResidueProperties.codonHash2.put("TCT","S");jalview.schemes.ResidueProperties.codonHash2.put("AGC","S");jalview.schemes.ResidueProperties.codonHash2.put("AGT",
"S");jalview.schemes.ResidueProperties.codonHash2.put("AGA","R");jalview.schemes.ResidueProperties.codonHash2.put("AGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGA","R");jalview.schemes.ResidueProperties.codonHash2.put("CGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGC","R");jalview.schemes.ResidueProperties.codonHash2.put("CGT","R");jalview.schemes.ResidueProperties.codonHash2.put("GGA","G");jalview.schemes.ResidueProperties.codonHash2.put("GGG","G");jalview.schemes.ResidueProperties.codonHash2.put("GGC",
"G");jalview.schemes.ResidueProperties.codonHash2.put("GGT","G");jalview.schemes.ResidueProperties.codonHash2.put("TGA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAG","*");jalview.schemes.ResidueProperties.codonHash2.put("TGG","W");jalview.schemes.ResidueProperties.codonHash2.put("TGC","C");jalview.schemes.ResidueProperties.codonHash2.put("TGT","C");jalview.schemes.ResidueProperties.codonHash2.put("ATA","I");jalview.schemes.ResidueProperties.codonHash2.put("ATC",
"I");jalview.schemes.ResidueProperties.codonHash2.put("ATT","I");jalview.schemes.ResidueProperties.codonHash2.put("ATG","M");jalview.schemes.ResidueProperties.codonHash2.put("CTA","L");jalview.schemes.ResidueProperties.codonHash2.put("CTG","L");jalview.schemes.ResidueProperties.codonHash2.put("CTC","L");jalview.schemes.ResidueProperties.codonHash2.put("CTT","L");jalview.schemes.ResidueProperties.codonHash2.put("TTA","L");jalview.schemes.ResidueProperties.codonHash2.put("TTG","L");jalview.schemes.ResidueProperties.codonHash2.put("GTA",
"V");jalview.schemes.ResidueProperties.codonHash2.put("GTG","V");jalview.schemes.ResidueProperties.codonHash2.put("GTC","V");jalview.schemes.ResidueProperties.codonHash2.put("GTT","V");jalview.schemes.ResidueProperties.codonHash2.put("TTC","F");jalview.schemes.ResidueProperties.codonHash2.put("TTT","F");jalview.schemes.ResidueProperties.buildAmbiguityCodonSet();jalview.schemes.ResidueProperties.Lys.add("AAA");jalview.schemes.ResidueProperties.Lys.add("AAG");jalview.schemes.ResidueProperties.Asn.add("AAC");
jalview.schemes.ResidueProperties.Asn.add("AAT");jalview.schemes.ResidueProperties.Gln.add("CAA");jalview.schemes.ResidueProperties.Gln.add("CAG");jalview.schemes.ResidueProperties.His.add("CAC");jalview.schemes.ResidueProperties.His.add("CAT");jalview.schemes.ResidueProperties.Glu.add("GAA");jalview.schemes.ResidueProperties.Glu.add("GAG");jalview.schemes.ResidueProperties.Asp.add("GAC");jalview.schemes.ResidueProperties.Asp.add("GAT");jalview.schemes.ResidueProperties.Tyr.add("TAC");jalview.schemes.ResidueProperties.Tyr.add("TAT");
jalview.schemes.ResidueProperties.Thr.add("ACA");jalview.schemes.ResidueProperties.Thr.add("ACG");jalview.schemes.ResidueProperties.Thr.add("ACC");jalview.schemes.ResidueProperties.Thr.add("ACT");jalview.schemes.ResidueProperties.Pro.add("CCA");jalview.schemes.ResidueProperties.Pro.add("CCG");jalview.schemes.ResidueProperties.Pro.add("CCC");jalview.schemes.ResidueProperties.Pro.add("CCT");jalview.schemes.ResidueProperties.Ala.add("GCA");jalview.schemes.ResidueProperties.Ala.add("GCG");jalview.schemes.ResidueProperties.Ala.add("GCC");
jalview.schemes.ResidueProperties.Ala.add("GCT");jalview.schemes.ResidueProperties.Ser.add("TCA");jalview.schemes.ResidueProperties.Ser.add("TCG");jalview.schemes.ResidueProperties.Ser.add("TCC");jalview.schemes.ResidueProperties.Ser.add("TCT");jalview.schemes.ResidueProperties.Ser.add("AGC");jalview.schemes.ResidueProperties.Ser.add("AGT");jalview.schemes.ResidueProperties.Arg.add("AGA");jalview.schemes.ResidueProperties.Arg.add("AGG");jalview.schemes.ResidueProperties.Arg.add("CGA");jalview.schemes.ResidueProperties.Arg.add("CGG");
jalview.schemes.ResidueProperties.Arg.add("CGC");jalview.schemes.ResidueProperties.Arg.add("CGT");jalview.schemes.ResidueProperties.Gly.add("GGA");jalview.schemes.ResidueProperties.Gly.add("GGG");jalview.schemes.ResidueProperties.Gly.add("GGC");jalview.schemes.ResidueProperties.Gly.add("GGT");jalview.schemes.ResidueProperties.STOP.add("TGA");jalview.schemes.ResidueProperties.STOP.add("TAA");jalview.schemes.ResidueProperties.STOP.add("TAG");jalview.schemes.ResidueProperties.Trp.add("TGG");jalview.schemes.ResidueProperties.Cys.add("TGC");
jalview.schemes.ResidueProperties.Cys.add("TGT");jalview.schemes.ResidueProperties.Ile.add("ATA");jalview.schemes.ResidueProperties.Ile.add("ATC");jalview.schemes.ResidueProperties.Ile.add("ATT");jalview.schemes.ResidueProperties.Met.add("ATG");jalview.schemes.ResidueProperties.Leu.add("CTA");jalview.schemes.ResidueProperties.Leu.add("CTG");jalview.schemes.ResidueProperties.Leu.add("CTC");jalview.schemes.ResidueProperties.Leu.add("CTT");jalview.schemes.ResidueProperties.Leu.add("TTA");jalview.schemes.ResidueProperties.Leu.add("TTG");
jalview.schemes.ResidueProperties.Val.add("GTA");jalview.schemes.ResidueProperties.Val.add("GTG");jalview.schemes.ResidueProperties.Val.add("GTC");jalview.schemes.ResidueProperties.Val.add("GTT");jalview.schemes.ResidueProperties.Phe.add("TTC");jalview.schemes.ResidueProperties.Phe.add("TTT");c$.propHash=c$.prototype.propHash=new java.util.Hashtable;c$.hydrophobic=c$.prototype.hydrophobic=new java.util.Hashtable;c$.polar=c$.prototype.polar=new java.util.Hashtable;c$.small=c$.prototype.small=new java.util.Hashtable;
c$.positive=c$.prototype.positive=new java.util.Hashtable;c$.negative=c$.prototype.negative=new java.util.Hashtable;c$.charged=c$.prototype.charged=new java.util.Hashtable;c$.aromatic=c$.prototype.aromatic=new java.util.Hashtable;c$.aliphatic=c$.prototype.aliphatic=new java.util.Hashtable;c$.tiny=c$.prototype.tiny=new java.util.Hashtable;c$.proline=c$.prototype.proline=new java.util.Hashtable;jalview.schemes.ResidueProperties.hydrophobic.put("I",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("L",
new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("V",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("C",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("A",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("G",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("M",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("F",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("Y",new Integer(1));
jalview.schemes.ResidueProperties.hydrophobic.put("W",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("H",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("K",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("X",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("-",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("*",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("R",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("E",
new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("D",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("N",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("S",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("T",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("P",new Integer(0));jalview.schemes.ResidueProperties.polar.put("Y",new Integer(1));jalview.schemes.ResidueProperties.polar.put("W",
new Integer(1));jalview.schemes.ResidueProperties.polar.put("H",new Integer(1));jalview.schemes.ResidueProperties.polar.put("K",new Integer(1));jalview.schemes.ResidueProperties.polar.put("R",new Integer(1));jalview.schemes.ResidueProperties.polar.put("E",new Integer(1));jalview.schemes.ResidueProperties.polar.put("Q",new Integer(1));jalview.schemes.ResidueProperties.polar.put("D",new Integer(1));jalview.schemes.ResidueProperties.polar.put("N",new Integer(1));jalview.schemes.ResidueProperties.polar.put("S",
new Integer(1));jalview.schemes.ResidueProperties.polar.put("T",new Integer(1));jalview.schemes.ResidueProperties.polar.put("X",new Integer(1));jalview.schemes.ResidueProperties.polar.put("-",new Integer(1));jalview.schemes.ResidueProperties.polar.put("*",new Integer(1));jalview.schemes.ResidueProperties.polar.put("I",new Integer(0));jalview.schemes.ResidueProperties.polar.put("L",new Integer(0));jalview.schemes.ResidueProperties.polar.put("V",new Integer(0));jalview.schemes.ResidueProperties.polar.put("C",
new Integer(0));jalview.schemes.ResidueProperties.polar.put("A",new Integer(0));jalview.schemes.ResidueProperties.polar.put("G",new Integer(0));jalview.schemes.ResidueProperties.polar.put("M",new Integer(0));jalview.schemes.ResidueProperties.polar.put("F",new Integer(0));jalview.schemes.ResidueProperties.polar.put("P",new Integer(0));jalview.schemes.ResidueProperties.small.put("I",new Integer(0));jalview.schemes.ResidueProperties.small.put("L",new Integer(0));jalview.schemes.ResidueProperties.small.put("V",
new Integer(1));jalview.schemes.ResidueProperties.small.put("C",new Integer(1));jalview.schemes.ResidueProperties.small.put("A",new Integer(1));jalview.schemes.ResidueProperties.small.put("G",new Integer(1));jalview.schemes.ResidueProperties.small.put("M",new Integer(0));jalview.schemes.ResidueProperties.small.put("F",new Integer(0));jalview.schemes.ResidueProperties.small.put("Y",new Integer(0));jalview.schemes.ResidueProperties.small.put("W",new Integer(0));jalview.schemes.ResidueProperties.small.put("H",
new Integer(0));jalview.schemes.ResidueProperties.small.put("K",new Integer(0));jalview.schemes.ResidueProperties.small.put("R",new Integer(0));jalview.schemes.ResidueProperties.small.put("E",new Integer(0));jalview.schemes.ResidueProperties.small.put("Q",new Integer(0));jalview.schemes.ResidueProperties.small.put("D",new Integer(1));jalview.schemes.ResidueProperties.small.put("N",new Integer(1));jalview.schemes.ResidueProperties.small.put("S",new Integer(1));jalview.schemes.ResidueProperties.small.put("T",
new Integer(1));jalview.schemes.ResidueProperties.small.put("P",new Integer(1));jalview.schemes.ResidueProperties.small.put("-",new Integer(1));jalview.schemes.ResidueProperties.small.put("*",new Integer(1));jalview.schemes.ResidueProperties.positive.put("I",new Integer(0));jalview.schemes.ResidueProperties.positive.put("L",new Integer(0));jalview.schemes.ResidueProperties.positive.put("V",new Integer(0));jalview.schemes.ResidueProperties.positive.put("C",new Integer(0));jalview.schemes.ResidueProperties.positive.put("A",
new Integer(0));jalview.schemes.ResidueProperties.positive.put("G",new Integer(0));jalview.schemes.ResidueProperties.positive.put("M",new Integer(0));jalview.schemes.ResidueProperties.positive.put("F",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Y",new Integer(0));jalview.schemes.ResidueProperties.positive.put("W",new Integer(0));jalview.schemes.ResidueProperties.positive.put("H",new Integer(1));jalview.schemes.ResidueProperties.positive.put("K",new Integer(1));jalview.schemes.ResidueProperties.positive.put("R",
new Integer(1));jalview.schemes.ResidueProperties.positive.put("E",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Q",new Integer(0));jalview.schemes.ResidueProperties.positive.put("D",new Integer(0));jalview.schemes.ResidueProperties.positive.put("N",new Integer(0));jalview.schemes.ResidueProperties.positive.put("S",new Integer(0));jalview.schemes.ResidueProperties.positive.put("T",new Integer(0));jalview.schemes.ResidueProperties.positive.put("P",new Integer(0));jalview.schemes.ResidueProperties.positive.put("-",
new Integer(1));jalview.schemes.ResidueProperties.positive.put("*",new Integer(1));jalview.schemes.ResidueProperties.negative.put("I",new Integer(0));jalview.schemes.ResidueProperties.negative.put("L",new Integer(0));jalview.schemes.ResidueProperties.negative.put("V",new Integer(0));jalview.schemes.ResidueProperties.negative.put("C",new Integer(0));jalview.schemes.ResidueProperties.negative.put("A",new Integer(0));jalview.schemes.ResidueProperties.negative.put("G",new Integer(0));jalview.schemes.ResidueProperties.negative.put("M",
new Integer(0));jalview.schemes.ResidueProperties.negative.put("F",new Integer(0));jalview.schemes.ResidueProperties.negative.put("Y",new Integer(0));jalview.schemes.ResidueProperties.negative.put("W",new Integer(0));jalview.schemes.ResidueProperties.negative.put("H",new Integer(0));jalview.schemes.ResidueProperties.negative.put("K",new Integer(0));jalview.schemes.ResidueProperties.negative.put("R",new Integer(0));jalview.schemes.ResidueProperties.negative.put("E",new Integer(1));jalview.schemes.ResidueProperties.negative.put("Q",
new Integer(0));jalview.schemes.ResidueProperties.negative.put("D",new Integer(1));jalview.schemes.ResidueProperties.negative.put("N",new Integer(0));jalview.schemes.ResidueProperties.negative.put("S",new Integer(0));jalview.schemes.ResidueProperties.negative.put("T",new Integer(0));jalview.schemes.ResidueProperties.negative.put("P",new Integer(0));jalview.schemes.ResidueProperties.negative.put("-",new Integer(1));jalview.schemes.ResidueProperties.negative.put("*",new Integer(1));jalview.schemes.ResidueProperties.charged.put("I",
new Integer(0));jalview.schemes.ResidueProperties.charged.put("L",new Integer(0));jalview.schemes.ResidueProperties.charged.put("V",new Integer(0));jalview.schemes.ResidueProperties.charged.put("C",new Integer(0));jalview.schemes.ResidueProperties.charged.put("A",new Integer(0));jalview.schemes.ResidueProperties.charged.put("G",new Integer(0));jalview.schemes.ResidueProperties.charged.put("M",new Integer(0));jalview.schemes.ResidueProperties.charged.put("F",new Integer(0));jalview.schemes.ResidueProperties.charged.put("Y",
new Integer(0));jalview.schemes.ResidueProperties.charged.put("W",new Integer(0));jalview.schemes.ResidueProperties.charged.put("H",new Integer(1));jalview.schemes.ResidueProperties.charged.put("K",new Integer(1));jalview.schemes.ResidueProperties.charged.put("R",new Integer(1));jalview.schemes.ResidueProperties.charged.put("E",new Integer(1));jalview.schemes.ResidueProperties.charged.put("Q",new Integer(0));jalview.schemes.ResidueProperties.charged.put("D",new Integer(1));jalview.schemes.ResidueProperties.charged.put("N",
new Integer(0));jalview.schemes.ResidueProperties.charged.put("S",new Integer(0));jalview.schemes.ResidueProperties.charged.put("T",new Integer(0));jalview.schemes.ResidueProperties.charged.put("P",new Integer(0));jalview.schemes.ResidueProperties.charged.put("-",new Integer(1));jalview.schemes.ResidueProperties.charged.put("*",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("I",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("L",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("V",
new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("A",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("F",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("Y",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("W",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("H",
new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("R",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("T",
new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("-",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("I",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("L",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("V",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("A",
new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("F",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Y",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("W",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("H",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("R",
new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("T",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("-",
new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("I",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("L",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("V",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("C",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("A",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("G",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("M",
new Integer(0));jalview.schemes.ResidueProperties.tiny.put("F",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Y",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("W",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("H",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("K",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("R",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("E",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Q",
new Integer(0));jalview.schemes.ResidueProperties.tiny.put("D",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("N",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("S",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("T",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("P",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("-",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("*",new Integer(1));jalview.schemes.ResidueProperties.proline.put("I",
new Integer(0));jalview.schemes.ResidueProperties.proline.put("L",new Integer(0));jalview.schemes.ResidueProperties.proline.put("V",new Integer(0));jalview.schemes.ResidueProperties.proline.put("C",new Integer(0));jalview.schemes.ResidueProperties.proline.put("A",new Integer(0));jalview.schemes.ResidueProperties.proline.put("G",new Integer(0));jalview.schemes.ResidueProperties.proline.put("M",new Integer(0));jalview.schemes.ResidueProperties.proline.put("F",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Y",
new Integer(0));jalview.schemes.ResidueProperties.proline.put("W",new Integer(0));jalview.schemes.ResidueProperties.proline.put("H",new Integer(0));jalview.schemes.ResidueProperties.proline.put("K",new Integer(0));jalview.schemes.ResidueProperties.proline.put("R",new Integer(0));jalview.schemes.ResidueProperties.proline.put("E",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Q",new Integer(0));jalview.schemes.ResidueProperties.proline.put("D",new Integer(0));jalview.schemes.ResidueProperties.proline.put("N",
new Integer(0));jalview.schemes.ResidueProperties.proline.put("S",new Integer(0));jalview.schemes.ResidueProperties.proline.put("T",new Integer(0));jalview.schemes.ResidueProperties.proline.put("P",new Integer(1));jalview.schemes.ResidueProperties.proline.put("-",new Integer(1));jalview.schemes.ResidueProperties.proline.put("*",new Integer(1));jalview.schemes.ResidueProperties.propHash.put("hydrophobic",jalview.schemes.ResidueProperties.hydrophobic);jalview.schemes.ResidueProperties.propHash.put("small",
jalview.schemes.ResidueProperties.small);jalview.schemes.ResidueProperties.propHash.put("positive",jalview.schemes.ResidueProperties.positive);jalview.schemes.ResidueProperties.propHash.put("negative",jalview.schemes.ResidueProperties.negative);jalview.schemes.ResidueProperties.propHash.put("charged",jalview.schemes.ResidueProperties.charged);jalview.schemes.ResidueProperties.propHash.put("aromatic",jalview.schemes.ResidueProperties.aromatic);jalview.schemes.ResidueProperties.propHash.put("aliphatic",
jalview.schemes.ResidueProperties.aliphatic);jalview.schemes.ResidueProperties.propHash.put("tiny",jalview.schemes.ResidueProperties.tiny);jalview.schemes.ResidueProperties.propHash.put("proline",jalview.schemes.ResidueProperties.proline);jalview.schemes.ResidueProperties.propHash.put("polar",jalview.schemes.ResidueProperties.polar);for(var b=w(23,23,0),c=w(23,23,0),f=w(23,23,0),a=0;23>a;a++){for(var l=0,k=0,g=0,e="",e=jalview.schemes.ResidueProperties.aa.length>a?e+jalview.schemes.ResidueProperties.aa[a]:
"-",j=a+1;23>j;j++){var n="",n=jalview.schemes.ResidueProperties.aa.length>j?n+jalview.schemes.ResidueProperties.aa[j]:"-";b[a][j]=0;c[a][j]=0;f[a][j]=0;for(var x=jalview.schemes.ResidueProperties.propHash.keys();x.hasMoreElements();){var u=x.nextElement(),D=jalview.schemes.ResidueProperties.propHash.get(u);null!=D.get(e)&&null!=D.get(n)&&(u=D.get(e).intValue(),D=D.get(n).intValue(),c[a][j]+=u==D&&0<u?2:0,c[j][a]+=u==D&&0<u?2:0,b[a][j]+=u==D?2:0,b[j][a]+=u==D?2:0,f[a][j]+=u==D?1+2*u:0,f[j][a]+=u==
D?1+2*u:0)}l<b[a][j]&&(l=b[a][j]);k<c[a][j]&&(k=c[a][j]);g<f[a][j]&&(g=f[a][j])}b[a][a]=l;c[a][a]=k;f[a][a]=g}jalview.schemes.ResidueProperties.scoreMatrices.put("PID",new jalview.analysis.scoremodels.PIDScoreModel);jalview.schemes.ResidueProperties.scoreMatrices.put("Displayed Features",new jalview.analysis.scoremodels.FeatureScoreModel);G(c$,"toDssp3State",null);jalview.schemes.ResidueProperties.toDssp3State=new java.util.Hashtable;jalview.schemes.ResidueProperties.toDssp3State.put("H","H");jalview.schemes.ResidueProperties.toDssp3State.put("E",
"E");jalview.schemes.ResidueProperties.toDssp3State.put("C"," ");jalview.schemes.ResidueProperties.toDssp3State.put(" "," ");jalview.schemes.ResidueProperties.toDssp3State.put("T"," ");jalview.schemes.ResidueProperties.toDssp3State.put("B","E");jalview.schemes.ResidueProperties.toDssp3State.put("G","H");jalview.schemes.ResidueProperties.toDssp3State.put("I","H");jalview.schemes.ResidueProperties.toDssp3State.put("X"," ");G(c$,"toRNAssState",null,"RNAcloseParen",X(255,!1));jalview.schemes.ResidueProperties.toRNAssState=
new java.util.Hashtable;jalview.schemes.ResidueProperties.toRNAssState.put(")","(");jalview.schemes.ResidueProperties.toRNAssState.put("(","(");jalview.schemes.ResidueProperties.toRNAssState.put("]","[");jalview.schemes.ResidueProperties.toRNAssState.put("[","[");jalview.schemes.ResidueProperties.toRNAssState.put("{","{");jalview.schemes.ResidueProperties.toRNAssState.put("}","{");jalview.schemes.ResidueProperties.toRNAssState.put(">",">");jalview.schemes.ResidueProperties.toRNAssState.put("<",">");
jalview.schemes.ResidueProperties.toRNAssState.put("A","A");jalview.schemes.ResidueProperties.toRNAssState.put("a","A");jalview.schemes.ResidueProperties.toRNAssState.put("B","B");jalview.schemes.ResidueProperties.toRNAssState.put("b","B");jalview.schemes.ResidueProperties.toRNAssState.put("C","C");jalview.schemes.ResidueProperties.toRNAssState.put("c","C");jalview.schemes.ResidueProperties.toRNAssState.put("D","D");jalview.schemes.ResidueProperties.toRNAssState.put("d","D");jalview.schemes.ResidueProperties.toRNAssState.put("E",
"E");jalview.schemes.ResidueProperties.toRNAssState.put("e","E");jalview.schemes.ResidueProperties.toRNAssState.put("F","F");jalview.schemes.ResidueProperties.toRNAssState.put("f","F");jalview.schemes.ResidueProperties.toRNAssState.put("G","G");jalview.schemes.ResidueProperties.toRNAssState.put("g","G");jalview.schemes.ResidueProperties.toRNAssState.put("H","H");jalview.schemes.ResidueProperties.toRNAssState.put("h","H");jalview.schemes.ResidueProperties.toRNAssState.put("I","I");jalview.schemes.ResidueProperties.toRNAssState.put("i",
"I");jalview.schemes.ResidueProperties.toRNAssState.put("J","J");jalview.schemes.ResidueProperties.toRNAssState.put("j","J");jalview.schemes.ResidueProperties.toRNAssState.put("K","K");jalview.schemes.ResidueProperties.toRNAssState.put("k","K");jalview.schemes.ResidueProperties.toRNAssState.put("L","L");jalview.schemes.ResidueProperties.toRNAssState.put("l","L");jalview.schemes.ResidueProperties.toRNAssState.put("M","M");jalview.schemes.ResidueProperties.toRNAssState.put("m","M");jalview.schemes.ResidueProperties.toRNAssState.put("N",
"N");jalview.schemes.ResidueProperties.toRNAssState.put("n","N");jalview.schemes.ResidueProperties.toRNAssState.put("O","O");jalview.schemes.ResidueProperties.toRNAssState.put("o","O");jalview.schemes.ResidueProperties.toRNAssState.put("P","P");jalview.schemes.ResidueProperties.toRNAssState.put("p","P");jalview.schemes.ResidueProperties.toRNAssState.put("Q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("R","R");jalview.schemes.ResidueProperties.toRNAssState.put("r",
"R");jalview.schemes.ResidueProperties.toRNAssState.put("S","S");jalview.schemes.ResidueProperties.toRNAssState.put("s","S");jalview.schemes.ResidueProperties.toRNAssState.put("T","T");jalview.schemes.ResidueProperties.toRNAssState.put("t","T");jalview.schemes.ResidueProperties.toRNAssState.put("U","U");jalview.schemes.ResidueProperties.toRNAssState.put("u","U");jalview.schemes.ResidueProperties.toRNAssState.put("V","V");jalview.schemes.ResidueProperties.toRNAssState.put("v","V");jalview.schemes.ResidueProperties.toRNAssState.put("W",
"W");jalview.schemes.ResidueProperties.toRNAssState.put("w","W");jalview.schemes.ResidueProperties.toRNAssState.put("X","X");jalview.schemes.ResidueProperties.toRNAssState.put("x","X");jalview.schemes.ResidueProperties.toRNAssState.put("Y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("Z","Z");jalview.schemes.ResidueProperties.toRNAssState.put("z","Z");for(a=0;a<jalview.schemes.ResidueProperties.RNAcloseParen.length;a++)jalview.schemes.ResidueProperties.RNAcloseParen[a]=
!1;for(var m,a=jalview.schemes.ResidueProperties.toRNAssState.keySet().iterator();a.hasNext()&&((m=a.next())||1);)jalview.schemes.ResidueProperties.RNAcloseParen[m.charCodeAt(0)]=m.charAt(0)!=jalview.schemes.ResidueProperties.toRNAssState.get(m).charAt(0)});p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI","$.ViewBasedAnalysisI"],"jalview.analysis.scoremodels.FeatureScoreModel",["jalview.util.Comparison","java.util.ArrayList","$.Arrays","$.Hashtable"],function(){c$=s(function(){this.fr=
null;r(this,arguments)},jalview.analysis.scoremodels,"FeatureScoreModel",null,[jalview.api.analysis.ScoreModelI,jalview.api.analysis.ViewBasedAnalysisI]);e(c$,"configureFromAlignmentView",function(a){this.fr=a.cloneFeatureRenderer();return!0},"jalview.api.AlignmentViewPanel");e(c$,"findDistances",function(a){var b=0,c=java.util.Arrays.asList(this.fr.getDisplayedFeatureTypes());null!=c&&(b=c.size());var c=a.getVisibleAlignment(jalview.util.Comparison.GapChars.charAt(0)).getSequencesArray(),f=c.length,
l=a.getWidth();a=Q(f,f,0);if(0==b){for(var d,g=0;g<a.length&&((d=a[g])||1);g++)for(b=0;b<d.length;d[b++]=0);return a}for(d=0;d<l;d++){for(var e=new java.util.ArrayList,b=0;b<f;b++){for(var j=new java.util.Hashtable,n=this.fr.findFeaturesAtRes(c[b],c[b].findPosition(d)).iterator();n.hasNext()&&((g=n.next())||1);)j.put(g.getType(),g);e.add(j)}for(b=0;b<f-1;b++){0==d&&(a[b][b]=0);for(j=b+1;j<f;j++){var n=0,x=e.get(b),u,D=e.get(j);x.size()>D.size()?u=D:(u=x,x=D);for(var m,D=x.keySet().iterator();D.hasNext()&&
((m=D.next())||1);)null!=u.get(m)&&n++;a[b][j]+=x.size()+u.size()-2*n;a[j][b]+=a[b][j]}}}for(b=0;b<f;b++)for(j=b+1;j<f;j++)a[b][j]/=l,a[j][b]=a[b][j];return a},"jalview.datamodel.AlignmentView");e(c$,"getName",function(){return"Sequence Feature Similarity"});e(c$,"isDNA",function(){return!0});e(c$,"isProtein",function(){return!0});e(c$,"toString",function(){return"Score between sequences based on hamming distance between binary vectors marking features displayed at each column"})});p("jalview.api.analysis");
M(jalview.api.analysis,"ScoreModelI");p("jalview.api.analysis");M(jalview.api.analysis,"ViewBasedAnalysisI");p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI"],"jalview.analysis.scoremodels.PIDScoreModel",["jalview.util.Comparison"],function(){c$=B(jalview.analysis.scoremodels,"PIDScoreModel",null,jalview.api.analysis.ScoreModelI);e(c$,"findDistances",function(a){a=a.getSequenceStrings(jalview.util.Comparison.GapChars.charAt(0));for(var b=a.length,c=Q(b,b,0),f=0;f<b-1;f++)for(var l=
f;l<b;l++)l==f?c[f][f]=0:(c[f][l]=100-jalview.util.Comparison.PID(a[f],a[l]),c[l][f]=c[f][l]);return c},"jalview.datamodel.AlignmentView");e(c$,"getName",function(){return"PID"});e(c$,"isDNA",function(){return!0});e(c$,"isProtein",function(){return!0})});p("jalview.schemes");q(["jalview.analysis.scoremodels.PairwiseSeqScoreModel","jalview.api.analysis.ScoreModelI"],"jalview.schemes.ScoreMatrix",["jalview.schemes.ResidueProperties","java.lang.StringBuffer"],function(){c$=s(function(){this.matrix=this.name=
null;this.type=0;r(this,arguments)},jalview.schemes,"ScoreMatrix",jalview.analysis.scoremodels.PairwiseSeqScoreModel,jalview.api.analysis.ScoreModelI);e(c$,"getName",function(){return this.name});m(c$,function(a,b,c){t(this,jalview.schemes.ScoreMatrix,[]);this.matrix=b;this.type=c;this.name=a},"~S,~A,~N");e(c$,"isDNA",function(){return 1==this.type});e(c$,"isProtein",function(){return 0==this.type});e(c$,"getMatrix",function(){return this.matrix});d(c$,"getPairwiseScore",function(a,b){return this.getPairwiseScore(a.charAt(0),
b.charAt(0))},"~S,~S");d(c$,"getPairwiseScore",function(a,b){var c=0;try{var f=0==this.type?jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)]:jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)],l=0==this.type?jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(0)]:jalview.schemes.ResidueProperties.nucleotideIndex[b.charCodeAt(0)],c=this.matrix[f][l]}catch(d){if(!y(d,Exception))throw d;}return c},"~S,~S");e(c$,"toString",function(){return this.outputMatrix(!1)});d(c$,"outputMatrix",
function(a){var b=new StringBuffer,c=0==this.type?jalview.schemes.ResidueProperties.aaIndex:jalview.schemes.ResidueProperties.nucleotideIndex,f=0==this.type?23:10,l=!0;a&&b.append('<table border="1">');for(var d="A";"Z">=d;d=String.fromCharCode(d.charCodeAt(0)+1))if(0<=c[d.charCodeAt(0)]&&c[d.charCodeAt(0)]<f){if(l){b.append(a?"<tr><td></td>":"");for(var g="A";"Z">=g;g=String.fromCharCode(g.charCodeAt(0)+1))0<=c[g.charCodeAt(0)]&&c[g.charCodeAt(0)]<f&&b.append((a?"<td>&nbsp;":"\t")+g+(a?"&nbsp;</td>":
""));l=!1;b.append(a?"</tr>\n":"\n")}a&&b.append("<tr>");b.append((a?"<td>":"")+d+(a?"</td>":""));for(g="A";"Z">=g;g=String.fromCharCode(g.charCodeAt(0)+1))0<=c[g.charCodeAt(0)]&&c[g.charCodeAt(0)]<f&&b.append((a?"<td>":"\t")+this.matrix[c[d.charCodeAt(0)]][c[g.charCodeAt(0)]]+(a?"</td>":""));b.append(a?"</tr>\n":"\n")}a&&b.append("</table>");return b.toString()},"~B")});p("jalview.analysis.scoremodels");q(["jalview.api.analysis.ScoreModelI"],"jalview.analysis.scoremodels.PairwiseSeqScoreModel",["jalview.util.Comparison"],
function(){c$=B(jalview.analysis.scoremodels,"PairwiseSeqScoreModel",null,jalview.api.analysis.ScoreModelI);e(c$,"findDistances",function(a){a=a.getSequenceStrings(jalview.util.Comparison.GapChars.charAt(0));for(var b=a.length,c=Q(b,b,0),f=0,l=a[0].length,d=0;d<b-1;d++)for(var g=d;g<b;g++){for(var e=0,j=0;j<l;j++)try{e+=this.getPairwiseScore(a[d].charAt(j),a[g].charAt(j))}catch(n){if(y(n,Exception))System.err.println("err creating "+this.getName()+" tree"),n.printStackTrace();else throw n;}c[d][g]=
e;e>f&&(f=e)}for(d=0;d<b-1;d++)for(g=d;g<b;g++)c[d][g]=f-c[d][g],c[g][d]=c[d][g];return c},"jalview.datamodel.AlignmentView")});p("jalview.datamodel");q(["jalview.datamodel.ASequence","$.SequenceI","jalview.jsdev.RegExp"],"jalview.datamodel.Sequence","jalview.analysis.AlignSeq jalview.datamodel.AlignmentAnnotation $.DBRefEntry $.DBRefSource $.PDBEntry $.SequenceFeature jalview.schemes.ResidueProperties jalview.util.Comparison $.StringUtils java.lang.StringBuffer java.util.ArrayList $.Vector".split(" "),
function(){c$=s(function(){this.description=this.sequence=this.name=this.datasetSequence=null;this.end=this.start=0;this.annotation=this.rna=this.dbrefs=this.vamsasId=this.pdbIds=null;this.index=-1;this.endrx=this.limitrx=this.sequenceFeatures=null;r(this,arguments)},jalview.datamodel,"Sequence",jalview.datamodel.ASequence,jalview.datamodel.SequenceI);J(c$,function(){this.limitrx=jalview.jsdev.RegExp.newRegex(["[/][0-9]{1,}[-][0-9]{1,}$"]);this.endrx=jalview.jsdev.RegExp.newRegex(["[0-9]{1,}$"])});
m(c$,function(a,b,c,f){t(this,jalview.datamodel.Sequence,[]);this.initSeqAndName(a,b.toCharArray(),c,f)},"~S,~S,~N,~N");m(c$,function(a,b,c,f){t(this,jalview.datamodel.Sequence,[]);this.initSeqAndName(a,b,c,f)},"~S,~A,~N,~N");d(c$,"initSeqAndName",function(a,b,c,f){this.name=a;this.sequence=b;this.start=c;this.end=f;this.parseId();this.checkValidRange()},"~S,~A,~N,~N");d(c$,"parseId",function(){null==this.name&&(System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."),
this.name="");this.limitrx.search(this.name)&&(this.name=this.limitrx.left(),this.endrx.search(this.limitrx.stringMatched()),this.setStart(Integer.parseInt(this.limitrx.stringMatched().substring(1,this.endrx.matchedFrom()-1))),this.setEnd(Integer.parseInt(this.endrx.stringMatched())))});d(c$,"checkValidRange",function(){for(var a=0,b=0;b<this.sequence.length;b++)jalview.util.Comparison.isGap(this.sequence[b])||a++;0<a&&(a+=this.start-1);this.end<a&&(this.end=a)});m(c$,function(a,b){this.construct(a,
b,1,-1)},"~S,~S");m(c$,function(a){this.construct(a,a.getAnnotation())},"jalview.datamodel.SequenceI");m(c$,function(a,b){t(this,jalview.datamodel.Sequence,[]);this.initSeqFrom(a,b)},"jalview.datamodel.SequenceI,~A");d(c$,"initSeqFrom",function(a,b){this.initSeqAndName(a.getName(),a.getSequence(),a.getStart(),a.getEnd());this.description=a.getDescription();if(null!=a.getSequenceFeatures())for(var c=a.getSequenceFeatures(),f=0;f<c.length;f++)this.addSequenceFeature(new jalview.datamodel.SequenceFeature(c[f]));
this.setDatasetSequence(a.getDatasetSequence());if(null==this.datasetSequence&&null!=a.getDBRef()){c=a.getDBRef();for(f=0;f<c.length;f++)this.addDBRef(new jalview.datamodel.DBRefEntry(c[f]))}if(null!=a.getAnnotation()){c=a.getAnnotation();for(f=0;f<c.length;f++)if(null!=c[f]){var l=null==b;if(!l)for(var d=0;!l&&d<b.length;d++)l=b[d]===c[f];l&&(l=new jalview.datamodel.AlignmentAnnotation(c[f]),this.addAlignmentAnnotation(l))}}if(null!=a.getPDBId())for(f=a.getPDBId().elements();f.hasMoreElements();)this.addPDBId(new jalview.datamodel.PDBEntry(f.nextElement()))},
"jalview.datamodel.SequenceI,~A");d(c$,"setSequenceFeatures",function(a){this.sequenceFeatures=a},"~A");e(c$,"addSequenceFeature",function(a){null==this.sequenceFeatures&&(this.sequenceFeatures=[]);for(var b=0;b<this.sequenceFeatures.length;b++)if(this.sequenceFeatures[b].equals(a))return;b=Array(this.sequenceFeatures.length+1);System.arraycopy(this.sequenceFeatures,0,b,0,this.sequenceFeatures.length);b[this.sequenceFeatures.length]=a;this.sequenceFeatures=b},"jalview.datamodel.SequenceFeature");
e(c$,"deleteFeature",function(a){if(null!=this.sequenceFeatures){for(var b=0,b=0;b<this.sequenceFeatures.length&&!this.sequenceFeatures[b].equals(a);b++);if(b!=this.sequenceFeatures.length)if(a=this.sequenceFeatures.length,2>a)this.sequenceFeatures=null;else{var c=Array(a-1);System.arraycopy(this.sequenceFeatures,0,c,0,b);b<a&&System.arraycopy(this.sequenceFeatures,b+1,c,b,this.sequenceFeatures.length-b-1);this.sequenceFeatures=c}}},"jalview.datamodel.SequenceFeature");d(c$,"getSequenceFeatures",
function(){for(var a=this.sequenceFeatures,b=this,c=0;null==a&&null!=b.getDatasetSequence()&&10>c++;)b=b.getDatasetSequence(),a=b.sequenceFeatures;return a});e(c$,"addPDBId",function(a){null==this.pdbIds&&(this.pdbIds=new java.util.Vector);this.pdbIds.contains(a)?jalview.datamodel.Sequence.updatePDBEntry(this.pdbIds.get(this.pdbIds.indexOf(a)),a):this.pdbIds.addElement(a)},"jalview.datamodel.PDBEntry");c$.updatePDBEntry=d(c$,"updatePDBEntry",function(a,b){null!=b.getFile()&&a.setFile(b.getFile())},
"jalview.datamodel.PDBEntry,jalview.datamodel.PDBEntry");d(c$,"setPDBId",function(a){this.pdbIds=a},"java.util.Vector");d(c$,"getPDBId",function(){return this.pdbIds});e(c$,"getDisplayId",function(a){var b=new StringBuffer(this.name);a&&b.append("/"+this.start+"-"+this.end);return b.toString()},"~B");e(c$,"setName",function(a){this.name=a;this.parseId()},"~S");d(c$,"getName",function(){return this.name});e(c$,"setStart",function(a){this.start=a},"~N");d(c$,"getStart",function(){return this.start});
e(c$,"setEnd",function(a){this.end=a},"~N");d(c$,"getEnd",function(){return this.end});e(c$,"getLength",function(){return this.sequence.length});d(c$,"setSequence",function(a){this.sequence=a.toCharArray();this.checkValidRange()},"~S");d(c$,"getSequenceAsString",function(){return String.instantialize(this.sequence)});d(c$,"getSequenceAsString",function(a,b){return String.instantialize(this.getSequence(a,b))},"~N,~N");d(c$,"getSequence",function(){return this.sequence});d(c$,"getSequence",function(a,
b){0>a&&(a=0);if(a>=this.sequence.length)return N(0,"\x00");b>=this.sequence.length&&(b=this.sequence.length);var c=N(b-a,"\x00");System.arraycopy(this.sequence,a,c,0,b-a);return c},"~N,~N");e(c$,"getSubSequence",function(a,b){0>a&&(a=0);var c=this.getSequence(a,b);if(0==c.length)return null;var f=this.findPosition(a),l=this.findPosition(b)-1,c=new jalview.datamodel.Sequence(this.getName(),c,f,l);c.setDescription(this.description);null!=this.datasetSequence?c.setDatasetSequence(this.datasetSequence):
c.setDatasetSequence(this);return c},"~N,~N");e(c$,"getCharAt",function(a){return a<this.sequence.length?this.sequence[a]:" "},"~N");d(c$,"setDescription",function(a){this.description=a},"~S");d(c$,"getDescription",function(){return this.description});e(c$,"findIndex",function(a){for(var b=this.start,c=0;c<this.sequence.length&&b<=this.end&&b<=a;)jalview.util.Comparison.isGap(this.sequence[c])||b++,c++;return b==this.end&&b<a?this.end+1:c},"~N");e(c$,"findPosition",function(a){for(var b=0,c=this.start,
f=this.sequence.length;b<a&&b<f;)jalview.util.Comparison.isGap(this.sequence[b])||c++,b++;return c},"~N");e(c$,"gapMap",function(){for(var a=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(this.sequence)),a=w(a.length,0),b=0,c=0;b<this.sequence.length;)jalview.util.Comparison.isGap(this.sequence[b])||(a[c++]=b),b++;return a});e(c$,"findPositionMap",function(){for(var a=w(this.sequence.length,0),b=0,c=this.start,f=this.sequence.length;b<f;)a[b]=c,jalview.util.Comparison.isGap(this.sequence[b])||
c++,b++;return a});e(c$,"getInsertions",function(){for(var a=new java.util.ArrayList,b=-1,c=0,f=this.sequence.length;c<f;)jalview.util.Comparison.isGap(this.sequence[c])?-1==b&&(b=c):-1!=b&&(a.add(w(-1,[b,c-1])),b=-1),c++;-1!=b&&a.add(w(-1,[b,c-1]));return a});e(c$,"deleteChars",function(a,b){var c=this.start,f=this.end;if(!(a>=this.sequence.length||0>a)){for(var l=jalview.util.StringUtils.deleteChars(this.sequence,a,b),d=!1,g=-1,e=-1,j=!1,n=!1,x=a;x<b;x++)if(23!=jalview.schemes.ResidueProperties.aaIndex[this.sequence[x].charCodeAt(0)])if(d)f--;
else if(n||(e=this.findIndex(this.start)-1,n=!0),e==x){c=this.findPosition(b);break}else if(j||(g=this.findIndex(this.end)-1,j=!0),g<b){f=this.findPosition(a-1);break}else d=!0,f--;d&&null!=this.datasetSequence&&(d=new jalview.datamodel.Sequence(this.datasetSequence),d.deleteChars(a,b),this.datasetSequence=d);this.start=c;this.end=f;this.sequence=l}},"~N,~N");d(c$,"insertCharAt",function(a,b,c){var f=N(this.sequence.length+b,"\x00");a>=this.sequence.length?(System.arraycopy(this.sequence,0,f,0,this.sequence.length),
a=this.sequence.length):System.arraycopy(this.sequence,0,f,0,a);for(var l=a;0<b;)f[l++]=c,b--;a<this.sequence.length&&System.arraycopy(this.sequence,a,f,l,this.sequence.length-a);this.sequence=f},"~N,~N,~S");d(c$,"insertCharAt",function(a,b){this.insertCharAt(a,1,b)},"~N,~S");e(c$,"getVamsasId",function(){return this.vamsasId});e(c$,"setVamsasId",function(a){this.vamsasId=a},"~S");d(c$,"setDBRef",function(a){this.dbrefs=a},"~A");d(c$,"getDBRef",function(){return null==this.dbrefs&&null!=this.datasetSequence&&
this!==this.datasetSequence?this.datasetSequence.getDBRef():this.dbrefs});e(c$,"addDBRef",function(a){null==this.dbrefs&&(this.dbrefs=[]);var b,c=this.dbrefs.length;for(b=0;b<c;b++)if(this.dbrefs[b].equalRef(a)){null!=a.getMap()&&null==this.dbrefs[b].getMap()&&(this.dbrefs[b]=a);return}b=Array(c+1);System.arraycopy(this.dbrefs,0,b,0,c);b[b.length-1]=a;this.dbrefs=b},"jalview.datamodel.DBRefEntry");d(c$,"setDatasetSequence",function(a){this.datasetSequence=a},"jalview.datamodel.SequenceI");d(c$,"getDatasetSequence",
function(){return this.datasetSequence});d(c$,"getAnnotation",function(){return null==this.annotation?null:this.annotation.toArray(Array(this.annotation.size()))});e(c$,"hasAnnotation",function(a){return null==this.annotation?!1:this.annotation.contains(a)},"jalview.datamodel.AlignmentAnnotation");d(c$,"addAlignmentAnnotation",function(a){null==this.annotation&&(this.annotation=new java.util.Vector);this.annotation.contains(a)||this.annotation.addElement(a);a.setSequenceRef(this)},"jalview.datamodel.AlignmentAnnotation");
e(c$,"removeAlignmentAnnotation",function(a){null!=this.annotation&&(this.annotation.removeElement(a),0==this.annotation.size()&&(this.annotation=null))},"jalview.datamodel.AlignmentAnnotation");d(c$,"isValidDatasetSequence",function(){if(null!=this.datasetSequence)return!1;for(var a=0;a<this.sequence.length;a++)if(jalview.util.Comparison.isGap(this.sequence[a]))return!1;return!0});e(c$,"deriveSequence",function(){var a=new jalview.datamodel.Sequence(this);null!=this.datasetSequence?a.setDatasetSequence(this.datasetSequence):
this.isValidDatasetSequence()?a.setDatasetSequence(this):(a.setSequence(jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(this.sequence))),this.setDatasetSequence(a),a.setSequenceFeatures(this.getSequenceFeatures()),a=this);return a});e(c$,"createDatasetSequence",function(){if(null==this.datasetSequence&&(this.datasetSequence=new jalview.datamodel.Sequence(this.getName(),jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,this.getSequenceAsString()),
this.getStart(),this.getEnd()),this.datasetSequence.setSequenceFeatures(this.getSequenceFeatures()),this.datasetSequence.setDescription(this.getDescription()),this.setSequenceFeatures(null),this.datasetSequence.setDBRef(this.getDBRef()),this.setDBRef(null),this.datasetSequence.setPDBId(this.getPDBId()),this.setPDBId(null),this.datasetSequence.updatePDBIds(),null!=this.annotation))for(var a,b=this.annotation.iterator();b.hasNext()&&((a=b.next())||1);){var c=new jalview.datamodel.AlignmentAnnotation(a);
c.sequenceRef=this.datasetSequence;c.adjustForAlignment();this.datasetSequence.addAlignmentAnnotation(c)}return this.datasetSequence});e(c$,"setAlignmentAnnotation",function(a){null!=this.annotation&&this.annotation.removeAllElements();if(null!=a)for(var b=0;b<a.length;b++)null!=a[b]&&this.addAlignmentAnnotation(a[b])},"~A");d(c$,"getAnnotation",function(a){if(null==this.annotation||0==this.annotation.size())return null;for(var b=new java.util.Vector,c=this.annotation.elements();c.hasMoreElements();){var f=
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else if(a.dontMatch&&"1"<=a.c&&"9">=a.c)c=a.c.charCodeAt(0)-48,f=new com.stevesoft.pat.StrPos(a),f.inc(),!f.dontMatch&&("0"<=f.c&&"9">=f.c)&&(c=10*c+(f.c.charCodeAt(0)-48),a.inc()),this.add(new com.stevesoft.pat.BackMatch(c));else if(a.dontMatch&&"b"==a.c)this.add(new com.stevesoft.pat.Boundary);else if(a.match("\b"))this.add(new com.stevesoft.pat.Boundary);else if(a.match("$"))this.add(new com.stevesoft.pat.End(!0));else if(a.dontMatch&&"Z"==a.c)this.add(new com.stevesoft.pat.End(!1));else if(a.match("."))this.add(new com.stevesoft.pat.Any);
else if(a.incMatch("(??")){c=new StringBuffer;for(f=new StringBuffer;!a.match(")")&&!a.match(":");)c.append(a.c),a.inc();if(a.incMatch(":"))for(;!a.match(")");)f.append(a.c),a.inc();var l=c.toString();v(com.stevesoft.pat.Regex.validators.get(l),String)?(c=com.stevesoft.pat.Regex.validators.get(l),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c,l),this.add(f.thePattern)):(c=new com.stevesoft.pat.Custom(c.toString()),null!=c.v&&(l=c.v.arg(f.toString()),
null!=l&&(l.argsave=f.toString(),f=c.v.pattern,c.v=l,l.pattern=f),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c.v.pattern,l),c.sub=f.thePattern,c.sub.add(new com.stevesoft.pat.CustomEndpoint(c)),c.sub.setParent(c),this.add(c)))}else if(a.match("(")){b.parenLevel++;f=new com.stevesoft.pat.Regex(null,"");a.inc();if(a.incMatch("?:"))f.or=new com.stevesoft.pat.Or;else if(a.incMatch("?="))f.or=new com.stevesoft.pat.lookAhead(!1);else if(a.incMatch("?!"))f.or=
new com.stevesoft.pat.lookAhead(!0);else if(a.match("?")){a.inc();do"i"==a.c&&(b.ignoreCase=!0),"Q"==a.c&&(b.dontMatchInQuotes=!0),"o"==a.c&&(b.optimizeMe=!0),"g"==a.c&&(b.gFlag=!0),"s"==a.c&&(b.sFlag=!0),"m"==a.c&&(b.mFlag=!0),a.inc();while(!a.match(")")&&!a.$eos);f=null;b.parenLevel--;a.$eos&&com.stevesoft.pat.RegSyntaxError.endItAll("Unclosed ()")}else f.or=b.noBackRefs?new com.stevesoft.pat.Or:new com.stevesoft.pat.OrMark(b.val++);null!=f&&this.add(f._compileSP(a,b))}else if(a.match("^"))this.add(new com.stevesoft.pat.Start(!0));
else if(a.dontMatch&&"A"==a.c)this.add(new com.stevesoft.pat.Start(!1));else if(a.match("*"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInf);else if(a.match("+"))this.addMulti(new com.stevesoft.pat.patInt(1),new com.stevesoft.pat.patInf);else if(a.match("?"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInt(1));else if(a.match("{")){f=!1;c=new com.stevesoft.pat.StrPos(a);a.inc();var l=a.getPatInt(),d=null;a.match("}")?d=l:(a.match(",")||(f=!0),
a.inc(),d=a.match("}")?new com.stevesoft.pat.patInf:a.getPatInt());if(null==l||null==d)f=!0;f?(a.dup(c),this.add(new com.stevesoft.pat.oneChar(a.c))):this.addMulti(l,d)}else a.escMatch("x")&&this.next2Hex(a)?(a.inc(),f=this.getHexDigit(a),a.inc(),f=16*f+this.getHexDigit(a),this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(f)))):a.escMatch("c")?(a.inc(),a.c.charCodeAt(0)<com.stevesoft.pat.Ctrl.cmap.length?this.add(new com.stevesoft.pat.oneChar(com.stevesoft.pat.Ctrl.cmap[a.c.charCodeAt(0)])):
this.add(new com.stevesoft.pat.oneChar(a.c))):a.escMatch("f")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(12))):a.escMatch("a")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(7))):a.escMatch("t")?this.add(new com.stevesoft.pat.oneChar("\t")):a.escMatch("n")?this.add(new com.stevesoft.pat.oneChar("\n")):a.escMatch("r")?this.add(new com.stevesoft.pat.oneChar("\r")):a.escMatch("b")?this.add(new com.stevesoft.pat.oneChar("\b")):a.escMatch("e")?this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(27))):
(this.add(new com.stevesoft.pat.oneChar(a.c)),a.match(")")&&com.stevesoft.pat.RegSyntaxError.endItAll("Unmatched right paren in pattern"))},"com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings");d(c$,"_compile",function(a,b){this.minMatch=null;this.sFlag=this.mFlag=this.ignoreCase=this.gFlag=!1;var c=new com.stevesoft.pat.StrPos(a,0);this.thePattern=this._compileSP(c,b);this.pt.marks=null;return this.thePattern},"~S,com.stevesoft.pat.Rthings");d(c$,"_compileSP",function(a,b){for(;!(a.$eos||null!=this.or&&
a.match(")"));)this.compileSP(a,b),a.inc();a.match(")")?b.parenLevel--:a.$eos&&0!=b.parenLevel&&com.stevesoft.pat.RegSyntaxError.endItAll("Unclosed Parenthesis! lvl="+b.parenLevel);return null!=this.or?(null==this.p&&(this.p=new com.stevesoft.pat.NullPattern),this.or.addOr(this.p),this.or):null==this.p?new com.stevesoft.pat.NullPattern:this.p},"com.stevesoft.pat.StrPos,com.stevesoft.pat.Rthings");d(c$,"addMulti",function(a,b){var c,f;for(c=this.p;null!=c&&null!=c.next;c=c.next);if(null==c||c===this.p)f=
null;else for(f=this.p;f.next!==c;f=f.next);if(v(c,com.stevesoft.pat.Multi)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else if(v(c,com.stevesoft.pat.FastMulti)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else if(v(c,com.stevesoft.pat.DotMulti)&&0==a.intValue()&&1==b.intValue())c.matchFewest=!0;else{if(v(c,com.stevesoft.pat.Multi)||v(c,com.stevesoft.pat.DotMulti)||v(c,com.stevesoft.pat.FastMulti))throw new com.stevesoft.pat.RegSyntax("Syntax error.");null==f?this.p=com.stevesoft.pat.Regex.mkMulti(a,
b,this.p):f.next=com.stevesoft.pat.Regex.mkMulti(a,b,c)}},"com.stevesoft.pat.patInt,com.stevesoft.pat.patInt");c$.mkMulti=d(c$,"mkMulti",function(a,b,c){return v(c,com.stevesoft.pat.Any)&&null==c.next?new com.stevesoft.pat.DotMulti(a,b):com.stevesoft.pat.RegOpt.safe4fm(c)?new com.stevesoft.pat.FastMulti(a,b,c):new com.stevesoft.pat.Multi(a,b,c)},"com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern");d(c$,"matchBracket",function(a){var b;a.match("^")?(b=new com.stevesoft.pat.Bracket(!0),
a.inc()):b=new com.stevesoft.pat.Bracket(!1);for(a.match("]")&&com.stevesoft.pat.RegSyntaxError.endItAll("Unmatched []");!a.$eos&&!a.match("]");){var c=new com.stevesoft.pat.StrPos(a);c.inc();var f=new com.stevesoft.pat.StrPos(c);f.inc();if(c.match("-")&&!f.match("]"))c=new com.stevesoft.pat.StrPos(c),c.inc(),c.$eos||b.addOr(new com.stevesoft.pat.Range(a.c,c.c)),a.inc(),a.inc();else if(a.escMatch("Q"))for(a.inc();!a.escMatch("E");)b.addOr(new com.stevesoft.pat.oneChar(a.c)),a.inc();else a.escMatch("d")?
b.addOr(new com.stevesoft.pat.Range("0","9")):a.escMatch("s")?(b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(32))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(8),String.fromCharCode(10))),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(13)))):a.escMatch("w")?(b.addOr(new com.stevesoft.pat.Range("a","z")),b.addOr(new com.stevesoft.pat.Range("A","Z")),b.addOr(new com.stevesoft.pat.Range("0","9")),b.addOr(new com.stevesoft.pat.oneChar("_"))):a.escMatch("D")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),
String.fromCharCode(47))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(58),String.fromCharCode(65535)))):a.escMatch("S")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),String.fromCharCode(7))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(11),String.fromCharCode(12))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(14),String.fromCharCode(31))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(33),String.fromCharCode(65535)))):a.escMatch("W")?(b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(0),
String.fromCharCode(64))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(91),String.fromCharCode(94))),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(96))),b.addOr(new com.stevesoft.pat.Range(String.fromCharCode(123),String.fromCharCode(65535)))):a.escMatch("x")&&this.next2Hex(a)?(a.inc(),c=this.getHexDigit(a),a.inc(),c=16*c+this.getHexDigit(a),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(c)))):a.escMatch("a")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(7))):
a.escMatch("f")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(12))):a.escMatch("e")?b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(27))):a.escMatch("n")?b.addOr(new com.stevesoft.pat.oneChar("\n")):a.escMatch("t")?b.addOr(new com.stevesoft.pat.oneChar("\t")):a.escMatch("r")?b.addOr(new com.stevesoft.pat.oneChar("\r")):a.escMatch("c")?(a.inc(),a.c.charCodeAt(0)<com.stevesoft.pat.Ctrl.cmap.length?b.addOr(new com.stevesoft.pat.oneChar(com.stevesoft.pat.Ctrl.cmap[a.c.charCodeAt(0)])):
b.addOr(new com.stevesoft.pat.oneChar(a.c))):this.isOctalString(a)?(c=a.c.charCodeAt(0)-48,a.inc(),c=8*c+a.c.charCodeAt(0)-48,f=new com.stevesoft.pat.StrPos(a),f.inc(),this.isOctalDigit(f,!1)&&(a.inc(),c=8*c+a.c.charCodeAt(0)-48),b.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(c)))):b.addOr(new com.stevesoft.pat.oneChar(a.c));a.inc()}return b},"com.stevesoft.pat.StrPos");e(c$,"toString",function(){var a=new StringBuffer;"\\"!=this.esc&&(a.append("(?e="),a.append(this.esc),a.append(")"));
if(this.gFlag||this.mFlag||!com.stevesoft.pat.Regex.dotDoesntMatchCR||this.sFlag||this.ignoreCase||this.dontMatchInQuotes||this.optimized())a.append("(?"),this.ignoreCase&&a.append("i"),this.mFlag&&a.append("m"),(this.sFlag||!com.stevesoft.pat.Regex.dotDoesntMatchCR)&&a.append("s"),this.dontMatchInQuotes&&a.append("Q"),this.optimized()&&a.append("o"),this.gFlag&&a.append("g"),a.append(")");var b=this.thePattern.toString();"\\"!=this.esc&&(b=com.stevesoft.pat.Regex.reEscape(b,"\\",this.esc));a.append(b);
return a.toString()});c$.reEscape=d(c$,"reEscape",function(a,b,c){if(b==c)return a;var f,l=new StringBuffer;for(f=0;f<a.length;f++)a.charAt(f)==b&&f+1<a.length?(a.charAt(f+1)==b?l.append(b):(l.append(c),l.append(a.charAt(f+1))),f++):a.charAt(f)==c?(l.append(c),l.append(c)):l.append(a.charAt(f));return l.toString()},"~S,~S,~S");d(c$,"accept",function(a,b){return this.search(b)},"java.io.File,~S");c$.version=d(c$,"version",function(){return"lgpl release 1.5.3"});d(c$,"optimize",function(){this.optimized()||
null==this.thePattern||(this.minMatch=new com.stevesoft.pat.patInt(0),this.thePattern=com.stevesoft.pat.RegOpt.opt(this.thePattern,this.ignoreCase,this.dontMatchInQuotes),this.skipper=com.stevesoft.pat.Skip.findSkipRegex(this))});d(c$,"optimized",function(){return null!=this.minMatch});c$.perlCode=d(c$,"perlCode",function(a){return com.stevesoft.pat.parsePerl.parse(a)},"~S");d(c$,"isLiteral",function(){for(var a=this.thePattern;null!=a;){if(!v(a,com.stevesoft.pat.oneChar)&&!v(a,com.stevesoft.pat.Skipped))return!1;
a=a.next}return!0});d(c$,"countMinChars",function(){return this.thePattern.countMinChars()});d(c$,"countMaxChars",function(){return this.thePattern.countMaxChars()});d(c$,"isHexDigit",function(a){return!a.$eos&&!a.dontMatch&&("0"<=a.c&&"9">=a.c||"a"<=a.c&&"f">=a.c||"A"<=a.c&&"F">=a.c)},"com.stevesoft.pat.StrPos");d(c$,"isOctalDigit",function(a,b){return!a.$eos&&!(new Boolean(b^a.dontMatch)).valueOf()&&"0"<=a.c&&"7">=a.c},"com.stevesoft.pat.StrPos,~B");d(c$,"getHexDigit",function(a){return"0"<=a.c&&
"9">=a.c?a.c.charCodeAt(0)-48:"a"<=a.c&&"f">=a.c?a.c.charCodeAt(0)-97+10:a.c.charCodeAt(0)-65+10},"com.stevesoft.pat.StrPos");d(c$,"next2Hex",function(a){a=new com.stevesoft.pat.StrPos(a);a.inc();if(!this.isHexDigit(a))return!1;a.inc();return!this.isHexDigit(a)?!1:!0},"com.stevesoft.pat.StrPos");d(c$,"isOctalString",function(a){if(!this.isOctalDigit(a,!0))return!1;a=new com.stevesoft.pat.StrPos(a);a.inc();return!this.isOctalDigit(a,!1)?!1:!0},"com.stevesoft.pat.StrPos");G(c$,"BackRefOffset",1);c$.none=
c$.prototype.none=new com.stevesoft.pat.NoPattern;c$.validators=c$.prototype.validators=new java.util.Hashtable;com.stevesoft.pat.Regex.defineV("p","(?>1)",new com.stevesoft.pat.UnicodePunct);com.stevesoft.pat.Regex.defineV("P","(?>1)",new com.stevesoft.pat.NUnicodePunct);com.stevesoft.pat.Regex.defineV("s","(?>1)",new com.stevesoft.pat.UnicodeWhite);com.stevesoft.pat.Regex.defineV("S","(?>1)",new com.stevesoft.pat.NUnicodeWhite);com.stevesoft.pat.Regex.defineV("w","(?>1)",new com.stevesoft.pat.UnicodeW);
com.stevesoft.pat.Regex.defineV("W","(?>1)",new com.stevesoft.pat.NUnicodeW);com.stevesoft.pat.Regex.defineV("d","(?>1)",new com.stevesoft.pat.UnicodeDigit);com.stevesoft.pat.Regex.defineV("D","(?>1)",new com.stevesoft.pat.NUnicodeDigit);com.stevesoft.pat.Regex.defineV("m","(?>1)",new com.stevesoft.pat.UnicodeMath);com.stevesoft.pat.Regex.defineV("M","(?>1)",new com.stevesoft.pat.NUnicodeMath);com.stevesoft.pat.Regex.defineV("c","(?>1)",new com.stevesoft.pat.UnicodeCurrency);com.stevesoft.pat.Regex.defineV("C",
"(?>1)",new com.stevesoft.pat.NUnicodeCurrency);com.stevesoft.pat.Regex.defineV("a","(?>1)",new com.stevesoft.pat.UnicodeAlpha);com.stevesoft.pat.Regex.defineV("A","(?>1)",new com.stevesoft.pat.NUnicodeAlpha);com.stevesoft.pat.Regex.defineV("uc","(?>1)",new com.stevesoft.pat.UnicodeUpper);com.stevesoft.pat.Regex.defineV("lc","(?>1)",new com.stevesoft.pat.UnicodeLower);G(c$,"defaultMFlag",!1,"dotDoesntMatchCR",!0,"lasts",null,"lastbs",null,"back_slash","\\")});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.RegRes",
["java.lang.StringBuffer"],function(){c$=s(function(){this.marks=null;this.didMatch_=!1;this.src=null;this.numSubs_=this.matchFrom_=this.charsMatched_=0;r(this,arguments)},com.stevesoft.pat,"RegRes");d(c$,"getString",function(){return this.src.toString()});d(c$,"getStringLike",function(){return this.src});e(c$,"toString",function(){var a=new StringBuffer;a.append("match="+this.matchedFrom()+":"+this.charsMatched());if(!this.didMatch())return a.toString();for(var b=0;b<this.numSubs();b++){var c=b+
1;a.append(" sub("+c+")="+this.matchedFromI(c)+":"+this.charsMatchedI(c))}return a.toString()});d(c$,"copyOutOf",function(a){if(null==a.marks)this.marks=null;else try{this.marks=w(a.marks.length,0);for(var b=0;b<this.marks.length;b++)this.marks[b]=a.marks[b]}catch(c){}this.didMatch_=a.didMatch_;this.src=a.src;this.charsMatched_=a.charsMatched_;this.matchFrom_=a.matchFrom_;this.numSubs_=a.numSubs_},"com.stevesoft.pat.RegRes");d(c$,"equals",function(a){if(this.charsMatched_!=a.charsMatched_||(this.matchFrom_!=
a.matchFrom_||this.didMatch_!=a.didMatch_||this.numSubs_!=a.numSubs_||!this.src.unwrap().equals(a.src.unwrap()))||null==this.marks&&null!=a.marks||null!=this.marks&&null==a.marks)return!1;for(var b=1;b<=this.numSubs_;b++)if(this.matchedFromI(b)!=a.matchedFromI(b)||this.charsMatchedI(b)!=a.charsMatchedI(b))return!1;return!0},"com.stevesoft.pat.RegRes");d(c$,"stringMatched",function(){var a=this.matchedFrom(),b=this.charsMatched();return!this.didMatch_||0>a||0>b?null:this.src.substring(a,a+b)});d(c$,
"matchedFromI",function(a){return null==this.marks||a>this.numSubs_?-1:this.marks[a]},"~N");d(c$,"charsMatchedI",function(a){return null==this.marks||a>this.numSubs_||!this.didMatch_?-1:0>this.matchedFromI(a)?-1:this.marks[a+this.numSubs_]-this.matchedFromI(a)},"~N");d(c$,"matchedToI",function(a){return null==this.marks||a>this.numSubs_||!this.didMatch_?-1:this.marks[a+this.numSubs_]},"~N");d(c$,"stringMatchedI",function(a){var b=this.matchedFromI(a);a=this.charsMatchedI(a);return!this.didMatch_||
0>b||0>a?null:this.src.substring(b,b+a)},"~N");d(c$,"left",function(){var a=this.matchedFrom();return!this.didMatch_||0>a?null:this.src.substring(0,a)});d(c$,"leftI",function(a){a=this.matchedFromI(a);return!this.didMatch_||0>a?null:this.src.substring(0,a)},"~N");d(c$,"right",function(){var a=this.matchedFrom(),b=this.charsMatched();return!this.didMatch_||0>a||0>b?null:this.src.substring(a+b,this.src.length())});d(c$,"rightI",function(a){var b=this.matchedFromI(a);a=this.charsMatchedI(a);return!this.didMatch_||
0>b||0>a?null:this.src.substring(b+a,this.src.length())},"~N");d(c$,"matchedFrom",function(){return!this.didMatch_?-1:this.matchFrom_});d(c$,"charsMatched",function(){return!this.didMatch_||0>this.matchFrom_?-1:this.charsMatched_});d(c$,"matchedTo",function(){return!this.didMatch_?-1:this.matchFrom_+this.charsMatched_});d(c$,"numSubs",function(){return this.numSubs_});d(c$,"didMatch",function(){return this.didMatch_});d(c$,"matchFrom",function(){return this.matchedFrom()});d(c$,"substring",function(){return this.stringMatched()});
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String.fromCharCode(1056);a[4109]=String.fromCharCode(32768);a[4110]=String.fromCharCode(65535);a[4111]=String.fromCharCode(65407);a[4112]=String.fromCharCode(43690);a[4113]=String.fromCharCode(43690);a[4114]=String.fromCharCode(43690);a[4115]=String.fromCharCode(21930);a[4116]=String.fromCharCode(43861);a[4117]=String.fromCharCode(43690);a[4118]=String.fromCharCode(43690);a[4119]=String.fromCharCode(54442);a[4120]=String.fromCharCode(12585);a[4121]=String.fromCharCode(20004);a[4122]=String.fromCharCode(10538);
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a[4155]=String.fromCharCode(65535);a[4156]=String.fromCharCode(32767);a[4157]="c";a[4158]=String.fromCharCode(168)});c$.title_f=d(c$,"title_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.title=new com.stevesoft.pat.Bits(a);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[13]=String.fromCharCode(32768);a[14]=String.fromCharCode(65535);a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(43690);a[17]=String.fromCharCode(43690);
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a[37]=String.fromCharCode(65535);a[38]=String.fromCharCode(65535);a[39]=String.fromCharCode(65535);a[40]=String.fromCharCode(65535);a[41]=String.fromCharCode(65535);a[42]=String.fromCharCode(511);a[57]=String.fromCharCode(1);a[58]=String.fromCharCode(61440);a[59]=String.fromCharCode(65535);a[60]=String.fromCharCode(32767);a[61]="c";a[62]=String.fromCharCode(43688);a[63]=String.fromCharCode(7);a[67]=String.fromCharCode(65535);a[68]=String.fromCharCode(65535);a[69]=String.fromCharCode(57342);a[70]=
String.fromCharCode(43690);a[71]=String.fromCharCode(43690);a[72]=String.fromCharCode(2);a[73]=String.fromCharCode(43690);a[74]=String.fromCharCode(43690);a[75]=String.fromCharCode(43690);a[76]=String.fromCharCode(4372);a[77]=String.fromCharCode(43690);a[78]=String.fromCharCode(35498);a[79]=String.fromCharCode(554);a[86]=String.fromCharCode(65534);a[87]=String.fromCharCode(65535);a[88]=String.fromCharCode(255);a[269]=String.fromCharCode(65535);a[270]=String.fromCharCode(65535);a[271]=String.fromCharCode(127);
a[480]=String.fromCharCode(43690);a[481]=String.fromCharCode(43690);a[482]=String.fromCharCode(43690);a[483]=String.fromCharCode(43690);a[484]=String.fromCharCode(43690);a[485]=String.fromCharCode(43690);a[486]=String.fromCharCode(43690);a[487]=String.fromCharCode(43690);a[488]=String.fromCharCode(43690);a[489]=String.fromCharCode(4074);a[490]=String.fromCharCode(43690);a[491]=String.fromCharCode(43690);a[492]=String.fromCharCode(43690);a[493]=String.fromCharCode(43690);a[494]=String.fromCharCode(43690);
a[495]=String.fromCharCode(682);a[496]=String.fromCharCode(255);a[497]=String.fromCharCode(63);a[498]=String.fromCharCode(255);a[499]=String.fromCharCode(255);a[500]=String.fromCharCode(63);a[501]=String.fromCharCode(255);a[502]=String.fromCharCode(255);a[503]=String.fromCharCode(16383);a[504]=String.fromCharCode(255);a[505]=String.fromCharCode(255);a[506]=String.fromCharCode(255);a[507]=String.fromCharCode(223);a[508]=String.fromCharCode(220);a[509]=String.fromCharCode(207);a[510]=String.fromCharCode(255);
a[511]=String.fromCharCode(220);a[519]=String.fromCharCode(32768);a[528]=String.fromCharCode(50176);a[529]=String.fromCharCode(8);a[530]=String.fromCharCode(49152);a[531]=String.fromCharCode(16);a[4016]=String.fromCharCode(127);a[4017]=String.fromCharCode(248);a[4084]=String.fromCharCode(65534);a[4085]=String.fromCharCode(2047);a[4102]=String.fromCharCode(65534);a[4103]=String.fromCharCode(2047);a[4106]=String.fromCharCode(1024);a[4107]=String.fromCharCode(1056);a[4109]=String.fromCharCode(32768);
a[4110]=String.fromCharCode(65535);a[4111]=String.fromCharCode(65407);a[4112]=String.fromCharCode(43690);a[4113]=String.fromCharCode(43690);a[4114]=String.fromCharCode(43690);a[4115]=String.fromCharCode(21930);a[4116]=String.fromCharCode(43861);a[4117]=String.fromCharCode(43690);a[4118]=String.fromCharCode(43690);a[4119]=String.fromCharCode(54442);a[4120]=String.fromCharCode(12585);a[4121]=String.fromCharCode(20004);a[4122]=String.fromCharCode(10538);a[4123]=String.fromCharCode(9809);a[4124]=String.fromCharCode(21056);
a[4125]=String.fromCharCode(46421);a[4126]=String.fromCharCode(43690);a[4127]=String.fromCharCode(43049);a[4128]=String.fromCharCode(43690);a[4129]=String.fromCharCode(170);a[4133]=String.fromCharCode(65535);a[4134]=String.fromCharCode(65535);a[4135]=String.fromCharCode(65535);a[4136]=String.fromCharCode(65535);a[4137]=String.fromCharCode(65535);a[4138]=String.fromCharCode(511);a[4153]=String.fromCharCode(1);a[4154]=String.fromCharCode(61440);a[4155]=String.fromCharCode(65535);a[4156]=String.fromCharCode(32767);
a[4157]="c";a[4158]=String.fromCharCode(168)});c$.currency_f=d(c$,"currency_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.currency=new com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(16);a[10]=String.fromCharCode(60);a[159]=String.fromCharCode(12);a[227]=String.fromCharCode(32768);a[522]=String.fromCharCode(8191);a[4070]=String.fromCharCode(512);a[4080]=String.fromCharCode(16);a[4094]="c";a[4098]=String.fromCharCode(16);a[4106]=String.fromCharCode(60)});c$.decimal_digit_f=d(c$,"decimal_digit_f",
function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.decimal_digit=new com.stevesoft.pat.Bits(a);a[3]=String.fromCharCode(1023);a[102]=String.fromCharCode(1023);a[111]=String.fromCharCode(1023);a[150]=String.fromCharCode(65472);a[158]=String.fromCharCode(65472);a[166]=String.fromCharCode(65472);a[174]=String.fromCharCode(65472);a[182]=String.fromCharCode(65472);a[190]=String.fromCharCode(65408);a[198]=String.fromCharCode(65472);a[206]=String.fromCharCode(65472);a[214]=String.fromCharCode(65472);
a[229]=String.fromCharCode(1023);a[237]=String.fromCharCode(1023);a[242]=String.fromCharCode(1023);a[4081]=String.fromCharCode(1023);a[4099]=String.fromCharCode(1023)});c$.math_f=d(c$,"math_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.math=new com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(2048);a[3]=String.fromCharCode(28672);a[7]=String.fromCharCode(20480);a[10]=String.fromCharCode(4096);a[11]=String.fromCharCode(2);a[13]=String.fromCharCode(128);a[15]=String.fromCharCode(128);
a[516]=String.fromCharCode(16);a[519]=String.fromCharCode(7168);a[520]=String.fromCharCode(7168);a[537]=String.fromCharCode(31);a[541]=String.fromCharCode(20);a[544]=String.fromCharCode(65535);a[545]=String.fromCharCode(65535);a[546]=String.fromCharCode(65535);a[547]=String.fromCharCode(65535);a[548]=String.fromCharCode(65535);a[549]=String.fromCharCode(65535);a[550]=String.fromCharCode(65535);a[551]=String.fromCharCode(65535);a[552]=String.fromCharCode(65535);a[553]=String.fromCharCode(65535);a[554]=
String.fromCharCode(65535);a[555]=String.fromCharCode(65535);a[556]=String.fromCharCode(65535);a[557]=String.fromCharCode(65535);a[558]=String.fromCharCode(65535);a[559]=String.fromCharCode(3);a[560]=String.fromCharCode(3840);a[562]=String.fromCharCode(3);a[4018]=String.fromCharCode(512);a[4070]="t";a[4080]=String.fromCharCode(2048);a[4081]=String.fromCharCode(28672);a[4085]=String.fromCharCode(20480);a[4094]=String.fromCharCode(7940);a[4098]=String.fromCharCode(2048);a[4099]=String.fromCharCode(28672);
a[4103]=String.fromCharCode(20480);a[4106]=String.fromCharCode(4096);a[4107]=String.fromCharCode(2);a[4109]=String.fromCharCode(128);a[4111]=String.fromCharCode(128)});c$.letter_f=d(c$,"letter_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.letter=new com.stevesoft.pat.Bits(a);a[4]=String.fromCharCode(65534);a[5]=String.fromCharCode(2047);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[12]=String.fromCharCode(65535);
a[13]=String.fromCharCode(65407);a[14]=String.fromCharCode(65535);a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(65535);a[17]=String.fromCharCode(65535);a[18]=String.fromCharCode(65535);a[19]=String.fromCharCode(65535);a[20]=String.fromCharCode(65535);a[21]=String.fromCharCode(65535);a[22]=String.fromCharCode(65535);a[23]=String.fromCharCode(65535);a[24]=String.fromCharCode(65535);a[25]=String.fromCharCode(65535);a[26]=String.fromCharCode(65535);a[27]=String.fromCharCode(65535);a[28]=
String.fromCharCode(65535);a[29]=String.fromCharCode(65535);a[30]=String.fromCharCode(65535);a[31]=String.fromCharCode(64575);a[32]=String.fromCharCode(65535);a[33]=String.fromCharCode(255);a[37]=String.fromCharCode(65535);a[38]=String.fromCharCode(65535);a[39]=String.fromCharCode(65535);a[40]=String.fromCharCode(65535);a[41]=String.fromCharCode(65535);a[42]=String.fromCharCode(511);a[43]=String.fromCharCode(63999);a[44]=String.fromCharCode(3);a[45]=String.fromCharCode(3);a[46]=String.fromCharCode(31);
a[55]=String.fromCharCode(1024);a[56]=String.fromCharCode(55104);a[57]=String.fromCharCode(65535);a[58]=String.fromCharCode(65531);a[59]=String.fromCharCode(65535);a[60]=String.fromCharCode(32767);a[61]=String.fromCharCode(21631);a[62]=String.fromCharCode(65533);a[63]=String.fromCharCode(15);a[64]=String.fromCharCode(57342);a[65]=String.fromCharCode(65535);a[66]=String.fromCharCode(65535);a[67]=String.fromCharCode(65535);a[68]=String.fromCharCode(65535);a[69]=String.fromCharCode(57342);a[70]=String.fromCharCode(65535);
a[71]=String.fromCharCode(65535);a[72]=String.fromCharCode(3);a[73]=String.fromCharCode(65535);a[74]=String.fromCharCode(65535);a[75]=String.fromCharCode(65535);a[76]=String.fromCharCode(6559);a[77]=String.fromCharCode(65535);a[78]=String.fromCharCode(53247);a[79]=String.fromCharCode(831);a[83]=String.fromCharCode(65534);a[84]=String.fromCharCode(65535);a[85]=String.fromCharCode(639);a[86]=String.fromCharCode(65534);a[87]=String.fromCharCode(65535);a[88]=String.fromCharCode(255);a[93]=String.fromCharCode(65535);
a[94]=String.fromCharCode(2047);a[95]=String.fromCharCode(7);a[98]=String.fromCharCode(65534);a[99]=String.fromCharCode(2047);a[100]=String.fromCharCode(2047);a[103]=String.fromCharCode(65534);a[104]=String.fromCharCode(65535);a[105]=String.fromCharCode(65535);a[106]=String.fromCharCode(65535);a[107]=String.fromCharCode(31999);a[108]=String.fromCharCode(32767);a[109]=String.fromCharCode(47);a[110]=String.fromCharCode(96);a[144]=String.fromCharCode(65504);a[145]=String.fromCharCode(65535);a[146]=String.fromCharCode(65535);
a[147]=String.fromCharCode(9215);a[149]=String.fromCharCode(65280);a[150]=String.fromCharCode(3);a[152]=String.fromCharCode(40928);a[153]=String.fromCharCode(65529);a[154]=String.fromCharCode(65023);a[155]=String.fromCharCode(965);a[157]=String.fromCharCode(45056);a[158]=String.fromCharCode(3);a[159]=String.fromCharCode(3);a[160]=String.fromCharCode(34784);a[161]=String.fromCharCode(65529);a[162]=String.fromCharCode(65023);a[163]=String.fromCharCode(877);a[165]=String.fromCharCode(24064);a[167]=String.fromCharCode(28);
a[168]=String.fromCharCode(45024);a[169]=String.fromCharCode(65531);a[170]=String.fromCharCode(65023);a[171]=String.fromCharCode(9197);a[174]=String.fromCharCode(1);a[176]=String.fromCharCode(40928);a[177]=String.fromCharCode(65529);a[178]=String.fromCharCode(65023);a[179]=String.fromCharCode(9165);a[181]=String.fromCharCode(45056);a[182]=String.fromCharCode(3);a[184]=String.fromCharCode(51168);a[185]=String.fromCharCode(54845);a[186]=String.fromCharCode(50968);a[187]=String.fromCharCode(959);a[192]=
String.fromCharCode(57312);a[193]=String.fromCharCode(65533);a[194]=String.fromCharCode(65023);a[195]=String.fromCharCode(1007);a[198]=String.fromCharCode(3);a[200]=String.fromCharCode(57312);a[201]=String.fromCharCode(65533);a[202]=String.fromCharCode(65023);a[203]=String.fromCharCode(1007);a[205]=String.fromCharCode(16384);a[206]=String.fromCharCode(3);a[208]=String.fromCharCode(57312);a[209]=String.fromCharCode(65533);a[210]=String.fromCharCode(65023);a[211]=String.fromCharCode(1023);a[214]=String.fromCharCode(3);
a[224]=String.fromCharCode(65534);a[225]=String.fromCharCode(65535);a[226]=String.fromCharCode(32767);a[227]=String.fromCharCode(13);a[228]=String.fromCharCode(127);a[232]=String.fromCharCode(9622);a[233]=String.fromCharCode(65264);a[234]=String.fromCharCode(27822);a[235]=String.fromCharCode(8205);a[236]=String.fromCharCode(95);a[237]=String.fromCharCode(12288);a[244]=String.fromCharCode(65279);a[245]=String.fromCharCode(65535);a[246]=String.fromCharCode(1023);a[266]=String.fromCharCode(65535);a[267]=
String.fromCharCode(65535);a[268]=String.fromCharCode(63);a[269]=String.fromCharCode(65535);a[270]=String.fromCharCode(65535);a[271]=String.fromCharCode(127);a[272]=String.fromCharCode(65535);a[273]=String.fromCharCode(65535);a[274]=String.fromCharCode(65535);a[275]=String.fromCharCode(65535);a[276]=String.fromCharCode(65535);a[277]=String.fromCharCode(33791);a[278]=String.fromCharCode(65535);a[279]=String.fromCharCode(65535);a[280]=String.fromCharCode(65535);a[281]=String.fromCharCode(65535);a[282]=
String.fromCharCode(65287);a[283]=String.fromCharCode(65535);a[284]=String.fromCharCode(65535);a[285]=String.fromCharCode(65535);a[286]=String.fromCharCode(65535);a[287]=String.fromCharCode(1023);a[480]=String.fromCharCode(65535);a[481]=String.fromCharCode(65535);a[482]=String.fromCharCode(65535);a[483]=String.fromCharCode(65535);a[484]=String.fromCharCode(65535);a[485]=String.fromCharCode(65535);a[486]=String.fromCharCode(65535);a[487]=String.fromCharCode(65535);a[488]=String.fromCharCode(65535);
a[489]=String.fromCharCode(4095);a[490]=String.fromCharCode(65535);a[491]=String.fromCharCode(65535);a[492]=String.fromCharCode(65535);a[493]=String.fromCharCode(65535);a[494]=String.fromCharCode(65535);a[495]=String.fromCharCode(1023);a[496]=String.fromCharCode(65535);a[497]=String.fromCharCode(16191);a[498]=String.fromCharCode(65535);a[499]=String.fromCharCode(65535);a[500]=String.fromCharCode(16191);a[501]=String.fromCharCode(43775);a[502]=String.fromCharCode(65535);a[503]=String.fromCharCode(16383);
a[504]=String.fromCharCode(65535);a[505]=String.fromCharCode(65535);a[506]=String.fromCharCode(65535);a[507]=String.fromCharCode(24543);a[508]=String.fromCharCode(8156);a[509]=String.fromCharCode(4047);a[510]=String.fromCharCode(8191);a[511]=String.fromCharCode(8156);a[519]=String.fromCharCode(32768);a[528]=String.fromCharCode(64644);a[529]=String.fromCharCode(16175);a[530]=String.fromCharCode(64848);a[531]=String.fromCharCode(507);a[768]=String.fromCharCode(32);a[771]=String.fromCharCode(62);a[772]=
String.fromCharCode(65534);a[773]=String.fromCharCode(65535);a[774]=String.fromCharCode(65535);a[775]=String.fromCharCode(65535);a[776]=String.fromCharCode(65535);a[777]=String.fromCharCode(30751);a[778]=String.fromCharCode(65534);a[779]=String.fromCharCode(65535);a[780]=String.fromCharCode(65535);a[781]=String.fromCharCode(65535);a[782]=String.fromCharCode(65535);a[783]=String.fromCharCode(30719);a[784]=String.fromCharCode(65504);a[785]=String.fromCharCode(65535);a[786]=String.fromCharCode(8191);
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a[1257]=String.fromCharCode(65535);a[1258]=String.fromCharCode(65535);a[1259]=String.fromCharCode(65535);a[1260]=String.fromCharCode(65535);a[1261]=String.fromCharCode(65535);a[1262]=String.fromCharCode(65535);a[1263]=String.fromCharCode(65535);a[1264]=String.fromCharCode(65535);a[1265]=String.fromCharCode(65535);a[1266]=String.fromCharCode(65535);a[1267]=String.fromCharCode(65535);a[1268]=String.fromCharCode(65535);a[1269]=String.fromCharCode(65535);a[1270]=String.fromCharCode(65535);a[1271]=String.fromCharCode(65535);
a[1272]=String.fromCharCode(65535);a[1273]=String.fromCharCode(65535);a[1274]=String.fromCharCode(65535);a[1275]=String.fromCharCode(65535);a[1276]=String.fromCharCode(65535);a[1277]=String.fromCharCode(65535);a[1278]=String.fromCharCode(65535);a[1279]=String.fromCharCode(65535);a[1280]=String.fromCharCode(65535);a[1281]=String.fromCharCode(65535);a[1282]=String.fromCharCode(65535);a[1283]=String.fromCharCode(65535);a[1284]=String.fromCharCode(65535);a[1285]=String.fromCharCode(65535);a[1286]=String.fromCharCode(65535);
a[1287]=String.fromCharCode(65535);a[1288]=String.fromCharCode(65535);a[1289]=String.fromCharCode(65535);a[1290]=String.fromCharCode(65535);a[1291]=String.fromCharCode(65535);a[1292]=String.fromCharCode(65535);a[1293]=String.fromCharCode(65535);a[1294]=String.fromCharCode(65535);a[1295]=String.fromCharCode(65535);a[1296]=String.fromCharCode(65535);a[1297]=String.fromCharCode(65535);a[1298]=String.fromCharCode(65535);a[1299]=String.fromCharCode(65535);a[1300]=String.fromCharCode(65535);a[1301]=String.fromCharCode(65535);
a[1302]=String.fromCharCode(65535);a[1303]=String.fromCharCode(65535);a[1304]=String.fromCharCode(65535);a[1305]=String.fromCharCode(65535);a[1306]=String.fromCharCode(65535);a[1307]=String.fromCharCode(65535);a[1308]=String.fromCharCode(65535);a[1309]=String.fromCharCode(65535);a[1310]=String.fromCharCode(65535);a[1311]=String.fromCharCode(65535);a[1312]=String.fromCharCode(65535);a[1313]=String.fromCharCode(65535);a[1314]=String.fromCharCode(65535);a[1315]=String.fromCharCode(65535);a[1316]=String.fromCharCode(65535);
a[1317]=String.fromCharCode(65535);a[1318]=String.fromCharCode(65535);a[1319]=String.fromCharCode(65535);a[1320]=String.fromCharCode(65535);a[1321]=String.fromCharCode(65535);a[1322]=String.fromCharCode(65535);a[1323]=String.fromCharCode(65535);a[1324]=String.fromCharCode(65535);a[1325]=String.fromCharCode(65535);a[1326]=String.fromCharCode(65535);a[1327]=String.fromCharCode(65535);a[1328]=String.fromCharCode(65535);a[1329]=String.fromCharCode(65535);a[1330]=String.fromCharCode(65535);a[1331]=String.fromCharCode(65535);
a[1332]=String.fromCharCode(65535);a[1333]=String.fromCharCode(65535);a[1334]=String.fromCharCode(65535);a[1335]=String.fromCharCode(65535);a[1336]=String.fromCharCode(65535);a[1337]=String.fromCharCode(65535);a[1338]=String.fromCharCode(65535);a[1339]=String.fromCharCode(65535);a[1340]=String.fromCharCode(65535);a[1341]=String.fromCharCode(65535);a[1342]=String.fromCharCode(65535);a[1343]=String.fromCharCode(65535);a[1344]=String.fromCharCode(65535);a[1345]=String.fromCharCode(65535);a[1346]=String.fromCharCode(65535);
a[1347]=String.fromCharCode(65535);a[1348]=String.fromCharCode(65535);a[1349]=String.fromCharCode(65535);a[1350]=String.fromCharCode(65535);a[1351]=String.fromCharCode(65535);a[1352]=String.fromCharCode(65535);a[1353]=String.fromCharCode(65535);a[1354]=String.fromCharCode(65535);a[1355]=String.fromCharCode(65535);a[1356]=String.fromCharCode(65535);a[1357]=String.fromCharCode(65535);a[1358]=String.fromCharCode(65535);a[1359]=String.fromCharCode(65535);a[1360]=String.fromCharCode(65535);a[1361]=String.fromCharCode(65535);
a[1362]=String.fromCharCode(65535);a[1363]=String.fromCharCode(65535);a[1364]=String.fromCharCode(65535);a[1365]=String.fromCharCode(65535);a[1366]=String.fromCharCode(65535);a[1367]=String.fromCharCode(65535);a[1368]=String.fromCharCode(65535);a[1369]=String.fromCharCode(65535);a[1370]=String.fromCharCode(65535);a[1371]=String.fromCharCode(65535);a[1372]=String.fromCharCode(65535);a[1373]=String.fromCharCode(65535);a[1374]=String.fromCharCode(65535);a[1375]=String.fromCharCode(65535);a[1376]=String.fromCharCode(65535);
a[1377]=String.fromCharCode(65535);a[1378]=String.fromCharCode(65535);a[1379]=String.fromCharCode(65535);a[1380]=String.fromCharCode(65535);a[1381]=String.fromCharCode(65535);a[1382]=String.fromCharCode(65535);a[1383]=String.fromCharCode(65535);a[1384]=String.fromCharCode(65535);a[1385]=String.fromCharCode(65535);a[1386]=String.fromCharCode(65535);a[1387]=String.fromCharCode(65535);a[1388]=String.fromCharCode(65535);a[1389]=String.fromCharCode(65535);a[1390]=String.fromCharCode(65535);a[1391]=String.fromCharCode(65535);
a[1392]=String.fromCharCode(65535);a[1393]=String.fromCharCode(65535);a[1394]=String.fromCharCode(65535);a[1395]=String.fromCharCode(65535);a[1396]=String.fromCharCode(65535);a[1397]=String.fromCharCode(65535);a[1398]=String.fromCharCode(65535);a[1399]=String.fromCharCode(65535);a[1400]=String.fromCharCode(65535);a[1401]=String.fromCharCode(65535);a[1402]=String.fromCharCode(65535);a[1403]=String.fromCharCode(65535);a[1404]=String.fromCharCode(65535);a[1405]=String.fromCharCode(65535);a[1406]=String.fromCharCode(65535);
a[1407]=String.fromCharCode(65535);a[1408]=String.fromCharCode(65535);a[1409]=String.fromCharCode(65535);a[1410]=String.fromCharCode(65535);a[1411]=String.fromCharCode(65535);a[1412]=String.fromCharCode(65535);a[1413]=String.fromCharCode(65535);a[1414]=String.fromCharCode(65535);a[1415]=String.fromCharCode(65535);a[1416]=String.fromCharCode(65535);a[1417]=String.fromCharCode(65535);a[1418]=String.fromCharCode(65535);a[1419]=String.fromCharCode(65535);a[1420]=String.fromCharCode(65535);a[1421]=String.fromCharCode(65535);
a[1422]=String.fromCharCode(65535);a[1423]=String.fromCharCode(65535);a[1424]=String.fromCharCode(65535);a[1425]=String.fromCharCode(65535);a[1426]=String.fromCharCode(65535);a[1427]=String.fromCharCode(65535);a[1428]=String.fromCharCode(65535);a[1429]=String.fromCharCode(65535);a[1430]=String.fromCharCode(65535);a[1431]=String.fromCharCode(65535);a[1432]=String.fromCharCode(65535);a[1433]=String.fromCharCode(65535);a[1434]=String.fromCharCode(65535);a[1435]=String.fromCharCode(65535);a[1436]=String.fromCharCode(65535);
a[1437]=String.fromCharCode(65535);a[1438]=String.fromCharCode(65535);a[1439]=String.fromCharCode(65535);a[1440]=String.fromCharCode(65535);a[1441]=String.fromCharCode(65535);a[1442]=String.fromCharCode(65535);a[1443]=String.fromCharCode(65535);a[1444]=String.fromCharCode(65535);a[1445]=String.fromCharCode(65535);a[1446]=String.fromCharCode(65535);a[1447]=String.fromCharCode(65535);a[1448]=String.fromCharCode(65535);a[1449]=String.fromCharCode(65535);a[1450]=String.fromCharCode(65535);a[1451]=String.fromCharCode(65535);
a[1452]=String.fromCharCode(65535);a[1453]=String.fromCharCode(65535);a[1454]=String.fromCharCode(65535);a[1455]=String.fromCharCode(65535);a[1456]=String.fromCharCode(65535);a[1457]=String.fromCharCode(65535);a[1458]=String.fromCharCode(65535);a[1459]=String.fromCharCode(65535);a[1460]=String.fromCharCode(65535);a[1461]=String.fromCharCode(65535);a[1462]=String.fromCharCode(65535);a[1463]=String.fromCharCode(65535);a[1464]=String.fromCharCode(65535);a[1465]=String.fromCharCode(65535);a[1466]=String.fromCharCode(65535);
a[1467]=String.fromCharCode(65535);a[1468]=String.fromCharCode(65535);a[1469]=String.fromCharCode(65535);a[1470]=String.fromCharCode(65535);a[1471]=String.fromCharCode(65535);a[1472]=String.fromCharCode(65535);a[1473]=String.fromCharCode(65535);a[1474]=String.fromCharCode(65535);a[1475]=String.fromCharCode(65535);a[1476]=String.fromCharCode(65535);a[1477]=String.fromCharCode(65535);a[1478]=String.fromCharCode(65535);a[1479]=String.fromCharCode(65535);a[1480]=String.fromCharCode(65535);a[1481]=String.fromCharCode(65535);
a[1482]=String.fromCharCode(65535);a[1483]=String.fromCharCode(65535);a[1484]=String.fromCharCode(65535);a[1485]=String.fromCharCode(65535);a[1486]=String.fromCharCode(65535);a[1487]=String.fromCharCode(65535);a[1488]=String.fromCharCode(65535);a[1489]=String.fromCharCode(65535);a[1490]=String.fromCharCode(65535);a[1491]=String.fromCharCode(65535);a[1492]=String.fromCharCode(65535);a[1493]=String.fromCharCode(65535);a[1494]=String.fromCharCode(65535);a[1495]=String.fromCharCode(65535);a[1496]=String.fromCharCode(65535);
a[1497]=String.fromCharCode(65535);a[1498]=String.fromCharCode(65535);a[1499]=String.fromCharCode(65535);a[1500]=String.fromCharCode(65535);a[1501]=String.fromCharCode(65535);a[1502]=String.fromCharCode(65535);a[1503]=String.fromCharCode(65535);a[1504]=String.fromCharCode(65535);a[1505]=String.fromCharCode(65535);a[1506]=String.fromCharCode(65535);a[1507]=String.fromCharCode(65535);a[1508]=String.fromCharCode(65535);a[1509]=String.fromCharCode(65535);a[1510]=String.fromCharCode(65535);a[1511]=String.fromCharCode(65535);
a[1512]=String.fromCharCode(65535);a[1513]=String.fromCharCode(65535);a[1514]=String.fromCharCode(65535);a[1515]=String.fromCharCode(65535);a[1516]=String.fromCharCode(65535);a[1517]=String.fromCharCode(65535);a[1518]=String.fromCharCode(65535);a[1519]=String.fromCharCode(65535);a[1520]=String.fromCharCode(65535);a[1521]=String.fromCharCode(65535);a[1522]=String.fromCharCode(65535);a[1523]=String.fromCharCode(65535);a[1524]=String.fromCharCode(65535);a[1525]=String.fromCharCode(65535);a[1526]=String.fromCharCode(65535);
a[1527]=String.fromCharCode(65535);a[1528]=String.fromCharCode(65535);a[1529]=String.fromCharCode(65535);a[1530]=String.fromCharCode(65535);a[1531]=String.fromCharCode(65535);a[1532]=String.fromCharCode(65535);a[1533]=String.fromCharCode(65535);a[1534]=String.fromCharCode(65535);a[1535]=String.fromCharCode(65535);a[1536]=String.fromCharCode(65535);a[1537]=String.fromCharCode(65535);a[1538]=String.fromCharCode(65535);a[1539]=String.fromCharCode(65535);a[1540]=String.fromCharCode(65535);a[1541]=String.fromCharCode(65535);
a[1542]=String.fromCharCode(65535);a[1543]=String.fromCharCode(65535);a[1544]=String.fromCharCode(65535);a[1545]=String.fromCharCode(65535);a[1546]=String.fromCharCode(65535);a[1547]=String.fromCharCode(65535);a[1548]=String.fromCharCode(65535);a[1549]=String.fromCharCode(65535);a[1550]=String.fromCharCode(65535);a[1551]=String.fromCharCode(65535);a[1552]=String.fromCharCode(65535);a[1553]=String.fromCharCode(65535);a[1554]=String.fromCharCode(65535);a[1555]=String.fromCharCode(65535);a[1556]=String.fromCharCode(65535);
a[1557]=String.fromCharCode(65535);a[1558]=String.fromCharCode(65535);a[1559]=String.fromCharCode(65535);a[1560]=String.fromCharCode(65535);a[1561]=String.fromCharCode(65535);a[1562]=String.fromCharCode(65535);a[1563]=String.fromCharCode(65535);a[1564]=String.fromCharCode(65535);a[1565]=String.fromCharCode(65535);a[1566]=String.fromCharCode(65535);a[1567]=String.fromCharCode(65535);a[1568]=String.fromCharCode(65535);a[1569]=String.fromCharCode(65535);a[1570]=String.fromCharCode(65535);a[1571]=String.fromCharCode(65535);
a[1572]=String.fromCharCode(65535);a[1573]=String.fromCharCode(65535);a[1574]=String.fromCharCode(65535);a[1575]=String.fromCharCode(65535);a[1576]=String.fromCharCode(65535);a[1577]=String.fromCharCode(65535);a[1578]=String.fromCharCode(65535);a[1579]=String.fromCharCode(65535);a[1580]=String.fromCharCode(65535);a[1581]=String.fromCharCode(65535);a[1582]=String.fromCharCode(65535);a[1583]=String.fromCharCode(65535);a[1584]=String.fromCharCode(65535);a[1585]=String.fromCharCode(65535);a[1586]=String.fromCharCode(65535);
a[1587]=String.fromCharCode(65535);a[1588]=String.fromCharCode(65535);a[1589]=String.fromCharCode(65535);a[1590]=String.fromCharCode(65535);a[1591]=String.fromCharCode(65535);a[1592]=String.fromCharCode(65535);a[1593]=String.fromCharCode(65535);a[1594]=String.fromCharCode(65535);a[1595]=String.fromCharCode(65535);a[1596]=String.fromCharCode(65535);a[1597]=String.fromCharCode(65535);a[1598]=String.fromCharCode(65535);a[1599]=String.fromCharCode(65535);a[1600]=String.fromCharCode(65535);a[1601]=String.fromCharCode(65535);
a[1602]=String.fromCharCode(65535);a[1603]=String.fromCharCode(65535);a[1604]=String.fromCharCode(65535);a[1605]=String.fromCharCode(65535);a[1606]=String.fromCharCode(65535);a[1607]=String.fromCharCode(65535);a[1608]=String.fromCharCode(65535);a[1609]=String.fromCharCode(65535);a[1610]=String.fromCharCode(65535);a[1611]=String.fromCharCode(65535);a[1612]=String.fromCharCode(65535);a[1613]=String.fromCharCode(65535);a[1614]=String.fromCharCode(65535);a[1615]=String.fromCharCode(65535);a[1616]=String.fromCharCode(65535);
a[1617]=String.fromCharCode(65535);a[1618]=String.fromCharCode(65535);a[1619]=String.fromCharCode(65535);a[1620]=String.fromCharCode(65535);a[1621]=String.fromCharCode(65535);a[1622]=String.fromCharCode(65535);a[1623]=String.fromCharCode(65535);a[1624]=String.fromCharCode(65535);a[1625]=String.fromCharCode(65535);a[1626]=String.fromCharCode(65535);a[1627]=String.fromCharCode(65535);a[1628]=String.fromCharCode(65535);a[1629]=String.fromCharCode(65535);a[1630]=String.fromCharCode(65535);a[1631]=String.fromCharCode(65535);
a[1632]=String.fromCharCode(65535);a[1633]=String.fromCharCode(65535);a[1634]=String.fromCharCode(65535);a[1635]=String.fromCharCode(65535);a[1636]=String.fromCharCode(65535);a[1637]=String.fromCharCode(65535);a[1638]=String.fromCharCode(65535);a[1639]=String.fromCharCode(65535);a[1640]=String.fromCharCode(65535);a[1641]=String.fromCharCode(65535);a[1642]=String.fromCharCode(65535);a[1643]=String.fromCharCode(65535);a[1644]=String.fromCharCode(65535);a[1645]=String.fromCharCode(65535);a[1646]=String.fromCharCode(65535);
a[1647]=String.fromCharCode(65535);a[1648]=String.fromCharCode(65535);a[1649]=String.fromCharCode(65535);a[1650]=String.fromCharCode(65535);a[1651]=String.fromCharCode(65535);a[1652]=String.fromCharCode(65535);a[1653]=String.fromCharCode(65535);a[1654]=String.fromCharCode(65535);a[1655]=String.fromCharCode(65535);a[1656]=String.fromCharCode(65535);a[1657]=String.fromCharCode(65535);a[1658]=String.fromCharCode(65535);a[1659]=String.fromCharCode(65535);a[1660]=String.fromCharCode(65535);a[1661]=String.fromCharCode(65535);
a[1662]=String.fromCharCode(65535);a[1663]=String.fromCharCode(65535);a[1664]=String.fromCharCode(65535);a[1665]=String.fromCharCode(65535);a[1666]=String.fromCharCode(65535);a[1667]=String.fromCharCode(65535);a[1668]=String.fromCharCode(65535);a[1669]=String.fromCharCode(65535);a[1670]=String.fromCharCode(65535);a[1671]=String.fromCharCode(65535);a[1672]=String.fromCharCode(65535);a[1673]=String.fromCharCode(65535);a[1674]=String.fromCharCode(65535);a[1675]=String.fromCharCode(65535);a[1676]=String.fromCharCode(65535);
a[1677]=String.fromCharCode(65535);a[1678]=String.fromCharCode(65535);a[1679]=String.fromCharCode(65535);a[1680]=String.fromCharCode(65535);a[1681]=String.fromCharCode(65535);a[1682]=String.fromCharCode(65535);a[1683]=String.fromCharCode(65535);a[1684]=String.fromCharCode(65535);a[1685]=String.fromCharCode(65535);a[1686]=String.fromCharCode(65535);a[1687]=String.fromCharCode(65535);a[1688]=String.fromCharCode(65535);a[1689]=String.fromCharCode(65535);a[1690]=String.fromCharCode(65535);a[1691]=String.fromCharCode(65535);
a[1692]=String.fromCharCode(65535);a[1693]=String.fromCharCode(65535);a[1694]=String.fromCharCode(65535);a[1695]=String.fromCharCode(65535);a[1696]=String.fromCharCode(65535);a[1697]=String.fromCharCode(65535);a[1698]=String.fromCharCode(65535);a[1699]=String.fromCharCode(65535);a[1700]=String.fromCharCode(65535);a[1701]=String.fromCharCode(65535);a[1702]=String.fromCharCode(65535);a[1703]=String.fromCharCode(65535);a[1704]=String.fromCharCode(65535);a[1705]=String.fromCharCode(65535);a[1706]=String.fromCharCode(65535);
a[1707]=String.fromCharCode(65535);a[1708]=String.fromCharCode(65535);a[1709]=String.fromCharCode(65535);a[1710]=String.fromCharCode(65535);a[1711]=String.fromCharCode(65535);a[1712]=String.fromCharCode(65535);a[1713]=String.fromCharCode(65535);a[1714]=String.fromCharCode(65535);a[1715]=String.fromCharCode(65535);a[1716]=String.fromCharCode(65535);a[1717]=String.fromCharCode(65535);a[1718]=String.fromCharCode(65535);a[1719]=String.fromCharCode(65535);a[1720]=String.fromCharCode(65535);a[1721]=String.fromCharCode(65535);
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(b-=f[1]+1-f[0]);while(a>f[1]&&c<this.hiddenColumns.size());if(a>f[0]&&a<f[1])return f[0]+a-b}return b},"~N");d(c$,"findHiddenRegionPosition",function(a){var b=0;if(null!=this.hiddenColumns){var c=0,f=0;do{b=this.hiddenColumns.elementAt(c);if(0==a)return b[0];f+=b[1]+1-b[0];b=b[1]+1;c++}while(c<a+1);b-=f}return b},"~N");d(c$,"getHiddenBoundaryRight",function(a){if(null!=this.hiddenColumns){var b=0;do{var c=this.hiddenColumns.elementAt(b);if(a<c[0])return c[0];b++}while(b<this.hiddenColumns.size())}return a},
"~N");d(c$,"getHiddenBoundaryLeft",function(a){if(null!=this.hiddenColumns){var b=this.hiddenColumns.size()-1;do{var c=this.hiddenColumns.elementAt(b);if(a>c[1])return c[1];b--}while(-1<b)}return a},"~N");d(c$,"hideSelectedColumns",function(){for(;0<this.size();){var a=this.getSelected().firstElement().intValue();this.hideColumns(a)}});d(c$,"hideColumns",function(a,b){null==this.hiddenColumns&&(this.hiddenColumns=new java.util.Vector);for(var c=!1,f=!1,d=0;d<this.hiddenColumns.size();d++){var k=this.hiddenColumns.elementAt(d);
if(a<=k[1]&&b>=k[0]){this.hiddenColumns.removeElementAt(d);f=!0;break}else if(b<k[0]&&a<k[0]){this.hiddenColumns.insertElementAt(w(-1,[a,b]),d);c=!0;break}}f?this.hideColumns(a,b):c||this.hiddenColumns.addElement(w(-1,[a,b]))},"~N,~N");d(c$,"hideColumns",function(a){var b=a;for(a+=1;this.contains(b);)this.removeElement(b),b--;for(;this.contains(a);)this.removeElement(a),a++;b++;a--;b>a&&(b=a);this.hideColumns(b,a)},"~N");d(c$,"revealAllHiddenColumns",function(){if(null!=this.hiddenColumns)for(var a=
0;a<this.hiddenColumns.size();a++)for(var b=this.hiddenColumns.elementAt(a),c=b[0];c<b[1]+1;c++)this.addElement(c);this.hiddenColumns=null});d(c$,"revealHiddenColumns",function(a){for(var b=0;b<this.hiddenColumns.size();b++){var c=this.hiddenColumns.elementAt(b);if(a==c[0]){for(a=c[0];a<c[1]+1;a++)this.addElement(a);this.hiddenColumns.removeElement(c);break}}0==this.hiddenColumns.size()&&(this.hiddenColumns=null)},"~N");d(c$,"isVisible",function(a){if(null!=this.hiddenColumns)for(var b=0;b<this.hiddenColumns.size();b++){var c=
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b);return k},"~N,~N,~A");d(c$,"getVisibleContigs",function(a,b){if(null!=this.hiddenColumns&&0<this.hiddenColumns.size()){for(var c=new java.util.ArrayList,f=this.getHiddenColumns(),d=a,k,g,e=0;d<b&&e<f.size();e++)k=f.get(e),g=k[0],k=k[1],k<d||(g>d&&c.add(w(-1,[d,g-1])),d=k+1);d<b&&c.add(w(-1,[d,b-1]));f=w(2*c.size(),0);d=0;for(e=c.size();d<e;d++)g=c.get(d),c.set(d,null),f[2*d]=g[0],f[2*d+1]=g[1];c.clear();return f}return w(-1,[a,b-1])},"~N,~N");d(c$,"makeVisibleAnnotation",function(a){this.makeVisibleAnnotation(-1,
-1,a)},"jalview.datamodel.AlignmentAnnotation");d(c$,"makeVisibleAnnotation",function(a,b,c){if(null!=c.annotations)if(a==b&&-1==b&&(a=0,b=c.annotations.length),null!=this.hiddenColumns&&0<this.hiddenColumns.size()){for(var f=new java.util.Vector,d=null,k=this.getHiddenColumns(),g=a,d=b,e,j,n=0,x=0;x<k.size();x++)if(e=k.get(x),j=e[0],e=e[1],!(j<a)){g=Math.min(g,e+1);d=Math.min(d,j);if(g>d)break;f.addElement(d=Array(d-g));System.arraycopy(c.annotations,g,d,0,d.length);n+=d.length;g=e+1;d=b}b>g&&(f.addElement(d=
Array(b-g+1)),d.length+g<=c.annotations.length?System.arraycopy(c.annotations,g,d,0,d.length):System.arraycopy(c.annotations,g,d,0,c.annotations.length-g),n+=d.length);if(0!=n){c.annotations=Array(n);var n=0,u;for(a=f.iterator();a.hasNext()&&((u=a.next())||1);)System.arraycopy(u,0,c.annotations,n,u.length),n+=u.length}}else c.restrict(a,b)},"~N,~N,jalview.datamodel.AlignmentAnnotation");d(c$,"invertColumnSelection",function(a,b){for(var c=null!=this.hiddenColumns&&0<this.hiddenColumns.size(),f=a;f<
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this.hiddenColumns&&0<this.hiddenColumns.size())this.addElementsFrom(a);else{var b;for(a=a.getSelected().iterator();a.hasNext()&&((b=a.next())||1);)this.addElement(b.intValue())}},"jalview.datamodel.ColumnSelection");c$.propagateInsertions=d(c$,"propagateInsertions",function(a,b,c){var f=b.getGapCharacter();c=c.getAlignmentAndColumnSelection(f);f=c[1];f.propagateInsertions(a,b,c[0][0]);return f},"jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.AlignmentView");d(c$,"propagateInsertions",
function(a,b,c){var f=b.getGapCharacter();this.pruneDeletions(jalview.util.ShiftList.parseMap(c.gapMap()));for(var d=this.getVisibleContigs(0,a.getLength()),k=0,g=0;g<d.length;g+=2){if(d[g]>k){for(var e=new StringBuffer,j=0,n=d[g]-k;j<n;j++)e.append(f);j=0;for(n=b.getHeight();j<n;j++){var x=b.getSequenceAt(j);if(x!==a)if(x=b.getSequenceAt(j).getSequenceAsString(),x.length<=k+0){var u=k+0-x.length-1;if(0<u)for(x+=e;0<(u=k+0-x.length-1);)if(u>=e.length())x+=e.toString();else{var m=N(u,"\x00");e.getChars(0,
u,m,0);x+=m.toString()}}else b.getSequenceAt(j).setSequence(x.substring(0,k+0)+e.toString()+x.substring(k+0))}}k=d[g+1]+1}if(0+k<a.getLength()){e=new StringBuffer;j=0;for(n=a.getLength()-k-0;j<n;j++)e.append(f);j=0;for(n=b.getHeight();j<n;j++)if(x=b.getSequenceAt(j),x!==a){x=x.getSequenceAsString();for(u=c.getLength()-x.length;0<u;)u>=e.length()?x+=e.toString():(m=N(u,"\x00"),e.getChars(0,u,m,0),x+=m.toString()),u=c.getLength()-x.length}}},"jalview.datamodel.SequenceI,jalview.datamodel.AlignmentI,jalview.datamodel.SequenceI");
d(c$,"hasSelectedColumns",function(){return null!=this.selected&&0<this.selected.size()});d(c$,"hasHiddenColumns",function(){return null!=this.hiddenColumns&&0<this.hiddenColumns.size()});d(c$,"hasManyHiddenColumns",function(){return null!=this.hiddenColumns&&1<this.hiddenColumns.size()});d(c$,"hideInsertionsFor",function(a){var b;for(a=a.getInsertions().iterator();a.hasNext()&&((b=a.next())||1);)this.hideColumns(b[0],b[1])},"jalview.datamodel.SequenceI");d(c$,"filterAnnotations",function(a,b){this.revealAllHiddenColumns();
this.clear();var c=0;do{if(null!=a[c]){var f=!1;b.getThresholdType()===jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD&&a[c].value>=b.getThresholdValue()&&(f=!0);b.getThresholdType()===jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD&&a[c].value<=b.getThresholdValue()&&(f=!0);b.isFilterAlphaHelix()&&"H"==a[c].secondaryStructure&&(f=!0);b.isFilterBetaSheet()&&"E"==a[c].secondaryStructure&&(f=!0);b.isFilterTurn()&&
"S"==a[c].secondaryStructure&&(f=!0);var d=b.getRegexString();if(null!=d&&!b.getRegexSearchFields().isEmpty()){var k=b.getRegexSearchFields();try{k.contains(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING)&&a[c].displayCharacter.matches(d)&&(f=!0)}catch(g){if(y(g,java.util.regex.PatternSyntaxException))a[c].displayCharacter.equals(d)&&(f=!0);else throw g;}k.contains(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION)&&
(null!=a[c].description&&a[c].description.matches(d))&&(f=!0)}f&&this.addElement(c)}c++}while(c<a.length);return!1},"~A,jalview.viewmodel.annotationfilter.AnnotationFilterParameter")});p("jalview.util");q(null,"jalview.util.ShiftList",["java.util.ArrayList"],function(){c$=s(function(){this.shifts=null;r(this,arguments)},jalview.util,"ShiftList");m(c$,function(){this.shifts=new java.util.ArrayList});d(c$,"addShift",function(a,b){for(var c=0,f=null;c<this.shifts.size()&&(f=this.shifts.get(c))[0]<a;)c++;
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function(a){var b=null;if(null!=a&&0<a.length)for(var b=new jalview.util.ShiftList,c=0,f=0;c<a.length;f++,c++)f!=a[c]&&(b.addShift(f,a[c]-f),f=a[c]);return b},"~A");d(c$,"getShifts",function(){return this.shifts})});p("jalview.viewmodel.annotationfilter");q(["java.lang.Enum","java.util.ArrayList"],"jalview.viewmodel.annotationfilter.AnnotationFilterParameter",null,function(){c$=s(function(){this.thresholdType=null;this.thresholdValue=0;this.filterTurn=this.filterBetaSheet=this.filterAlphaHelix=!1;
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this.hidecols=a.hidecols,this.hidereps=a.hidereps,this.idColour=a.idColour,this.outlineColour=a.outlineColour,this.seqrep=a.seqrep,this.textColour=a.textColour,this.textColour2=a.textColour2,this.thresholdTextColour=a.thresholdTextColour,this.width=a.width,this.ignoreGapsInConsensus=a.ignoreGapsInConsensus,null!=a.conserve&&this.recalcConservation())},"jalview.datamodel.SequenceGroup");d(c$,"getSelectionAsNewSequences",function(a){for(var b=this.sequences.size(),c=Array(b),f=this.getSequencesInOrder(a),
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"getSequences",function(){return this.sequences});d(c$,"getSequences",function(a){if(null==a)return this.sequences;for(var b=new java.util.ArrayList,c,f=this.sequences.iterator();f.hasNext()&&((c=f.next())||1);)if(b.add(c),a.containsKey(c))for(var d,k=a.get(c).getSequences().iterator();k.hasNext()&&((d=k.next())||1);)d!==c&&!b.contains(d)&&b.add(d);return b},"java.util.Map");d(c$,"getSequencesAsArray",function(a){a=this.getSequences(a);return null==a?null:a.toArray(Array(a.size()))},"java.util.Map");
d(c$,"adjustForRemoveLeft",function(a){this.startRes>=a&&(this.startRes-=a);if(this.endRes>=a)this.endRes-=a,this.startRes>this.endRes&&(this.startRes=0);else return!1;return!0},"~N");d(c$,"adjustForRemoveRight",function(a){if(this.startRes>a)return!1;this.endRes>=a&&(this.endRes=a);return!0},"~N");d(c$,"getName",function(){return this.groupName});d(c$,"getDescription",function(){return this.description});d(c$,"setName",function(a){this.groupName=a},"~S");d(c$,"setDescription",function(a){this.description=
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null==this.conservation))try{var a=jalview.analysis.AAFrequency.calculate(this.sequences,this.startRes,this.endRes+1,this.showSequenceLogo);null!=this.consensus&&this._updateConsensusRow(a,this.sequences.size());null!=this.cs&&this.cs.setConsensus(a);if(null!=this.conservation||null!=this.cs&&this.cs.conservationApplied()){var b=new jalview.analysis.Conservation(this.groupName,jalview.schemes.ResidueProperties.propHash,3,this.sequences,this.startRes,this.endRes+1);b.calculate();b.verdict(!1,this.consPercGaps);
null!=this.conservation&&this._updateConservationRow(b);null!=this.cs&&this.cs.conservationApplied()&&this.cs.setConservation(b)}null!=this.cs&&this.cs.alignmentChanged(null!=this.context?this.context:this,null)}catch(c){if(y(c,OutOfMemoryError))System.out.println("Out of memory loading groups: "+c);else throw c;}});d(c$,"_updateConservationRow",function(a){null==this.conservation&&this.getConservation();this.conservation.label="Conservation for "+this.getName();this.conservation.description="Conservation for group "+
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if(!b)return d;if(k<d.length){c=d;for(d=Array(k);0<=--k;)d[k]=c[k],c[k]=null}return d},"jalview.datamodel.AlignmentI,~B");d(c$,"getIdColour",function(){return this.idColour});d(c$,"setIdColour",function(a){this.idColour=a},"java.awt.Color");e(c$,"getSeqrep",function(){return this.seqrep});e(c$,"setSeqrep",function(a){this.seqrep=a},"jalview.datamodel.SequenceI");e(c$,"hasSeqrep",function(){return null!=this.seqrep});d(c$,"setHidereps",function(a){this.hidereps=a},"~B");d(c$,"isHidereps",function(){return this.hidereps});
d(c$,"setHideCols",function(a){this.hidecols=a},"~B");d(c$,"isHideCols",function(){return this.hidecols});d(c$,"intersect",function(a,b){var c=new jalview.datamodel.SequenceGroup(this),f=this.getSequencesInOrder(a);c.sequences=new java.util.ArrayList;for(var d=0;null!=f&&d<f.length;d++)(null==b||b.containsKey(f[d]))&&c.sequences.add(f[d]);return c},"jalview.datamodel.AlignmentI,java.util.Map");d(c$,"getShowNonconserved",function(){return this.showNonconserved});d(c$,"setShowNonconserved",function(a){this.showNonconserved=
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d(c$,"setConservationRow",function(a){null==this.conservation&&(this.conservation=a)},"jalview.datamodel.AlignmentAnnotation");d(c$,"getConservationRow",function(){null==this.conservation&&(this.conservation=new jalview.datamodel.AlignmentAnnotation("","",Array(1),0,11,1));this.conservation.hasText=!0;this.conservation.autoCalculated=!0;this.conservation.groupRef=this;this.conservation.label="Conservation for "+this.getName();this.conservation.description="Conservation for group "+this.getName()+
" less than "+this.consPercGaps+"% gaps";return this.conservation});d(c$,"hasAnnotationRows",function(){return null!=this.consensus||null!=this.conservation});d(c$,"getConsensusSeq",function(){this.getConsensus();for(var a=new StringBuffer,b=0;b<this.consensus.annotations.length;b++)null!=this.consensus.annotations[b]&&("["==this.consensus.annotations[b].description.charAt(0)?a.append(this.consensus.annotations[b].description.charAt(1)):a.append(this.consensus.annotations[b].displayCharacter));a=
new jalview.datamodel.Sequence("Group"+this.getName()+" Consensus",a.toString());a.setDescription("Percentage Identity Consensus "+(this.ignoreGapsInConsensus?" without gaps":""));return a});d(c$,"setIgnoreGapsConsensus",function(a){this.ignoreGapsInConsensus!=a&&null!=this.consensus&&(this.ignoreGapsInConsensus=a,this.recalcConservation());this.ignoreGapsInConsensus=a},"~B");d(c$,"getIgnoreGapsConsensus",function(){return this.ignoreGapsInConsensus});d(c$,"setshowSequenceLogo",function(a){this.showSequenceLogo!=
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e(c$,"getAlignmentAnnotation",function(){for(var a=new java.util.ArrayList,b,c=this.sequences.iterator();c.hasNext()&&((b=c.next())||1);){var f=b.getAnnotation();if(null!=f)for(var d,k=0;k<f.length&&((d=f[k])||1);k++)d.groupRef===this&&a.add(d)}null!=this.consensus&&a.add(this.consensus);null!=this.conservation&&a.add(this.conservation);return a.toArray([])});e(c$,"findAnnotation",function(a){for(var b=new java.util.ArrayList,c,f=0,d=this.getAlignmentAnnotation();f<d.length&&((c=d[f])||1);f++)c.getCalcId()===
a&&b.add(c);return b},"~S");e(c$,"findAnnotations",function(a,b,c){for(var f=new java.util.ArrayList,d,k=0,g=this.getAlignmentAnnotation();k<g.length&&((d=g[k])||1);k++)null!=d.getCalcId()&&(d.getCalcId().equals(b)&&null!=d.sequenceRef&&d.sequenceRef===a&&null!=d.label&&d.label.equals(c))&&f.add(d);return f},"jalview.datamodel.SequenceI,~S,~S");d(c$,"hasAnnotation",function(a){if(null!=a&&!"".equals(a))for(var b,c=0,f=this.getAlignmentAnnotation();c<f.length&&((b=f[c])||1);c++)if(b.getCalcId()===
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q(null,"jalview.analysis.AAFrequency","jalview.analysis.CodingUtils jalview.datamodel.Annotation jalview.util.Format $.MappingUtils $.QuickSort java.lang.Float $.StringBuilder java.util.Arrays $.Hashtable".split(" "),function(){c$=B(jalview.analysis,"AAFrequency");c$.calculate=d(c$,"calculate",function(a,c,f){return jalview.analysis.AAFrequency.calculate(a,c,f,!1)},"java.util.List,~N,~N");c$.calculate=d(c$,"calculate",function(a,c,f,d){for(var k=Array(a.size()),g=0,e=0;e<a.size();e++)k[e]=a.get(e),
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m)m="-";"-"==m?p[45]++:("a"<=m&&"z">=m&&(m=String.fromCharCode(m.charCodeAt(0)+-32)),e++,p[m.charCodeAt(0)]++)}else p[45]++;if(1==x)u=String.valueOf(m),g=1;else for(n=65;90>=n;n++)1>p[n]||p[n]<g||(p[n]>g?u=jalview.analysis.AAFrequency.CHARS[n-65]:p[n]==g&&(u+=jalview.analysis.AAFrequency.CHARS[n-65]),g=p[n]);0==u.length&&(u="-");k&&c.put("P",E(-1,[p,w(-1,[x,e])]));c.put("C",new Integer(g));c.put("R",u);p=100*g/x;c.put("G",new Float(p));0<e&&(p=100*g/e);c.put("N",new Float(p));d[j]=c}},"~A,~N,~N,~A,~B");
c$.completeConsensus=d(c$,"completeConsensus",function(a,c,f,d,e,g,h){jalview.analysis.AAFrequency.completeConsensus(a,c,f,d,e,g,null,h)},"jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N");c$.completeConsensus=d(c$,"completeConsensus",function(a,c,f,d,e,g,h,j){if(!(null==a||null==a.annotations||a.annotations.length<d))for(j=jalview.analysis.AAFrequency.getPercentageFormat(j);f<d;f++){var n;if(f>=c.length||null==(n=c[f]))a.annotations[f]=null;else{var x=n.get(e?"N":"G");if(null==x)a.annotations[f]=
null;else{var x=x.floatValue(),u=n.get("R").toString(),m=new StringBuilder(64);1<u.length?(m.append("[").append(u).append("] "),u="+"):m.append(n.get("R")+" ");var p=n.get("P");if(null!=p&&g){var q=p[1][0],s=p[1][1],q=e?s:q;m.setLength(0);if(null!=h)for(s=0;s<h.length;s++){var r=100*p[0][h[s].charCodeAt(0)]/q;m.append(0==s?"":"; ").append(h[s]).append(" ").append(null!=j?j.formDouble(r):I(r)).append("%")}else{for(var t=N(p[0].length,"\x00"),r=Q(p[0].length,0),s=0;s<t.length;s++)t[s]=String.fromCharCode(s),
r[s]=p[0][s];jalview.util.QuickSort.sortFloatChar(r,t);for(var v=0,s=t.length-1;0<p[0][t[s].charCodeAt(0)];s--){var w=t[s];"-"!=w&&(r=100*p[0][w.charCodeAt(0)]/q,m.append(0==v?"":"; ").append(w).append(" ").append(null!=j?j.formDouble(r):I(r)).append("%"),v++)}}}else m.append(null!=j?j.formDouble(x):I(x)).append("%");a.annotations[f]=new jalview.datamodel.Annotation(u,m.toString()," ",x)}}}},"jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~A,~N");c$.getPercentageFormat=d(c$,"getPercentageFormat",
function(a){for(var c=0;10<=a;)c++,a/=10;return 1>=c?null:new jalview.util.Format("%3."+(c-1)+"f")},"~N");c$.extractProfile=d(c$,"extractProfile",function(a,c){var f=w(64,0),d=a.get("P");if(null==d)return null;for(var e=N(d[0].length,"\x00"),g=Q(d[0].length,0),h=0;h<e.length;h++)e[h]=String.fromCharCode(h),g[h]=d[0][h];jalview.util.QuickSort.sortFloatChar(g,e);for(var g=2,j=0,n=0,x=d[1][c?1:0],h=e.length-1;0<d[0][e[h].charCodeAt(0)];h--)if("-"!=e[h]){f[g++]=e[h].charCodeAt(0);var u=I(100*d[0][e[h].charCodeAt(0)]/
x);f[g++]=u;j+=u;n++}f[0]=n;f[1]=j;d=w(f.length+1,0);d[0]=0;System.arraycopy(f,0,d,1,f.length);return d},"java.util.Hashtable,~B");c$.extractCdnaProfile=d(c$,"extractCdnaProfile",function(a,c){var f=a.get("P"),d=w(f.length-2,0);System.arraycopy(f,2,d,0,f.length-2);var e=w(3+2*d.length,0);e[0]=2;for(var g=N(d.length,"\x00"),h=0;h<g.length;h++)g[h]=String.fromCharCode(h);jalview.util.QuickSort.sortIntChar(d,g);for(var j=0,n=0,x=3,f=c?f[1]:f[0],h=g.length-1;0<=h;h--){var u=d[h];if(0==u)break;n++;e[x++]=
g[h].charCodeAt(0);u=F(100*u/f);e[x++]=u;j+=u}e[2]=j;e[1]=n;return java.util.Arrays.copyOfRange(e,0,x)},"java.util.Hashtable,~B");c$.calculateCdna=d(c$,"calculateCdna",function(a,c,f,d,e){for(var g=a.getGapCharacter();d<e;d++){var h=new java.util.Hashtable,j=w(66,0);j[0]=a.getSequences().size();for(var n=0,x,u=a.getSequences().iterator();u.hasNext()&&((x=u.next())||1);)if(x.getCharAt(d)!=g){var m=jalview.util.MappingUtils.findCodonFor(x,d,c),m=jalview.analysis.CodingUtils.encodeCodon(m);0<=m&&(j[m+
2]++,n++)}j[1]=n;h.put("P",j);f[d]=h}},"jalview.datamodel.AlignmentI,java.util.Set,~A,~N,~N");c$.completeCdnaConsensus=d(c$,"completeCdnaConsensus",function(a,c,f,d){if(!(null==a||null==a.annotations||a.annotations.length<c.length)){a.scaleColLabel=!0;for(var e=0;e<c.length;e++){var g=c[e];if(null!=g){for(var h=g.get("P"),g=0,j=N(h.length-2,"\x00"),n=2;n<h.length;n++){var x=h[n];j[n-2]=String.fromCharCode(n-2);g+=x}var u=w(h.length-2,0);System.arraycopy(h,2,u,0,h.length-2);jalview.util.QuickSort.sortIntChar(u,
j);var n=j[j.length-1].charCodeAt(0),h=u[j.length-1],m=String.valueOf(jalview.analysis.CodingUtils.decodeCodon(n));1<u.length&&u[j.length-2]==n&&(m="+");for(var p=100*u[u.length-1]/g,q=new StringBuilder(32),s=new StringBuilder,r=null,t=null,v=jalview.analysis.AAFrequency.getPercentageFormat(d),n=j.length-1;0<=n;n--){x=u[n];if(0==x){0<s.length()&&q.append(s).append(": ").append(r).append("% ");break}var y=j[n].charCodeAt(0),r=F(100*x/g),y=String.valueOf(jalview.analysis.CodingUtils.decodeCodon(y)),
r=null==v?Integer.toString(r):v.formLong(r);if(f||x==h)r.equals(t)&&0<n?s.append(0==s.length()?"":", "):(0<s.length()&&q.append(s).append(": ").append(t).append("% "),s.setLength(0)),s.append(y),t=r}a.annotations[e]=new jalview.datamodel.Annotation(m,q.toString()," ",p)}}}},"jalview.datamodel.AlignmentAnnotation,~A,~B,~N");G(c$,"TO_UPPER_CASE",-32,"MAXCOUNT","C","MAXRESIDUE","R","PID_GAPS","G","PID_NOGAPS","N","PROFILE","P","ENCODED_CHARS","E");c$.CHARS=c$.prototype.CHARS=Array(26);for(var a="A";"Z">=
a;a=String.fromCharCode(a.charCodeAt(0)+1))jalview.analysis.AAFrequency.CHARS[a.charCodeAt(0)-65]=String.valueOf(a)});p("jalview.analysis");c$=B(jalview.analysis,"CodingUtils");c$.encodeCodon=d(c$,"encodeCodon",function(a){return null==a?-1:jalview.analysis.CodingUtils.encodeCodon(a[2])+(jalview.analysis.CodingUtils.encodeCodon(a[1])<<2)+(jalview.analysis.CodingUtils.encodeCodon(a[0])<<4)},"~A");c$.encodeCodon=d(c$,"encodeCodon",function(a){var b=-2147483648;switch(a){case "A":case "a":b=0;break;
case "C":case "c":b=1;break;case "G":case "g":b=2;break;case "T":case "t":case "U":case "u":b=3}return b},"~S");c$.decodeCodon=d(c$,"decodeCodon",function(a){var b=N(3,"\x00");b[2]=jalview.analysis.CodingUtils.decodeNucleotide(a&3);a>>>=2;b[1]=jalview.analysis.CodingUtils.decodeNucleotide(a&3);b[0]=jalview.analysis.CodingUtils.decodeNucleotide(a>>>2&3);return b},"~N");c$.decodeNucleotide=d(c$,"decodeNucleotide",function(a){var b="0";switch(a){case 0:b="A";break;case 1:b="C";break;case 2:b="G";break;
case 3:b="T"}return b},"~N");G(c$,"CODON_ENCODING_BITSHIFT",2);p("jalview.analysis");q(null,"jalview.analysis.Conservation","jalview.datamodel.Annotation $.Sequence jalview.schemes.ResidueProperties jalview.util.Comparison java.awt.Color java.lang.Character $.Double $.StringBuffer java.util.Hashtable $.Vector".split(" "),function(){c$=s(function(){this.sequences=null;this.end=this.start=0;this.seqNums=null;this.maxLength=0;this.seqNumsChanged=!1;this.total=null;this.canonicaliseAa=!0;this.qualityRange=
this.quality=null;this.consString="";this.propHash=this.consSequence=null;this.threshold=0;this.name="";this.consSymbs=this.cons2=null;r(this,arguments)},jalview.analysis,"Conservation");J(c$,function(){this.qualityRange=Array(2)});m(c$,function(a,b,c,f,d,e){this.name=a;this.propHash=b;this.threshold=c;this.start=d;this.end=e;this.maxLength=e-d+1;var g;a=f.size();this.sequences=b=Array(a);try{for(g=0;g<a;g++)b[g]=f.get(g),b[g].getLength()>this.maxLength&&(this.maxLength=b[g].getLength())}catch(h){if(y(h,
ArrayIndexOutOfBoundsException))this.sequences=[],this.maxLength=0;else throw h;}},"~S,java.util.Hashtable,~N,java.util.List,~N,~N");d(c$,"calcSeqNum",function(a){var b=null,c=null,b=this.sequences.length;if(-1<a&&a<b)if(b=this.sequences[a].getSequenceAsString(),this.seqNums.size()<=a&&this.seqNums.addElement(w(b.length+1,0)),b.hashCode()!=this.seqNums.elementAt(a)[0]){var f,d;this.seqNumsChanged=!0;d=b.length;this.maxLength<d&&(this.maxLength=d);c=w(d+1,0);c[0]=b.hashCode();for(f=1;f<=d;f++)c[f]=
jalview.schemes.ResidueProperties.aaIndex[b.charCodeAt(f-1)];this.seqNums.setElementAt(c,a)}else System.out.println("SEQUENCE HAS BEEN DELETED!!!");else System.err.println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n")},"~N");d(c$,"calculate",function(){var a,b,c,f=this.sequences.length,d,e,g=null,h;this.total=Array(this.maxLength);for(var j=this.start;j<=this.end;j++){d=w(255,0);for(a=0;a<f;a++)if(this.sequences[a].getLength()>j){b=this.sequences[a].getCharAt(j);if(this.canonicaliseAa)b=
String.fromCharCode(jalview.schemes.ResidueProperties.aaIndex[this.sequences[a].getCharAt(j).charCodeAt(0)]),b=20<b.charCodeAt(0)?"-":jalview.schemes.ResidueProperties.aa[b.charCodeAt(0)].charAt(0);else{if("."==b||" "==b)b="-";!this.canonicaliseAa&&("a"<=b&&"z">=b)&&(b=String.fromCharCode(b.charCodeAt(0)-32))}d[b.charCodeAt(0)]++}else d[45]++;c=F(this.threshold*f/100);a=new java.util.Hashtable;for(var n="-";"Z">n;n=String.fromCharCode(n.charCodeAt(0)+1))if(d[n.charCodeAt(0)]>c){g=String.valueOf(n);
for(h=this.propHash.keys();h.hasMoreElements();)e=h.nextElement(),b=this.propHash.get(e),a.containsKey(e)?!1==a.get(e).equals(b.get(g))&&a.put(e,new Integer(-1)):b.containsKey(g)?a.put(e,b.get(g)):a.put(e,b.get("-"))}0<this.total.length&&(this.total[j-this.start]=a)}});d(c$,"countConsNGaps",function(a){var b=0,c=0,f=0,d=w(2,0),e="$",g,h=this.sequences.length,j;for(g=0;g<h;g++)a>=this.sequences[g].getLength()?b++:(j=this.sequences[g].getCharAt(a),jalview.util.Comparison.isGap(j)?b++:(f++,1==f?(e=j,
c++):e==j&&c++));d[0]=f==c?1:0;d[1]=b;return d},"~N");d(c$,"verdict",function(a,b){for(var c=new StringBuffer,f,d,e,g,h,j,n=0;n<this.start;n++)c.append("-");this.consSymbs=Array(this.end-this.start+1);for(n=this.start;n<=this.end;n++)if(e=this.countConsNGaps(n),f=e[1],f=100*f/this.sequences.length,this.consSymbs[n-this.start]=String.instantialize(),b>f){h=this.total[n-this.start];g=0;for(j=h.keys();j.hasMoreElements();)f=j.nextElement(),d=h.get(f),a?1==d.intValue()&&(this.consSymbs[n-this.start]=
f+" "+this.consSymbs[n-this.start],g++):-1!=d.intValue()&&(this.consSymbs[n-this.start]=0==d.intValue()?this.consSymbs[n-this.start]+" !"+f:f+" "+this.consSymbs[n-this.start],g++);10>g?c.append(""+g):c.append(1==e[0]?"*":"+")}else c.append("-");this.consSequence=new jalview.datamodel.Sequence(this.name,c.toString(),this.start,this.end)},"~B,~N");d(c$,"getConsSequence",function(){return this.consSequence});d(c$,"findQuality",function(){this.findQuality(0,this.maxLength-1)});d(c$,"percentIdentity2",
function(){this.seqNums=new java.util.Vector;for(var a=0,b=this.sequences.length,a=0;a<b;a++)this.calcSeqNum(a);if(null==this.cons2||this.seqNumsChanged){this.cons2=w(this.maxLength,24,0);for(b=0;24>b;b++)for(a=0;a<this.maxLength;a++)this.cons2[a][b]=0;for(var c,b=0;b<this.sequences.length;){c=this.seqNums.elementAt(b);for(a=1;a<c.length;a++)this.cons2[a-1][c[a]]++;for(a=c.length-1;a<this.maxLength;a++)this.cons2[a][23]++;b++}}});d(c$,"findQuality",function(a,b){this.quality=new java.util.Vector;
var c=-1E4,f=jalview.schemes.ResidueProperties.getBLOSUM62();this.percentIdentity2();var d=this.seqNums.size(),e=w(d,0),g,h,j,n,x,u,m,p,q;for(u=0;u<d;u++)e[u]=this.seqNums.elementAt(u).length-1;for(u=a;u<=b;u++){h=0;n=U(24,0);for(g=0;24>g;g++){for(j=n[g]=0;24>j;j++)n[g]+=this.cons2[u][j]*f[g][j]+4;n[g]/=d}for(p=0;p<d;p++){g=0;x=U(24,0);q=u<e[p]?this.seqNums.elementAt(p)[u+1]:23;for(m=0;23>m;m++)j=f[m][q]+4,x[m]=n[m]-j,g+=x[m]*x[m];h+=Math.sqrt(g)}c<h&&(c=h);this.quality.addElement(new Double(h))}e=
-1E4;for(u=a;u<=b;u++)f=this.quality.elementAt(u).doubleValue(),f=(c-f)*(d-this.cons2[u][23])/d,this.quality.setElementAt(new Double(f),u),f>e&&(e=f);this.qualityRange[0]=new Double(0);this.qualityRange[1]=new Double(e)},"~N,~N");d(c$,"completeAnnotations",function(a,b,c,f){c=this.getConsSequence().getSequence();var d=0,e=0,g;null!=a.annotations&&a.annotations.length<f&&(a.annotations=Array(f));null!=b&&(b.graphMax=this.qualityRange[1].floatValue(),null!=b.annotations&&b.annotations.length<f&&(b.annotations=
Array(f)),d=this.qualityRange[0].floatValue(),e=this.qualityRange[1].floatValue());for(var h=0;h<f;h++){var j=0;g=c[h];Character.isDigit(g)?j=g.charCodeAt(0)-48:"*"==g?j=11:"+"==g&&(j=10);var n=j-0,n=n/11;a.annotations[h]=new jalview.datamodel.Annotation(String.valueOf(g),this.consSymbs[h-this.start]," ",j,new java.awt.Color(0.3+0.7*n,0+0.9*n,0+0*n));null!=b&&(j=this.quality.elementAt(h).floatValue(),n=j-d,n/=e,b.annotations[h]=new jalview.datamodel.Annotation(" ",String.valueOf(j)," ",j,new java.awt.Color(0.3+
0.7*n,0+0.9*n,0+0*n)))}},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.AlignmentAnnotation,~N,~N");c$.calculateConservation=d(c$,"calculateConservation",function(a,b,c,f,d,e,g,h,j){a=new jalview.analysis.Conservation(a,b,c,f,d,e);return jalview.analysis.Conservation.calculateConservation(a,g,h,j)},"~S,java.util.Hashtable,~N,java.util.List,~N,~N,~B,~N,~B");c$.calculateConservation=d(c$,"calculateConservation",function(a,b,c,f){a.calculate();a.verdict(b,c);f&&a.findQuality();return a},"jalview.analysis.Conservation,~B,~N,~B")});
p("jalview.datamodel");q(["jalview.datamodel.AlignmentI","$.HiddenSequences","java.util.ArrayList","$.Collections","$.LinkedHashSet"],"jalview.datamodel.Alignment","jalview.analysis.AlignmentUtils jalview.datamodel.AlignmentAnnotation $.CigarArray $.SeqCigar $.Sequence jalview.util.Comparison $.MessageManager java.lang.Error java.util.HashSet $.Hashtable $.Vector".split(" "),function(){c$=s(function(){this.groups=this.sequences=this.dataset=null;this.gapCharacter="-";this.type=1;this.$hasRNAStructure=
!1;this.codonFrameList=this.alignmentProperties=this.hiddenSequences=this.annotations=null;this.alignmentRefs=0;this.seqrep=null;r(this,arguments)},jalview.datamodel,"Alignment",null,jalview.datamodel.AlignmentI);J(c$,function(){this.groups=java.util.Collections.synchronizedList(new java.util.ArrayList);this.hiddenSequences=new jalview.datamodel.HiddenSequences(this);this.codonFrameList=new java.util.LinkedHashSet});d(c$,"initAlignment",function(a){var b=0;this.type=jalview.util.Comparison.isNucleotide(a)?
1:0;this.sequences=java.util.Collections.synchronizedList(new java.util.ArrayList);for(b=0;b<a.length;b++)this.sequences.add(a[b])},"~A");m(c$,function(a){for(var b=a.getSequencesArray(),c=0;c<b.length;c++)b[c]=new jalview.datamodel.Sequence(b[c]);this.codonFrameList=a.codonFrameList;this.initAlignment(b)},"jalview.datamodel.AlignmentI");m(c$,function(a){this.initAlignment(a)},"~A");c$.createAlignment=d(c$,"createAlignment",function(){throw Error(jalview.util.MessageManager.getString("error.alignment_cigararray_not_implemented"));
},"jalview.datamodel.CigarArray");d(c$,"getSequences",function(){return this.sequences});d(c$,"getSequences",function(){return this.sequences},"java.util.Map");d(c$,"getSequencesArray",function(){return null==this.sequences?null:this.sequences.toArray(Array(this.sequences.size()))});e(c$,"getSequencesByName",function(){return jalview.analysis.AlignmentUtils.getSequencesByName(this)});e(c$,"getSequenceAt",function(a){return-1<a&&a<this.sequences.size()?this.sequences.get(a):null},"~N");e(c$,"addSequence",
function(a){null!=this.dataset&&(null==a.getDatasetSequence()&&(a=a.deriveSequence()),this.getDataset().addSequence(a.getDatasetSequence()));null==this.sequences?this.initAlignment(E(-1,[a])):this.sequences.add(a);null!=this.hiddenSequences&&this.hiddenSequences.adjustHeightSequenceAdded()},"jalview.datamodel.SequenceI");e(c$,"setSequenceAt",function(a,b){this.deleteSequence(a);this.sequences.set(a,b)},"~N,jalview.datamodel.SequenceI");d(c$,"getGroups",function(){return this.groups});e(c$,"finalize",
function(){null!=this.getDataset()&&this.getDataset().removeAlignmentRef();this.hiddenSequences=this.annotations=this.groups=this.sequences=this.dataset=null});d(c$,"removeAlignmentRef",function(){0==--this.alignmentRefs&&this.finalize()});d(c$,"deleteSequence",function(a){this.deleteSequence(this.findIndex(a))},"jalview.datamodel.SequenceI");d(c$,"deleteSequence",function(a){-1<a&&a<this.getHeight()&&(this.sequences.remove(a),this.hiddenSequences.adjustHeightSequenceDeleted(a))},"~N");e(c$,"findGroup",
function(a){for(var b=0;b<this.groups.size();b++){var c=this.groups.get(b);if(c.getSequences(null).contains(a))return c}return null},"jalview.datamodel.SequenceI");e(c$,"findAllGroups",function(a){for(var b=new java.util.ArrayList,c=this.groups.size(),f=0;f<c;f++){var d=this.groups.get(f);null==d||null==d.getSequences()?(this.deleteGroup(d),c--):d.getSequences().contains(a)&&b.add(d)}a=Array(b.size());return b.toArray(a)},"jalview.datamodel.SequenceI");e(c$,"addGroup",function(a){if(!this.groups.contains(a)){if(0<
this.hiddenSequences.getSize()){var b,c=a.getSize();for(b=0;b<c;b++)this.sequences.contains(a.getSequenceAt(b))||(a.deleteSequence(a.getSequenceAt(b),!1),c--,b--);if(1>a.getSize())return}a.setContext(this);this.groups.add(a)}},"jalview.datamodel.SequenceGroup");d(c$,"removeAnnotationForGroup",function(a){if(!(null==this.annotations||0==this.annotations.length)){var b=Array(this.annotations.length),c=Array(this.annotations.length),f,d,e;if(null==a)for(e=d=f=0;f<this.annotations.length;f++)null!=this.annotations[f].groupRef?
b[d++]=this.annotations[f]:c[e++]=this.annotations[f];else for(e=d=f=0;f<this.annotations.length;f++)this.annotations[f].groupRef===a?b[d++]=this.annotations[f]:c[e++]=this.annotations[f];if(0<d){for(f=0;f<d;f++)this.unhookAnnotation(b[f]),b[f]=null;a=Array(e);for(f=0;f<e;f++)a[f]=c[f];this.annotations=a}}},"jalview.datamodel.SequenceGroup");e(c$,"deleteAllGroups",function(){null!=this.annotations&&this.removeAnnotationForGroup(null);for(var a,b=this.groups.iterator();b.hasNext()&&((a=b.next())||
1);)a.setContext(null);this.groups.clear()});e(c$,"deleteGroup",function(a){this.groups.contains(a)&&(this.removeAnnotationForGroup(a),this.groups.remove(a),a.setContext(null))},"jalview.datamodel.SequenceGroup");d(c$,"findName",function(a){return this.findName(a,!1)},"~S");d(c$,"findName",function(a,b){return this.findName(null,a,b)},"~S,~B");d(c$,"findName",function(a,b,c){var f=0,d=null,d=null;if(null!=a){for(d=!1;f<this.sequences.size();)if(this.getSequenceAt(f++)===a){d=!0;break}d||(f=0)}for(;f<
this.sequences.size();){d=this.getSequenceAt(f);d=d.getName();if(d.equals(b)||c&&d.equalsIgnoreCase(b))return this.getSequenceAt(f);f++}return null},"jalview.datamodel.SequenceI,~S,~B");e(c$,"findSequenceMatch",function(a){for(var b=new java.util.Vector,c=0;c<this.sequences.size();)this.getSequenceAt(c).getName().equals(a)&&b.addElement(this.getSequenceAt(c)),c++;a=Array(b.size());for(c=0;c<a.length;c++)a[c]=b.elementAt(c);return a},"~S");d(c$,"findIndex",function(a){for(var b=0;b<this.sequences.size();){if(a===
this.getSequenceAt(b))return b;b++}return-1},"jalview.datamodel.SequenceI");d(c$,"findIndex",function(a){for(var b=0;b<this.sequences.size();){if(a.involvesSequence(this.getSequenceAt(b)))return b;b++}return-1},"jalview.datamodel.SearchResults");e(c$,"getHeight",function(){return this.sequences.size()});e(c$,"getWidth",function(){for(var a=-1,b=0;b<this.sequences.size();b++)this.getSequenceAt(b).getLength()>a&&(a=this.getSequenceAt(b).getLength());return a});e(c$,"setGapCharacter",function(a){this.gapCharacter=
a;for(var b,c=this.sequences.iterator();c.hasNext()&&((b=c.next())||1);)b.setSequence(b.getSequenceAsString().$replace(".",a).$replace("-",a).$replace(" ",a))},"~S");d(c$,"getGapCharacter",function(){return this.gapCharacter});d(c$,"isAligned",function(){return this.isAligned(!1)});d(c$,"isAligned",function(a){var b=this.getWidth();if(null==this.hiddenSequences||0==this.hiddenSequences.getSize())a=!0;for(var c=0;c<this.sequences.size();c++)if((a||!this.hiddenSequences.isHidden(this.getSequenceAt(c)))&&
this.getSequenceAt(c).getLength()!=b)return!1;return!0},"~B");e(c$,"deleteAllAnnotations",function(a){for(var b=!1,c,f=0,d=this.getAlignmentAnnotation();f<d.length&&((c=d[f])||1);f++)if(!c.autoCalculated||a)this.deleteAnnotation(c),b=!0;return b},"~B");d(c$,"deleteAnnotation",function(a){return this.deleteAnnotation(a,!0)},"jalview.datamodel.AlignmentAnnotation");d(c$,"deleteAnnotation",function(a,b){var c=1;null!=this.annotations&&(c=this.annotations.length);if(1>c)return!1;for(var f=Array(c-1),
d=!1,e=0,g=0;g<c;g++)this.annotations[g]===a?d=!0:e<f.length&&(f[e++]=this.annotations[g]);d&&(this.annotations=f,b&&this.unhookAnnotation(a));return d},"jalview.datamodel.AlignmentAnnotation,~B");d(c$,"unhookAnnotation",function(a){null!=a.sequenceRef&&a.sequenceRef.removeAlignmentAnnotation(a);null!=a.groupRef&&(a.groupRef=null)},"jalview.datamodel.AlignmentAnnotation");d(c$,"addAnnotation",function(a){this.addAnnotation(a,-1)},"jalview.datamodel.AlignmentAnnotation");d(c$,"addAnnotation",function(a,
b){null!=a.getRNAStruc()&&(this.$hasRNAStructure=!0);var c=1;null!=this.annotations&&(c=this.annotations.length+1);var f=Array(c),d=0;-1==b||b>=c?f[c-1]=a:f[b]=a;if(1<c)for(var e=0,d=0;d<c-1;d++,e++)e==b&&e++,e<f.length&&(f[e]=this.annotations[d]);this.annotations=f},"jalview.datamodel.AlignmentAnnotation,~N");e(c$,"setAnnotationIndex",function(a,b){if(!(null==a||null==this.annotations||this.annotations.length-1<b)){var c=this.annotations.length,f=Array(c);f[b]=a;for(var d=0;d<c;d++)d!=b&&(f[d]=d<
b?this.annotations[d]:this.annotations[d-1]);this.annotations=f}},"jalview.datamodel.AlignmentAnnotation,~N");d(c$,"getAlignmentAnnotation",function(){return this.annotations});e(c$,"setNucleotide",function(a){this.type=a?1:0},"~B");d(c$,"isNucleotide",function(){return 1==this.type?!0:!1});e(c$,"hasRNAStructure",function(){return this.$hasRNAStructure});e(c$,"setDataset",function(a){if(null==this.dataset&&null==a){for(var b=Array(this.getHeight()),c=0;c<this.getHeight();c++)a=this.getSequenceAt(c),
b[c]=null!=a.getDatasetSequence()?a.getDatasetSequence():a.createDatasetSequence();this.dataset=new jalview.datamodel.Alignment(b)}else if(null==this.dataset&&null!=a){this.dataset=a;for(c=0;c<this.getHeight();c++)if(a=this.getSequenceAt(c),b=a.getDatasetSequence(),null==b)b=a.createDatasetSequence(),this.dataset.addSequence(b);else{for(;null!=b.getDatasetSequence();)b=b.getDatasetSequence();-1==this.dataset.findIndex(b)&&this.dataset.addSequence(b)}}this.dataset.addAlignmentRef()},"jalview.datamodel.Alignment");
d(c$,"addAlignmentRef",function(){this.alignmentRefs++});e(c$,"getDataset",function(){return this.dataset});e(c$,"padGaps",function(){for(var a=!1,b=-1,c,f=0;f<this.sequences.size();f++){c=this.getSequenceAt(f);for(var d=c.getLength();d>b;d--)if(d>b&&!jalview.util.Comparison.isGap(c.getCharAt(d))){b=d;break}}b++;for(f=0;f<this.sequences.size();f++)c=this.getSequenceAt(f),d=c.getLength(),d<b?(c.insertCharAt(d,b-d,this.gapCharacter),a=!0):c.getLength()>b&&c.deleteChars(b,c.getLength());return a});e(c$,
"justify",function(a){for(var b=!1,c=-1,f=w(2*this.sequences.size(),0),d,e=0;e<this.sequences.size();e++){d=this.getSequenceAt(e);f[2*e]=d.findIndex(d.getStart());f[2*e+1]=d.findIndex(d.getStart()+d.getLength());for(var g=!1,h=0,j=d.getLength();h<j;h++)jalview.util.Comparison.isGap(d.getCharAt(h))||(g?(f[2*e+1]=h,h-f[2*e]>c&&(c=h-f[2*e])):(f[2*e]=h,g=!0))}c++;for(e=0;e<this.sequences.size();e++)d=this.getSequenceAt(e),g=1+f[2*e+1]-f[2*e],h=c-g,g=d.getLength(),a?(g>f[2*e+1]&&(d.deleteChars(f[2*e+1]+
1,g),b=!0),f[2*e]>h?(d.deleteChars(0,f[2*e]-h),b=!0):f[2*e]<h&&(d.insertCharAt(0,h-f[2*e],this.gapCharacter),b=!0)):(0<f[2*e]&&(d.deleteChars(0,f[2*e]),b=!0,f[2*e+1]-=f[2*e],g-=f[2*e]),g>c?(d.deleteChars(c+1,g),b=!0):g<c&&(d.insertCharAt(g,c-g,this.gapCharacter),b=!0));return b},"~B");d(c$,"getHiddenSequences",function(){return this.hiddenSequences});e(c$,"getCompactAlignment",function(){for(var a=Array(this.sequences.size()),b=0,c,f=this.sequences.iterator();f.hasNext()&&((c=f.next())||1);)a[b++]=
new jalview.datamodel.SeqCigar(c);a=new jalview.datamodel.CigarArray(a);a.addOperation("M",this.getWidth());return a});e(c$,"setProperty",function(a,b){null==this.alignmentProperties&&(this.alignmentProperties=new java.util.Hashtable);this.alignmentProperties.put(a,b)},"~O,~O");d(c$,"getProperty",function(a){return null!=this.alignmentProperties?this.alignmentProperties.get(a):null},"~O");d(c$,"getProperties",function(){return this.alignmentProperties});e(c$,"addCodonFrame",function(a){null!=a&&this.codonFrameList.add(a)},
"jalview.datamodel.AlignedCodonFrame");e(c$,"getCodonFrame",function(a){if(null==a)return null;for(var b=new java.util.ArrayList,c,f=this.codonFrameList.iterator();f.hasNext()&&((c=f.next())||1);)c.involvesSequence(a)&&b.add(c);return b},"jalview.datamodel.SequenceI");e(c$,"setCodonFrames",function(a){this.codonFrameList=a},"java.util.Set");d(c$,"getCodonFrames",function(){return this.codonFrameList});e(c$,"removeCodonFrame",function(a){return null==a||null==this.codonFrameList?!1:this.codonFrameList.remove(a)},
"jalview.datamodel.AlignedCodonFrame");e(c$,"append",function(a){a===this&&System.err.println("Self append may cause a deadlock.");var b=a.getGapCharacter()==this.getGapCharacter(),c=a.getGapCharacter(),f=null!=a.getHiddenSequences()&&null!=a.getHiddenSequences().hiddenSequences?a.getHiddenSequences().getFullAlignment().getSequences():a.getSequences();if(null!=f)for(var d,f=f.iterator();f.hasNext()&&((d=f.next())||1);){if(!b)for(var e=d.getSequence(),g=0;g<e.length;g++)e[g]==c&&(e[g]=this.gapCharacter);
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this.length||null==this.refCigars||0==this.refCigars.length)return null;a=this.getArrayofSequenceAndDeletions(a);for(var b=Array(a.length),c=0;c<this.refCigars.length;c++)b[c]=a[c][0];return b},"~S");d(c$,"applyDeletions",function(){var a=null;if(0==this.length)return null;for(var b=0,c=0,f=0,d=0;d<this.length;)if("D"!=this.operation[d])"M"==this.operation[d]&&(b+=this.range[d]),c+=this.range[d++];else{null==a&&(a=new java.util.Vector);var e=b,g=b+this.range[d]-1;a.addElement(w(-1,[c+f,this.range[d]]));
f+=this.range[d]-1;System.arraycopy(this.operation,d+1,this.operation,d,this.length-d);System.arraycopy(this.range,d+1,this.range,d,this.length-d);this.length--;for(var h=0;h<this.refCigars.length;h++)this.refCigars[h].deleteRange(e,g)}if(null!=a){b=w(2*a.size(),0);c=0;for(f=a.size();c<f;c++)d=a.elementAt(c),b[2*c]=d[0],b[2*c+1]=d[1],a.setElementAt(null,c);return b}return null});d(c$,"getSeqCigarArray",function(){if(!this.isSeqCigarArray())return null;for(var a=Array(this.refCigars.length),b=0;b<
this.refCigars.length;b++)a[b]=this.refCigars[b];return a})});p("jalview.datamodel");q(null,"jalview.datamodel.CigarBase","jalview.util.MessageManager java.lang.Error $.Exception $.StringBuffer java.util.Vector JU.AU".split(" "),function(){c$=s(function(){this.length=0;this._inc_length=10;this.range=this.operation=null;r(this,arguments)},jalview.datamodel,"CigarBase");m(c$,function(){});d(c$,"getSequenceAndDeletions",function(a,b){var c=0,f=JU.AU.newInt2(this.length),d=null,e=new StringBuffer,g=0,
h=0,j=0,n=0,x=0,u=0,m=-1,p=!1;if(0==this.length)return null;null!=a&&(c=a.length);for(var q=!0,s=0;s<this.length;s++)switch(this.operation[s]){case "D":p||(f[++m]=w(-1,[g,0,h]));g+=this.range[s];f[m][1]=g-1;p=!0;break;case "I":for(var p=!1,r=0;r<this.range[s];r++)e.append(b),h++;break;case "M":p=!1;q&&(j=g,n=h,q=!1);if(null!=a)if(x=g+this.range[s],x>c)for(e.append(a.substring(g,c));x-- >=c;)e.append(b);else e.append(a.substring(g,x));h+=this.range[s];g+=this.range[s];x=g-1;u=h;break;default:throw Error(jalview.util.MessageManager.formatMessage("error.unknown_seq_cigar_operation",
E(-1,[(new StringBuffer(this.operation[s].charCodeAt(0))).toString()])));}0<++m&&(d=w(m,0),System.arraycopy(f,0,d,0,m));return E(-1,[null!=a?e.toString():null,w(-1,[j,n,x,u]),d])},"~S,~S");d(c$,"compact_operations",function(){var a=1;if(null!=this.operation)for(var b=this.operation[0];a<this.length;)if(b==this.operation[a]){this.range[a-1]+=this.range[a];var c=this.length-a;0<c&&(System.arraycopy(this.range,a+1,this.range,a,c),System.arraycopy(this.operation,a+1,this.operation,a,c));this.length--}else b=
this.operation[a++]});c$.parseCigarString=d(c$,"parseCigarString",function(a){for(var b=0,c=0,f=a.length;c<f;c++){var d=a.charAt(c);("M"==d||45==d.charCodeAt(0)||"I"==d||41==d.charCodeAt(0)||"D"==d||36==d.charCodeAt(0))&&b++}for(var e=N(b,"\x00"),b=w(b,0),g=0,c=0,f=a.length;c<f;){var h=c;do d=a.charAt(h++);while("0"<=d&&"9">=d&&h<f);if(h>=f&&"0"<=d&&"9">=d)throw new Exception(jalview.util.MessageManager.getString("exception.unterminated_cigar_string"));try{var j=a.substring(c,h-1);b[g]=Integer.parseInt(j);
c=h}catch(n){if(y(n,Exception))throw Error(jalview.util.MessageManager.getString("error.implementation_bug_parse_cigar_string"));throw n;}"a"<=d&&"z">=d&&(d=String.fromCharCode(d.charCodeAt(0)-32));if("M"==d||"I"==d||"D"==d)e[g++]=d;else throw new Exception(jalview.util.MessageManager.formatMessage("exception.unexpected_operation_cigar_string_pos",E(-1,[(new StringBuffer(d.charCodeAt(0))).toString(),Integer.$valueOf(c).toString(),a])));}return E(-1,[e,b])},"~S");d(c$,"addOperation",function(a,b){"a"<=
a&&"z">=a&&(a=String.fromCharCode(a.charCodeAt(0)-32));if("M"!=a&&"D"!=a&&"I"!=a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_invalid_operation_string"));if(0!=b){if(0>b)throw Error(jalview.util.MessageManager.getString("error.invalid_range_string"));null==this.operation&&(this.operation=N(this._inc_length,"\x00"),this.range=w(this._inc_length,0));if(this.length+1==this.operation.length){var c=this.operation;this.operation=N(this.length+1+this._inc_length,"\x00");
System.arraycopy(c,0,this.operation,0,this.length);c=this.range;this.range=w(this.length+1+this._inc_length,0);System.arraycopy(c,0,this.range,0,this.length)}0<this.length&&this.operation[this.length-1]==a?this.length--:this.range[this.length]=0;this.operation[this.length]=a;this.range[this.length++]+=b}},"~S,~N");d(c$,"deleteRange",function(a,b){var c=0;if(0==this.length)return c;if(0>a||a>b)throw Error(jalview.util.MessageManager.getString("error.implementation_error_delete_range_out_of_bounds"));
var f=0,d=1+b-a,e=this.length,g=0,h=!1,j=this.operation,n=this.range;this.length=0;this.range=this.operation=null;for(this.compact_operations();g<e&&f<=b&&0<d;)if("D"==j[g])this.addDeleted(n[g++]);else{var x=n[g];if(!h){if(f+x<=a){this.addOperation(j[g],n[g]);f+=n[g++];continue}h=!0;0<a-f&&(this.addOperation(j[g],a-f),x-=a-f)}if(g<e&&h&&0<d&&0<x){switch(j[g]){case "M":d>x?(this.addDeleted(x),c+=x):(c+=d,this.addDeleted(d),0<x-d&&this.addOperation("M",x-d),x=d=0);break;case "I":0<x-d&&(this.addInsertion(x-
d),d=0);break;case "D":throw Error(jalview.util.MessageManager.getString("error.implementation_error"));default:throw Error(jalview.util.MessageManager.formatMessage("error.implementation_error_unknown_operation",E(-1,[(new StringBuffer(j[g].charCodeAt(0))).toString()])));}d-=x;++g}}for(;g<e;)this.addOperation(j[g],n[g++]);return c},"~N,~N");d(c$,"hasDeletedRegions",function(){for(var a=0;a<this.length;a++)if("D"==this.operation[a])return!0;return!1});d(c$,"getDeletedRegions",function(){if(0==this.length)return null;
for(var a=new java.util.Vector,b=0,c=0,f=0;f<this.length;f++)switch(this.operation[f]){case "M":b+=this.range[f];case "I":c+=this.range[f];break;case "D":a.addElement(w(-1,[c,b,this.range[f]])),b+=this.range[f]}if(0==a.size())return null;b=w(3*a.size(),0);f=0;for(c=a.size();f<c;f++){var d=a.elementAt(f);b[3*f]=d[0];b[3*f+1]=d[1];b[3*f+2]=d[2]}return b});d(c$,"getFullWidth",function(){var a=0;if(null!=this.range)for(var b=0;b<this.length;b++)a+=this.range[b];return a});d(c$,"getWidth",function(){var a=
0;if(null!=this.range)for(var b=0;b<this.length;b++)if("M"==this.operation[b]||"I"==this.operation[b])a+=this.range[b];return a});d(c$,"addInsertion",function(a){this.addOperation("I",a)},"~N");d(c$,"addDeleted",function(a){this.addOperation("D",a)},"~N");d(c$,"getCigarstring",function(){for(var a=new StringBuffer,b=0;b<this.length;b++)a.append(""+this.range[b]),a.append(this.operation[b]);return a.toString()});G(c$,"D","D","I","I","M","M","_case_shift",String.fromCharCode(32))});p("jalview.datamodel");
q(["jalview.datamodel.CigarSimple"],"jalview.datamodel.CigarCigar",null,function(){c$=s(function(){this.refCigar=null;r(this,arguments)},jalview.datamodel,"CigarCigar",jalview.datamodel.CigarSimple);m(c$,function(a){t(this,jalview.datamodel.CigarCigar);this.refCigar=a},"jalview.datamodel.SeqCigar");e(c$,"getSequenceString",function(a){if(0==this.length)return"";var b=this.refCigar.getSequenceString(a);return null!=b?0==this.length?"":this.getSequenceAndDeletions(b,a)[0]:null},"~S")});p("jalview.datamodel");
q(["jalview.datamodel.CigarBase"],"jalview.datamodel.CigarSimple",null,function(){c$=B(jalview.datamodel,"CigarSimple",jalview.datamodel.CigarBase)});p("jalview.datamodel");q(["jalview.datamodel.CigarSimple"],"jalview.datamodel.SeqCigar","jalview.analysis.AlignSeq $.SeqsetUtils jalview.datamodel.Sequence jalview.util.Comparison $.MessageManager $.ShiftList java.lang.Error $.StringBuffer java.util.Hashtable".split(" "),function(){c$=s(function(){this.end=this.start=0;this.selGroups=this.seqProps=this.refseq=
null;r(this,arguments)},jalview.datamodel,"SeqCigar",jalview.datamodel.CigarSimple);d(c$,"getRefSeq",function(){return this.refseq});d(c$,"getStart",function(){return this.start});d(c$,"getEnd",function(){return this.end});e(c$,"getSequenceString",function(a){return 0==this.length?"":this.getSequenceAndDeletions(this.refseq.getSequenceAsString(this.start,this.end),a)[0]},"~S");d(c$,"getSeq",function(a){if(null==this.refseq||0==this.length)return null;a=this.getSequenceAndDeletions(this.refseq.getSequenceAsString(this.start,
this.end),a);if(null==a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));var b=a[1];a=new jalview.datamodel.Sequence(this.refseq.getName(),a[0],this.refseq.getStart()+this.start+b[0],this.refseq.getStart()+this.start+(0==b[2]?-1:b[2]));a.setDescription(this.refseq.getDescription());var b=a.getStart(),c=a.getEnd();null!=this.seqProps&&jalview.analysis.SeqsetUtils.SeqCharacterUnhash(a,this.seqProps);a.setDatasetSequence(this.refseq);
a.setStart(b);a.setEnd(c);return a},"~S");d(c$,"_setSeq",function(a,b,c,f){var d=!1;if(null==a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_set_seq_null"));if(0>c)throw Error(jalview.util.MessageManager.formatMessage("error.implementation_error_s",E(-1,[Integer.$valueOf(c).toString()])));var e=a.getSequenceAsString();if(0==f||f<c||f>e.length)f=e.length;this.start=a.findPosition(c)-a.getStart();this.end=a.findPosition(f)-a.getStart();var g=this.end-this.start,h=a.getDatasetSequence();
null==h&&(h=jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,String.instantialize(e)),g=h.length,h=g==a.getLength()?a:new jalview.datamodel.Sequence(a.getName(),h,a.getStart(),a.getStart()+h.length-1));h.getStart()<a.getStart()&&(e=a.getStart()-h.getStart(),b?(this.addDeleted(c+e),this.start=0):this.start+=e,this.end+=e);g!=f-c&&(d=!0);this.refseq=h;this.seqProps=jalview.analysis.SeqsetUtils.SeqCharacterHash(a);if(this.end>h.getLength())throw Error(jalview.util.MessageManager.getString("error.implementation_error_seqcigar_possible"));
return d},"jalview.datamodel.SequenceI,~B,~N,~N");m(c$,function(a,b,c){t(this,jalview.datamodel.SeqCigar);if(null==a)throw Error(jalview.util.MessageManager.getString("error.implmentation_bug_seq_null"));if(b.length!=c.length)throw Error(jalview.util.MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));if(null!=b){this.operation=N(b.length+this._inc_length,"\x00");this.range=w(b.length+this._inc_length,0);if(this._setSeq(a,!1,0,0))throw Error(jalview.util.MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
a=this.length;for(var f=0;f<b.length;a++,f++){var d=b[f];if("M"!=d&&"I"!=d&&"D"!=d)throw Error(jalview.util.MessageManager.formatMessage("error.implementation_bug_cigar_operation",E(-1,[Integer.$valueOf(f).toString(),Integer.$valueOf(d.charCodeAt(0)).toString(),Integer.$valueOf(77).toString(),Integer.$valueOf(73).toString(),Integer.$valueOf(68).toString()])));this.operation[a]=d;this.range[a]=c[f]}this.length+=b.length}else if(this.range=this.operation=null,this.length=0,this._setSeq(a,!1,0,0))throw Error(jalview.util.MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
},"jalview.datamodel.SequenceI,~A,~A");d(c$,"addMatch",function(a){this.addOperation("M",a)},"~N");c$.addSequenceOps=d(c$,"addSequenceOps",function(a,b,c,f,d){var e="\x00",g=0,h=0,j=b.getLength();for(d||(h=c);h<=f;)d=h<j?jalview.util.Comparison.isGap(b.getCharAt(h)):!0,c<=h&&h<=f?(d?(0<g&&"I"!=e&&(a.addOperation(e,g),g=0),e="I"):(0<g&&"M"!=e&&(a.addOperation(e,g),g=0),e="M"),g++):d||(0<g&&"D"!=e&&(a.addOperation(e,g),g=0),e="D",g++),h++;0<g&&a.addOperation(e,g)},"jalview.datamodel.CigarBase,jalview.datamodel.SequenceI,~N,~N,~B");
m(c$,function(a){t(this,jalview.datamodel.SeqCigar);if(null==a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_for_new_cigar"));this._setSeq(a,!1,0,0);jalview.datamodel.SeqCigar.addSequenceOps(this,a,0,a.getLength()-1,!1)},"jalview.datamodel.SequenceI");m(c$,function(a,b,c){t(this,jalview.datamodel.SeqCigar);if(null==a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_for_new_cigar"));this._setSeq(a,!1,b,c+1);jalview.datamodel.SeqCigar.addSequenceOps(this,
a,b,c,!1)},"jalview.datamodel.SequenceI,~N,~N");c$.parseCigar=d(c$,"parseCigar",function(a,b){var c=jalview.datamodel.CigarBase.parseCigarString(b);return new jalview.datamodel.SeqCigar(a,c[0],c[1])},"jalview.datamodel.SequenceI,~S");c$.createAlignmentSequences=d(c$,"createAlignmentSequences",function(a,b,c,f){for(var d=Array(a.length),e=Array(a.length),g=Array(a.length),h=Array(a.length),j=0;j<a.length;j++){g[j]=a[j].getRefSeq().getSequenceAsString(a[j].start,a[j].end);h[j]=a[j].getSequenceAndDeletions(g[j],
b);if(null==h[j])throw Error(jalview.util.MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations",E(-1,[Integer.$valueOf(j).toString()])));e[j]=new StringBuffer(h[j][0])}for(var n=new jalview.util.ShiftList,j=0;j<a.length;j++){var x=h[j][2];if(null!=x)for(var u=0;u<x.length;u++){for(var m=x[u],p=N(m[1]-m[0]+1,"\x00"),q=0;q<p.length;q++)p[q]=b;for(var s=n.shift(m[2]),q=0;q<a.length;q++)if(q!=j){if(e[q].length()<=s)for(var r=s-e[q].length();0<r;r--)e[q].append(b);e[q].insert(s,
p)}else e[q].insert(s,g[j].substring(m[0],m[1]+1));n.addShift(m[2],p.length);null==f&&c.hideColumns(s,s+p.length-1)}}for(j=0;j<a.length;j++)b=h[j][1],g=a[j].getRefSeq(),d[j]=new jalview.datamodel.Sequence(g.getName(),e[j].toString(),g.getStart()+a[j].start+b[0],g.getStart()+a[j].start+(0==b[2]?-1:b[2])),d[j].setDatasetSequence(g),d[j].setDescription(g.getDescription());if(null!=f)for(j=0;j<f.length;j+=3)c.hideColumns(f[j+1],f[j+1]+f[j+2]-1);return d},"~A,~S,jalview.datamodel.ColumnSelection,~A");
d(c$,"setGroupMembership",function(a){null==this.selGroups&&(this.selGroups=new java.util.Hashtable);this.selGroups.put(a,w(0,0))},"~O");d(c$,"removeGroupMembership",function(a){return null!=this.selGroups&&this.selGroups.containsKey(a)?(this.selGroups.remove(a),!0):!1},"~O");d(c$,"clearMemberships",function(){null!=this.selGroups&&this.selGroups.clear();this.selGroups=null});d(c$,"getAllMemberships",function(){if(null==this.selGroups)return null;for(var a=Array(this.selGroups.size()),b=this.selGroups.keys(),
c=0;b.hasMoreElements();c++)a[c]=b.nextElement();return a});d(c$,"isMemberOf",function(a){return null!=this.selGroups&&null!=this.selGroups.get(a)},"~O")});p("jalview.analysis");q(null,"jalview.analysis.SeqsetUtils","jalview.analysis.AlignSeq $.SequenceIdMatcher jalview.datamodel.Sequence jalview.util.Comparison java.util.Hashtable $.Vector".split(" "),function(){c$=B(jalview.analysis,"SeqsetUtils");c$.SeqCharacterHash=d(c$,"SeqCharacterHash",function(a){var b=new java.util.Hashtable;b.put("Name",
a.getName());b.put("Start",new Integer(a.getStart()));b.put("End",new Integer(a.getEnd()));null!=a.getDescription()&&b.put("Description",a.getDescription());var c=new java.util.Vector,f=a.getSequenceFeatures();if(null!=f&&0<f.length)for(var d=0;d<f.length;d++)c.addElement(f[d]);b.put("SeqFeatures",c);b.put("PdbId",null!=a.getPDBId()?a.getPDBId():new java.util.Vector);b.put("datasetSequence",null!=a.getDatasetSequence()?a.getDatasetSequence():new jalview.datamodel.Sequence("THISISAPLACEHOLDER",""));
return b},"jalview.datamodel.SequenceI");c$.SeqCharacterUnhash=d(c$,"SeqCharacterUnhash",function(a,b){var c=!0;if(null==b)return!1;var f=b.get("Name"),d=b.get("Start"),e=b.get("End"),g=b.get("SeqFeatures"),h=b.get("PdbId"),j=b.get("Description"),n=b.get("datasetSequence");null==f?c=!1:a.setName(f);null!=h&&0<h.size()&&a.setPDBId(h);null!=d&&null!=e&&(a.setStart(d.intValue()),a.setEnd(e.intValue()));if(null!=g&&0<g.size()){f=Array(g.size());d=0;for(e=g.size();d<e;d++)f[d]=g.elementAt(d);a.setSequenceFeatures(f)}null!=
j&&a.setDescription(j);null!=n&&!(n.getName().equals("THISISAPLACEHOLDER")&&0==n.getLength())&&a.setDatasetSequence(n);return c},"jalview.datamodel.SequenceI,java.util.Hashtable");c$.unique_name=d(c$,"unique_name",function(a){return String.instantialize("Sequence"+a)},"~N");c$.uniquify=d(c$,"uniquify",function(a,b){for(var c=new java.util.Hashtable,f=0;f<a.length;f++){var d=jalview.analysis.SeqsetUtils.unique_name(f);c.put(d,jalview.analysis.SeqsetUtils.SeqCharacterHash(a[f]));b&&a[f].setName(d)}return c},
"~A,~B");c$.deuniquify=d(c$,"deuniquify",function(a,b){return jalview.analysis.SeqsetUtils.deuniquify(a,b,!0)},"java.util.Hashtable,~A");c$.deuniquify=d(c$,"deuniquify",function(a,b,c){for(var f=new jalview.analysis.SequenceIdMatcher(b),d=null,e=a.keys(),g=new java.util.Vector,d=0,h=b.length;d<h;d++)g.addElement(b[d]);for(;e.hasMoreElements();)b=e.nextElement(),v(b,String)&&(null!=(d=f.findIdMatch(b))?(b=a.get(b),g.removeElement(d),jalview.analysis.SeqsetUtils.SeqCharacterUnhash(d,b)):c||System.err.println("Can't find '"+
b+"' in uniquified alignment"));if(0<g.size()&&!c){System.err.println("Did not find matches for :");for(d=g.elements();d.hasMoreElements();System.out.println(d.nextElement().getName()));return!1}return!0},"java.util.Hashtable,~A,~B");c$.getNonEmptySequenceSet=d(c$,"getNonEmptySequenceSet",function(a){for(var b=X(a.length,!1),c=0,f=0,d=a.length;f<d;f++)0==jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars,a[f].getSequenceAsString()).length?b[f]=!1:(b[f]=!0,c++);if(0==c)return null;
for(var c=Array(c),f=0,d=a.length,e=0;f<d;f++)b[f]&&(c[e++]=a[f]);return c},"~A")});p("jalview.datamodel");q(null,"jalview.datamodel.FeatureProperties",["jalview.datamodel.DBRefSource"],function(){c$=B(jalview.datamodel,"FeatureProperties");c$.isCodingFeature=d(c$,"isCodingFeature",function(a,b){return b.equalsIgnoreCase("CDS")?null==a||a.equalsIgnoreCase(jalview.datamodel.DBRefSource.EMBL)||a.equalsIgnoreCase(jalview.datamodel.DBRefSource.EMBLCDS):!1},"~S,~S");c$.getCodingFeature=d(c$,"getCodingFeature",
function(a){return jalview.datamodel.DBRefSource.EMBL.equalsIgnoreCase(a)||jalview.datamodel.DBRefSource.EMBLCDS.equalsIgnoreCase(a)?"CDS":null},"~S");G(c$,"EMBL_CODING_FEATURE","CDS","EXONPOS","exon number","EXONPRODUCT","product")});p("jalview.util");q(["java.util.HashMap"],"jalview.util.DBRefUtils","jalview.datamodel.DBRefEntry $.DBRefSource $.PDBEntry jalview.jsdev.RegExp java.util.ArrayList $.Hashtable".split(" "),function(){c$=B(jalview.util,"DBRefUtils");c$.selectRefs=d(c$,"selectRefs",function(a,
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this.ignoreGapsInConsensusCalculation)):a.setThreshold(0,this.ignoreGapsInConsensusCalculation),b&&(a.setConsensus(this.hconsensus),a.setConservation(this.hconservation)),a.alignmentChanged(this.alignment,this.hiddenRepSequences));if(this.getColourAppliesToAllGroups())for(var c,f=this.getAlignment().getGroups().iterator();f.hasNext()&&((c=f.next())||1);)null==a?c.cs=null:(c.cs=a.applyTo(c,this.getHiddenRepSequences()),c.setConsPercGaps(this.ConsPercGaps),this.getAbovePIDThreshold()||v(a,jalview.schemes.PIDColourScheme)||
v(a,jalview.schemes.Blosum62ColourScheme)?(c.cs.setThreshold(this.viewStyle.getThreshold(),this.isIgnoreGapsConsensus()),b=!0):c.cs.setThreshold(0,this.isIgnoreGapsConsensus()),this.getConservationSelected()?(c.cs.setConservationApplied(!0),b=!0):c.cs.setConservation(null),b?c.recalcConservation():c.cs.alignmentChanged(c,this.hiddenRepSequences))},"jalview.schemes.ColourSchemeI");e(c$,"getGlobalColourScheme",function(){return this.globalColourScheme});e(c$,"setConservation",function(a){this.hconservation=
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this.conservation&&this.autoCalculateConsensus&&null==this.calculator.getRegisteredWorkersOfClass(jalview.workers.ConservationThread)&&this.calculator.registerWorker(new jalview.workers.ConservationThread(this,a))},"jalview.api.AlignmentViewPanel");d(c$,"updateConsensus",function(a){if(null!=this.consensus&&this.autoCalculateConsensus){null==this.calculator.getRegisteredWorkersOfClass(jalview.workers.ConsensusThread)&&this.calculator.registerWorker(new jalview.workers.ConsensusThread(this,a));var b=
this.getAlignment();!b.isNucleotide()&&null!=b.getCodonFrames()&&!b.getCodonFrames().isEmpty()&&null==this.calculator.getRegisteredWorkersOfClass(jalview.workers.ComplementConsensusThread)&&this.calculator.registerWorker(new jalview.workers.ComplementConsensusThread(this,a))}},"jalview.api.AlignmentViewPanel");d(c$,"updateStrucConsensus",function(a){this.autoCalculateStrucConsensus&&(null==this.strucConsensus&&this.alignment.isNucleotide()&&this.alignment.hasRNAStructure())&&this.initRNAStructure();
null!=this.strucConsensus&&this.autoCalculateStrucConsensus&&null==this.calculator.getRegisteredWorkersOfClass(jalview.workers.StrucConsensusThread)&&this.calculator.registerWorker(new jalview.workers.StrucConsensusThread(this,a))},"jalview.api.AlignmentViewPanel");d(c$,"isCalcInProgress",function(){return this.calculator.isWorking()});e(c$,"isCalculationInProgress",function(a){return!a.autoCalculated?!1:this.calculator.workingInvolvedWith(a)?!0:!1},"jalview.datamodel.AlignmentAnnotation");e(c$,"isClosed",
function(){return null==this.alignment});e(c$,"getCalcManager",function(){return this.calculator});e(c$,"isShowSequenceLogo",function(){return this.showSequenceLogo});d(c$,"setShowSequenceLogo",function(a){a!=this.showSequenceLogo&&(this.showSequenceLogo=a,this.calculator.updateAnnotationFor(jalview.workers.ConsensusThread),this.calculator.updateAnnotationFor(jalview.workers.ComplementConsensusThread),this.calculator.updateAnnotationFor(jalview.workers.StrucConsensusThread));this.showSequenceLogo=
a},"~B");d(c$,"setShowConsensusHistogram",function(a){this.showConsensusHistogram=a},"~B");d(c$,"isShowGroupConservation",function(){return this.showGroupConservation});d(c$,"setShowGroupConservation",function(a){this.showGroupConservation=a},"~B");d(c$,"isShowGroupConsensus",function(){return this.showGroupConsensus});d(c$,"setShowGroupConsensus",function(a){this.showGroupConsensus=a},"~B");e(c$,"isShowConsensusHistogram",function(){return this.showConsensusHistogram});e(c$,"getSelectionGroup",function(){return this.selectionGroup});
e(c$,"setSelectionGroup",function(a){this.selectionGroup=a},"jalview.datamodel.SequenceGroup");d(c$,"setHiddenColumns",function(a){this.colSel=a},"jalview.datamodel.ColumnSelection");e(c$,"getColumnSelection",function(){return this.colSel});e(c$,"setColumnSelection",function(a){this.colSel=a;null!=a&&this.updateHiddenColumns()},"jalview.datamodel.ColumnSelection");e(c$,"getHiddenRepSequences",function(){return this.hiddenRepSequences});e(c$,"setHiddenRepSequences",function(a){this.hiddenRepSequences=
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this.alignment.hashCode()+"");return this.sequenceSetID});e(c$,"getViewId",function(){null==this.viewId&&(this.viewId=this.getSequenceSetId()+"."+this.hashCode()+"");return this.viewId});d(c$,"setIgnoreGapsConsensus",function(a,b){this.ignoreGapsInConsensusCalculation=a;null!=b&&(this.updateConsensus(b),null!=this.globalColourScheme&&this.globalColourScheme.setThreshold(this.globalColourScheme.getThreshold(),this.ignoreGapsInConsensusCalculation))},"~B,jalview.api.AlignmentViewPanel");d(c$,"isSelectionGroupChanged",
function(a){var b=null==this.selectionGroup||0==this.selectionGroup.getSize()?-1:this.selectionGroup.hashCode();return-1!=b&&b!=this.sgrouphash?(a&&(this.sgrouphash=b),!0):!1},"~B");d(c$,"isColSelChanged",function(a){var b=null==this.colSel||0==this.colSel.size()?-1:this.colSel.hashCode();return-1!=b&&b!=this.colselhash?(a&&(this.colselhash=b),!0):!1},"~B");e(c$,"isIgnoreGapsConsensus",function(){return this.ignoreGapsInConsensusCalculation});d(c$,"addPropertyChangeListener",function(a){this.changeSupport.addPropertyChangeListener(a)},
"java.beans.PropertyChangeListener");d(c$,"removePropertyChangeListener",function(a){this.changeSupport.removePropertyChangeListener(a)},"java.beans.PropertyChangeListener");d(c$,"firePropertyChange",function(a,b,c){this.changeSupport.firePropertyChange(a,b,c)},"~S,~O,~O");d(c$,"hideSelectedColumns",function(){1>this.colSel.size()||(this.colSel.hideSelectedColumns(),this.setSelectionGroup(null))});d(c$,"hideColumns",function(a,b){a==b?this.colSel.hideColumns(a):this.colSel.hideColumns(a,b)},"~N,~N");
d(c$,"showColumn",function(a){this.colSel.revealHiddenColumns(a)},"~N");d(c$,"showAllHiddenColumns",function(){this.colSel.revealAllHiddenColumns()});d(c$,"showAllHiddenSeqs",function(){if(0<this.alignment.getHiddenSequences().getSize()){null==this.selectionGroup&&(this.selectionGroup=new jalview.datamodel.SequenceGroup,this.selectionGroup.setEndRes(this.alignment.getWidth()-1));for(var a,b=this.alignment.getHiddenSequences().showAll(this.hiddenRepSequences).iterator();b.hasNext()&&((a=b.next())||
1);)this.selectionGroup.addSequence(a,!1),this.setSequenceAnnotationsVisible(a,!0);this.hiddenRepSequences=null;this.firePropertyChange("alignment",null,this.alignment.getSequences());this.sendSelection()}});d(c$,"showSequence",function(a){a=this.alignment.getHiddenSequences().showSequence(a,this.hiddenRepSequences);if(0<a.size()){null==this.selectionGroup&&(this.selectionGroup=new jalview.datamodel.SequenceGroup,this.selectionGroup.setEndRes(this.alignment.getWidth()-1));var b;for(a=a.iterator();a.hasNext()&&
((b=a.next())||1);)this.selectionGroup.addSequence(b,!1),this.setSequenceAnnotationsVisible(b,!0);this.firePropertyChange("alignment",null,this.alignment.getSequences());this.sendSelection()}},"~N");d(c$,"hideAllSelectedSeqs",function(){if(!(null==this.selectionGroup||1>this.selectionGroup.getSize())){var a=this.selectionGroup.getSequencesInOrder(this.alignment);this.hideSequence(a);this.setSelectionGroup(null)}});d(c$,"hideSequence",function(a){if(null!=a){for(var b=0;b<a.length;b++)this.alignment.getHiddenSequences().hideSequence(a[b]),
this.setSequenceAnnotationsVisible(a[b],!1);this.firePropertyChange("alignment",null,this.alignment.getSequences())}},"~A");d(c$,"setSequenceAnnotationsVisible",function(a,b){for(var c,f=0,d=this.alignment.getAlignmentAnnotation();f<d.length&&((c=d[f])||1);f++)c.sequenceRef===a&&(c.visible=b)},"jalview.datamodel.SequenceI,~B");d(c$,"hideRepSequences",function(a,b){var c=b.getSize();if(!(2>c)){null==this.hiddenRepSequences&&(this.hiddenRepSequences=new java.util.Hashtable);this.hiddenRepSequences.put(a,
b);for(var f=Array(c-1),d=0,e=0;e<c;e++)if(b.getSequenceAt(e)!==a){if(d==c-1)return;f[d++]=b.getSequenceAt(e)}b.setSeqrep(a);b.setHidereps(!0);this.hideSequence(f)}},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup");d(c$,"isHiddenRepSequence",function(a){return this.alignment.getSeqrep()===a||null!=this.hiddenRepSequences&&this.hiddenRepSequences.containsKey(a)},"jalview.datamodel.SequenceI");d(c$,"getRepresentedSequences",function(a){return null==this.hiddenRepSequences?null:this.hiddenRepSequences.get(a)},
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b)}else a=this.selectionGroup.getSelectionAsNewSequences(this.alignment);return a});e(c$,"getSequenceSelection",function(){var a=null;null!=this.selectionGroup&&(a=this.selectionGroup.getSequencesInOrder(this.alignment));null==a&&(a=this.alignment.getSequencesArray());return a});e(c$,"getViewAsCigars",function(a){return new jalview.datamodel.CigarArray(this.alignment,this.colSel,a?this.selectionGroup:null)},"~B");d(c$,"getAlignmentView",function(a){return this.getAlignmentView(a,!1)},"~B");d(c$,"getAlignmentView",
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b=Array(f);if(null!=this.colSel&&this.colSel.hasHiddenColumns())b=this.colSel.getVisibleSequenceStrings(d,e,c);else for(a=0;a<f;a++)b[a]=c[a].getSequenceAsString(d,e);return b},"~B");e(c$,"getVisibleRegionBoundaries",function(a,b){var c=new java.util.ArrayList,f=a,d=b;do null!=this.colSel&&this.colSel.hasHiddenColumns()&&(0==f&&(f=this.colSel.adjustForHiddenColumns(f)),d=this.colSel.getHiddenBoundaryRight(f),f==d&&(d=b),d>b&&(d=b)),c.add(w(-1,[f,d])),null!=this.colSel&&this.colSel.hasHiddenColumns()&&
(f=this.colSel.adjustForHiddenColumns(d),f=this.colSel.getHiddenBoundaryLeft(f)+1);while(d<b);w(c.size(),2,0);return c},"~N,~N");e(c$,"getVisibleAlignmentAnnotation",function(a){var b=new java.util.ArrayList,c;if(null!=(c=this.alignment.getAlignmentAnnotation()))for(var f,d=0;d<c.length&&((f=c[d])||1);d++){var e=new jalview.datamodel.AlignmentAnnotation(f);a&&null!=this.selectionGroup?this.colSel.makeVisibleAnnotation(this.selectionGroup.getStartRes(),this.selectionGroup.getEndRes(),e):this.colSel.makeVisibleAnnotation(e);
b.add(e)}return b},"~B");e(c$,"isPadGaps",function(){return this.padGaps});e(c$,"setPadGaps",function(a){this.padGaps=a},"~B");e(c$,"alignmentChanged",function(a){this.isPadGaps()&&this.alignment.padGaps();this.autoCalculateConsensus&&this.updateConsensus(a);null!=this.hconsensus&&this.autoCalculateConsensus&&this.updateConservation(a);this.autoCalculateStrucConsensus&&this.updateStrucConsensus(a);a=this.alignment.getWidth();var b=this.alignment.getGroups();if(null!=b)for(var c,b=b.iterator();b.hasNext()&&
((c=b.next())||1);)c.getEndRes()>a&&c.setEndRes(a-1);null!=this.selectionGroup&&this.selectionGroup.getEndRes()>a&&this.selectionGroup.setEndRes(a-1);this.resetAllColourSchemes();this.calculator.restartWorkers()},"jalview.api.AlignmentViewPanel");d(c$,"resetAllColourSchemes",function(){var a=this.globalColourScheme;null!=a&&(a.alignmentChanged(this.alignment,this.hiddenRepSequences),a.setConsensus(this.hconsensus),a.conservationApplied()&&a.setConservation(jalview.analysis.Conservation.calculateConservation("All",
jalview.schemes.ResidueProperties.propHash,3,this.alignment.getSequences(),0,this.alignment.getWidth(),!1,this.getConsPercGaps(),!1)));for(var b,a=this.alignment.getGroups().iterator();a.hasNext()&&((b=a.next())||1);)null!=b.cs&&b.cs.alignmentChanged(b,this.hiddenRepSequences),b.recalcConservation()});d(c$,"initAutoAnnotation",function(){null==this.hconsensus&&!this.$isDataset&&(this.alignment.isNucleotide()?this.initRNAStructure():(this.initConservation(),this.initQuality()),this.consensus=new jalview.datamodel.AlignmentAnnotation("Consensus",
"PID",Array(1),0,100,1),this.initConsensus(this.consensus),this.initComplementConsensus())});d(c$,"initComplementConsensus",function(){if(!this.alignment.isNucleotide()){var a=this.alignment.getCodonFrames();null!=a&&!a.isEmpty()&&(this.complementConsensus=new jalview.datamodel.AlignmentAnnotation("cDNA Consensus","PID for cDNA",Array(1),0,100,1),this.initConsensus(this.complementConsensus))}});d(c$,"initConsensus",function(a){a.hasText=!0;a.autoCalculated=!0;this.showConsensus&&this.alignment.addAnnotation(a)},
"jalview.datamodel.AlignmentAnnotation");d(c$,"initConservation",function(){this.showConservation&&null==this.conservation&&(this.conservation=new jalview.datamodel.AlignmentAnnotation("Conservation","Conservation of total alignment less than "+this.getConsPercGaps()+"% gaps",Array(1),0,11,1),this.conservation.hasText=!0,this.conservation.autoCalculated=!0,this.alignment.addAnnotation(this.conservation))});d(c$,"initQuality",function(){this.showQuality&&null==this.quality&&(this.quality=new jalview.datamodel.AlignmentAnnotation("Quality",
"Alignment Quality based on Blosum62 scores",Array(1),0,11,1),this.quality.hasText=!0,this.quality.autoCalculated=!0,this.alignment.addAnnotation(this.quality))});d(c$,"initRNAStructure",function(){this.alignment.hasRNAStructure()&&null==this.strucConsensus&&(this.strucConsensus=new jalview.datamodel.AlignmentAnnotation("StrucConsensus","PID",Array(1),0,100,1),this.strucConsensus.hasText=!0,this.strucConsensus.autoCalculated=!0,this.showConsensus&&this.alignment.addAnnotation(this.strucConsensus))});
e(c$,"calcPanelHeight",function(){var a=this.getAlignment().getAlignmentAnnotation(),b=0,c=this.getCharHeight();if(null!=a)for(var f=new java.util.BitSet,d,e=0;e<a.length&&((d=a[e])||1);e++)if(null==d)System.err.println("Null annotation row: ignoring.");else if(d.visible){if(-1<d.graphGroup)if(f.get(d.graphGroup))continue;else f.set(d.graphGroup);d.height=0;d.hasText&&(d.height+=c);d.hasIcons&&(d.height+=16);0<d.graph&&(d.height+=d.graphHeight);0==d.height&&(d.height=20);b+=d.height}0==b&&(b=20);
return b});e(c$,"updateGroupAnnotationSettings",function(a,b){var c=!1,f=this.isShowGroupConservation(),d=this.isShowGroupConsensus(),e=this.isShowSequenceLogo(),g=this.isShowConsensusHistogram(),h=this.isNormaliseSequenceLogo(),c=this.alignment.getAlignmentAnnotation(),j=new java.util.ArrayList;if(null!=c)for(var n=0;n<c.length;n++)c[n].autoCalculated&&null!=c[n].groupRef&&(j.add(c[n].groupRef),this.alignment.deleteAnnotation(c[n],!1));if(null!=this.alignment.getGroups())for(var x,n=this.alignment.getGroups().iterator();n.hasNext()&&
((x=n.next())||1);){c=!1;if(a||!b&&!j.contains(x))x.setshowSequenceLogo(e),x.setShowConsensusHistogram(g),x.setNormaliseSequenceLogo(h);f&&(c=!0,this.alignment.addAnnotation(x.getConservationRow(),0));d&&(c=!0,this.alignment.addAnnotation(x.getConsensus(),0));c&&x.recalcConservation()}j.clear()},"~B,~B");d(c$,"isDisplayReferenceSeq",function(){return this.alignment.hasSeqrep()&&this.viewStyle.isDisplayReferenceSeq()});d(c$,"setDisplayReferenceSeq",function(a){this.viewStyle.setDisplayReferenceSeq(a)},
"~B");d(c$,"isColourByReferenceSeq",function(){return this.alignment.hasSeqrep()&&this.viewStyle.isColourByReferenceSeq()});e(c$,"getSequenceColour",function(a){a=this.sequenceColours.get(a);return null==a?java.awt.Color.white:a},"jalview.datamodel.SequenceI");e(c$,"setSequenceColour",function(a,b){null==b?this.sequenceColours.remove(a):this.sequenceColours.put(a,b)},"jalview.datamodel.SequenceI,java.awt.Color");e(c$,"updateSequenceIdColours",function(){for(var a,b=this.alignment.getGroups().iterator();b.hasNext()&&
((a=b.next())||1);)if(null!=a.idColour)for(var c,f=a.getSequences(this.getHiddenRepSequences()).iterator();f.hasNext()&&((c=f.next())||1);)this.sequenceColours.put(c,a.idColour)});e(c$,"clearSequenceColours",function(){this.sequenceColours.clear()});d(c$,"getCodingComplement",function(){return this.codingComplement});d(c$,"setCodingComplement",function(a){this===a?System.err.println("Ignoring recursive setCodingComplement request"):(this.codingComplement=a,a.getCodingComplement()!==this&&a.setCodingComplement(this))},
"jalview.api.AlignViewportI");e(c$,"isNucleotide",function(){return null==this.getAlignment()?!1:this.getAlignment().isNucleotide()});e(c$,"getFeaturesDisplayed",function(){return this.featuresDisplayed});e(c$,"setFeaturesDisplayed",function(a){this.featuresDisplayed=a},"jalview.api.FeaturesDisplayedI");e(c$,"areFeaturesDisplayed",function(){return null!=this.featuresDisplayed&&0<this.featuresDisplayed.getRegisterdFeaturesCount()});d(c$,"setShowSequenceFeatures",function(a){this.viewStyle.setShowSequenceFeatures(a)},
"~B");d(c$,"isShowSequenceFeatures",function(){return this.viewStyle.isShowSequenceFeatures()});d(c$,"setShowSequenceFeaturesHeight",function(a){this.viewStyle.setShowSequenceFeaturesHeight(a)},"~B");d(c$,"isShowSequenceFeaturesHeight",function(){return this.viewStyle.isShowSequenceFeaturesHeight()});d(c$,"setShowAnnotation",function(a){this.viewStyle.setShowAnnotation(a)},"~B");d(c$,"isShowAnnotation",function(){return this.viewStyle.isShowAnnotation()});d(c$,"isRightAlignIds",function(){return this.viewStyle.isRightAlignIds()});
d(c$,"setRightAlignIds",function(a){this.viewStyle.setRightAlignIds(a)},"~B");d(c$,"getConservationSelected",function(){return this.viewStyle.getConservationSelected()});d(c$,"setShowBoxes",function(a){this.viewStyle.setShowBoxes(a)},"~B");d(c$,"getTextColour",function(){return this.viewStyle.getTextColour()});d(c$,"getTextColour2",function(){return this.viewStyle.getTextColour2()});d(c$,"getThresholdTextColour",function(){return this.viewStyle.getThresholdTextColour()});d(c$,"isConservationColourSelected",
function(){return this.viewStyle.isConservationColourSelected()});d(c$,"isRenderGaps",function(){return this.viewStyle.isRenderGaps()});d(c$,"isShowColourText",function(){return this.viewStyle.isShowColourText()});d(c$,"setConservationColourSelected",function(a){this.viewStyle.setConservationColourSelected(a)},"~B");d(c$,"setShowColourText",function(a){this.viewStyle.setShowColourText(a)},"~B");d(c$,"setTextColour",function(a){this.viewStyle.setTextColour(a)},"java.awt.Color");d(c$,"setThresholdTextColour",
function(a){this.viewStyle.setThresholdTextColour(a)},"~N");d(c$,"setTextColour2",function(a){this.viewStyle.setTextColour2(a)},"java.awt.Color");e(c$,"getViewStyle",function(){return new jalview.viewmodel.styles.ViewStyle(this.viewStyle)});e(c$,"setViewStyle",function(a){this.viewStyle=new jalview.viewmodel.styles.ViewStyle(a)},"jalview.api.ViewStyleI");d(c$,"sameStyle",function(a){return this.viewStyle.sameStyle(a)},"jalview.api.ViewStyleI");d(c$,"getIdWidth",function(){return this.viewStyle.getIdWidth()});
d(c$,"setIdWidth",function(a){this.viewStyle.setIdWidth(a)},"~N");d(c$,"isCentreColumnLabels",function(){return this.viewStyle.isCentreColumnLabels()});d(c$,"setCentreColumnLabels",function(a){this.viewStyle.setCentreColumnLabels(a)},"~B");d(c$,"setShowDBRefs",function(a){this.viewStyle.setShowDBRefs(a)},"~B");d(c$,"isShowDBRefs",function(){return this.viewStyle.isShowDBRefs()});d(c$,"isShowNPFeats",function(){return this.viewStyle.isShowNPFeats()});d(c$,"setShowNPFeats",function(a){this.viewStyle.setShowNPFeats(a)},
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d(c$,"setHistoryList",function(a){this.historyList=a},"java.util.Deque");d(c$,"getHistoryList",function(){return this.historyList});d(c$,"setRedoList",function(a){this.redoList=a},"java.util.Deque");d(c$,"getRedoList",function(){return this.redoList});e(c$,"getVamsasSource",function(){return this});d(c$,"getSortAnnotationsBy",function(){return this.sortAnnotationsBy});d(c$,"setSortAnnotationsBy",function(a){this.sortAnnotationsBy=a},"jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");d(c$,
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["java.lang.Boolean"],function(){c$=s(function(){this.abovePIDThreshold=!1;this.charWidth=this.charHeight=0;this.idWidth=-1;this.displayReferenceSeq=this.conservationColourSelected=this.colourByReferenceSeq=this.shownpfeats=this.showdbrefs=this.centreColumnLabels=this.colourAppliesToAllGroups=!1;this.increment=0;this.renderGaps=!0;this.scaleAboveWrapped=this.rightAlignIds=!1;this.scaleRightWrapped=this.scaleLeftWrapped=!0;this.seqNameItalics=!1;this.showBoxes=this.showAnnotation=!0;this.showColourText=
!1;this.showJVSuffix=this.showHiddenMarkers=!0;this.showSequenceFeatures=this.showSeqFeaturesHeight=!1;this.showText=!0;this.showUnconserved=!1;this.textColour2=this.textColour=null;this.thresholdTextColour=this.threshold=0;this.upperCasebold=!1;this.fontName=null;this.fontSize=0;this.scaleProteinAsCdna=!0;this.wrapAlignment=!1;this.fontStyle=this.wrappedWidth=0;r(this,arguments)},jalview.viewmodel.styles,"ViewStyle",null,jalview.api.ViewStyleI);J(c$,function(){this.textColour=java.awt.Color.black;
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this.setDisplayReferenceSeq(a.isDisplayReferenceSeq());this.setFontName(a.getFontName());this.setFontSize(a.getFontSize());this.setFontStyle(a.getFontStyle());this.setIdWidth(a.getIdWidth());this.setIncrement(a.getIncrement());this.setRenderGaps(a.isRenderGaps());this.setRightAlignIds(a.isRightAlignIds());this.setScaleAboveWrapped(a.getScaleAboveWrapped());this.setScaleLeftWrapped(a.getScaleLeftWrapped());this.setScaleProteinAsCdna(a.isScaleProteinAsCdna());this.setScaleRightWrapped(a.getScaleRightWrapped());
this.setSeqNameItalics(a.isSeqNameItalics());this.setShowAnnotation(a.isShowAnnotation());this.setShowBoxes(a.getShowBoxes());this.setShowColourText(a.isShowColourText());this.setShowDBRefs(a.isShowDBRefs());this.setShowHiddenMarkers(a.getShowHiddenMarkers());this.setShowJVSuffix(a.getShowJVSuffix());this.setShowNPFeats(a.isShowNPFeats());this.setShowSequenceFeaturesHeight(a.isShowSequenceFeaturesHeight());this.setShowSequenceFeatures(a.isShowSequenceFeatures());this.setShowText(a.getShowText());
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this.getFontSize()==a.getFontSize()&&this.getFontStyle()==a.getFontStyle()&&this.getIdWidth()==a.getIdWidth()&&this.getIncrement()==a.getIncrement()&&this.isRenderGaps()==a.isRenderGaps()&&this.isRightAlignIds()==a.isRightAlignIds()&&this.getScaleAboveWrapped()==a.getScaleAboveWrapped()&&this.getScaleLeftWrapped()==a.getScaleLeftWrapped()&&this.isScaleProteinAsCdna()==a.isScaleProteinAsCdna()&&this.getScaleRightWrapped()==a.getScaleRightWrapped()&&this.isSeqNameItalics()==a.isSeqNameItalics()&&this.isShowAnnotation()==
a.isShowAnnotation()&&this.getShowBoxes()==a.getShowBoxes()&&this.isShowColourText()==a.isShowColourText()&&this.isShowDBRefs()==a.isShowDBRefs()&&this.getShowHiddenMarkers()==a.getShowHiddenMarkers()&&this.getShowJVSuffix()==a.getShowJVSuffix()&&this.isShowNPFeats()==a.isShowNPFeats()&&this.isShowSequenceFeaturesHeight()==a.isShowSequenceFeaturesHeight()&&this.isShowSequenceFeatures()==a.isShowSequenceFeatures()&&this.getShowText()==a.getShowText()&&this.getShowUnconserved()==a.getShowUnconserved()&&
this.getThreshold()==a.getThreshold()&&this.getThresholdTextColour()==a.getThresholdTextColour()&&this.isUpperCasebold()==a.isUpperCasebold()&&this.getWrapAlignment()==a.getWrapAlignment()&&this.getWrappedWidth()==a.getWrappedWidth();return b=(b=(b=b&&String.valueOf(this.getFontName()).equals(String.valueOf(a.getFontName())))&&String.valueOf(this.getTextColour()).equals(String.valueOf(a.getTextColour())))&&String.valueOf(this.getTextColour2()).equals(String.valueOf(a.getTextColour2()))},"~O");e(c$,
"hashCode",function(){var a,b=1;a=0+b++*Boolean.$valueOf(this.abovePIDThreshold).hashCode();a+=b++*Boolean.$valueOf(this.centreColumnLabels).hashCode();a+=b++*Boolean.$valueOf(this.colourAppliesToAllGroups).hashCode();a+=b++*Boolean.$valueOf(this.displayReferenceSeq).hashCode();a+=b++*Boolean.$valueOf(this.renderGaps).hashCode();a+=b++*Boolean.$valueOf(this.rightAlignIds).hashCode();a+=b++*Boolean.$valueOf(this.scaleProteinAsCdna).hashCode();a+=b++*Boolean.$valueOf(this.scaleRightWrapped).hashCode();
a+=b++*Boolean.$valueOf(this.seqNameItalics).hashCode();a+=b++*Boolean.$valueOf(this.showAnnotation).hashCode();a+=b++*Boolean.$valueOf(this.showBoxes).hashCode();a+=b++*Boolean.$valueOf(this.showdbrefs).hashCode();a+=b++*Boolean.$valueOf(this.showJVSuffix).hashCode();a+=b++*Boolean.$valueOf(this.showSequenceFeatures).hashCode();a+=b++*Boolean.$valueOf(this.showUnconserved).hashCode();a+=b++*Boolean.$valueOf(this.wrapAlignment).hashCode();a+=b++*this.charHeight;a+=b++*this.charWidth;a+=b++*this.fontSize;
a+=b++*this.fontStyle;a+=b++*this.idWidth;return a+=String.valueOf(this.fontName).hashCode()});d(c$,"isUpperCasebold",function(){return this.upperCasebold});e(c$,"setUpperCasebold",function(a){this.upperCasebold=a},"~B");d(c$,"getAbovePIDThreshold",function(){return this.abovePIDThreshold});d(c$,"getCharHeight",function(){return this.charHeight});d(c$,"getCharWidth",function(){return this.charWidth});d(c$,"getColourAppliesToAllGroups",function(){return this.colourAppliesToAllGroups});d(c$,"getColourText",
function(){return this.showColourText});d(c$,"getConservationSelected",function(){return this.conservationColourSelected});d(c$,"getIncrement",function(){return this.increment});d(c$,"getScaleAboveWrapped",function(){return this.scaleAboveWrapped});d(c$,"getScaleLeftWrapped",function(){return this.scaleLeftWrapped});d(c$,"getScaleRightWrapped",function(){return this.scaleRightWrapped});d(c$,"getShowBoxes",function(){return this.showBoxes});d(c$,"getShowHiddenMarkers",function(){return this.showHiddenMarkers});
d(c$,"getShowJVSuffix",function(){return this.showJVSuffix});d(c$,"getShowText",function(){return this.showText});d(c$,"getShowUnconserved",function(){return this.showUnconserved});d(c$,"getTextColour",function(){return this.textColour});d(c$,"getTextColour2",function(){return this.textColour2});d(c$,"getThreshold",function(){return this.threshold});d(c$,"getThresholdTextColour",function(){return this.thresholdTextColour});d(c$,"getWrapAlignment",function(){return this.wrapAlignment});d(c$,"getWrappedWidth",
function(){return this.wrappedWidth});d(c$,"isColourByReferenceSeq",function(){return this.colourByReferenceSeq});d(c$,"isConservationColourSelected",function(){return this.conservationColourSelected});d(c$,"isDisplayReferenceSeq",function(){return this.displayReferenceSeq});d(c$,"isRenderGaps",function(){return this.renderGaps});d(c$,"isRightAlignIds",function(){return this.rightAlignIds});d(c$,"isSeqNameItalics",function(){return this.seqNameItalics});d(c$,"isShowAnnotation",function(){return this.showAnnotation});
d(c$,"isShowColourText",function(){return this.showColourText});d(c$,"isShowSequenceFeaturesHeight",function(){return this.showSeqFeaturesHeight});d(c$,"isShowSequenceFeatures",function(){return this.showSequenceFeatures});e(c$,"setAbovePIDThreshold",function(a){this.abovePIDThreshold=a},"~B");e(c$,"setCharHeight",function(a){this.charHeight=a},"~N");e(c$,"setCharWidth",function(a){this.charWidth=a},"~N");e(c$,"setColourAppliesToAllGroups",function(a){this.colourAppliesToAllGroups=a},"~B");e(c$,"setColourByReferenceSeq",
function(a){this.colourByReferenceSeq=a},"~B");e(c$,"setColourText",function(a){this.showColourText=a},"~B");e(c$,"setConservationColourSelected",function(a){this.conservationColourSelected=a},"~B");e(c$,"setConservationSelected",function(a){this.conservationColourSelected=a},"~B");e(c$,"setDisplayReferenceSeq",function(a){this.displayReferenceSeq=a},"~B");e(c$,"setIncrement",function(a){this.increment=a},"~N");e(c$,"setRenderGaps",function(a){this.renderGaps=a},"~B");e(c$,"setRightAlignIds",function(a){this.rightAlignIds=
a},"~B");e(c$,"setScaleAboveWrapped",function(a){this.scaleAboveWrapped=a},"~B");e(c$,"setScaleLeftWrapped",function(a){this.scaleLeftWrapped=a},"~B");e(c$,"setScaleRightWrapped",function(a){this.scaleRightWrapped=a},"~B");e(c$,"setSeqNameItalics",function(a){this.seqNameItalics=a},"~B");e(c$,"setShowAnnotation",function(a){this.showAnnotation=a},"~B");e(c$,"setShowBoxes",function(a){this.showBoxes=a},"~B");e(c$,"setShowColourText",function(a){this.showColourText=a},"~B");e(c$,"setShowHiddenMarkers",
function(a){this.showHiddenMarkers=a},"~B");e(c$,"setShowJVSuffix",function(a){this.showJVSuffix=a},"~B");e(c$,"setShowSequenceFeaturesHeight",function(a){this.showSeqFeaturesHeight=a},"~B");e(c$,"setShowSequenceFeatures",function(a){this.showSequenceFeatures=a},"~B");e(c$,"setShowText",function(a){this.showText=a},"~B");e(c$,"setShowUnconserved",function(a){this.showUnconserved=a},"~B");e(c$,"setTextColour",function(a){this.textColour=a},"java.awt.Color");e(c$,"setTextColour2",function(a){this.textColour2=
a},"java.awt.Color");e(c$,"setThreshold",function(a){this.threshold=a},"~N");e(c$,"setThresholdTextColour",function(a){this.thresholdTextColour=a},"~N");e(c$,"setWrapAlignment",function(a){this.wrapAlignment=a},"~B");e(c$,"setWrappedWidth",function(a){this.wrappedWidth=a},"~N");e(c$,"sameStyle",function(a){return this.equals(a)},"jalview.api.ViewStyleI");d(c$,"getFontName",function(){return this.fontName});d(c$,"getFontSize",function(){return this.fontSize});d(c$,"getFontStyle",function(){return this.fontStyle});
e(c$,"setFontName",function(a){this.fontName=a},"~S");e(c$,"setFontSize",function(a){this.fontSize=a},"~N");e(c$,"setFontStyle",function(a){this.fontStyle=a},"~N");d(c$,"getIdWidth",function(){return this.idWidth});e(c$,"setIdWidth",function(a){this.idWidth=a},"~N");d(c$,"isCentreColumnLabels",function(){return this.centreColumnLabels});e(c$,"setCentreColumnLabels",function(a){this.centreColumnLabels=a},"~B");d(c$,"isShowDBRefs",function(){return this.showdbrefs});e(c$,"setShowDBRefs",function(a){this.showdbrefs=
a},"~B");d(c$,"isShowNPFeats",function(){return this.shownpfeats});e(c$,"setShowNPFeats",function(a){this.shownpfeats=a},"~B");d(c$,"isScaleProteinAsCdna",function(){return this.scaleProteinAsCdna});e(c$,"setScaleProteinAsCdna",function(a){this.scaleProteinAsCdna=a},"~B")});p("jalview.workers");q(["jalview.api.AlignCalcManagerI","java.util.ArrayList","$.Collections","$.HashSet","$.Hashtable"],"jalview.workers.AlignCalcManager",null,function(){c$=s(function(){this.canUpdate=this.updating=this.inProgress=
this.blackList=this.restartable=null;r(this,arguments)},jalview.workers,"AlignCalcManager",null,jalview.api.AlignCalcManagerI);J(c$,function(){this.restartable=java.util.Collections.synchronizedList(new java.util.ArrayList);this.blackList=java.util.Collections.synchronizedList(new java.util.ArrayList);this.inProgress=java.util.Collections.synchronizedMap(new java.util.Hashtable);this.updating=java.util.Collections.synchronizedMap(new java.util.Hashtable);this.canUpdate=new java.util.HashSet});e(c$,
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return null==a?0:a.size()},"jalview.api.AlignCalcWorkerI");e(c$,"notifyWorking",function(a){if(null!=this.inProgress.get(a.getClass()))return!1;this.inProgress.put(a.getClass(),a);return!0},"jalview.api.AlignCalcWorkerI");e(c$,"workerComplete",function(a){this.inProgress.remove(a.getClass());var b=this.updating.get(a.getClass());null!=b&&(b.remove(a),this.canUpdate.add(a))},"jalview.api.AlignCalcWorkerI");e(c$,"workerCannotRun",function(a){this.blackList.add(a.getClass())},"jalview.api.AlignCalcWorkerI");
d(c$,"isBlackListed",function(a){return this.blackList.contains(a)},"Class");e(c$,"startWorker",function(a){var b=a;b.isAlive()&&(b.interrupt(),a=a.getNewWorker());a.setName(a.getClass().getName());a.start()},"jalview.api.AlignCalcWorkerI");d(c$,"isWorking",function(a){return null!=a&&this.inProgress.get(a.getClass())===a},"jalview.api.AlignCalcWorkerI");d(c$,"isWorking",function(){return 0<this.inProgress.size()});e(c$,"registerWorker",function(a){this.restartable.contains(a)||this.restartable.add(a);
this.startWorker(a)},"jalview.api.AlignCalcWorkerI");e(c$,"restartWorkers",function(){for(var a,b=this.restartable.iterator();b.hasNext()&&((a=b.next())||1);)this.startWorker(a)});e(c$,"workingInvolvedWith",function(a){for(var b,c=this.inProgress.values().iterator();c.hasNext()&&((b=c.next())||1);)if(b.involves(a))return!0;for(var f,d=this.updating.values().iterator();d.hasNext()&&((f=d.next())||1);)for(c=f.iterator();c.hasNext()&&((b=c.next())||1);)if(b.involves(a))return!0;return!1},"jalview.datamodel.AlignmentAnnotation");
e(c$,"updateAnnotationFor",function(a){for(var b,c=0,f=this.canUpdate.toArray([]);c<f.length&&((b=f[c])||1);c++)a.equals(b.getClass())&&b.updateAnnotation()},"Class");e(c$,"getRegisteredWorkersOfClass",function(a){for(var b=new java.util.ArrayList,c,f=0,d=this.canUpdate.toArray(Array(this.canUpdate.size()));f<d.length&&((c=d[f])||1);f++)a.equals(c.getClass())&&b.add(c);return 0==b.size()?null:b},"Class");e(c$,"startRegisteredWorkersOfClass",function(a){var b=this.getRegisteredWorkersOfClass(a);if(null==
b)return!1;for(var c,b=b.iterator();b.hasNext()&&((c=b.next())||1);)this.isPending(c)?System.err.println("Pending exists for "+a):this.startWorker(c);return!0},"Class");e(c$,"workerMayRun",function(a){this.blackList.contains(a.getClass())&&this.blackList.remove(a.getClass())},"jalview.api.AlignCalcWorkerI");e(c$,"removeRegisteredWorkersOfClass",function(a){this.getRegisteredWorkersOfClass(a);for(var b=new java.util.ArrayList,c=new java.util.HashSet,f,d=this.restartable.iterator();d.hasNext()&&((f=
d.next())||1);)a.equals(f.getClass())&&(b.add(f),c.add(f));this.restartable.removeAll(b);for(d=this.canUpdate.iterator();d.hasNext()&&((f=d.next())||1);)a.equals(f.getClass())&&(b.add(f),c.add(f));this.canUpdate.removeAll(b)},"Class")});p("jalview.api");M(jalview.api,"AlignCalcManagerI");p("java.util");q(["java.util.AbstractCollection","$.Iterator","java.util.Deque"],"java.util.ArrayDeque","java.lang.AssertionError $.IllegalStateException $.NullPointerException java.lang.reflect.Array java.util.Arrays $.ConcurrentModificationException $.NoSuchElementException".split(" "),
function(){c$=s(function(){this.elements=null;this.tail=this.head=0;H("java.util.ArrayDeque.DeqIterator")||java.util.ArrayDeque.$ArrayDeque$DeqIterator$();H("java.util.ArrayDeque.DescendingIterator")||java.util.ArrayDeque.$ArrayDeque$DescendingIterator$();r(this,arguments)},java.util,"ArrayDeque",java.util.AbstractCollection,[java.util.Deque,Cloneable,java.io.Serializable]);d(c$,"allocateElements",function(a){var b=8;a>=b&&(b=a,b|=b>>>1,b|=b>>>2,b|=b>>>4,b|=b>>>8,b|=b>>>16,b++,0>b&&(b>>>=1));this.elements=
Array(b)},"~N");d(c$,"doubleCapacity",function(){var a=this.head,b=this.elements.length,c=b-a,f=b<<1;if(0>f)throw new IllegalStateException("Sorry, deque too big");f=Array(f);System.arraycopy(this.elements,a,f,0,c);System.arraycopy(this.elements,0,f,c,a);this.elements=f;this.head=0;this.tail=b});d(c$,"copyElements",function(a){if(this.head<this.tail)System.arraycopy(this.elements,this.head,a,0,this.size());else if(this.head>this.tail){var b=this.elements.length-this.head;System.arraycopy(this.elements,
this.head,a,0,b);System.arraycopy(this.elements,0,a,b,this.tail)}return a},"~A");m(c$,function(){t(this,java.util.ArrayDeque,[]);this.elements=Array(16)});m(c$,function(a){t(this,java.util.ArrayDeque,[]);this.allocateElements(a)},"~N");m(c$,function(a){t(this,java.util.ArrayDeque,[]);this.allocateElements(a.size());this.addAll(a)},"java.util.Collection");e(c$,"addFirst",function(a){if(null==a)throw new NullPointerException;this.elements[this.head=this.head-1&this.elements.length-1]=a;this.head==this.tail&&
this.doubleCapacity()},"~O");e(c$,"addLast",function(a){if(null==a)throw new NullPointerException;this.elements[this.tail]=a;(this.tail=this.tail+1&this.elements.length-1)==this.head&&this.doubleCapacity()},"~O");e(c$,"offerFirst",function(a){this.addFirst(a);return!0},"~O");e(c$,"offerLast",function(a){this.addLast(a);return!0},"~O");e(c$,"removeFirst",function(){var a=this.pollFirst();if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"removeLast",function(){var a=this.pollLast();
if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"pollFirst",function(){var a=this.head,b=this.elements[a];if(null==b)return null;this.elements[a]=null;this.head=a+1&this.elements.length-1;return b});e(c$,"pollLast",function(){var a=this.tail-1&this.elements.length-1,b=this.elements[a];if(null==b)return null;this.elements[a]=null;this.tail=a;return b});e(c$,"getFirst",function(){var a=this.elements[this.head];if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,
"getLast",function(){var a=this.elements[this.tail-1&this.elements.length-1];if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"peekFirst",function(){return this.elements[this.head]});e(c$,"peekLast",function(){return this.elements[this.tail-1&this.elements.length-1]});e(c$,"removeFirstOccurrence",function(a){if(null==a)return!1;for(var b=this.elements.length-1,c=this.head,f;null!=(f=this.elements[c]);){if(a.equals(f))return this.$delete(c),!0;c=c+1&b}return!1},"~O");e(c$,"removeLastOccurrence",
function(a){if(null==a)return!1;for(var b=this.elements.length-1,c=this.tail-1&b,f;null!=(f=this.elements[c]);){if(a.equals(f))return this.$delete(c),!0;c=c-1&b}return!1},"~O");e(c$,"add",function(a){this.addLast(a);return!0},"~O");e(c$,"offer",function(a){return this.offerLast(a)},"~O");d(c$,"remove",function(){return this.removeFirst()});e(c$,"poll",function(){return this.pollFirst()});e(c$,"element",function(){return this.getFirst()});e(c$,"peek",function(){return this.peekFirst()});e(c$,"push",
function(a){this.addFirst(a)},"~O");e(c$,"pop",function(){return this.removeFirst()});d(c$,"checkInvariants",function(){});d(c$,"$delete",function(a){this.checkInvariants();var b=this.elements,c=b.length-1,f=this.head,d=this.tail,e=a-f&c,g=d-a&c;if(e>=(d-f&c))throw new java.util.ConcurrentModificationException;if(e<g)return f<=a?System.arraycopy(b,f,b,f+1,e):(System.arraycopy(b,0,b,1,a),b[0]=b[c],System.arraycopy(b,f,b,f+1,c-f)),b[f]=null,this.head=f+1&c,!1;a<d?(System.arraycopy(b,a+1,b,a,g),this.tail=
d-1):(System.arraycopy(b,a+1,b,a,c-a),b[c]=b[0],System.arraycopy(b,1,b,0,d),this.tail=d-1&c);return!0},"~N");e(c$,"size",function(){return this.tail-this.head&this.elements.length-1});e(c$,"isEmpty",function(){return this.head==this.tail});e(c$,"iterator",function(){return C(java.util.ArrayDeque.DeqIterator,this,null)});e(c$,"descendingIterator",function(){return C(java.util.ArrayDeque.DescendingIterator,this,null)});e(c$,"contains",function(a){if(null==a)return!1;for(var b=this.elements.length-1,
c=this.head,f;null!=(f=this.elements[c]);){if(a.equals(f))return!0;c=c+1&b}return!1},"~O");d(c$,"remove",function(a){return this.removeFirstOccurrence(a)},"~O");e(c$,"clear",function(){var a=this.head,b=this.tail;if(a!=b){this.head=this.tail=0;var c=this.elements.length-1;do this.elements[a]=null,a=a+1&c;while(a!=b)}});d(c$,"toArray",function(){return this.copyElements(Array(this.size()))});d(c$,"toArray",function(a){var b=this.size();a.length<b&&(a=java.lang.reflect.Array.newInstance(a.getClass().getComponentType(),
b));this.copyElements(a);a.length>b&&(a[b]=null);return a},"~A");d(c$,"clone",function(){try{var a=K(this,java.util.ArrayDeque,"clone",[]);a.elements=java.util.Arrays.copyOf(this.elements,this.elements.length);return a}catch(b){if(y(b,CloneNotSupportedException))throw new AssertionError;throw b;}});c$.$ArrayDeque$DeqIterator$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.fence=this.cursor=0;this.lastRet=-1;r(this,arguments)},java.util.ArrayDeque,"DeqIterator",null,java.util.Iterator);
J(c$,function(){this.cursor=this.b$["java.util.ArrayDeque"].head;this.fence=this.b$["java.util.ArrayDeque"].tail});e(c$,"hasNext",function(){return this.cursor!=this.fence});e(c$,"next",function(){if(this.cursor==this.fence)throw new java.util.NoSuchElementException;var a=this.b$["java.util.ArrayDeque"].elements[this.cursor];if(this.b$["java.util.ArrayDeque"].tail!=this.fence||null==a)throw new java.util.ConcurrentModificationException;this.lastRet=this.cursor;this.cursor=this.cursor+1&this.b$["java.util.ArrayDeque"].elements.length-
1;return a});e(c$,"remove",function(){if(0>this.lastRet)throw new IllegalStateException;this.b$["java.util.ArrayDeque"].$delete(this.lastRet)&&(this.cursor=this.cursor-1&this.b$["java.util.ArrayDeque"].elements.length-1,this.fence=this.b$["java.util.ArrayDeque"].tail);this.lastRet=-1});c$=z()};c$.$ArrayDeque$DescendingIterator$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.fence=this.cursor=0;this.lastRet=-1;r(this,arguments)},java.util.ArrayDeque,"DescendingIterator",null,java.util.Iterator);
J(c$,function(){this.cursor=this.b$["java.util.ArrayDeque"].tail;this.fence=this.b$["java.util.ArrayDeque"].head});e(c$,"hasNext",function(){return this.cursor!=this.fence});e(c$,"next",function(){if(this.cursor==this.fence)throw new java.util.NoSuchElementException;this.cursor=this.cursor-1&this.b$["java.util.ArrayDeque"].elements.length-1;var a=this.b$["java.util.ArrayDeque"].elements[this.cursor];if(this.b$["java.util.ArrayDeque"].head!=this.fence||null==a)throw new java.util.ConcurrentModificationException;
this.lastRet=this.cursor;return a});e(c$,"remove",function(){if(0>this.lastRet)throw new IllegalStateException;this.b$["java.util.ArrayDeque"].$delete(this.lastRet)||(this.cursor=this.cursor+1&this.b$["java.util.ArrayDeque"].elements.length-1,this.fence=this.b$["java.util.ArrayDeque"].head);this.lastRet=-1});c$=z()};G(c$,"MIN_INITIAL_CAPACITY",8)});p("java.util");q(["java.util.Queue"],"java.util.Deque",null,function(){M(java.util,"Deque",java.util.Queue)});p("jalview.datamodel");q(null,"jalview.datamodel.AlignmentView",
"jalview.datamodel.Alignment $.CigarArray $.ColumnSelection $.SeqCigar $.SequenceGroup jalview.util.MessageManager $.ShiftList java.lang.Error java.util.ArrayList $.Vector".split(" "),function(){c$=s(function(){this.contigs=this.sequences=null;this.firstCol=this.width=0;this.scGroups=null;this.$isNa=!1;H("jalview.datamodel.AlignmentView.ScGroup")||jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$();this.selected=null;r(this,arguments)},jalview.datamodel,"AlignmentView");d(c$,"isNa",function(){return this.$isNa});
m(c$,function(a,b,c,f,d){this.construct(new jalview.datamodel.CigarArray(a,f?b:null,d?c:null),d&&null!=c?c.getStartRes():0);this.$isNa=a.isNucleotide();null!=c&&0<c.getSize()?(c.getSequences(null),this.selected=new java.util.Vector,b=c.getSequencesInOrder(a,d)):b=a.getSequencesArray();f=new java.util.ArrayList;var e=new java.util.ArrayList;a=a.getGroups();e.addAll(a);var g=a=null;if(null!=e){if(null!=c&&d){a=c.getStartRes();for(var g=c.getEndRes(),h=new java.util.ArrayList,j,e=e.iterator();e.hasNext()&&
((j=e.next())||1);)j.getStartRes()>g||j.getEndRes()<a||(j.getStartRes()<a&&j.setStartRes(a),j.getEndRes()>g&&j.setEndRes(g),j.setStartRes(j.getStartRes()-a+1),j.setEndRes(j.getEndRes()-a+1),h.add(j));e=h}a=Array(e.size());g=X(e.size(),!1);for(h=0;h<a.length;h++)j=e.get(h),a[h]=C(jalview.datamodel.AlignmentView.ScGroup,this,null),a[h].sg=new jalview.datamodel.SequenceGroup(j),g[h]=!1,f.add(j.getSequences())}for(h=e=0;h<b.length;h++)if(null!=b[h]){null!=c&&(0<c.getSize()&&!d)&&(this.sequences[e].setGroupMembership(this.selected),
this.selected.addElement(this.sequences[e]));if(null!=f)for(j=0;j<a.length;j++)f.get(j).contains(b[h])&&(this.sequences[e].setGroupMembership(a[j]),a[j].sg.deleteSequence(b[h],!1),a[j].seqs.addElement(this.sequences[e]),g[j]||(null==this.scGroups&&(this.scGroups=new java.util.ArrayList),g[j]=!0,this.scGroups.add(a[j])));e++}for(j=0;j<a.length;j++){c=a[j].sg.getSequencesAsArray(null);for(d=0;d<c.length;d++)a[j].sg.deleteSequence(c[d],!1);a[j]=null}},"jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup,~B,~B,~B");
m(c$,function(a){if(!a.isSeqCigarArray())throw Error(jalview.util.MessageManager.getString("error.implementation_error_can_only_make_alignmnet_from_cigararray"));this.contigs=a.getDeletedRegions();this.sequences=a.getSeqCigarArray();this.width=a.getWidth()},"jalview.datamodel.CigarArray");m(c$,function(a,b){this.construct(a);this.firstCol=b},"jalview.datamodel.CigarArray,~N");d(c$,"setSequences",function(a){this.sequences=a},"~A");d(c$,"setContigs",function(a){this.contigs=a},"~A");d(c$,"getSequences",
function(){return this.sequences});d(c$,"getContigs",function(){return this.contigs});d(c$,"getAlignmentAndColumnSelection",function(a){var b=new jalview.datamodel.ColumnSelection;return E(-1,[jalview.datamodel.SeqCigar.createAlignmentSequences(this.sequences,a,b,this.contigs),b])},"~S");d(c$,"getVisibleAlignment",function(a){a=this.getVisibleSeqs(a);a=new jalview.datamodel.Alignment(a);this.addPrunedGroupsInOrder(a,-1,-1,!0);return a},"~S");d(c$,"addPrunedGroupsInOrder",function(a,b,c,f){var d=!1;
-1<b&&b<=c&&(d=!0);var e=a.getSequencesArray(),g=null!=this.scGroups?this.scGroups.size():0;if(0<g){for(var h=Array(g),j=0;j<g;j++){var n=this.scGroups.get(j).sg;d&&(n.getStartRes()>c||n.getEndRes()<b)?h[j]=null:(h[j]=new jalview.datamodel.SequenceGroup(n),d&&!f&&(h[j].getStartRes()<b?h[j].setStartRes(0):(h[j].setStartRes(h[j].getStartRes()-b),h[j].setEndRes(h[j].getEndRes()-b)),h[j].getEndRes()>c-b&&h[j].setEndRes(c-b)))}if(f&&null!=this.contigs){j=0;f=new jalview.util.ShiftList;d&&f.addShift(b,
-b);for(n=0;n<this.contigs.length;n+=3)f.addShift(j+this.contigs[n+1],this.contigs[n+2]-this.contigs[n+1]),j=this.contigs[n+1]+this.contigs[n+2];for(j=0;j<h.length;j++)if(null!=h[j]){var n=h[j].getStartRes(),x=h[j].getEndRes();d&&(n<b&&(n=b),x>c&&(x=c));n=f.shift(n);x=f.shift(x);h[j].setStartRes(n);h[j].setEndRes(x)}}for(b=0;b<e.length;b++)for(j=0;j<g;j++)null!=h[j]&&this.sequences[b].isMemberOf(this.scGroups.get(j))&&h[j].addSequence(e[b],!1);for(j=0;j<g;j++)null!=h[j]&&0<h[j].getSize()&&a.addGroup(h[j]),
h[j]=null}},"jalview.datamodel.AlignmentI,~N,~N,~B");d(c$,"getVisibleSeqs",function(){for(var a=Array(this.sequences.length),b=0,c=this.sequences.length;b<c;b++)a[b]=this.sequences[b].getSeq("-");for(var f=this.getSequenceStrings("-"),b=0,c=a.length;b<c;b++)a[b].setSequence(f[b]);return a},"~S");d(c$,"getVisibleContigAlignments",function(a){var b=0,c=this.getVisibleContigs();a=this.getVisibleContigs(a);for(var f=Array(a.length),b=0;b<a.length;b++)f[b]=new jalview.datamodel.Alignment(a[b]),null!=this.scGroups&&
0<this.scGroups.size()&&this.addPrunedGroupsInOrder(f[b],c[2*b],c[2*b+1],!0);return f},"~S");d(c$,"getSequenceStrings",function(a){for(var b=Array(this.sequences.length),c=0;c<this.sequences.length;c++){var f=this.sequences[c].getSequenceString(a);if(null!=this.contigs){b[c]="";for(var d=0,e=0;e<this.contigs.length;e+=3)b[c]+=f.substring(d,this.contigs[e+1]),d=this.contigs[e+1]+this.contigs[e+2];b[c]+=f.substring(d)}else b[c]=f}return b},"~S");d(c$,"getWidth",function(){return this.width});d(c$,"setWidth",
function(a){this.width=a},"~N");d(c$,"getVisibleContigs",function(a){var b;b=1;if(null==this.sequences||0>=this.width)return null;if(null!=this.contigs&&0<this.contigs.length){var c=0;b=0;for(var f=this.width,d=0;d<this.contigs.length;d+=3)0<this.contigs[d+1]-c&&b++,f+=this.contigs[d+2],c=this.contigs[d+1]+this.contigs[d+2];c<f&&b++;b=Array(b);for(var e=c=0,d=0;d<this.contigs.length;d+=3){if(0<this.contigs[d+1]-c){for(var g=Array(this.sequences.length),h=0;h<g.length;h++)g[h]=this.sequences[h].getSeq(a).getSubSequence(c,
this.contigs[d+1]);b[e]=g;e++}c=this.contigs[d+1]+this.contigs[d+2]}if(c<f){g=Array(this.sequences.length);for(h=0;h<g.length;h++)g[h]=this.sequences[h].getSeq(a).getSubSequence(c,f+1);b[e]=g}}else{b=Array(1);b[0]=Array(this.sequences.length);for(h=0;h<this.sequences.length;h++)b[0][h]=this.sequences[h].getSeq(a)}return b},"~S");d(c$,"getUpdatedView",function(a,b,c){if(null==this.sequences||0>=this.width)throw Error(jalview.util.MessageManager.getString("error.empty_view_cannot_be_updated"));if(null==
a)throw Error("nvismsa==null. use getAlignmentAndColumnSelection() instead.");if(null!=this.contigs&&0<this.contigs.length){var f=Array(this.sequences.length),d=new jalview.datamodel.ColumnSelection;if(null!=this.contigs&&0<this.contigs.length){for(var e=0,g=0,h=this.width,j=0,n=0;n<this.contigs.length;n+=3){h+=this.contigs[n+2];if(0<this.contigs[n+1]-e){var x=0;if(null!=a[j]){var e=a[j],u=null==b?null:b[j];j++;if(e.length!=this.sequences.length)throw Error(jalview.util.MessageManager.formatMessage("error.mismatch_between_number_of_sequences_in_block",
E(-1,[Integer.$valueOf(j).toString(),Integer.$valueOf(e.length).toString(),Integer.$valueOf(this.sequences.length).toString()])));for(var x=e[0].getLength(),m=0;m<e.length;m++)null==f[m]?f[m]=e[m]:(f[m].setSequence(f[m].getSequenceAsString()+e[m].getSequenceAsString()),e[m].getStart()<=e[m].getEnd()&&f[m].setEnd(e[m].getEnd()),null!=u&&u.updateSequence(e[m],f[m]))}else{for(m=0;m<this.sequences.length;m++)u=this.sequences[m].getSeq(c).getSubSequence(e,this.contigs[n+1]),x<u.getLength()&&(x=u.getLength()),
null==f[m]?f[m]=u:(f[m].setSequence(f[m].getSequenceAsString()+u.getSequenceAsString()),u.getEnd()>=u.getStart()&&f[m].setEnd(u.getEnd()));j++}g+=x}e=this.contigs[n+1]+this.contigs[n+2];for(m=0;m<this.sequences.length;m++)x=this.sequences[m].getSeq(c).getSubSequence(this.contigs[n+1],e),null==f[m]?f[m]=x:(f[m].setSequence(f[m].getSequenceAsString()+x.getSequenceAsString()),x.getEnd()>=x.getStart()&&f[m].setEnd(x.getEnd()));d.hideColumns(g,g+this.contigs[n+2]-1);g+=this.contigs[n+2]}if(j<a.length)if(x=
0,null!=a[j]){e=a[j];u=null!=b?b[j]:null;e[0].getLength();for(m=0;m<e.length;m++)null==f[m]?f[m]=e[m]:(f[m].setSequence(f[m].getSequenceAsString()+e[m].getSequenceAsString()),e[m].getEnd()>=e[m].getStart()&&f[m].setEnd(e[m].getEnd()),null!=u&&u.updateSequence(e[m],f[m]))}else if(e<h)for(m=0;m<this.sequences.length;m++)u=this.sequences[m].getSeq(c).getSubSequence(e,h+1),x<u.getLength()&&(x=u.getLength()),null==f[m]?f[m]=u:(f[m].setSequence(f[m].getSequenceAsString()+u.getSequenceAsString()),u.getEnd()>=
u.getStart()&&f[m].setEnd(u.getEnd()))}return E(-1,[f,d])}if(1!=a.length)throw Error(jalview.util.MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",E(-1,[Integer.$valueOf(a.length).toString()])));return null!=a[0]?E(-1,[a[0],new jalview.datamodel.ColumnSelection]):this.getAlignmentAndColumnSelection(c)},"~A,~A,~S");d(c$,"getVisibleContigs",function(){if(null!=this.contigs&&0<this.contigs.length){for(var a=0,b=0,c=this.width,f=0;f<this.contigs.length;f+=
3)0<this.contigs[f+1]-a&&b++,c+=this.contigs[f+2],a=this.contigs[f+1]+this.contigs[f+2];a<c&&b++;for(var d=w(2*b,0),f=a=b=0;f<this.contigs.length;f+=3)0<this.contigs[f+1]-a&&(d[b]=a,d[b+1]=this.contigs[f+1]-1,b+=2),a=this.contigs[f+1]+this.contigs[f+2];a<c&&(d[b]=a,d[b+1]=c);return d}return w(-1,[0,this.width])});d(c$,"getAlignmentOrigin",function(){return this.firstCol});d(c$,"getVisibleContigMapFor",function(a){var b=null,c=this.getVisibleContigs(),f=0,d=0;if(null!=c){for(var b=w(a.length,0),e=
0;e<c.length;e+=2){for(;f<a.length&&a[f]<c[e];)f++;for(;f<a.length&&a[f]<=c[e+1];)b[d++]=f++}a=w(d,0);System.arraycopy(b,0,a,0,d);b=a}return b},"~A");d(c$,"getEditedSequences",function(a,b){for(var c=this.getSequences(),f=Array(c.length),d=0,e=c.length;d<e;d++)f[d]=c[d].getSeq(a);if(b){c=this.getSequenceStrings(a);for(d=0;d<c.length;d++)f[d].setSequence(c[d]),c[d]=null}return f},"~S,~B");c$.summariseAlignmentView=d(c$,"summariseAlignmentView",function(a,b){b.print("View has "+a.sequences.length+" of which ");
null==a.selected?b.print("None"):b.print(" "+a.selected.size());b.println(" are selected.");b.print("View is "+a.getWidth()+" columns wide");var c=0,f=a.getContigs();if(null!=f){for(var c=a.width,d=0;d<f.length;d+=3)c+=f[d+2];b.println("with "+c+" visible columns spread over "+F(f.length/3)+" regions.")}else b.println(".");if(null!=a.scGroups){b.println("There are "+a.scGroups.size()+" groups defined on the view.");for(d=0;d<a.scGroups.size();d++){c=a.scGroups.get(d);b.println("Group "+d+": Name = "+
c.sg.getName()+" Contains "+c.seqs.size()+" Seqs.");b.println("This group runs from "+c.sg.getStartRes()+" to "+c.sg.getEndRes());for(f=0;f<c.seqs.size();f++)c.seqs.elementAt(f).isMemberOf(c)||b.println("** WARNING: sequence "+c.seqs.elementAt(f).toString()+" is not marked as member of group.")}c=a.getVisibleAlignment("-");if(null!=c&&(b.println("Vis. alignment is "+c.getWidth()+" wide and has "+c.getHeight()+" seqs."),null!=c.getGroups()&&0<c.getGroups().size()))for(var d=1,e,c=c.getGroups().iterator();c.hasNext()&&
((e=c.next())||1);)b.println("Group "+d++ +" begins at column "+e.getStartRes()+" and ends at "+e.getEndRes())}},"jalview.datamodel.AlignmentView,java.io.PrintStream");c$.testSelectionViews=d(c$,"testSelectionViews",function(a,b,c){System.out.println("Testing standard view creation:\n");var f=null;try{System.out.println("View with no hidden columns, no limit to selection, no groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!1,!1,!1),jalview.datamodel.AlignmentView.summariseAlignmentView(f,
System.out)}catch(d){if(y(d,Exception))d.printStackTrace(),System.err.println("Failed to generate alignment with selection but no groups marked.");else throw d;}try{System.out.println("View with no hidden columns, no limit to selection, and all groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!1,!1,!0),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(e){if(y(e,Exception))e.printStackTrace(),System.err.println("Failed to generate alignment with selection marked but no groups marked.");
else throw e;}try{System.out.println("View with no hidden columns, limited to selection and no groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!1,!0,!1),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(g){if(y(g,Exception))g.printStackTrace(),System.err.println("Failed to generate alignment with selection restricted but no groups marked.");else throw g;}try{System.out.println("View with no hidden columns, limited to selection, and all groups to be collected:"),
f=new jalview.datamodel.AlignmentView(a,b,c,!1,!0,!0),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(h){if(y(h,Exception))h.printStackTrace(),System.err.println("Failed to generate alignment with selection restricted and groups marked.");else throw h;}try{System.out.println("View *with* hidden columns, no limit to selection, no groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!0,!1,!1),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(j){if(y(j,
Exception))j.printStackTrace(),System.err.println("Failed to generate alignment with selection but no groups marked.");else throw j;}try{System.out.println("View *with* hidden columns, no limit to selection, and all groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!0,!1,!0),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(n){if(y(n,Exception))n.printStackTrace(),System.err.println("Failed to generate alignment with selection marked but no groups marked.");
else throw n;}try{System.out.println("View *with* hidden columns, limited to selection and no groups to be collected:"),f=new jalview.datamodel.AlignmentView(a,b,c,!0,!0,!1),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(m){if(y(m,Exception))m.printStackTrace(),System.err.println("Failed to generate alignment with selection restricted but no groups marked.");else throw m;}try{System.out.println("View *with* hidden columns, limited to selection, and all groups to be collected:"),
f=new jalview.datamodel.AlignmentView(a,b,c,!0,!0,!0),jalview.datamodel.AlignmentView.summariseAlignmentView(f,System.out)}catch(u){if(y(u,Exception))u.printStackTrace(),System.err.println("Failed to generate alignment with selection restricted and groups marked.");else throw u;}},"jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");c$.$AlignmentView$ScGroup$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.sg=this.seqs=null;r(this,arguments)},
jalview.datamodel.AlignmentView,"ScGroup");m(c$,function(){this.seqs=new java.util.Vector});c$=z()}});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],"jalview.schemes.Blosum62ColourScheme",["jalview.schemes.ResidueProperties","jalview.util.Comparison","java.awt.Color"],function(){c$=B(jalview.schemes,"Blosum62ColourScheme",jalview.schemes.ResidueColourScheme);e(c$,"findColourSeq",function(a,b){"a"<=a&&"z">=a&&(a=String.fromCharCode(a.charCodeAt(0)-32));if(null==this.consensus||b>=this.consensus.length||
null==this.consensus[b]||0!=this.threshold&&!this.aboveThreshold(a,b))return java.awt.Color.white;var c;if(jalview.util.Comparison.isGap(a))return java.awt.Color.white;c=this.consensus[b].get("R");if(-1<c.indexOf(a))c=new java.awt.Color(154,154,255);else{var f=0,d=0,e=c.length;do f+=jalview.schemes.ResidueProperties.getBLOSUM62(c.charAt(d),a);while(++d<e);c=0<f?new java.awt.Color(204,204,255):java.awt.Color.white}this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI");
d(c$,"applyTo",function(a,b){return K(this,jalview.schemes.Blosum62ColourScheme,"applyTo",[a,b])},"jalview.datamodel.AnnotatedCollectionI,java.util.Map")});p("jalview.schemes");q(["jalview.schemes.ColourSchemeI"],"jalview.schemes.ResidueColourScheme",["jalview.util.Comparison","$.MessageManager","java.awt.Color","java.lang.Error"],function(){c$=s(function(){this.symbolIndex=null;this.conservationColouring=!1;this.colors=null;this.threshold=0;this.ignoreGaps="G";this.conservation=this.consensus=null;
this.conservationLength=0;this.inc=30;r(this,arguments)},jalview.schemes,"ResidueColourScheme",null,jalview.schemes.ColourSchemeI);m(c$,function(a,b,c){this.symbolIndex=a;this.colors=b;this.threshold=c},"~A,~A,~N");m(c$,function(a){this.symbolIndex=a},"~A");m(c$,function(){this.symbolIndex=null});e(c$,"findColour",function(a){return null==this.colors?java.awt.Color.white:this.colors[this.symbolIndex[a.charCodeAt(0)]]},"~S");e(c$,"findColourSeq",function(a,b){var c;c=null!=this.colors&&null!=this.symbolIndex&&
0==this.threshold||this.aboveThreshold(a,b)?this.colors[this.symbolIndex[a.charCodeAt(0)]]:java.awt.Color.white;this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI");e(c$,"getThreshold",function(){return this.threshold});e(c$,"setThreshold",function(a,b){this.threshold=a;this.ignoreGaps=b?"N":"G"},"~N,~B");d(c$,"aboveThreshold",function(a,b){"a"<=a&&"z">=a&&(a=String.fromCharCode(a.charCodeAt(0)-32));return null==this.consensus||this.consensus.length<
b||null==this.consensus[b]?!1:-1!=this.consensus[b].get("C").intValue()&&this.consensus[b].contains(String.valueOf(a))&&this.consensus[b].get(this.ignoreGaps).floatValue()>=this.threshold?!0:!1},"~S,~N");e(c$,"conservationApplied",function(){return this.conservationColouring});e(c$,"setConservationApplied",function(a){this.conservationColouring=a},"~B");e(c$,"setConservationInc",function(a){this.inc=a},"~N");e(c$,"getConservationInc",function(){return this.inc});e(c$,"setConsensus",function(a){null!=
a&&(this.consensus=a)},"~A");e(c$,"setConservation",function(a){if(null==a)this.conservationColouring=!1,this.conservation=null;else{this.conservationColouring=!0;var b,c=a.getConsSequence().getLength();this.conservation=N(c,"\x00");for(b=0;b<c;b++)this.conservation[b]=a.getConsSequence().getCharAt(b);this.conservationLength=this.conservation.length}},"jalview.analysis.Conservation");d(c$,"applyConservation",function(a,b){if(this.conservationLength>b&&"*"!=this.conservation[b]&&"+"!=this.conservation[b])if(jalview.util.Comparison.isGap(this.conservation[b]))a=
java.awt.Color.white;else{var c=11-(this.conservation[b].charCodeAt(0)-48);if(0==c)return java.awt.Color.white;var f=a.getRed(),d=a.getGreen(),e=a.getBlue(),g,h;g=(255-f)*(c/10);h=(255-d)*(c/10);c=(255-e)*(c/10);f+=this.inc/20*g;d+=this.inc/20*h;e+=this.inc/20*c;a=255<f||255<d||255<e?java.awt.Color.white:new java.awt.Color(f,d,e)}return a},"java.awt.Color,~N");e(c$,"alignmentChanged",function(){},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");e(c$,"applyTo",function(){try{return this.getClass().newInstance()}catch(a){if(y(a,
Exception))throw Error(jalview.util.MessageManager.formatMessage("error.implementation_error_cannot_duplicate_colour_scheme",E(-1,[this.getClass().getName()])),a);throw a;}},"jalview.datamodel.AnnotatedCollectionI,java.util.Map")});p("jalview.schemes");M(jalview.schemes,"ColourSchemeI");p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],"jalview.schemes.PIDColourScheme",["jalview.schemes.ResidueProperties","jalview.util.Comparison","java.awt.Color"],function(){c$=s(function(){this.group=
this.thresholds=this.pidColours=null;r(this,arguments)},jalview.schemes,"PIDColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.PIDColourScheme,[]);this.pidColours=jalview.schemes.ResidueProperties.pidColours;this.thresholds=jalview.schemes.ResidueProperties.pidThresholds});e(c$,"findColourSeq",function(a,b){"a"<=a&&"z">=a&&(a=String.fromCharCode(a.charCodeAt(0)-32));if(null==this.consensus||(b>=this.consensus.length||null==this.consensus[b])||0!=this.threshold&&
!this.aboveThreshold(a,b))return java.awt.Color.white;var c=java.awt.Color.white,f=0;if(this.consensus.length<=b)return java.awt.Color.white;if(-1!=Integer.parseInt(this.consensus[b].get("C").toString())&&this.consensus[b].contains(String.valueOf(a))&&(f=this.consensus[b].get(this.ignoreGaps).floatValue(),!jalview.util.Comparison.isGap(a)))for(var d=0;d<this.thresholds.length;d++)if(f>this.thresholds[d]){c=this.pidColours[d];break}this.conservationColouring&&(c=this.applyConservation(c,b));return c},
"~S,~N,jalview.datamodel.SequenceI")});p("jalview.workers");q(["jalview.workers.ConsensusThread"],"jalview.workers.ComplementConsensusThread",["jalview.analysis.AAFrequency"],function(){c$=s(function(){this.mappings=null;r(this,arguments)},jalview.workers,"ComplementConsensusThread",jalview.workers.ConsensusThread);e(c$,"getNewWorker",function(){return new jalview.workers.ComplementConsensusThread(this.alignViewport,this.ap)});e(c$,"getConsensusAnnotation",function(){return this.alignViewport.getComplementConsensusAnnotation()});
e(c$,"getViewportConsensus",function(){return this.alignViewport.getComplementConsensusHash()});d(c$,"initializeCalc",function(){this.mappings=this.alignment.getCodonFrames();return null!=this.mappings&&!this.mappings.isEmpty()&&K(this,jalview.workers.ComplementConsensusThread,"initializeCalc",[])});e(c$,"computeConsensus",function(){for(var a=0;3>a;a++)try{jalview.analysis.AAFrequency.calculateCdna(this.alignment,this.mappings,this.hconsensus,this.iFirst,this.iLast);break}catch(b){if(!y(b,java.util.ConcurrentModificationException))throw b;
}});e(c$,"finalizeCalc",function(){this.alignViewport.setComplementConsensusHash(this.hconsensus)});e(c$,"deriveConsensus",function(a,b){jalview.analysis.AAFrequency.completeCdnaConsensus(a,b,this.alignViewport.isShowSequenceLogo(),this.getSequences().length)},"jalview.datamodel.AlignmentAnnotation,~A")});p("jalview.workers");q(["jalview.api.AlignCalcWorkerI","jalview.workers.AlignCalcWorker"],"jalview.workers.ConsensusThread",["jalview.analysis.AAFrequency"],function(){c$=s(function(){this.aseqs=
this.hconsensus=null;r(this,arguments)},jalview.workers,"ConsensusThread",jalview.workers.AlignCalcWorker,jalview.api.AlignCalcWorkerI);e(c$,"getNewWorker",function(){return new jalview.workers.ConsensusThread(this.alignViewport,this.ap)});e(c$,"run1",function(a){for(;!Thread.interrupted();){if(this.alignViewport.isClosed()){this.abortAndDestroy();break}try{switch(a){case 0:if(this.calcMan.isPending(this))return;this.calcMan.notifyStart(this);if(null==this.getConsensusAnnotation()||this.calcMan.isPending(this)){this.calcMan.workerComplete(this);
return}a=3;break;case 3:for(;!this.calcMan.notifyWorking(this);){null!=this.ap&&this.ap.paintAlignment(!1);try{if(this.sleepAndReturn(200,a))return}catch(b){if(y(b,InterruptedException)){a=2;break}else throw b;}}if(this.alignViewport.isClosed()){this.abortAndDestroy();a=2;break}this.alignment=this.alignViewport.getAlignment();this.aWidth=-1;if(null==this.alignment||0>(this.aWidth=this.alignment.getWidth()))a=2;this.eraseConsensus(this.aWidth);a=this.initializeCalc()?4:2;break;case 4:this.iFirst=this.iLast;
this.iLast=Math.min(this.iLast+this.nPer,this.aWidth);if(this.iLast==this.iFirst)a=2;else if(this.computeConsensus(),this.sleepAndReturn(0,a))return;break;case 2:this.finalizeCalc();this.updateAlignment();this.notifyDone();return}}catch(c){if(y(c,OutOfMemoryError)){var f=c;this.calcMan.workerCannotRun(this);this.ap.raiseOOMWarning("calculating consensus",f)}else f=c,System.out.println("Error in ConsensusThread: "+f),f.printStackTrace(),this.calcMan.workerComplete(this)}}},"~N");d(c$,"initializeCalc",
function(){this.iLast=0;this.hconsensus=Array(this.aWidth);this.aseqs=this.getSequences();return!0});d(c$,"computeConsensus",function(){this.started=System.currentTimeMillis();jalview.analysis.AAFrequency.calculate(this.aseqs,this.iFirst,this.iLast,this.hconsensus,!0);500>System.currentTimeMillis()-this.started&&(this.nPer*=2)});d(c$,"finalizeCalc",function(){this.alignViewport.setSequenceConsensusHash(this.hconsensus)});d(c$,"updateAlignment",function(){this.setColourSchemeConsensus(this.hconsensus);
this.updateResultAnnotation(!0)});d(c$,"eraseConsensus",function(a){this.getConsensusAnnotation().annotations=Array(a)},"~N");d(c$,"getSequences",function(){return this.alignViewport.getAlignment().getSequencesArray()});d(c$,"setColourSchemeConsensus",function(a){var b=this.alignViewport.getGlobalColourScheme();null!=b&&b.setConsensus(a)},"~A");d(c$,"getConsensusAnnotation",function(){return this.alignViewport.getAlignmentConsensusAnnotation()});e(c$,"updateAnnotation",function(){this.updateResultAnnotation(!1)});
d(c$,"updateResultAnnotation",function(a){var b=this.getConsensusAnnotation(),c=this.getViewportConsensus();(a||!this.calcMan.isWorking(this)&&null!=b&&null!=c)&&this.deriveConsensus(b,c)},"~B");d(c$,"deriveConsensus",function(a,b){var c=this.getSequences().length;jalview.analysis.AAFrequency.completeConsensus(a,b,0,b.length,this.alignViewport.isIgnoreGapsConsensus(),this.alignViewport.isShowSequenceLogo(),c)},"jalview.datamodel.AlignmentAnnotation,~A");d(c$,"getViewportConsensus",function(){return this.alignViewport.getSequenceConsensusHash()})});
p("jalview.api");M(jalview.api,"AlignCalcWorkerI",Runnable);p("jalview.workers");q(["jalview.api.AlignCalcWorkerI","swingjs.JSThread"],"jalview.workers.AlignCalcWorker",null,function(){c$=s(function(){this.iLast=this.iFirst=0;this.nPer=2;this.started=0;this.alignment=null;this.aWidth=0;this.ourAnnots=this.ap=this.calcMan=this.alignViewport=null;r(this,arguments)},jalview.workers,"AlignCalcWorker",swingjs.JSThread,jalview.api.AlignCalcWorkerI);m(c$,function(a,b){t(this,jalview.workers.AlignCalcWorker,
[null,"AlignCalcWorker"]);this.alignViewport=a;this.calcMan=a.getCalcManager();this.ap=b},"jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");d(c$,"abortAndDestroy",function(){null!=this.calcMan&&this.calcMan.workerComplete(this);this.ap=this.calcMan=this.alignViewport=null});e(c$,"involves",function(a){return null!=this.ourAnnots&&this.ourAnnots.contains(a)},"jalview.datamodel.AlignmentAnnotation");e(c$,"removeOurAnnotation",function(){if(null!=this.ourAnnots&&null!=this.alignViewport)for(var a=
this.alignViewport.getAlignment(),b,c=this.ourAnnots.iterator();c.hasNext()&&((b=c.next())||1);)a.deleteAnnotation(b,!0)});d(c$,"notifyDone",function(){null!=this.ap&&this.ap.paintAlignment(!0);this.calcMan.workerComplete(this)});G(c$,"LOOP_STANDBY",3,"LOOP_CALCULATE",4,"MS_MAX",500)});p("jalview.workers");q(["jalview.api.AlignCalcWorkerI","jalview.workers.AlignCalcWorker"],"jalview.workers.ConservationThread",["jalview.analysis.Conservation","jalview.schemes.ResidueProperties","java.util.ArrayList"],
function(){c$=s(function(){this.ConsPercGaps=25;this.quality=this.conservation=this.cons=null;r(this,arguments)},jalview.workers,"ConservationThread",jalview.workers.AlignCalcWorker,jalview.api.AlignCalcWorkerI);e(c$,"getNewWorker",function(){return new jalview.workers.ConservationThread(this.alignViewport,this.ap)});m(c$,function(a,b){t(this,jalview.workers.ConservationThread,[a,b]);this.ConsPercGaps=a.getConsPercGaps()},"jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");e(c$,"run1",function(a){for(;!Thread.interrupted();)try{switch(a){case 0:if(this.calcMan.isPending(this))return;
this.calcMan.notifyStart(this);a=3;break;case 3:for(;!this.calcMan.notifyWorking(this);){null!=this.ap&&this.ap.paintAlignment(!1);try{if(this.sleepAndReturn(200,a))return}catch(b){if(y(b,InterruptedException)){a=2;break}else throw b;}}if(this.alignViewport.isClosed()){this.abortAndDestroy();a=2;break}var c=new java.util.ArrayList;this.alignment=this.alignViewport.getAlignment();this.conservation=this.alignViewport.getAlignmentConservationAnnotation();this.quality=this.alignViewport.getAlignmentQualityAnnot();
c.add(this.conservation);c.add(this.quality);this.ourAnnots=c;this.ConsPercGaps=this.alignViewport.getConsPercGaps();if(null==this.alignment||0>(this.aWidth=this.alignment.getWidth())){this.calcMan.workerComplete(this);return}a=4;break;case 4:this.iFirst=this.iLast;this.nPer=this.aWidth+1;this.iLast=Math.min(this.iLast+this.nPer,this.aWidth);if(this.iLast==this.iFirst)a=2;else if(this.computeConsensus(),this.sleepAndReturn(0,a))return;break;case 2:this.updateResultAnnotation(!0);this.notifyDone();
return}}catch(f){if(y(f,OutOfMemoryError)){var d=f;this.calcMan.workerCannotRun(this);this.ap.raiseOOMWarning("calculating conservation",d)}else d=f,System.out.println("Error in ConsensusThread: "+d),d.printStackTrace(),this.calcMan.workerComplete(this)}},"~N");d(c$,"computeConsensus",function(){this.cons=jalview.analysis.Conservation.calculateConservation("All",jalview.schemes.ResidueProperties.propHash,3,this.alignment.getSequences(),0,this.aWidth-1,!1,this.ConsPercGaps,null!=this.quality)});d(c$,
"updateResultAnnotation",function(a){if(a||!this.calcMan.isWorking(this)&&null!=this.cons&&null!=this.conservation&&null!=this.quality)this.alignViewport.setConservation(this.cons),this.cons.completeAnnotations(this.conservation,this.quality,0,this.aWidth)},"~B");e(c$,"updateAnnotation",function(){this.updateResultAnnotation(!1)})});p("jalview.workers");q(["jalview.api.AlignCalcWorkerI","jalview.workers.AlignCalcWorker"],"jalview.workers.StrucConsensusThread",["jalview.analysis.StructureFrequency"],
function(){c$=s(function(){this.hStrucConsensus=this.strucConsensus=this.rnaStruc=null;this.nseq=-1;this.arr=this.aa=null;r(this,arguments)},jalview.workers,"StrucConsensusThread",jalview.workers.AlignCalcWorker,jalview.api.AlignCalcWorkerI);e(c$,"getNewWorker",function(){return new jalview.workers.StrucConsensusThread(this.alignViewport,this.ap)});e(c$,"run1",function(a){if(this.alignViewport.isClosed())this.abortAndDestroy();else for(;!Thread.interrupted();)try{switch(a){case 0:if(this.calcMan.isPending(this))return;
this.calcMan.notifyStart(this);a=3;break;case 3:for(;!this.calcMan.notifyWorking(this);){null!=this.ap&&this.ap.paintAlignment(!1);try{if(this.sleepAndReturn(200,a))return}catch(b){if(y(b,InterruptedException)){a=2;break}else throw b;}}if(this.alignViewport.isClosed()){this.abortAndDestroy();a=2;break}this.alignment=this.alignViewport.getAlignment();this.aWidth=-1;if(null==this.alignment||0>(this.aWidth=this.alignment.getWidth()))a=2;this.strucConsensus=this.alignViewport.getAlignmentStrucConsensusAnnotation();
this.hStrucConsensus=this.alignViewport.getRnaStructureConsensusHash();this.strucConsensus.annotations=null;this.strucConsensus.annotations=Array(this.aWidth);this.hStrucConsensus=Array(this.aWidth);this.aa=this.alignViewport.getAlignment().getAlignmentAnnotation();for(var c=0;c<this.aa.length;c++)if(null!=this.aa[c].getRNAStruc()&&this.aa[c].isValidStruc()){this.rnaStruc=this.aa[c];break}if(null==this.rnaStruc||!this.rnaStruc.isValidStruc()){this.calcMan.workerComplete(this);return}this.arr=this.alignment.getSequencesArray();
this.nseq=this.arr.length;a=4;break;case 4:this.iFirst=this.iLast;this.iLast=Math.min(this.iLast+this.nPer,this.aWidth);if(this.iLast==this.iFirst)a=2;else if(jalview.analysis.StructureFrequency.calculate(this.arr,0,this.alignment.getWidth(),this.hStrucConsensus,!0,this.rnaStruc),this.sleepAndReturn(0,a))return;break;case 2:this.alignViewport.setRnaStructureConsensusHash(this.hStrucConsensus);this.updateResultAnnotation(!0);null!=this.alignViewport.getGlobalColourScheme()&&this.alignViewport.getGlobalColourScheme().setConsensus(this.hStrucConsensus);
this.notifyDone();return}}catch(f){y(f,OutOfMemoryError)?(c=f,this.calcMan.workerCannotRun(this),this.ap.raiseOOMWarning("calculating RNA structure consensus",c)):(c=f,System.out.println("Error in ConsensusThread: "+c),c.printStackTrace(),this.calcMan.workerComplete(this))}},"~N");e(c$,"updateAnnotation",function(){this.updateResultAnnotation(!1)});d(c$,"updateResultAnnotation",function(a){(a||!this.calcMan.isWorking(this)&&null!=this.strucConsensus&&null!=this.hStrucConsensus)&&jalview.analysis.StructureFrequency.completeConsensus(this.strucConsensus,
this.hStrucConsensus,0,this.hStrucConsensus.length,this.alignViewport.isIgnoreGapsConsensus(),this.alignViewport.isShowSequenceLogo(),this.nseq)},"~B")});p("jalview.analysis");q(null,"jalview.analysis.StructureFrequency","jalview.datamodel.Annotation jalview.util.Format $.QuickSort java.lang.Float java.util.Hashtable JU.AU".split(" "),function(){c$=B(jalview.analysis,"StructureFrequency");c$.findPair=d(c$,"findPair",function(a,b){for(var c=0;c<a.length;c++)if(a[c].getBegin()==b)return a[c].getEnd();
return-1},"~A,~N");c$.calculate=d(c$,"calculate",function(a,b,c,f,d,e){var g,h=e.getRNAStruc().toCharArray();e=e._rnasecstr;var j,n,m=0,u,p=-1,q,s=a.length,r,t,v=!0;for(u=b;u<c;u++){b=new java.util.Hashtable;g="-";r=w(255,0);t=w(255,255,0);p=-1;j=u<h.length?h[u]:"-";if("."==j||" "==j)j="-";if("("!=j&&"["!=j)"-"==j&&r[45]++;else if(p=jalview.analysis.StructureFrequency.findPair(e,u),-1<p)for(q=0;q<s;q++)if(null==a[q])System.err.println("WARNING: Consensus skipping null sequence - possible race condition.");
else{j=a[q].getCharAt(u);if("."==j||" "==j)j="-";"-"==j?r[45]++:(n=a[q].getCharAt(p),!0==jalview.analysis.StructureFrequency.checkBpType(j,n)&&(r[40]++,g="(",v=!0),!1==jalview.analysis.StructureFrequency.checkBpType(j,n)&&(v=!1,r[91]++,g="["),t[j.charCodeAt(0)][n.charCodeAt(0)]++)}d&&(b.put("P",E(-1,[r,w(-1,[s,s-r[45]])])),b.put("B",t));!0==v&&(m=r[40]);!1==v&&(m=r[91]);b.put("C",new Integer(m));b.put("R",g);j=100*m/s;b.put("G",new Float(j));null==f[u]&&(f[u]=b);0<p&&(r[41]=r[40],r[93]=r[91],r[40]=
0,r[91]=0,b=new java.util.Hashtable,!0==v&&(g=")"),!1==v&&(g="]"),d&&(b.put("P",E(-1,[r,w(-1,[s,s-r[45]])])),b.put("B",t)),b.put("C",new Integer(m)),b.put("R",g),j=100*m/s,b.put("G",new Float(j)),f[p]=b)}},"~A,~N,~N,~A,~B,jalview.datamodel.AlignmentAnnotation");c$.checkBpType=d(c$,"checkBpType",function(a,b){"Z"<a&&(a=String.fromCharCode(a.charCodeAt(0)-32));"Z"<b&&(b=String.fromCharCode(b.charCodeAt(0)-32));switch(a){case "A":switch(b){case "T":return!0;case "U":return!0}break;case "C":switch(b){case "G":return!0}break;
case "T":switch(b){case "A":return!0;case "G":return!0}break;case "G":switch(b){case "C":return!0;case "T":return!0;case "U":return!0}break;case "U":switch(b){case "A":return!0;case "G":return!0}}return!1},"~S,~S");c$.completeConsensus=d(c$,"completeConsensus",function(a,b,c,f,d,e,g){var h,j;if(!(null==a||null==a.annotations||a.annotations.length<f)){j="%3.1f";for(var n=2;100<g;)n++,g/=10;2<n&&(j="%"+(2+n)+"."+n+"f");for(g=new jalview.util.Format(j);c<f;c++){var m;if(c>=b.length||null==(m=b[c]))a.annotations[c]=
null;else if(j=d?m.get("N"):m.get("G"),null==j)a.annotations[c]=null;else{j=j.floatValue();var n=m.get("R").toString(),u=m.get("R")+" ";1<n.length&&(u="["+n+"] ",n="+");h=m.get("P");var p=m.get("B");if(null!=p&&e){for(var u="",q=JU.AU.newInt2(625),s=Q(625,0),r=0,t=65;90>t;t++)for(var v=65;90>v;v++)q[r]=w(-1,[t,v]),s[r]=p[t][v],r++;jalview.util.QuickSort.sortFloatObject(s,q);p=0;r=h[1][d?1:0];for(t=624;0<t;t--)0<s[t]&&(h=100*s[t]/r,u+=(0==p?"":"; ")+String.fromCharCode(q[t][0])+String.fromCharCode(q[t][1])+
" "+g.formDouble(h)+"%",p++)}else u+=g.formDouble(j)+"%";a.annotations[c]=new jalview.datamodel.Annotation(n,u," ",j)}}}},"jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~B,~B,~N");c$.extractProfile=d(c$,"extractProfile",function(a,b){var c=w(74,0),f=a.get("P"),d=a.get("B");if(null==f)return null;for(var e=JU.AU.newInt2(625),g=Q(625,0),h=0,j=65;90>j;j++)for(var n=65;90>n;n++)e[h]=w(-1,[j,n]),g[h]=d[j][n],h++;jalview.util.QuickSort.sortFloatObject(g,e);d=0;c[1]=0;h=2;f=f[1][b?1:0];for(j=624;0<j;j--)0<
g[j]&&(c[h++]=e[j][0],c[h++]=e[j][1],c[h]=I(100*g[j]/f),c[1]+=c[h++],d++);c[0]=d;e=w(c.length+1,0);e[0]=1;System.arraycopy(c,0,e,1,c.length);return e},"java.util.Hashtable,~B");G(c$,"STRUCTURE_PROFILE_LENGTH",74,"MAXCOUNT","C","MAXRESIDUE","R","PID_GAPS","G","PID_NOGAPS","N","PROFILE","P","PAIRPROFILE","B")});p("jalview.schemes");q(null,"jalview.schemes.ColourSchemeProperty","jalview.schemes.Blosum62ColourScheme $.BuriedColourScheme $.ClustalxColourScheme $.HelixColourScheme $.HydrophobicColourScheme $.NucleotideColourScheme $.PIDColourScheme $.PurinePyrimidineColourScheme $.RNAHelicesColour $.StrandColourScheme $.TCoffeeColourScheme $.TaylorColourScheme $.TurnColourScheme $.UserColourScheme $.ZappoColourScheme jalview.util.ColorUtils java.awt.Color".split(" "),
function(){c$=B(jalview.schemes,"ColourSchemeProperty");c$.getColourIndexFromName=d(c$,"getColourIndexFromName",function(a){var b=-1;a.equalsIgnoreCase("Clustal")?b=2:a.equalsIgnoreCase("Blosum62")?b=3:a.equalsIgnoreCase("% Identity")?b=4:a.equalsIgnoreCase("Zappo")?b=5:a.equalsIgnoreCase("Taylor")?b=6:a.equalsIgnoreCase("Hydrophobic")?b=7:a.equalsIgnoreCase("Helix Propensity")?b=8:a.equalsIgnoreCase("Strand Propensity")?b=9:a.equalsIgnoreCase("Turn Propensity")?b=10:a.equalsIgnoreCase("Buried Index")?
b=11:a.equalsIgnoreCase("Nucleotide")?b=12:a.equalsIgnoreCase("T-Coffee Scores")?b=15:a.equalsIgnoreCase("User Defined")?b=0:a.equalsIgnoreCase("None")?b=1:a.equalsIgnoreCase("Purine/Pyrimidine")?b=13:a.equalsIgnoreCase("RNA Interaction type")?b=17:a.equalsIgnoreCase("RNA Helices")&&(b=16);return b},"~S");c$.getColourName=d(c$,"getColourName",function(a){var b=1;if(v(a,jalview.schemes.ClustalxColourScheme))b=2;else if(v(a,jalview.schemes.Blosum62ColourScheme))b=3;else if(v(a,jalview.schemes.PIDColourScheme))b=
4;else if(v(a,jalview.schemes.ZappoColourScheme))b=5;else if(v(a,jalview.schemes.TaylorColourScheme))b=6;else if(v(a,jalview.schemes.HydrophobicColourScheme))b=7;else if(v(a,jalview.schemes.HelixColourScheme))b=8;else if(v(a,jalview.schemes.StrandColourScheme))b=9;else if(v(a,jalview.schemes.TurnColourScheme))b=10;else if(v(a,jalview.schemes.BuriedColourScheme))b=11;else if(v(a,jalview.schemes.NucleotideColourScheme))b=12;else if(v(a,jalview.schemes.PurinePyrimidineColourScheme))b=13;else if(v(a,
jalview.schemes.TCoffeeColourScheme))b=15;else if(v(a,jalview.schemes.RNAHelicesColour))b=16;else if(v(a,jalview.schemes.UserColourScheme)){if(null!=a.getName()&&0<a.getName().length)return a.getName();b=0}return jalview.schemes.ColourSchemeProperty.getColourName(b)},"jalview.schemes.ColourSchemeI");c$.getColourName=d(c$,"getColourName",function(a){var b=null;switch(a){case 2:b="Clustal";break;case 3:b="Blosum62";break;case 4:b="% Identity";break;case 5:b="Zappo";break;case 6:b="Taylor";break;case 7:b=
"Hydrophobic";break;case 8:b="Helix Propensity";break;case 9:b="Strand Propensity";break;case 10:b="Turn Propensity";break;case 11:b="Buried Index";break;case 12:b="Nucleotide";break;case 13:b="Purine/Pyrimidine";break;case 15:b="T-Coffee Scores";break;case 17:b="RNA Interaction type";break;case 16:b="RNA Helices";break;case 0:b="User Defined";break;default:b="None"}return b},"~N");c$.getColour=d(c$,"getColour",function(a,b){if(-1==jalview.schemes.ColourSchemeProperty.getColourIndexFromName(b))if(-1==
b.indexOf("="))try{return new jalview.schemes.UserColourScheme(b)}catch(c){if(!y(c,Exception))throw c;}else try{(new jalview.schemes.UserColourScheme("white")).parseAppletParameter(b)}catch(f){if(!y(f,Exception))throw f;}return jalview.schemes.ColourSchemeProperty.getColour(a,jalview.schemes.ColourSchemeProperty.getColourIndexFromName(b))},"jalview.datamodel.AnnotatedCollectionI,~S");c$.getColour=d(c$,"getColour",function(a,b){var c=null;switch(b){case 2:c=new jalview.schemes.ClustalxColourScheme(a,
null);break;case 3:c=new jalview.schemes.Blosum62ColourScheme;break;case 4:c=new jalview.schemes.PIDColourScheme;break;case 5:c=new jalview.schemes.ZappoColourScheme;break;case 6:c=new jalview.schemes.TaylorColourScheme;break;case 7:c=new jalview.schemes.HydrophobicColourScheme;break;case 8:c=new jalview.schemes.HelixColourScheme;break;case 9:c=new jalview.schemes.StrandColourScheme;break;case 10:c=new jalview.schemes.TurnColourScheme;break;case 11:c=new jalview.schemes.BuriedColourScheme;break;case 12:c=
new jalview.schemes.NucleotideColourScheme;break;case 13:c=new jalview.schemes.PurinePyrimidineColourScheme;break;case 15:c=new jalview.schemes.TCoffeeColourScheme(a);break;case 16:c=new jalview.schemes.RNAHelicesColour(a);break;case 0:for(var c=Array(24),f=0;24>f;f++)c[f]=java.awt.Color.white;c=new jalview.schemes.UserColourScheme(c)}return c},"jalview.datamodel.AnnotatedCollectionI,~N");c$.getAWTColorFromName=d(c$,"getAWTColorFromName",function(a){var b=null;a=a.toLowerCase();a.equals("black")?
b=java.awt.Color.black:a.equals("blue")?b=java.awt.Color.blue:a.equals("cyan")?b=java.awt.Color.cyan:a.equals("darkGray")?b=java.awt.Color.darkGray:a.equals("gray")?b=java.awt.Color.gray:a.equals("green")?b=java.awt.Color.green:a.equals("lightGray")?b=java.awt.Color.lightGray:a.equals("magenta")?b=java.awt.Color.magenta:a.equals("orange")?b=java.awt.Color.orange:a.equals("pink")?b=java.awt.Color.pink:a.equals("red")?b=java.awt.Color.red:a.equals("white")?b=java.awt.Color.white:a.equals("yellow")&&
(b=java.awt.Color.yellow);return b},"~S");c$.initRnaHelicesShading=d(c$,"initRnaHelicesShading",function(a){var b=0;if(null==jalview.schemes.ColourSchemeProperty.rnaHelices)jalview.schemes.ColourSchemeProperty.rnaHelices=Array(a+1);else if(null!=jalview.schemes.ColourSchemeProperty.rnaHelices&&jalview.schemes.ColourSchemeProperty.rnaHelices.length<=a){var c=Array(a+1);System.arraycopy(jalview.schemes.ColourSchemeProperty.rnaHelices,0,c,0,jalview.schemes.ColourSchemeProperty.rnaHelices.length);b=jalview.schemes.ColourSchemeProperty.rnaHelices.length;
jalview.schemes.ColourSchemeProperty.rnaHelices=c}else return;for(;b<=a;b++)jalview.schemes.ColourSchemeProperty.rnaHelices[b]=jalview.util.ColorUtils.generateRandomColor(java.awt.Color.white)},"~N");G(c$,"UNDEFINED",-1,"USER_DEFINED",0,"NONE",1,"CLUSTAL",2,"BLOSUM",3,"PID",4,"ZAPPO",5,"TAYLOR",6,"HYDROPHOBIC",7,"HELIX",8,"STRAND",9,"TURN",10,"BURIED",11,"NUCLEOTIDE",12,"PURINEPYRIMIDINE",13,"COVARIATION",14,"TCOFFEE",15,"RNAHELIX",16,"RNAINTERACTION",17,"FIRST_COLOUR",1,"LAST_COLOUR",17,"rnaHelices",
null)});p("jalview.schemes");q(["jalview.schemes.ScoreColourScheme"],"jalview.schemes.BuriedColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"BuriedColourScheme",jalview.schemes.ScoreColourScheme);m(c$,function(){t(this,jalview.schemes.BuriedColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.buried,0.05,4.6])});e(c$,"makeColour",function(a){return new java.awt.Color(0,1-a,a)},"~N")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],
"jalview.schemes.ScoreColourScheme",["jalview.schemes.ResidueProperties","jalview.util.Comparison","java.awt.Color"],function(){c$=s(function(){this.max=this.min=0;this.scores=null;r(this,arguments)},jalview.schemes,"ScoreColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(a,b,c,f){t(this,jalview.schemes.ScoreColourScheme,[a]);this.scores=b;this.min=c;this.max=f;var d=b.length;this.colors=Array(b.length);for(a=0;a<d;a++){var e=(b[a]-c)/(f-c);1<e&&(e=1);0>e&&(e=0);this.colors[a]=this.makeColour(e)}},
"~A,~A,~N,~N");e(c$,"findColourSeq",function(a,b){if(0<this.threshold&&!this.aboveThreshold(a,b)||jalview.util.Comparison.isGap(a))return java.awt.Color.white;var c=this.colors[jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)]];this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI");d(c$,"makeColour",function(a){return new java.awt.Color(a,0,1-a)},"~N")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme","java.util.HashMap"],
["jalview.schemes.ConsensusColour","$.ClustalxColourScheme"],["jalview.schemes.Consensus","$.ResidueProperties","java.awt.Color"],function(){c$=s(function(){this.residueColour=this.colours=this.cons2=null;this.size=0;this.conses=null;this.includeGaps=!0;r(this,arguments)},jalview.schemes,"ClustalxColourScheme",jalview.schemes.ResidueColourScheme);J(c$,function(){this.conses=Array(32)});m(c$,function(a,b){t(this,jalview.schemes.ClustalxColourScheme,[]);this.alignmentChanged(a,b)},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");
e(c$,"alignmentChanged",function(a,b){var c=a.getWidth(),f=a.getSequences(b);this.cons2=w(c,24,0);this.includeGaps=this.isIncludeGaps();for(var d=0;24>d;d++)for(var e=0;e<c;e++)this.cons2[e][d]=0;for(var d=0,g,h,j=f.iterator();j.hasNext()&&((h=j.next())||1);){g=h.getSequence();for(var n=g.length-1,e=0;e<=n;e++)c=g.length-1<e?23:jalview.schemes.ResidueProperties.aaIndex[g[e].charCodeAt(0)],this.cons2[e][c]++;d++}this.size=f.size();this.makeColours()},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");
d(c$,"makeColours",function(){this.conses[0]=new jalview.schemes.Consensus("WLVIMAFCYHP",60);this.conses[1]=new jalview.schemes.Consensus("WLVIMAFCYHP",80);this.conses[2]=new jalview.schemes.Consensus("ED",50);this.conses[3]=new jalview.schemes.Consensus("KR",60);this.conses[4]=new jalview.schemes.Consensus("G",50);this.conses[5]=new jalview.schemes.Consensus("N",50);this.conses[6]=new jalview.schemes.Consensus("QE",50);this.conses[7]=new jalview.schemes.Consensus("P",50);this.conses[8]=new jalview.schemes.Consensus("TS",
50);this.conses[26]=new jalview.schemes.Consensus("A",85);this.conses[27]=new jalview.schemes.Consensus("C",85);this.conses[10]=new jalview.schemes.Consensus("E",85);this.conses[11]=new jalview.schemes.Consensus("F",85);this.conses[12]=new jalview.schemes.Consensus("G",85);this.conses[13]=new jalview.schemes.Consensus("H",85);this.conses[14]=new jalview.schemes.Consensus("I",85);this.conses[15]=new jalview.schemes.Consensus("L",85);this.conses[16]=new jalview.schemes.Consensus("M",85);this.conses[17]=
new jalview.schemes.Consensus("N",85);this.conses[18]=new jalview.schemes.Consensus("P",85);this.conses[19]=new jalview.schemes.Consensus("Q",85);this.conses[20]=new jalview.schemes.Consensus("R",85);this.conses[21]=new jalview.schemes.Consensus("S",85);this.conses[22]=new jalview.schemes.Consensus("T",85);this.conses[23]=new jalview.schemes.Consensus("V",85);this.conses[24]=new jalview.schemes.Consensus("W",85);this.conses[25]=new jalview.schemes.Consensus("Y",85);this.conses[28]=new jalview.schemes.Consensus("K",
85);this.conses[29]=new jalview.schemes.Consensus("D",85);this.conses[30]=new jalview.schemes.Consensus("G",0);this.conses[31]=new jalview.schemes.Consensus("P",0);this.colours=Array(11);var a=Array(1);a[0]=this.conses[30];this.colours[7]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.ORANGE),a);var b=Array(1);b[0]=this.conses[31];this.colours[8]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.YELLOW),
b);Array(1)[0]=this.conses[27];this.colours[9]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.PINK),a);a=Array(14);a[0]=this.conses[0];a[1]=this.conses[1];a[2]=this.conses[26];a[3]=this.conses[27];a[4]=this.conses[11];a[5]=this.conses[13];a[6]=this.conses[14];a[7]=this.conses[15];a[8]=this.conses[16];a[9]=this.conses[23];a[10]=this.conses[24];a[11]=this.conses[25];a[12]=this.conses[18];a[13]=this.conses[19];this.colours[0]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.BLUE),
a);this.colours[10]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.CYAN),a);a=Array(5);a[0]=this.conses[8];a[1]=this.conses[21];a[2]=this.conses[22];a[3]=this.conses[0];a[4]=this.conses[1];this.colours[1]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.GREEN),a);a=Array(3);a[0]=this.conses[17];a[1]=this.conses[29];a[2]=this.conses[5];this.colours[2]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.GREEN),
a);a=Array(6);a[0]=this.conses[6];a[1]=this.conses[19];a[2]=this.conses[22];a[3]=this.conses[3];a[4]=this.conses[28];a[5]=this.conses[20];this.colours[3]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.GREEN),a);a=Array(4);a[0]=this.conses[3];a[1]=this.conses[28];a[2]=this.conses[20];a[3]=this.conses[19];this.colours[4]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.RED),a);a=Array(6);a[0]=this.conses[3];
a[1]=this.conses[29];a[2]=this.conses[10];a[3]=this.conses[6];a[4]=this.conses[19];a[5]=this.conses[2];this.colours[5]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.MAGENTA),a);a=Array(5);a[0]=this.conses[3];a[1]=this.conses[29];a[2]=this.conses[10];a[3]=this.conses[17];a[4]=this.conses[2];this.colours[6]=new jalview.schemes.ConsensusColour(jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.MAGENTA),a);this.residueColour=Array(20);
this.residueColour[0]=this.colours[0];this.residueColour[1]=this.colours[4];this.residueColour[2]=this.colours[2];this.residueColour[3]=this.colours[6];this.residueColour[4]=this.colours[0];this.residueColour[5]=this.colours[3];this.residueColour[6]=this.colours[5];this.residueColour[7]=this.colours[7];this.residueColour[8]=this.colours[10];this.residueColour[9]=this.colours[0];this.residueColour[10]=this.colours[0];this.residueColour[11]=this.colours[4];this.residueColour[12]=this.colours[0];this.residueColour[13]=
this.colours[0];this.residueColour[14]=this.colours[8];this.residueColour[15]=this.colours[1];this.residueColour[16]=this.colours[1];this.residueColour[17]=this.colours[0];this.residueColour[18]=this.colours[10];this.residueColour[19]=this.colours[0]});e(c$,"findColour",function(){return java.awt.Color.pink},"~S");e(c$,"findColourSeq",function(a,b){var c;if(this.cons2.length<=b||this.includeGaps&&0!=this.threshold&&!this.aboveThreshold(a,b))return java.awt.Color.white;var f=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)];
c=java.awt.Color.white;if(19<f)return c;for(var d=0;d<this.residueColour[f].conses.length;d++)this.residueColour[f].conses[d].isConserved(this.cons2,b,this.size,this.includeGaps)&&(c=this.residueColour[f].c);4==f&&this.conses[27].isConserved(this.cons2,b,this.size,this.includeGaps)&&(c=jalview.schemes.ClustalxColourScheme.colhash.get(java.awt.Color.PINK));this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI");d(c$,"isIncludeGaps",function(){return this.includeGaps});
d(c$,"setIncludeGaps",function(a){this.includeGaps=a},"~B");e(c$,"applyTo",function(a,b){var c=new jalview.schemes.ClustalxColourScheme(a,b);c.includeGaps=this.includeGaps;return c},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");G(c$,"EIGHTY_FIVE",85,"FIFTY",50,"EIGHTY",80,"SIXTY",60);c$.colhash=c$.prototype.colhash=new java.util.HashMap;jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.RED,new java.awt.Color(0.9,0.2,0.1));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.BLUE,
new java.awt.Color(0.5,0.7,0.9));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.GREEN,new java.awt.Color(0.1,0.8,0.1));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.ORANGE,new java.awt.Color(0.9,0.6,0.3));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.CYAN,new java.awt.Color(0.1,0.7,0.7));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.PINK,new java.awt.Color(0.9,0.5,0.5));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.MAGENTA,
new java.awt.Color(0.8,0.3,0.8));jalview.schemes.ClustalxColourScheme.colhash.put(java.awt.Color.YELLOW,new java.awt.Color(0.8,0.8,0));c$=s(function(){this.c=this.conses=null;r(this,arguments)},jalview.schemes,"ConsensusColour");m(c$,function(a,b){this.conses=b;this.c=a},"java.awt.Color,~A")});p("jalview.schemes");q(null,"jalview.schemes.Consensus",["jalview.schemes.ResidueProperties"],function(){c$=s(function(){this.mask=null;this.threshold=0;this.maskstr=null;r(this,arguments)},jalview.schemes,
"Consensus");m(c$,function(a,b){this.maskstr=a;this.setMask(a);this.threshold=b},"~S,~N");d(c$,"setMask",function(a){this.mask=this.setNums(a)},"~S");d(c$,"isConserved",function(a,b,c){return this.isConserved(a,b,c,!0)},"~A,~N,~N");d(c$,"isConserved",function(a,b,c,f){var d=0;f||(c-=a[b][a[b].length-1]);for(f=0;f<this.mask.length;f++)d+=a[b][this.mask[f]];return d>this.threshold*c/100?!0:!1},"~A,~N,~N,~B");d(c$,"setNums",function(a){for(var b=w(a.length,0),c=0;c<a.length;)b[c]=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(c)],
c++;return b},"~S")});p("jalview.schemes");q(["jalview.schemes.ScoreColourScheme"],"jalview.schemes.HelixColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"HelixColourScheme",jalview.schemes.ScoreColourScheme);m(c$,function(){t(this,jalview.schemes.HelixColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.helix,0.57,1.51])});e(c$,"makeColour",function(a){return new java.awt.Color(a,1-a,a)},"~N")});p("jalview.schemes");
q(["jalview.schemes.ScoreColourScheme"],"jalview.schemes.HydrophobicColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"HydrophobicColourScheme",jalview.schemes.ScoreColourScheme);m(c$,function(){t(this,jalview.schemes.HydrophobicColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.hyd,-3.9,4.5])});e(c$,"makeColour",function(a){return new java.awt.Color(a,0,1-a)},"~N")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],
"jalview.schemes.NucleotideColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"NucleotideColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.NucleotideColourScheme,[jalview.schemes.ResidueProperties.nucleotideIndex,jalview.schemes.ResidueProperties.nucleotide,0])});e(c$,"findColour",function(a){return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)]]},"~S");e(c$,"findColourSeq",function(a,
b){var c;if(0==this.threshold||this.aboveThreshold(a,b))try{c=this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)]]}catch(f){if(y(f,Exception))return java.awt.Color.white;throw f;}else return java.awt.Color.white;this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],"jalview.schemes.PurinePyrimidineColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],
function(){c$=B(jalview.schemes,"PurinePyrimidineColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.PurinePyrimidineColourScheme,[jalview.schemes.ResidueProperties.purinepyrimidineIndex,jalview.schemes.ResidueProperties.purinepyrimidine,0])});d(c$,"findColour",function(a){return this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[a.charCodeAt(0)]]},"~S");d(c$,"findColour",function(a,b){var c;if(0==this.threshold||this.aboveThreshold(a,b))try{c=
this.colors[jalview.schemes.ResidueProperties.purinepyrimidineIndex[a.charCodeAt(0)]]}catch(f){if(y(f,Exception))return java.awt.Color.white;throw f;}else return java.awt.Color.white;this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme","java.util.Hashtable"],"jalview.schemes.RNAHelicesColour",["jalview.schemes.ResidueProperties","jalview.util.ColorUtils","java.awt.Color"],function(){c$=s(function(){this.positionsToHelix=
this.helixcolorhash=null;this.numHelix=0;this.annotation=null;this.lastrefresh=-1;r(this,arguments)},jalview.schemes,"RNAHelicesColour",jalview.schemes.ResidueColourScheme);J(c$,function(){this.helixcolorhash=new java.util.Hashtable;this.positionsToHelix=new java.util.Hashtable});m(c$,function(a){t(this,jalview.schemes.RNAHelicesColour,[jalview.schemes.ResidueProperties.nucleotideIndex]);this.annotation=a;this.refresh()},"jalview.datamodel.AlignmentAnnotation");m(c$,function(a){t(this,jalview.schemes.RNAHelicesColour,
[jalview.schemes.ResidueProperties.nucleotideIndex]);this.alignmentChanged(a,null)},"jalview.datamodel.AnnotatedCollectionI");e(c$,"alignmentChanged",function(a){a=a.getAlignmentAnnotation();for(var b=0;b<a.length;b++)if(null!=a[b].getRNAStruc()){this.annotation=a[b];break}this.refresh()},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");d(c$,"refresh",function(){if(null!=this.annotation&&(null==this.annotation._rnasecstr||this.lastrefresh!=this.annotation._rnasecstr.hashCode())&&this.annotation.isValidStruc()){this.annotation.getRNAStruc();
this.lastrefresh=this.annotation._rnasecstr.hashCode();this.numHelix=0;this.positionsToHelix=new java.util.Hashtable;for(var a=0;a<this.annotation._rnasecstr.length;a++)this.positionsToHelix.put(new Integer(this.annotation._rnasecstr[a].getBegin()),this.annotation._rnasecstr[a].getFeatureGroup()),this.positionsToHelix.put(new Integer(this.annotation._rnasecstr[a].getEnd()),this.annotation._rnasecstr[a].getFeatureGroup()),Integer.parseInt(this.annotation._rnasecstr[a].getFeatureGroup())>this.numHelix&&
(this.numHelix=Integer.parseInt(this.annotation._rnasecstr[a].getFeatureGroup()));for(a=0;a<=this.numHelix;a++)this.helixcolorhash.containsKey(Integer.toString(a))||this.helixcolorhash.put(Integer.toString(a),jalview.util.ColorUtils.generateRandomColor(java.awt.Color.white))}});e(c$,"findColour",function(a){return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[a.charCodeAt(0)]]},"~S");e(c$,"findColourSeq",function(a,b){this.refresh();var c=
java.awt.Color.white,f=null,f=this.positionsToHelix.get(new Integer(b));null!=f&&(c=this.helixcolorhash.get(f));return c},"~S,~N,jalview.datamodel.SequenceI")});p("jalview.util");q(null,"jalview.util.ColorUtils",["java.awt.Color","java.util.Random"],function(){c$=B(jalview.util,"ColorUtils");c$.generateRandomColor=d(c$,"generateRandomColor",function(a){var b=new java.util.Random,c=b.nextInt(256),f=b.nextInt(256),b=b.nextInt(256);null!=a&&(c=F((c+a.getRed())/2),f=F((f+a.getGreen())/2),b=F((b+a.getBlue())/
2));return new java.awt.Color(c,f,b)},"java.awt.Color");c$.toTkCode=d(c$,"toTkCode",function(a){return"#"+(16>a.getRed()?"0":"")+Integer.toHexString(a.getRed())+(16>a.getGreen()?"0":"")+Integer.toHexString(a.getGreen())+(16>a.getBlue()?"0":"")+Integer.toHexString(a.getBlue())},"java.awt.Color");c$.darkerThan=d(c$,"darkerThan",function(a){return null==a?null:a.darker().darker().darker()},"java.awt.Color");c$.brighterThan=d(c$,"brighterThan",function(a){return null==a?null:a.brighter().brighter().brighter()},
"java.awt.Color")});p("jalview.schemes");q(["jalview.schemes.ScoreColourScheme"],"jalview.schemes.StrandColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"StrandColourScheme",jalview.schemes.ScoreColourScheme);m(c$,function(){t(this,jalview.schemes.StrandColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.strand,0.37,1.7])});e(c$,"makeColour",function(a){return new java.awt.Color(a,a,1-a)},"~N")});p("jalview.schemes");
q(["jalview.schemes.ResidueColourScheme","java.awt.Color"],"jalview.schemes.TCoffeeColourScheme",["jalview.datamodel.AlignmentI","java.util.ArrayList","$.IdentityHashMap"],function(){c$=s(function(){this.seqMap=null;r(this,arguments)},jalview.schemes,"TCoffeeColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(a){t(this,jalview.schemes.TCoffeeColourScheme,[]);this.alignmentChanged(a,null)},"jalview.datamodel.AnnotatedCollectionI");e(c$,"alignmentChanged",function(a){var b=new java.util.ArrayList;
this.seqMap=new java.util.IdentityHashMap;var c=0,f;for(a=(v(a,jalview.datamodel.AlignmentI)?a:a.getContext()).findAnnotation("TCoffeeScore").iterator();a.hasNext()&&((f=a.next())||1);)if(null!=f.sequenceRef&&!f.belowAlignment){b.add(f);c<f.annotations.length&&(c=f.annotations.length);for(var d=Array(f.annotations.length),e=0,g,h=0,j=f.annotations;h<j.length&&((g=j[h])||1);h++)d[e++]=null!=g?g.colour:java.awt.Color.white;this.seqMap.put(f.sequenceRef,d)}},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");
e(c$,"findColourSeq",function(a,b,c){var f;return null==this.seqMap||null==(f=this.seqMap.get(c))||0>b||b>=f.length?java.awt.Color.white:f[b]},"~S,~N,jalview.datamodel.SequenceI");e(c$,"applyTo",function(a){return new jalview.schemes.TCoffeeColourScheme(a)},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");c$.$colors=c$.prototype.$colors=E(-1,[new java.awt.Color(102,102,255),new java.awt.Color(0,255,0),new java.awt.Color(102,255,0),new java.awt.Color(204,255,0),new java.awt.Color(255,255,0),
new java.awt.Color(255,204,0),new java.awt.Color(255,153,0),new java.awt.Color(255,102,0),new java.awt.Color(255,51,0),new java.awt.Color(255,34,0)])});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],"jalview.schemes.TaylorColourScheme",["jalview.schemes.ResidueProperties"],function(){c$=B(jalview.schemes,"TaylorColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.TaylorColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.taylor,
0])})});p("jalview.schemes");q(["jalview.schemes.ScoreColourScheme"],"jalview.schemes.TurnColourScheme",["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"TurnColourScheme",jalview.schemes.ScoreColourScheme);m(c$,function(){t(this,jalview.schemes.TurnColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.turn,0.47,1.56])});e(c$,"makeColour",function(a){return new java.awt.Color(a,1-a,1-a)},"~N")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],
"jalview.schemes.UserColourScheme",["jalview.schemes.ColourSchemeProperty","$.ResidueProperties","java.awt.Color","java.util.StringTokenizer"],function(){c$=s(function(){this.schemeName=this.lowerCaseColours=null;r(this,arguments)},jalview.schemes,"UserColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.UserColourScheme,[jalview.schemes.ResidueProperties.aaIndex])});m(c$,function(a){t(this,jalview.schemes.UserColourScheme,[jalview.schemes.ResidueProperties.aaIndex]);
this.colors=a},"~A");e(c$,"applyTo",function(){var a=new jalview.schemes.UserColourScheme(this.colors);null!=this.lowerCaseColours&&(a.schemeName=String.instantialize(this.schemeName),a.lowerCaseColours=Array(this.lowerCaseColours.length),System.arraycopy(this.lowerCaseColours,0,a.lowerCaseColours,0,this.lowerCaseColours.length));return a},"jalview.datamodel.AnnotatedCollectionI,java.util.Map");m(c$,function(a){t(this,jalview.schemes.UserColourScheme,[jalview.schemes.ResidueProperties.aaIndex]);var b=
this.getColourFromString(a);null==b&&(System.out.println("Unknown colour!! "+a),b=this.createColourFromName(a));this.colors=Array(24);for(var c=0;24>c;c++)this.colors[c]=b;this.schemeName=a},"~S");d(c$,"getColours",function(){return this.colors});d(c$,"getLowerCaseColours",function(){return this.lowerCaseColours});d(c$,"setName",function(a){this.schemeName=a},"~S");d(c$,"getName",function(){return this.schemeName});d(c$,"getColourFromString",function(a){a=a.trim();var b=null;try{var c=Integer.parseInt(a,
16),b=new java.awt.Color(c)}catch(f){if(!y(f,NumberFormatException))throw f;}null==b&&(b=jalview.schemes.ColourSchemeProperty.getAWTColorFromName(a));if(null==b)try{var d=new java.util.StringTokenizer(a,","),e=Integer.parseInt(d.nextToken()),g=Integer.parseInt(d.nextToken()),h=Integer.parseInt(d.nextToken()),b=new java.awt.Color(e,g,h)}catch(j){if(!y(j,Exception))throw j;}return b},"~S");d(c$,"createColourFromName",function(a){var b,c;c=a.length;var f=0,d=F(c/3),e=15*Math.abs(a.hashCode()%10);b=Math.abs(a.substring(f,
d).hashCode()+e)%210+20;f=d;d+=F(c/3);d>c&&(d=c);c=Math.abs(a.substring(f,d).hashCode()+e)%210+20;a=Math.abs(a.substring(d).hashCode()+e)%210+20;return new java.awt.Color(b,c,a)},"~S");d(c$,"parseAppletParameter",function(a){a=new java.util.StringTokenizer(a,";");var b,c=null,f,d;try{for(;a.hasMoreElements();){c=a.nextToken().trim();d=c.substring(0,c.indexOf("="));f=c.substring(c.indexOf("=")+1);for(b=new java.util.StringTokenizer(d," ,");b.hasMoreTokens();)if(c=b.nextToken(),-1!=jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt(0)]){var e=
jalview.schemes.ResidueProperties.aaIndex[c.charCodeAt(0)];if(c.equalsIgnoreCase("lowerCase")){null==this.lowerCaseColours&&(this.lowerCaseColours=Array(23));for(var g=0;23>g;g++)null==this.lowerCaseColours[g]&&(this.lowerCaseColours[g]=this.getColourFromString(f))}else c.equals(c.toLowerCase())?(null==this.lowerCaseColours&&(this.lowerCaseColours=Array(23)),this.lowerCaseColours[e]=this.getColourFromString(f)):this.colors[e]=this.getColourFromString(f)}}}catch(h){if(y(h,Exception))System.out.println("Error parsing userDefinedColours:\n"+
c+"\n"+h);else throw h;}},"~S");e(c$,"findColourSeq",function(a,b){var c;c=jalview.schemes.ResidueProperties.aaIndex[a.charCodeAt(0)];c=0==this.threshold||this.aboveThreshold(a,b)?null!=this.lowerCaseColours&&"a"<=a&&"z">=a?this.lowerCaseColours[c]:this.colors[c]:java.awt.Color.white;this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI");d(c$,"setLowerCaseColours",function(a){this.lowerCaseColours=a},"~A")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],
"jalview.schemes.ZappoColourScheme",["jalview.schemes.ResidueProperties"],function(){c$=B(jalview.schemes,"ZappoColourScheme",jalview.schemes.ResidueColourScheme);m(c$,function(){t(this,jalview.schemes.ZappoColourScheme,[jalview.schemes.ResidueProperties.aaIndex,jalview.schemes.ResidueProperties.zappo,0])})});p("jalview.structure");q(["java.util.ArrayList","$.HashMap","$.LinkedHashSet","$.Vector"],"jalview.structure.StructureSelectionManager","MCview.PDBfile jalview.analysis.AlignSeq jalview.commands.EditCommand $.OrderCommand jalview.datamodel.Mapping $.SearchResults jalview.io.AppletFormatAdapter jalview.structure.AtomSpec $.SecondaryStructureListener $.SequenceListener $.StructureListener $.StructureMapping $.VamsasListener jalview.util.MappingUtils $.MessageManager java.lang.Error $.NullPointerException $.StringBuilder java.util.Arrays $.Collections $.IdentityHashMap".split(" "),
function(){c$=s(function(){this.mappings=null;this.addTempFacAnnot=this.secStructServices=this.processSecondaryStructure=!1;this.pdbFileNameId=this.pdbIdFileName=this.sel_listeners=this.commandListeners=this.seqMappingRefCounts=this.seqmappings=null;this.relaySeqMappings=!0;this.listeners=null;this.handlingVamsasMo=!1;this.lastmsg=0;this.view_listeners=null;r(this,arguments)},jalview.structure,"StructureSelectionManager");J(c$,function(){this.mappings=new java.util.ArrayList;this.seqmappings=new java.util.LinkedHashSet;
this.seqMappingRefCounts=new java.util.HashMap;this.commandListeners=new java.util.ArrayList;this.sel_listeners=new java.util.ArrayList;this.pdbIdFileName=new java.util.HashMap;this.pdbFileNameId=new java.util.HashMap;this.listeners=new java.util.Vector;this.view_listeners=new java.util.Vector});d(c$,"isSecStructServices",function(){return this.secStructServices});d(c$,"setSecStructServices",function(a){this.secStructServices=a},"~B");d(c$,"isAddTempFacAnnot",function(){return this.addTempFacAnnot});
d(c$,"setAddTempFacAnnot",function(a){this.addTempFacAnnot=a},"~B");d(c$,"isProcessSecondaryStructure",function(){return this.processSecondaryStructure});d(c$,"setProcessSecondaryStructure",function(a){this.processSecondaryStructure=a},"~B");d(c$,"reportMapping",function(){if(this.mappings.isEmpty())System.err.println("reportMapping: No PDB/Sequence mappings.");else{System.err.println("reportMapping: There are "+this.mappings.size()+" mappings.");for(var a=0,b,c=this.mappings.iterator();c.hasNext()&&
((b=c.next())||1);)System.err.println("mapping "+a++ +" : "+b.pdbfile)}});d(c$,"registerPDBFile",function(a,b){this.pdbIdFileName.put(a,b);this.pdbFileNameId.put(b,a)},"~S,~S");d(c$,"findIdForPDBFile",function(a){return this.pdbFileNameId.get(a)},"~S");d(c$,"findFileForPDBId",function(a){return this.pdbIdFileName.get(a)},"~S");d(c$,"isPDBFileRegistered",function(a){return this.pdbFileNameId.containsKey(a)||this.pdbIdFileName.containsKey(a)},"~S");c$.getStructureSelectionManager=d(c$,"getStructureSelectionManager",
function(a){if(null==a&&null==jalview.structure.StructureSelectionManager.nullProvider){if(null!=jalview.structure.StructureSelectionManager.instances)throw Error(jalview.util.MessageManager.getString("error.implementation_error_structure_selection_manager_null"),new NullPointerException(jalview.util.MessageManager.getString("exception.ssm_context_is_null")));jalview.structure.StructureSelectionManager.nullProvider=new jalview.structure.StructureSelectionManager;return jalview.structure.StructureSelectionManager.nullProvider}null==
jalview.structure.StructureSelectionManager.instances&&(jalview.structure.StructureSelectionManager.instances=new java.util.IdentityHashMap);var b=jalview.structure.StructureSelectionManager.instances.get(a);null==b&&(b=null!=jalview.structure.StructureSelectionManager.nullProvider?jalview.structure.StructureSelectionManager.nullProvider:new jalview.structure.StructureSelectionManager,jalview.structure.StructureSelectionManager.instances.put(a,b));return b},"jalview.api.StructureSelectionManagerProvider");
d(c$,"setRelaySeqMappings",function(a){this.relaySeqMappings=a},"~B");d(c$,"isRelaySeqMappingsEnabled",function(){return this.relaySeqMappings});d(c$,"addStructureViewerListener",function(a){this.listeners.contains(a)||this.listeners.addElement(a)},"~O");d(c$,"alreadyMappedToFile",function(a){for(var b,c=this.mappings.iterator();c.hasNext()&&((b=c.next())||1);)if(b.getPdbId().equals(a))return b.pdbfile;return null},"~S");d(c$,"setMapping",function(a,b,c,f){return this.setMapping(!0,a,b,c,f)},"~A,~A,~S,~S");
d(c$,"setMapping",function(a,b,c,f,d){var e=this.processSecondaryStructure;if(this.isPDBFileRegistered(f))for(var g,h=0;h<b.length&&((g=b[h])||1);h++){for(var j=g;null!=j.getDatasetSequence();)j=j.getDatasetSequence();if(null!=j.getAnnotation())for(var n,m=0,j=j.getAnnotation();m<j.length&&((n=j[m])||1);m++)MCview.PDBfile.isCalcIdForFile(n,this.findIdForPDBFile(f))&&(e=!1)}g=null;try{g=new MCview.PDBfile(this.addTempFacAnnot,e,this.secStructServices,f,d),null!=g.id&&(0<g.id.trim().length&&jalview.io.AppletFormatAdapter.FILE.equals(d))&&
this.registerPDBFile(g.id.trim(),f)}catch(u){if(y(u,Exception))return u.printStackTrace(),null;throw u;}for(var p,e=0;e<b.length;e++){var q=!0;n=b[e];null!=c&&null!=c[e]?(q=!1,p=c[e]):-1<n.getName().indexOf("|")?(p=n.getName().substring(n.getName().lastIndexOf("|")+1),1<p.length&&(p=0==p.trim().length?" ":"")):p="";for(var s=-10,j=null,m=" ",h=null,r=!0,t,v=g.chains.iterator();v.hasNext()&&((t=v.next())||1);)if(!(0<p.length&&!p.equals(t.id)&&!q)){var z=jalview.analysis.AlignSeq.doGlobalNWAlignment(n,
t.sequence,t.isNa?"dna":"pep");if(r||z.maxscore>s||z.maxscore==s&&t.id.equals(p))r=!1,h=t,s=z.maxscore,j=z,m=t.id}if(null!=h){p=new StringBuilder(128);p.append(jalview.structure.StructureSelectionManager.NEWLINE).append("PDB Sequence is :").append(jalview.structure.StructureSelectionManager.NEWLINE).append("Sequence = ").append(h.sequence.getSequenceAsString());p.append(jalview.structure.StructureSelectionManager.NEWLINE).append("No of residues = ").append(h.residues.size()).append(jalview.structure.StructureSelectionManager.NEWLINE).append(jalview.structure.StructureSelectionManager.NEWLINE);
q=(H("jalview.structure.StructureSelectionManager$1")?0:jalview.structure.StructureSelectionManager.$StructureSelectionManager$1$(),C(jalview.structure.StructureSelectionManager$1,this,T("mappingDetails",p),System.out));j.printAlignment(q);p.append(jalview.structure.StructureSelectionManager.NEWLINE).append("PDB start/end ");p.append(String.valueOf(j.seq2start)).append(" ");p.append(String.valueOf(j.seq2end));p.append(jalview.structure.StructureSelectionManager.NEWLINE).append("SEQ start/end ");p.append(String.valueOf(j.seq1start+
n.getStart()-1)).append(" ");p.append(String.valueOf(j.seq1end+n.getEnd()-1));h.makeExactMapping(j,n);j=j.getMappingFromS1(!1);new jalview.datamodel.Mapping(j.getMap().getInverse());h.transferRESNUMFeatures(n,null);q=w(n.findPosition(n.getLength())+2,2,0);s=-1E4;r=0;do v=h.atoms.elementAt(r),s!=v.resNumber&&-1!=v.alignmentMapping&&(s=v.resNumber,q[v.alignmentMapping+1][0]=v.resNumber,q[v.alignmentMapping+1][1]=v.atomIndex),r++;while(r<h.atoms.size());d.equals(jalview.io.AppletFormatAdapter.PASTE)&&
(f="INLINE"+g.id);n=new jalview.structure.StructureMapping(n,f,g.id,m,q,p.toString());a&&this.mappings.add(n);h.transferResidueAnnotation(n,j)}}return g},"~B,~A,~A,~S,~S");d(c$,"removeStructureViewerListener",function(a,b){this.listeners.removeElement(a);if(v(a,jalview.structure.SequenceListener))for(var c=0;c<this.listeners.size();c++)v(this.listeners.elementAt(c),jalview.structure.StructureListener)&&this.listeners.elementAt(c).releaseReferences(a);if(null!=b){for(var f=new java.util.ArrayList(java.util.Arrays.asList(b)),
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if(d!=h&&c!==e.sequence){b.addResult(e.sequence,h,h);for(var d=h,c=e.sequence,j,n=this.seqmappings.iterator();n.hasNext()&&((j=n.next())||1);)j.markMappedRegion(e.sequence,h,b)}}var m;for(f=this.listeners.iterator();f.hasNext()&&((m=f.next())||1);)v(m,jalview.structure.SequenceListener)&&m.highlightSequence(b)}}},"java.util.List");d(c$,"mouseOverSequence",function(a,b,c,f){var d=this.handlingVamsasMo||!this.seqmappings.isEmpty(),e=null;-1==c&&(c=a.findPosition(b));for(var g=0;g<this.listeners.size();g++){var h=
this.listeners.elementAt(g);h!==f&&(v(h,jalview.structure.StructureListener)?this.highlightStructure(h,a,c):v(h,jalview.structure.SequenceListener)?d&&h.getVamsasSource()!==f&&this.relaySeqMappings&&(null==e&&(e=jalview.util.MappingUtils.buildSearchResults(a,c,this.seqmappings)),this.handlingVamsasMo&&e.addResult(a,c,c),h.highlightSequence(e)):v(h,jalview.structure.VamsasListener)&&!this.handlingVamsasMo?h.mouseOverSequence(a,b,f):v(h,jalview.structure.SecondaryStructureListener)&&h.mouseOverSequence(a,
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function(a,b,c){this.handlingVamsasMo=!0;var f=a.hashCode()*(1+b);this.lastmsg!=f&&(this.lastmsg=f,this.mouseOverSequence(a,b,-1,c));this.handlingVamsasMo=!1},"jalview.datamodel.SequenceI,~N,jalview.structure.VamsasSource");d(c$,"colourSequenceFromStructure",function(){return null},"jalview.datamodel.SequenceI,~S");d(c$,"structureSelectionChanged",function(){});d(c$,"sequenceSelectionChanged",function(){});d(c$,"sequenceColoursChanged",function(a){for(var b,c=0;c<this.listeners.size();c++)v(this.listeners.elementAt(c),
jalview.structure.StructureListener)&&(b=this.listeners.elementAt(c),b.updateColours(a))},"~O");d(c$,"getMapping",function(a){for(var b=new java.util.ArrayList,c,f=this.mappings.iterator();f.hasNext()&&((c=f.next())||1);)c.pdbfile.equals(a)&&b.add(c);return b.toArray(Array(b.size()))},"~S");d(c$,"printMappings",function(a,b){if(null==a||null==b||b.isEmpty())return"";for(var c=new StringBuilder(64),f,d=this.mappings.iterator();d.hasNext()&&((f=d.next())||1);)f.pdbfile.equals(a)&&b.contains(f.sequence)&&
(c.append(f.mappingDetails),c.append(jalview.structure.StructureSelectionManager.NEWLINE),c.append("====================="),c.append(jalview.structure.StructureSelectionManager.NEWLINE));c.append(jalview.structure.StructureSelectionManager.NEWLINE);return c.toString()},"~S,java.util.List");d(c$,"removeMappings",function(a){if(null!=a){var b;for(a=a.iterator();a.hasNext()&&((b=a.next())||1);)this.removeMapping(b)}},"java.util.Set");d(c$,"removeMapping",function(a){if(null!=a&&this.seqmappings.contains(a)){var b=
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this.seqMappingRefCounts.put(a,new Integer(1))))},"jalview.datamodel.AlignedCodonFrame");d(c$,"addSelectionListener",function(a){this.sel_listeners.contains(a)||this.sel_listeners.add(a)},"jalview.structure.SelectionListener");d(c$,"removeSelectionListener",function(a){this.sel_listeners.contains(a)&&this.sel_listeners.remove(a)},"jalview.structure.SelectionListener");d(c$,"sendSelection",function(a,b,c){for(var f,d=this.sel_listeners.iterator();d.hasNext()&&((f=d.next())||1);)f!==c&&f.selection(a,
b,c)},"jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource");d(c$,"sendViewPosition",function(a,b,c,f,d){if(null!=this.view_listeners&&0<this.view_listeners.size())for(var e=this.view_listeners.elements();e.hasMoreElements();){var g=e.nextElement();g!==a&&g.viewPosition(b,c,f,d,a)}},"jalview.api.AlignmentViewPanel,~N,~N,~N,~N");c$.release=d(c$,"release",function(a){if(null!=jalview.structure.StructureSelectionManager.instances){var b=jalview.structure.StructureSelectionManager.instances.get(a);
if(null!=b){jalview.structure.StructureSelectionManager.instances.remove(a);try{b.finalize()}catch(c){}}}},"jalview.api.StructureSelectionManagerProvider");d(c$,"registerPDBEntry",function(a){null!=a.getFile()&&0<a.getFile().trim().length&&this.registerPDBFile(a.getId(),a.getFile())},"jalview.datamodel.PDBEntry");d(c$,"addCommandListener",function(a){this.commandListeners.contains(a)||this.commandListeners.add(a)},"jalview.structure.CommandListener");d(c$,"hasCommandListener",function(a){return this.commandListeners.contains(a)},
"jalview.structure.CommandListener");d(c$,"removeCommandListener",function(a){return this.commandListeners.remove(a)},"jalview.structure.CommandListener");d(c$,"commandPerformed",function(a,b,c){for(var f,d=this.commandListeners.iterator();d.hasNext()&&((f=d.next())||1);)f.mirrorCommand(a,b,this,c)},"jalview.commands.CommandI,~B,jalview.structure.VamsasSource");d(c$,"mapCommand",function(a,b,c,f){return v(a,jalview.commands.EditCommand)?jalview.util.MappingUtils.mapEditCommand(a,b,c,f,this.seqmappings):
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System.lineSeparator();G(c$,"instances",null,"nullProvider",null)});p("MCview");q(["jalview.io.AlignFile"],"MCview.PDBfile","MCview.Atom $.PDBChain jalview.analysis.AlignSeq jalview.datamodel.Alignment $.AlignmentI $.PDBEntry jalview.io.FileParse jalview.util.MessageManager java.awt.Color java.io.IOException java.util.ArrayList $.Hashtable $.Vector".split(" "),function(){c$=s(function(){this.id=this.chains=null;this.visibleChainAnnotation=!1;this.$predictSecondaryStructure=!0;this.externalSecondaryStructure=
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0==f.indexOf("MODEL")&&(d=!0);0==f.indexOf("TER")&&(e=!0);if(d&&0==f.indexOf("ENDMDL"))break;if(0==f.indexOf("ATOM")||0==f.indexOf("HETATM")&&!e){e=!1;h=f.substring(12,15).trim();if(!h.equals("CA")&&!h.equals("P"))continue;var n=new MCview.Atom(f);c=this.findChain(n.chain);if(null!=c){if(n.resNumIns.trim().equals(g))continue}else c=new MCview.PDBChain(this.id,n.chain),this.chains.addElement(c);c.atoms.addElement(n);g=n.resNumIns.trim()}this.index++}this.makeResidueList();this.makeCaBondList();null==
this.id&&(this.id=this.inFile.getName());for(var m,u=this.chains.iterator();u.hasNext()&&((m=u.next())||1);){var p=this.postProcessChain(m);MCview.PDBfile.isRNA(p)?a.add(p):b.add(p)}this.$predictSecondaryStructure&&this.predictSecondaryStructure(a,b)}catch(q){if(y(q,OutOfMemoryError))throw System.out.println("OUT OF MEMORY LOADING PDB FILE"),new java.io.IOException(jalview.util.MessageManager.getString("exception.outofmemory_loading_pdb_file"));if(y(q,NumberFormatException))null!=f&&(System.err.println("Couldn't read number from line:"),
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0;c<b.length;c++)b[c].visible=this.visibleChainAnnotation,this.annotations.addElement(b[c]);return a},"MCview.PDBChain");c$.isCalcIdHandled=d(c$,"isCalcIdHandled",function(a){return null!=a&&MCview.PDBfile.CALC_ID_PREFIX.equals(a)},"~S");c$.isCalcIdForFile=d(c$,"isCalcIdForFile",function(a,b){return null!=a.getCalcId()&&MCview.PDBfile.CALC_ID_PREFIX.equals(a.getCalcId())&&b.equals(a.getProperty("PDBID"))},"jalview.datamodel.AlignmentAnnotation,~S");c$.relocateCalcId=d(c$,"relocateCalcId",function(a,
b){var c=MCview.PDBfile.CALC_ID_PREFIX.length,f=a.indexOf(MCview.PDBfile.CALC_ID_PREFIX,c),c=a.substring(c,f-1);return MCview.PDBfile.CALC_ID_PREFIX+b.get(c)+":"+a.substring(f)},"~S,java.util.Hashtable");d(c$,"markCalcIds",function(){for(var a,b=this.seqs.iterator();b.hasNext()&&((a=b.next())||1);)if(null!=a.getAnnotation())for(var c,f=0,d=a.getAnnotation();f<d.length&&((c=d[f])||1);f++){var e=c.getCalcId();null==e&&(e="");c.setCalcId(MCview.PDBfile.CALC_ID_PREFIX);c.setProperty("PDBID",this.id);
c.setProperty("oldCalcId",e)}});d(c$,"processPdbFileWithJmol",function(a){try{var b=W._4Name("jalview.ext.jmol.PDBFileWithJmol");if(null!=b){var c=b.getConstructor(E(-1,[jalview.io.FileParse])),f=E(-1,[new jalview.io.FileParse(this.getDataName(),this.type)]),d=c.newInstance(f),e=new jalview.datamodel.Alignment(b.getMethod("getSeqsAsArray",E(-1,[])).invoke(d,[]));b.getMethod("addAnnotations",E(-1,[jalview.datamodel.AlignmentI])).invoke(d,[e]);for(var g,h=e.getSequences().iterator();h.hasNext()&&((g=
h.next())||1);)null!=g.getDatasetSequence()?g.getDatasetSequence().getPDBId().clear():g.getPDBId().clear();this.replaceAndUpdateChains(a,e,"pep",!1)}}catch(j){if(!y(j,ClassNotFoundException))throw j;}},"java.util.List");d(c$,"replaceAndUpdateChains",function(a,b,c){a=jalview.analysis.AlignSeq.replaceMatchingSeqsWith(this.seqs,this.annotations,a,b,c,!1);var f;for(b=this.chains.iterator();b.hasNext()&&((f=b.next())||1);){c=0;for(var d,e=a.get(0).iterator();e.hasNext()&&((d=e.next())||1);)if(c++,d===
f.sequence||d.getDatasetSequence()===f.sequence){c=-c;break}0>c&&(c=-c-1,f.shadow=a.get(1).get(c),f.shadowMap=a.get(2).get(c).getMappingFromS1(!1))}},"java.util.List,jalview.datamodel.AlignmentI,~S,~B");d(c$,"processPdbFileWithAnnotate3d",function(a){try{var b=W._4Name("jalview.ws.jws1.Annotate3D");if(null!=b){for(var c=b.getConstructor(E(-1,[])).newInstance(E(-1,[])),f=b.getMethod("getRNAMLFor",E(-1,[jalview.io.FileParse])).invoke(c,E(-1,[new jalview.io.FileParse(this.getDataName(),this.type)])),
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d(c$,"makeCaBondList",function(){for(var a=0;a<this.chains.size();a++)this.chains.elementAt(a).makeCaBondList()});d(c$,"findChain",function(a){for(var b=0;b<this.chains.size();b++)if(this.chains.elementAt(b).id.equals(a))return this.chains.elementAt(b);return null},"~S");d(c$,"setChargeColours",function(){for(var a=0;a<this.chains.size();a++)this.chains.elementAt(a).setChargeColours()});d(c$,"setColours",function(a){for(var b=0;b<this.chains.size();b++)this.chains.elementAt(b).setChainColours(a)},
"jalview.schemes.ColourSchemeI");d(c$,"setChainColours",function(){for(var a=0;a<this.chains.size();a++)this.chains.elementAt(a).setChainColours(java.awt.Color.getHSBColor(1/a,0.4,1))});c$.isRNA=d(c$,"isRNA",function(a){var b,c=0;for(a=a.getSequence();c<a.length&&((b=a[c])||1);c++)if("A"!=b&&"C"!=b&&"G"!=b&&"U"!=b)return!1;return!0},"jalview.datamodel.SequenceI");G(c$,"CALC_ID_PREFIX","JalviewPDB")});p("jalview.io");q(["jalview.io.FileParse"],"jalview.io.AlignFile","jalview.datamodel.Sequence jalview.util.MessageManager java.io.IOException java.lang.Error java.util.ArrayList $.Hashtable $.Vector".split(" "),
function(){c$=s(function(){this.maxLength=this.noSeqs=0;this.properties=this.seqGroups=this.annotations=this.seqs=null;this.end=this.start=0;this.jvSuffix=!0;this.parseCalled=!1;this.newickStrings=null;r(this,arguments)},jalview.io,"AlignFile",jalview.io.FileParse);m(c$,function(){t(this,jalview.io.AlignFile,[]);this.initData()});m(c$,function(a,b){this.construct(!0,a,b)},"~S,~S");m(c$,function(a,b,c){t(this,jalview.io.AlignFile,[b,c]);this.initData();a&&this.doParse()},"~B,~S,~S");m(c$,function(a){this.construct(!0,
a)},"jalview.io.FileParse");m(c$,function(a,b){t(this,jalview.io.AlignFile,[b]);this.initData();a&&this.doParse()},"~B,jalview.io.FileParse");d(c$,"doParse",function(){if(this.parseCalled)throw new java.io.IOException("Implementation error: Parser called twice for same data.\nNeed to call initData() again before parsing can be reattempted.");this.parseCalled=!0;this.parse();for(var a=0,b=this.seqs.size();a<b;a++)this.seqs.get(a).setIndex(a)});d(c$,"getSeqs",function(){return this.seqs});d(c$,"getSeqGroups",
function(){return this.seqGroups});d(c$,"getSeqsAsArray",function(){for(var a=Array(this.seqs.size()),b=0;b<this.seqs.size();b++)a[b]=this.seqs.elementAt(b);return a});d(c$,"addAnnotations",function(a){this.addProperties(a);for(var b=0;b<this.annotations.size();b++){var c=this.annotations.elementAt(b);c.validateRangeAndDisplay();a.addAnnotation(c)}},"jalview.datamodel.AlignmentI");d(c$,"addSeqGroups",function(a){this.seqGroups=a.getGroups()},"jalview.datamodel.AlignmentI");d(c$,"addProperties",function(a){if(null!=
this.properties&&0<this.properties.size())for(var b=this.properties.keys(),c=this.properties.elements();b.hasMoreElements();)a.setProperty(b.nextElement(),c.nextElement())},"jalview.datamodel.AlignmentI");d(c$,"setAlignmentProperty",function(a,b){if(null==a)throw Error(jalview.util.MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));null!=b&&(null==this.properties&&(this.properties=new java.util.Hashtable),this.properties.put(a,b))},"~O,~O");d(c$,"getAlignmentProperty",
function(a){return null!=this.properties&&null!=a?this.properties.get(a):null},"~O");d(c$,"initData",function(){this.seqs=new java.util.Vector;this.annotations=new java.util.Vector;this.seqGroups=new java.util.ArrayList;this.parseCalled=!1});d(c$,"setSeqs",function(a){this.seqs=new java.util.Vector;for(var b=0;b<a.length;b++)this.seqs.addElement(a[b])},"~A");d(c$,"addJVSuffix",function(a){this.jvSuffix=a},"~B");d(c$,"parseId",function(a){var b=null;a=a.trim();var c=a.indexOf(" ");-1<c?(b=new jalview.datamodel.Sequence(a.substring(0,
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this.error=!1;this.dataIn.mark(2048)},"~S,~S");d(c$,"mark",function(){if(null!=this.dataIn)this.dataIn.mark(2048);else throw new java.io.IOException(jalview.util.MessageManager.getString("exception.no_init_source_stream"));});d(c$,"nextLine",function(){if(!this.error)return this.dataIn.readLine();throw new java.io.IOException(jalview.util.MessageManager.formatMessage("exception.invalid_source_stream",E(-1,[this.errormessage])));});d(c$,"isExporting",function(){return!this.error&&null==this.dataIn});
d(c$,"isValid",function(){return!this.error});d(c$,"close",function(){this.errormessage="EXCEPTION ON CLOSE";this.error=!0;this.dataIn.close();this.dataIn=null;this.errormessage="SOURCE IS CLOSED"});d(c$,"reset",function(){if(null!=this.dataIn&&!this.error)this.dataIn.reset();else throw new java.io.IOException(jalview.util.MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));});d(c$,"hasWarningMessage",function(){return null!=this.warningMessage&&0<this.warningMessage.length});
d(c$,"getWarningMessage",function(){return this.warningMessage});d(c$,"getInFile",function(){return null!=this.inFile?this.inFile.getAbsolutePath()+" ("+this.index+")":"From Paste + ("+this.index+")"});d(c$,"getDataName",function(){return this.dataName});d(c$,"setDataName",function(a){this.dataName=a},"~S");d(c$,"getReader",function(){return null!=this.dataIn?this.dataIn:null});d(c$,"getViewport",function(){return this.viewport});d(c$,"setViewport",function(a){this.viewport=a},"jalview.api.AlignViewportI");
d(c$,"getExportSettings",function(){return this.exportSettings});d(c$,"setExportSettings",function(a){this.exportSettings=a},"jalview.api.AlignExportSettingI");d(c$,"configureForView",function(a){null!=a&&this.setViewport(a.getAlignViewport())},"jalview.api.AlignmentViewPanel")});p("jalview.io");q(null,"jalview.io.AppletFormatAdapter","MCview.PDBfile jalview.datamodel.Alignment jalview.io.FileParse $.IdentifyFile jalview.jsdev.GenericFileAdapter jalview.util.MessageManager java.io.IOException java.lang.Exception $.StringBuffer".split(" "),
function(){c$=s(function(){this.viewpanel=null;this.serviceSecondaryStruct=this.localSecondaryStruct=this.annotFromStructure=!1;this.exportSettings=this.newline=this.inFile=this.alignFile=null;r(this,arguments)},jalview.io,"AppletFormatAdapter");J(c$,function(){this.newline=System.getProperty("line.separator")});m(c$,function(){});m(c$,function(a){this.viewpanel=a},"jalview.api.AlignmentViewPanel");m(c$,function(a,b){this.viewpanel=a;this.exportSettings=b},"jalview.api.AlignmentViewPanel,jalview.api.AlignExportSettingI");
c$.prettyPrint=d(c$,"prettyPrint",function(a){for(var b=new StringBuffer,c=0,f=a.length-1;c<f;c++)b.append(a[c]),b.append(", ");b.append(" and "+a[a.length-1]+".");return b.toString()},"~A");d(c$,"setNewlineString",function(a){this.newline=a},"~S");d(c$,"getNewlineString",function(){return this.newline});c$.isValidFormat=d(c$,"isValidFormat",function(a){return jalview.io.AppletFormatAdapter.isValidFormat(a,!1)},"~S");c$.isValidFormat=d(c$,"isValidFormat",function(a,b){for(var c,f=0,d=b?jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS:
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[a,b]):c.equals("BLC")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("BLCFile",[a,b]):c.equals("PIR")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PIRFile",[a,b]):c.equals("PFAM")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PfamFile",[a,b]):c.equals("JnetFile")?(this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("JPredFile",[a,b]),this.alignFile.removeNonSequences()):c.equals("PDB")?this.alignFile=new MCview.PDBfile(this.annotFromStructure,this.localSecondaryStruct,
this.serviceSecondaryStruct,a,b):c.equals("STH")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("StockholmFile",[a,b]):c.equals("SimpleBLAST")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("SimpleBlastFile",[a,b]):c.equals("PHYLIP")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PhylipFile",[a,b]):c.equals("JSON")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("JSONFile",[a,b]):c.equals("HTML")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("HtmlFile",
[a,b]):c.equals("RNAML")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("RnamlFile",[a,b]):c.equals("GFF v2 or v3")&&(this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("Gff3File",[a,b])),this.buildAlignmentFrom(this.alignFile)}catch(f){if(y(f,Exception)){f.printStackTrace();System.err.println("Failed to read alignment using the '"+c+"' reader.\n"+f);if(null!=f.getMessage()&&f.getMessage().startsWith(jalview.io.AppletFormatAdapter.INVALID_CHARACTERS))throw new java.io.IOException(f.getMessage());
if(b.equalsIgnoreCase("Paste"))try{return this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("FastaFile",[">UNKNOWN\n"+a,"Paste"]),this.buildAlignmentFrom(this.alignFile)}catch(d){if(y(d,Exception)){if(d.toString().startsWith(jalview.io.AppletFormatAdapter.INVALID_CHARACTERS))throw new java.io.IOException(f.getMessage());d.printStackTrace()}else throw d;}throw new java.io.IOException(jalview.io.AppletFormatAdapter.SUPPORTED_FORMATS);}throw f;}},"~S,~S,~S");d(c$,"readFromFile",function(a,b){this.inFile=
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this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PIRFile",[a]):b.equals("PFAM")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PfamFile",[a]):b.equals("JnetFile")?(this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("JPredFile",[a]),this.alignFile.removeNonSequences()):b.equals("PDB")?this.alignFile=new MCview.PDBfile(this.annotFromStructure,this.localSecondaryStruct,this.serviceSecondaryStruct,a):b.equals("STH")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("StockholmFile",
[a]):b.equals("RNAML")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("RnamlFile",[a]):b.equals("SimpleBLAST")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("SimpleBlastFile",[a]):b.equals("PHYLIP")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("PhylipFile",[a]):b.equals("GFF v2 or v3")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("Gff3File",[this.inFile,c]):b.equals("JSON")?this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("JSONFile",[a]):b.equals("HTML")&&
(this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("HtmlFile",[a])),this.buildAlignmentFrom(this.alignFile)}catch(f){if(y(f,Exception)){f.printStackTrace();System.err.println("Failed to read alignment using the '"+b+"' reader.\n"+f);if(null!=f.getMessage()&&f.getMessage().startsWith(jalview.io.AppletFormatAdapter.INVALID_CHARACTERS))throw new java.io.IOException(f.getMessage());if(c.equalsIgnoreCase("Paste"))try{return this.alignFile=jalview.jsdev.GenericFileAdapter.getFile("FastaFile",[">UNKNOWN\n"+
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this.alignFile.addGroups(a);return a},"jalview.io.AlignFile");d(c$,"formatSequences",function(a,b,c,f){var d=c.getAlignViewport().getAlignmentView(f,!1).getVisibleAlignment(c.getAlignViewport().getGapCharacter());f=c.getAlignViewport().getVisibleAlignmentAnnotation(f);if(null!=f){var e;for(f=f.iterator();f.hasNext()&&((e=f.next())||1);)d.addAnnotation(e)}this.viewpanel=c;return this.formatSequences(a,d,b)},"~S,~B,jalview.api.AlignmentViewPanel,~B");d(c$,"formatSequences",function(a,b,c){try{var f=
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jalview.jsdev.GenericFileAdapter.getFile("PIRFile",[]);else if(a.equalsIgnoreCase("PFAM"))f=jalview.jsdev.GenericFileAdapter.getFile("PfamFile",[]);else if(a.equalsIgnoreCase("STH"))f=jalview.jsdev.GenericFileAdapter.getFile("StockholmFile",[b]);else if(a.equalsIgnoreCase("AMSA"))f=jalview.jsdev.GenericFileAdapter.getFile("AMSAFile",[b]);else if(a.equalsIgnoreCase("PHYLIP"))f=jalview.jsdev.GenericFileAdapter.getFile("PhylipFile",[]);else if(a.equalsIgnoreCase("JSON"))f=jalview.jsdev.GenericFileAdapter.getFile("JSONFile",
[]);else if(a.equalsIgnoreCase("RNAML"))f=jalview.jsdev.GenericFileAdapter.getFile("RnamlFile",[]);else throw new Exception(jalview.util.MessageManager.getString("error.implementation_error_unknown_file_format_string"));f.setNewlineString(this.newline);f.addJVSuffix(c);f.setExportSettings(this.exportSettings);f.configureForView(this.viewpanel);null==this.viewpanel||null==this.viewpanel.getAlignment()||this.viewpanel.getAlignment()!==b?f.setSeqs(b.getSequencesArray()):f.setSeqs(this.viewpanel.getAlignment().getSequencesArray());
var d=f.print();f.hasWarningMessage()&&System.err.println("Warning raised when writing as "+a+" : "+f.getWarningMessage());return d}catch(e){if(y(e,Exception))System.err.println("Failed to write alignment as a '"+a+"' file\n"),e.printStackTrace();else throw e;}return null},"~S,jalview.datamodel.AlignmentI,~B");c$.checkProtocol=d(c$,"checkProtocol",function(a){var b=jalview.io.AppletFormatAdapter.FILE;a=a.toLowerCase().trim();if(0==a.indexOf("http:")||0==a.indexOf("https:")||0==a.indexOf("file:"))b=
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Exception))System.err.println("Exception checking resources: "+a+" "+e);else throw e;}f=-1<a.indexOf("://")?jalview.io.AppletFormatAdapter.URL:jalview.io.AppletFormatAdapter.FILE;d=null;try{c&&System.out.println("Trying to get contents of resource as "+f+":"),d=new jalview.io.FileParse(a,f),d.isValid()?c&&System.out.println("Successful."):d=null}catch(g){if(y(g,Exception))c&&System.err.println("Exception when accessing content: "+g),d=null;else throw g;}if(null==d){c&&System.out.println("Accessing as paste.");
f=jalview.io.AppletFormatAdapter.PASTE;d=null;try{d=new jalview.io.FileParse(a,f),d.isValid()||(d=null)}catch(h){if(y(h,Exception))System.err.println("Failed to access content as paste!"),h.printStackTrace(),d=null;else throw h;}}if(null==d)return null;if(null==b||0==b.length)return f;try{var j=(new jalview.io.IdentifyFile).Identify(a,f);if(null==j)return c&&System.out.println("Format not identified. Inaccessible file."),null;c&&System.out.println("Format identified as "+j+"and expected as "+b);if(j.equals(b))return c&&
System.out.println("Protocol identified as "+f),f;c&&System.out.println("File deemed not accessible via "+f);d.close()}catch(n){if(y(n,Exception))c&&(System.err.println("File deemed not accessible via "+f),n.printStackTrace());else throw n;}return null},"~S,~S,~B");d(c$,"getAlignFile",function(){return this.alignFile});d(c$,"setAlignFile",function(a){this.alignFile=a},"jalview.io.AlignFile");G(c$,"FILE","File","URL","URL","PASTE","Paste","CLASSLOADER","ClassLoader");c$.READABLE_FORMATS=c$.prototype.READABLE_FORMATS=
E(-1,"BLC;CLUSTAL;FASTA;MSF;PileUp;PIR;PFAM;STH;PDB;JnetFile;RNAML;PHYLIP;JSON;GFF v2 or v3;HTML".split(";"));c$.READABLE_EXTENSIONS=c$.prototype.READABLE_EXTENSIONS=E(-1,"fa, fasta, mfa, fastq;aln;pfam;msf;pir;blc;amsa;sto,stk;xml,rnaml;phy;json;.gff2,gff3;jar,jvp;html".split(";"));c$.READABLE_FNAMES=c$.prototype.READABLE_FNAMES=E(-1,"Fasta;Clustal;PFAM;MSF;PIR;BLC;AMSA;Stockholm;RNAML;PHYLIP;JSON;GFF v2 or v3;Jalview;HTML".split(";"));c$.WRITEABLE_FORMATS=c$.prototype.WRITEABLE_FORMATS=E(-1,"BLC CLUSTAL FASTA MSF PileUp PIR PFAM AMSA STH PHYLIP JSON".split(" "));
c$.WRITABLE_EXTENSIONS=c$.prototype.WRITABLE_EXTENSIONS=E(-1,"fa, fasta, mfa, fastq;aln;pfam;msf;pir;blc;amsa;sto,stk;phy;json;jvp".split(";"));c$.WRITABLE_FNAMES=c$.prototype.WRITABLE_FNAMES=E(-1,"Fasta Clustal PFAM MSF PIR BLC AMSA STH PHYLIP JSON Jalview".split(" "));G(c$,"INVALID_CHARACTERS","Contains invalid characters");c$.SUPPORTED_FORMATS=c$.prototype.SUPPORTED_FORMATS="Formats currently supported are\n"+jalview.io.AppletFormatAdapter.prettyPrint(jalview.io.AppletFormatAdapter.READABLE_FORMATS)});
p("jalview.io");q(null,"jalview.io.IdentifyFile",["jalview.io.FileParse"],function(){c$=B(jalview.io,"IdentifyFile");d(c$,"Identify",function(a,b){var c="UNIDENTIFIED FILE PARSING ERROR",f=null;try{if(f=new jalview.io.FileParse(a,b),f.isValid())return this.Identify(f)}catch(d){if(y(d,Exception))System.err.println("Error whilst identifying"),d.printStackTrace(System.err),c=d.getMessage();else throw d;}return null!=f?f.errormessage:c},"~S,~S");d(c$,"Identify",function(a){return this.Identify(a,!0)},
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function(){null!=this.blocks&&this.blocks.free();return 0});m(c$,function(a){this.z=a},"JU.ZStream");d(c$,"inflateInit",function(a){this.blocks=this.z.msg=null;this.wrap=0;0>a?a=-a:(this.wrap=(a>>4)+1,48>a&&(a&=15));if(8>a||15<a)return this.inflateEnd(),-2;null!=this.blocks&&this.wbits!=a&&(this.blocks.free(),this.blocks=null);this.wbits=a;this.blocks=new JU.InfBlocks(this.z,1<<a);this.inflateReset();return 0},"~N");d(c$,"inflate",function(a){var b,c;if(null==this.z||null==this.z.next_in)return 4==
a&&14==this.mode?0:-2;a=4==a?-5:0;for(b=-5;;)switch(this.mode){case 14:if(0==this.wrap){this.mode=7;break}try{b=this.readBytes(2,b,a)}catch(f){if(y(f,JU.Inflate.Return))return f.r;throw f;}if(0!=(this.wrap&2)&&35615==this.need){this.z.checksum=new JU.CRC32;this.checksum(2,this.need);null==this.gheader&&(this.gheader=new JU.GZIPHeader);this.mode=23;break}this.flags=0;this.method=this.need&255;c=this.need>>8&255;if(0==(this.wrap&1)||0!=((this.method<<8)+c)%31){this.mode=13;this.z.msg="incorrect header check";
break}if(8!=(this.method&15)){this.mode=13;this.z.msg="unknown compression method";break}if((this.method>>4)+8>this.wbits){this.mode=13;this.z.msg="invalid window size";break}this.z.checksum=new JU.Adler32;if(0==(c&32)){this.mode=7;break}this.mode=2;case 2:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need=(this.z.next_in[this.z.next_in_index++]&255)<<24&4278190080;this.mode=3;case 3:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need+=(this.z.next_in[this.z.next_in_index++]&
255)<<16&16711680;this.mode=4;case 4:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need+=(this.z.next_in[this.z.next_in_index++]&255)<<8&65280;this.mode=5;case 5:if(0==this.z.avail_in)return b;this.z.avail_in--;this.z.total_in++;this.need+=this.z.next_in[this.z.next_in_index++]&255;this.z.checksum.resetLong(this.need);this.mode=6;return 2;case 6:return this.mode=13,this.z.msg="need dictionary",this.marker=0,-2;case 7:b=this.blocks.proc(b);if(-3==b){this.mode=13;this.marker=
0;break}0==b&&(b=a);if(1!=b)return b;b=a;this.was=this.z.checksum.getValue();this.blocks.reset();if(0==this.wrap){this.mode=12;break}this.mode=8;case 8:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need=(this.z.next_in[this.z.next_in_index++]&255)<<24&4278190080;this.mode=9;case 9:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need+=(this.z.next_in[this.z.next_in_index++]&255)<<16&16711680;this.mode=10;case 10:if(0==this.z.avail_in)return b;
b=a;this.z.avail_in--;this.z.total_in++;this.need+=(this.z.next_in[this.z.next_in_index++]&255)<<8&65280;this.mode=11;case 11:if(0==this.z.avail_in)return b;b=a;this.z.avail_in--;this.z.total_in++;this.need+=this.z.next_in[this.z.next_in_index++]&255;0!=this.flags&&(this.need=((this.need&4278190080)>>24|(this.need&16711680)>>8|(this.need&65280)<<8|(this.need&65535)<<24)&4294967295);this.was!=this.need?this.z.msg="incorrect data check":0!=this.flags&&null!=this.gheader&&(this.gheader.crc=this.need);
this.mode=15;case 15:if(0!=this.wrap&&0!=this.flags){try{b=this.readBytes(4,b,a)}catch(d){if(y(d,JU.Inflate.Return))return d.r;throw d;}if(null!=this.z.msg&&this.z.msg.equals("incorrect data check")){this.mode=13;this.marker=5;break}if(this.need!=(this.z.total_out&4294967295)){this.z.msg="incorrect length check";this.mode=13;break}this.z.msg=null}else if(null!=this.z.msg&&this.z.msg.equals("incorrect data check")){this.mode=13;this.marker=5;break}this.mode=12;case 12:return 1;case 13:return-3;case 23:try{b=
this.readBytes(2,b,a)}catch(e){if(y(e,JU.Inflate.Return))return e.r;throw e;}this.flags=this.need&65535;if(8!=(this.flags&255)){this.z.msg="unknown compression method";this.mode=13;break}if(0!=(this.flags&57344)){this.z.msg="unknown header flags set";this.mode=13;break}0!=(this.flags&512)&&this.checksum(2,this.need);this.mode=16;case 16:try{b=this.readBytes(4,b,a)}catch(g){if(y(g,JU.Inflate.Return))return g.r;throw g;}null!=this.gheader&&(this.gheader.time=this.need);0!=(this.flags&512)&&this.checksum(4,
this.need);this.mode=17;case 17:try{b=this.readBytes(2,b,a)}catch(h){if(y(h,JU.Inflate.Return))return h.r;throw h;}null!=this.gheader&&(this.gheader.xflags=this.need&255,this.gheader.os=this.need>>8&255);0!=(this.flags&512)&&this.checksum(2,this.need);this.mode=18;case 18:if(0!=(this.flags&1024)){try{b=this.readBytes(2,b,a)}catch(j){if(y(j,JU.Inflate.Return))return j.r;throw j;}null!=this.gheader&&(this.gheader.extra=S(this.need&65535,0));0!=(this.flags&512)&&this.checksum(2,this.need)}else null!=
this.gheader&&(this.gheader.extra=null);this.mode=19;case 19:if(0!=(this.flags&1024))try{if(b=this.readBytes(b,a),null!=this.gheader){var n=this.tmp_string.toByteArray();this.tmp_string=null;if(n.length==this.gheader.extra.length)System.arraycopy(n,0,this.gheader.extra,0,n.length);else{this.z.msg="bad extra field length";this.mode=13;break}}}catch(m){if(y(m,JU.Inflate.Return))return m.r;throw m;}else null!=this.gheader&&(this.gheader.extra=null);this.mode=20;case 20:if(0!=(this.flags&2048))try{b=
this.readString(b,a),null!=this.gheader&&(this.gheader.name=this.tmp_string.toByteArray()),this.tmp_string=null}catch(u){if(y(u,JU.Inflate.Return))return u.r;throw u;}else null!=this.gheader&&(this.gheader.name=null);this.mode=21;case 21:if(0!=(this.flags&4096))try{b=this.readString(b,a),null!=this.gheader&&(this.gheader.comment=this.tmp_string.toByteArray()),this.tmp_string=null}catch(p){if(y(p,JU.Inflate.Return))return p.r;throw p;}else null!=this.gheader&&(this.gheader.comment=null);this.mode=
22;case 22:if(0!=(this.flags&512)){try{b=this.readBytes(2,b,a)}catch(q){if(y(q,JU.Inflate.Return))return q.r;throw q;}null!=this.gheader&&(this.gheader.hcrc=this.need&65535);if(this.need!=(this.z.checksum.getValue()&65535)){this.mode=13;this.z.msg="header crc mismatch";this.marker=5;break}}this.z.checksum=new JU.CRC32;this.mode=7;break;default:return-2}},"~N");d(c$,"inflateSetDictionary",function(a,b){if(null==this.z||6!=this.mode&&0!=this.wrap)return-2;var c=0,f=b;if(6==this.mode){var d=this.z.checksum.getValue();
this.z.checksum.reset();this.z.checksum.update(a,0,b);if(this.z.checksum.getValue()!=d)return-3}this.z.checksum.reset();f>=1<<this.wbits&&(f=(1<<this.wbits)-1,c=b-f);this.blocks.set_dictionary(a,c,f);this.mode=7;return 0},"~A,~N");d(c$,"inflateSync",function(){var a,b,c;if(null==this.z)return-2;13!=this.mode&&(this.mode=13,this.marker=0);if(0==(a=this.z.avail_in))return-5;b=this.z.next_in_index;for(c=this.marker;0!=a&&4>c;)this.z.next_in[b]==JU.Inflate.mark[c]?c++:c=0!=this.z.next_in[b]?0:4-c,b++,
a--;this.z.total_in+=b-this.z.next_in_index;this.z.next_in_index=b;this.z.avail_in=a;this.marker=c;if(4!=c)return-3;a=this.z.total_in;b=this.z.total_out;this.inflateReset();this.z.total_in=a;this.z.total_out=b;this.mode=7;return 0});d(c$,"inflateSyncPoint",function(){return null==this.z||null==this.blocks?-2:this.blocks.sync_point()});d(c$,"readBytes",function(a,b,c){-1==this.need_bytes&&(this.need_bytes=a,this.need=0);for(;0<this.need_bytes;){if(0==this.z.avail_in)throw C(JU.Inflate.Return,this,
null,b);b=c;this.z.avail_in--;this.z.total_in++;this.need|=(this.z.next_in[this.z.next_in_index++]&255)<<8*(a-this.need_bytes);this.need_bytes--}2==a?this.need&=65535:4==a&&(this.need&=4294967295);this.need_bytes=-1;return b},"~N,~N,~N");d(c$,"readString",function(a,b){null==this.tmp_string&&(this.tmp_string=new java.io.ByteArrayOutputStream);var c=0;do{if(0==this.z.avail_in)throw C(JU.Inflate.Return,this,null,a);a=b;this.z.avail_in--;this.z.total_in++;c=this.z.next_in[this.z.next_in_index];0!=c&&
this.tmp_string.write(this.z.next_in,this.z.next_in_index,1);this.z.checksum.update(this.z.next_in,this.z.next_in_index,1);this.z.next_in_index++}while(0!=c);return a},"~N,~N");d(c$,"readBytes",function(a,b){null==this.tmp_string&&(this.tmp_string=new java.io.ByteArrayOutputStream);for(;0<this.need;){if(0==this.z.avail_in)throw C(JU.Inflate.Return,this,null,a);a=b;this.z.avail_in--;this.z.total_in++;this.tmp_string.write(this.z.next_in,this.z.next_in_index,1);this.z.checksum.update(this.z.next_in,
this.z.next_in_index,1);this.z.next_in_index++;this.need--}return a},"~N,~N");d(c$,"checksum",function(a,b){for(var c=0;c<a;c++)this.crcbuf[c]=b&255,b>>=8;this.z.checksum.update(this.crcbuf,0,a)},"~N,~N");d(c$,"getGZIPHeader",function(){return this.gheader});d(c$,"inParsingHeader",function(){switch(this.mode){case 14:case 2:case 3:case 4:case 5:case 23:case 16:case 17:case 18:case 19:case 20:case 21:case 22:return!0;default:return!1}});c$.$Inflate$Return$=function(){A(self.c$);c$=s(function(){O(this,
arguments);this.r=0;r(this,arguments)},JU.Inflate,"Return",Exception);m(c$,function(a){t(this,JU.Inflate.Return,[]);this.r=a},"~N");c$=z()};G(c$,"PRESET_DICT",32,"Z_NO_FLUSH",0,"Z_PARTIAL_FLUSH",1,"Z_SYNC_FLUSH",2,"Z_FULL_FLUSH",3,"Z_FINISH",4,"Z_DEFLATED",8,"Z_OK",0,"Z_STREAM_END",1,"Z_NEED_DICT",2,"Z_STREAM_ERROR",-2,"Z_DATA_ERROR",-3,"Z_BUF_ERROR",-5,"DICT4",2,"DICT3",3,"DICT2",4,"DICT1",5,"DICT0",6,"BLOCKS",7,"CHECK4",8,"CHECK3",9,"CHECK2",10,"CHECK1",11,"DONE",12,"BAD",13,"HEAD",14,"LENGTH",
15,"TIME",16,"OS",17,"EXLEN",18,"EXTRA",19,"NAME",20,"COMMENT",21,"HCRC",22,"FLAGS",23,"mark",S(-1,[0,0,255,255]))});p("JU");q(null,"JU.GZIPHeader",["JU.ZStream","java.lang.IllegalArgumentException","$.InternalError"],function(){c$=s(function(){this.fhcrc=this.text=!1;this.xflags=this.time=0;this.os=255;this.comment=this.name=this.extra=null;this.crc=this.hcrc=0;this.done=!1;this.mtime=0;r(this,arguments)},JU,"GZIPHeader",null,Cloneable);d(c$,"setModifiedTime",function(a){this.mtime=a},"~N");d(c$,
"getModifiedTime",function(){return this.mtime});d(c$,"setOS",function(a){if(0<=a&&13>=a||255==a)this.os=a;else throw new IllegalArgumentException("os: "+a);},"~N");d(c$,"getOS",function(){return this.os});d(c$,"setName",function(a){this.name=JU.ZStream.getBytes(a)},"~S");d(c$,"getName",function(){if(null==this.name)return"";try{return String.instantialize(this.name,"ISO-8859-1")}catch(a){if(y(a,java.io.UnsupportedEncodingException))throw new InternalError(a.toString());throw a;}});d(c$,"setComment",
function(a){this.comment=JU.ZStream.getBytes(a)},"~S");d(c$,"getComment",function(){if(null==this.comment)return"";try{return String.instantialize(this.comment,"ISO-8859-1")}catch(a){if(y(a,java.io.UnsupportedEncodingException))throw new InternalError(a.toString());throw a;}});d(c$,"setCRC",function(a){this.crc=a},"~N");d(c$,"getCRC",function(){return this.crc});d(c$,"put",function(a){var b=0;this.text&&(b|=1);this.fhcrc&&(b|=2);null!=this.extra&&(b|=4);null!=this.name&&(b|=8);null!=this.comment&&
(b|=16);var c=0;1==a.level?c|=4:9==a.level&&(c|=2);a.put_short(35615);a.put_byteB(8);a.put_byteB(b);a.put_byteB(this.mtime);a.put_byteB(this.mtime>>8);a.put_byteB(this.mtime>>16);a.put_byteB(this.mtime>>24);a.put_byteB(c);a.put_byteB(this.os);null!=this.extra&&(a.put_byteB(this.extra.length),a.put_byteB(this.extra.length>>8),a.put_byte(this.extra,0,this.extra.length));null!=this.name&&(a.put_byte(this.name,0,this.name.length),a.put_byteB(0));null!=this.comment&&(a.put_byte(this.comment,0,this.comment.length),
a.put_byteB(0))},"JU.Deflate");d(c$,"clone",function(){var a=K(this,JU.GZIPHeader,"clone",[]),b;null!=a.extra&&(b=S(a.extra.length,0),System.arraycopy(a.extra,0,b,0,b.length),a.extra=b);null!=a.name&&(b=S(a.name.length,0),System.arraycopy(a.name,0,b,0,b.length),a.name=b);null!=a.comment&&(b=S(a.comment.length,0),System.arraycopy(a.comment,0,b,0,b.length),a.comment=b);return a});G(c$,"OS_MSDOS",0,"OS_AMIGA",1,"OS_VMS",2,"OS_UNIX",3,"OS_ATARI",5,"OS_OS2",6,"OS_MACOS",7,"OS_TOPS20",10,"OS_WIN32",11,
"OS_VMCMS",4,"OS_ZSYSTEM",8,"OS_CPM",9,"OS_QDOS",12,"OS_RISCOS",13,"OS_UNKNOWN",255)});p("JU");q(["JU.InfTree"],"JU.InfBlocks",["JU.InfCodes"],function(){c$=s(function(){this.index=this.table=this.left=this.mode=0;this.codes=this.tdi=this.tli=this.td=this.tl=this.bd=this.bl=this.tb=this.bb=this.blens=null;this.bitb=this.bitk=this.last=0;this.window=this.hufts=null;this.write=this.read=this.end=0;this.check=!1;this.z=this.inftree=null;r(this,arguments)},JU,"InfBlocks");J(c$,function(){this.bb=w(1,
0);this.tb=w(1,0);this.bl=w(1,0);this.bd=w(1,0);this.tli=w(1,0);this.tdi=w(1,0);this.inftree=new JU.InfTree});m(c$,function(a,b){this.z=a;this.codes=new JU.InfCodes(this.z,this);this.hufts=w(4320,0);this.window=S(b,0);this.end=b;this.check=0==a.istate.wrap?!1:!0;this.mode=0;this.tl=E(1,null);this.td=E(1,null);this.reset()},"JU.ZStream,~N");d(c$,"reset",function(){6==this.mode&&this.codes.free(this.z);this.read=this.write=this.bitb=this.bitk=this.mode=0;this.check&&this.z.checksum.reset()});d(c$,"proc",
function(a){var b,c,f,d,e,g,h;d=this.z.next_in_index;e=this.z.avail_in;c=this.bitb;f=this.bitk;g=this.write;for(h=g<this.read?this.read-g-1:this.end-g;;)switch(this.mode){case 0:for(;3>f;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}b=c&7;this.last=b&1;switch(b>>>1){case 0:c>>>=3;f-=3;b=f&7;c>>>=b;f-=b;this.mode=1;break;case 1:JU.InfTree.inflate_trees_fixed(this.bl,
this.bd,this.tl,this.td,this.z);this.codes.init(this.bl[0],this.bd[0],this.tl[0],0,this.td[0],0);c>>>=3;f-=3;this.mode=6;break;case 2:c>>>=3;f-=3;this.mode=3;break;case 3:return c>>>=3,f-=3,this.mode=9,this.z.msg="invalid block type",a=-3,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a)}break;case 1:for(;32>f;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,
this.z.next_in_index=d,this.write=g,this.inflate_flush(a);e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}if((~c>>>16&65535)!=(c&65535))return this.mode=9,this.z.msg="invalid stored block lengths",a=-3,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);this.left=c&65535;c=f=0;this.mode=0!=this.left?2:0!=this.last?7:0;break;case 2:if(0==e||0==h&&(g==this.end&&0!=this.read&&(g=0,h=g<this.read?this.read-g-1:this.end-g),
0==h&&(this.write=g,a=this.inflate_flush(a),g=this.write,h=g<this.read?this.read-g-1:this.end-g,g==this.end&&0!=this.read&&(g=0,h=g<this.read?this.read-g-1:this.end-g),0==h)))return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);a=0;b=this.left;b>e&&(b=e);b>h&&(b=h);System.arraycopy(this.z.next_in,d,this.window,g,b);d+=b;e-=b;g+=b;h-=b;if(0!=(this.left-=b))break;this.mode=0!=this.last?7:0;break;case 3:for(;14>
f;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}this.table=b=c&16383;if(29<(b&31)||29<(b>>5&31))return this.mode=9,this.z.msg="too many length or distance symbols",a=-3,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);b=258+(b&31)+(b>>5&31);if(null==
this.blens||this.blens.length<b)this.blens=w(b,0);else for(h=0;h<b;h++)this.blens[h]=0;c>>>=14;f-=14;this.index=0;this.mode=4;case 4:for(;this.index<4+(this.table>>>10);){for(;3>f;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}this.blens[JU.InfBlocks.border[this.index++]]=c&7;c>>>=3;f-=3}for(;19>this.index;)this.blens[JU.InfBlocks.border[this.index++]]=
0;this.bb[0]=7;b=this.inftree.inflate_trees_bits(this.blens,this.bb,this.tb,this.hufts,this.z);if(0!=b)return a=b,-3==a&&(this.blens=null,this.mode=9),this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);this.index=0;this.mode=5;case 5:for(;;){b=this.table;if(!(this.index<258+(b&31)+(b>>5&31)))break;var j,n;for(b=this.bb[0];f<b;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=
d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}b=this.hufts[3*(this.tb[0]+(c&JU.InfBlocks.inflate_mask[b]))+1];n=this.hufts[3*(this.tb[0]+(c&JU.InfBlocks.inflate_mask[b]))+2];if(16>n)c>>>=b,f-=b,this.blens[this.index++]=n;else{h=18==n?7:n-14;for(j=18==n?11:3;f<b+h;){if(0!=e)a=0;else return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);
e--;c|=(this.z.next_in[d++]&255)<<f;f+=8}c>>>=b;f-=b;j+=c&JU.InfBlocks.inflate_mask[h];c>>>=h;f-=h;h=this.index;b=this.table;if(h+j>258+(b&31)+(b>>5&31)||16==n&&1>h)return this.blens=null,this.mode=9,this.z.msg="invalid bit length repeat",a=-3,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);n=16==n?this.blens[h-1]:0;do this.blens[h++]=n;while(0!=--j);this.index=h}}this.tb[0]=-1;this.bl[0]=9;this.bd[0]=6;b=
this.table;b=this.inftree.inflate_trees_dynamic(257+(b&31),1+(b>>5&31),this.blens,this.bl,this.bd,this.tli,this.tdi,this.hufts,this.z);if(0!=b)return-3==b&&(this.blens=null,this.mode=9),a=b,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);this.codes.init(this.bl[0],this.bd[0],this.hufts,this.tli[0],this.hufts,this.tdi[0]);this.mode=6;case 6:this.bitb=c;this.bitk=f;this.z.avail_in=e;this.z.total_in+=d-this.z.next_in_index;
this.z.next_in_index=d;this.write=g;if(1!=(a=this.codes.proc(a)))return this.inflate_flush(a);a=0;this.codes.free(this.z);d=this.z.next_in_index;e=this.z.avail_in;c=this.bitb;f=this.bitk;g=this.write;h=g<this.read?this.read-g-1:this.end-g;if(0==this.last){this.mode=0;break}this.mode=7;case 7:this.write=g;a=this.inflate_flush(a);g=this.write;if(this.read!=this.write)return this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);
this.mode=8;case 8:return a=1,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);case 9:return a=-3,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a);default:return a=-2,this.bitb=c,this.bitk=f,this.z.avail_in=e,this.z.total_in+=d-this.z.next_in_index,this.z.next_in_index=d,this.write=g,this.inflate_flush(a)}},"~N");d(c$,
"free",function(){this.reset();this.hufts=this.window=null});d(c$,"set_dictionary",function(a,b,c){System.arraycopy(a,b,this.window,0,c);this.read=this.write=c},"~A,~N,~N");d(c$,"sync_point",function(){return 1==this.mode?1:0});d(c$,"inflate_flush",function(a){var b,c,f;c=this.z.next_out_index;f=this.read;b=(f<=this.write?this.write:this.end)-f;b>this.z.avail_out&&(b=this.z.avail_out);0!=b&&-5==a&&(a=0);this.z.avail_out-=b;this.z.total_out+=b;this.check&&0<b&&this.z.checksum.update(this.window,f,
b);System.arraycopy(this.window,f,this.z.next_out,c,b);c+=b;f+=b;f==this.end&&(f=0,this.write==this.end&&(this.write=0),b=this.write-f,b>this.z.avail_out&&(b=this.z.avail_out),0!=b&&-5==a&&(a=0),this.z.avail_out-=b,this.z.total_out+=b,this.check&&0<b&&this.z.checksum.update(this.window,f,b),System.arraycopy(this.window,f,this.z.next_out,c,b),c+=b,f+=b);this.z.next_out_index=c;this.read=f;return a},"~N");G(c$,"MANY",1440,"inflate_mask",w(-1,[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,
65535]),"border",w(-1,[16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),"Z_OK",0,"Z_STREAM_END",1,"Z_STREAM_ERROR",-2,"Z_DATA_ERROR",-3,"Z_BUF_ERROR",-5,"TYPE",0,"LENS",1,"STORED",2,"TABLE",3,"BTREE",4,"DTREE",5,"CODES",6,"DRY",7,"DONE",8,"BAD",9)});p("JU");c$=s(function(){this.x=this.u=this.r=this.c=this.v=this.hn=null;r(this,arguments)},JU,"InfTree");d(c$,"huft_build",function(a,b,c,f,d,e,g,h,j,n,m){var u,p,q,s,r,t,v,w,y,z;v=0;q=c;do this.c[a[b+v]]++,v++,q--;while(0!=q);if(this.c[0]==c)return g[0]=
-1,h[0]=0;t=h[0];for(s=1;15>=s&&0==this.c[s];s++);r=s;t<s&&(t=s);for(q=15;0!=q&&0==this.c[q];q--);p=q;t>q&&(t=q);h[0]=t;for(h=1<<s;s<q;s++,h<<=1)if(0>(h-=this.c[s]))return-3;if(0>(h-=this.c[q]))return-3;this.c[q]+=h;this.x[1]=s=0;v=1;for(w=2;0!=--q;)this.x[w]=s+=this.c[v],w++,v++;v=q=0;do{if(0!=(s=a[b+v]))m[this.x[s]++]=q;v++}while(++q<c);c=this.x[p];v=this.x[0]=q=0;b=-1;y=-t;for(z=w=this.u[0]=0;r<=p;r++)for(a=this.c[r];0!=a--;){for(;r>y+t;){b++;y+=t;z=p-y;z=z>t?t:z;if((u=1<<(s=r-y))>a+1)if(u-=a+
1,w=r,s<z)for(;++s<z&&!((u<<=1)<=this.c[++w]);)u-=this.c[w];z=1<<s;if(1440<n[0]+z)return-3;this.u[b]=w=n[0];n[0]+=z;0!=b?(this.x[b]=q,this.r[0]=s,this.r[1]=t,s=q>>>y-t,this.r[2]=w-this.u[b-1]-s,System.arraycopy(this.r,0,j,3*(this.u[b-1]+s),3)):g[0]=w}this.r[1]=r-y;v>=c?this.r[0]=192:m[v]<f?(this.r[0]=256>m[v]?0:96,this.r[2]=m[v++]):(this.r[0]=e[m[v]-f]+16+64,this.r[2]=d[m[v++]-f]);u=1<<r-y;for(s=q>>>y;s<z;s+=u)System.arraycopy(this.r,0,j,3*(w+s),3);for(s=1<<r-1;0!=(q&s);s>>>=1)q^=s;q^=s;for(s=(1<<
y)-1;(q&s)!=this.x[b];)b--,y-=t,s=(1<<y)-1}return 0!=h&&1!=p?-5:0},"~A,~N,~N,~N,~A,~A,~A,~A,~A,~A,~A");d(c$,"inflate_trees_bits",function(a,b,c,f,d){this.initWorkArea(19);this.hn[0]=0;a=this.huft_build(a,0,19,19,null,null,c,b,f,this.hn,this.v);if(-3==a)d.msg="oversubscribed dynamic bit lengths tree";else if(-5==a||0==b[0])d.msg="incomplete dynamic bit lengths tree",a=-3;return a},"~A,~A,~A,~A,JU.ZStream");d(c$,"inflate_trees_dynamic",function(a,b,c,f,d,e,g,h,j){this.initWorkArea(288);this.hn[0]=0;
e=this.huft_build(c,0,a,257,JU.InfTree.cplens,JU.InfTree.cplext,e,f,h,this.hn,this.v);if(0!=e||0==f[0])return-3==e?j.msg="oversubscribed literal/length tree":-4!=e&&(j.msg="incomplete literal/length tree",e=-3),e;this.initWorkArea(288);e=this.huft_build(c,a,b,0,JU.InfTree.cpdist,JU.InfTree.cpdext,g,d,h,this.hn,this.v);return 0!=e||0==d[0]&&257<a?(-3==e?j.msg="oversubscribed distance tree":-5==e?(j.msg="incomplete distance tree",e=-3):-4!=e&&(j.msg="empty distance tree with lengths",e=-3),e):0},"~N,~N,~A,~A,~A,~A,~A,~A,JU.ZStream");
c$.inflate_trees_fixed=d(c$,"inflate_trees_fixed",function(a,b,c,f){a[0]=9;b[0]=5;c[0]=JU.InfTree.fixed_tl;f[0]=JU.InfTree.fixed_td;return 0},"~A,~A,~A,~A,JU.ZStream");d(c$,"initWorkArea",function(a){null==this.hn&&(this.hn=w(1,0),this.v=w(a,0),this.c=w(16,0),this.r=w(3,0),this.u=w(15,0),this.x=w(16,0));this.v.length<a&&(this.v=w(a,0));for(var b=0;b<a;b++)this.v[b]=0;for(b=0;16>b;b++)this.c[b]=0;for(b=0;3>b;b++)this.r[b]=0;System.arraycopy(this.c,0,this.u,0,15);System.arraycopy(this.c,0,this.x,0,
16)},"~N");G(c$,"MANY",1440,"Z_OK",0,"Z_DATA_ERROR",-3,"Z_MEM_ERROR",-4,"Z_BUF_ERROR",-5,"fixed_bl",9,"fixed_bd",5,"fixed_tl",w(-1,[96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,192,80,7,10,0,8,96,0,8,32,0,9,160,0,8,0,0,8,128,0,8,64,0,9,224,80,7,6,0,8,88,0,8,24,0,9,144,83,7,59,0,8,120,0,8,56,0,9,208,81,7,17,0,8,104,0,8,40,0,9,176,0,8,8,0,8,136,0,8,72,0,9,240,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,200,81,7,13,0,8,100,0,8,36,0,9,168,0,8,4,0,8,132,0,8,68,0,9,232,80,7,8,
0,8,92,0,8,28,0,9,152,84,7,83,0,8,124,0,8,60,0,9,216,82,7,23,0,8,108,0,8,44,0,9,184,0,8,12,0,8,140,0,8,76,0,9,248,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,196,81,7,11,0,8,98,0,8,34,0,9,164,0,8,2,0,8,130,0,8,66,0,9,228,80,7,7,0,8,90,0,8,26,0,9,148,84,7,67,0,8,122,0,8,58,0,9,212,82,7,19,0,8,106,0,8,42,0,9,180,0,8,10,0,8,138,0,8,74,0,9,244,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,204,81,7,15,0,8,102,0,8,38,0,9,172,0,8,6,0,8,134,0,8,70,0,9,236,80,7,9,0,8,94,0,8,30,0,9,156,
84,7,99,0,8,126,0,8,62,0,9,220,82,7,27,0,8,110,0,8,46,0,9,188,0,8,14,0,8,142,0,8,78,0,9,252,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,194,80,7,10,0,8,97,0,8,33,0,9,162,0,8,1,0,8,129,0,8,65,0,9,226,80,7,6,0,8,89,0,8,25,0,9,146,83,7,59,0,8,121,0,8,57,0,9,210,81,7,17,0,8,105,0,8,41,0,9,178,0,8,9,0,8,137,0,8,73,0,9,242,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,202,81,7,13,0,8,101,0,8,37,0,9,170,0,8,5,0,8,133,0,8,69,0,9,234,80,7,8,0,8,93,0,8,29,0,9,154,84,7,83,0,8,125,0,
8,61,0,9,218,82,7,23,0,8,109,0,8,45,0,9,186,0,8,13,0,8,141,0,8,77,0,9,250,80,7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,198,81,7,11,0,8,99,0,8,35,0,9,166,0,8,3,0,8,131,0,8,67,0,9,230,80,7,7,0,8,91,0,8,27,0,9,150,84,7,67,0,8,123,0,8,59,0,9,214,82,7,19,0,8,107,0,8,43,0,9,182,0,8,11,0,8,139,0,8,75,0,9,246,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,206,81,7,15,0,8,103,0,8,39,0,9,174,0,8,7,0,8,135,0,8,71,0,9,238,80,7,9,0,8,95,0,8,31,0,9,158,84,7,99,0,8,127,0,8,63,0,9,222,82,7,27,
0,8,111,0,8,47,0,9,190,0,8,15,0,8,143,0,8,79,0,9,254,96,7,256,0,8,80,0,8,16,84,8,115,82,7,31,0,8,112,0,8,48,0,9,193,80,7,10,0,8,96,0,8,32,0,9,161,0,8,0,0,8,128,0,8,64,0,9,225,80,7,6,0,8,88,0,8,24,0,9,145,83,7,59,0,8,120,0,8,56,0,9,209,81,7,17,0,8,104,0,8,40,0,9,177,0,8,8,0,8,136,0,8,72,0,9,241,80,7,4,0,8,84,0,8,20,85,8,227,83,7,43,0,8,116,0,8,52,0,9,201,81,7,13,0,8,100,0,8,36,0,9,169,0,8,4,0,8,132,0,8,68,0,9,233,80,7,8,0,8,92,0,8,28,0,9,153,84,7,83,0,8,124,0,8,60,0,9,217,82,7,23,0,8,108,0,8,44,0,
9,185,0,8,12,0,8,140,0,8,76,0,9,249,80,7,3,0,8,82,0,8,18,85,8,163,83,7,35,0,8,114,0,8,50,0,9,197,81,7,11,0,8,98,0,8,34,0,9,165,0,8,2,0,8,130,0,8,66,0,9,229,80,7,7,0,8,90,0,8,26,0,9,149,84,7,67,0,8,122,0,8,58,0,9,213,82,7,19,0,8,106,0,8,42,0,9,181,0,8,10,0,8,138,0,8,74,0,9,245,80,7,5,0,8,86,0,8,22,192,8,0,83,7,51,0,8,118,0,8,54,0,9,205,81,7,15,0,8,102,0,8,38,0,9,173,0,8,6,0,8,134,0,8,70,0,9,237,80,7,9,0,8,94,0,8,30,0,9,157,84,7,99,0,8,126,0,8,62,0,9,221,82,7,27,0,8,110,0,8,46,0,9,189,0,8,14,0,8,142,
0,8,78,0,9,253,96,7,256,0,8,81,0,8,17,85,8,131,82,7,31,0,8,113,0,8,49,0,9,195,80,7,10,0,8,97,0,8,33,0,9,163,0,8,1,0,8,129,0,8,65,0,9,227,80,7,6,0,8,89,0,8,25,0,9,147,83,7,59,0,8,121,0,8,57,0,9,211,81,7,17,0,8,105,0,8,41,0,9,179,0,8,9,0,8,137,0,8,73,0,9,243,80,7,4,0,8,85,0,8,21,80,8,258,83,7,43,0,8,117,0,8,53,0,9,203,81,7,13,0,8,101,0,8,37,0,9,171,0,8,5,0,8,133,0,8,69,0,9,235,80,7,8,0,8,93,0,8,29,0,9,155,84,7,83,0,8,125,0,8,61,0,9,219,82,7,23,0,8,109,0,8,45,0,9,187,0,8,13,0,8,141,0,8,77,0,9,251,80,
7,3,0,8,83,0,8,19,85,8,195,83,7,35,0,8,115,0,8,51,0,9,199,81,7,11,0,8,99,0,8,35,0,9,167,0,8,3,0,8,131,0,8,67,0,9,231,80,7,7,0,8,91,0,8,27,0,9,151,84,7,67,0,8,123,0,8,59,0,9,215,82,7,19,0,8,107,0,8,43,0,9,183,0,8,11,0,8,139,0,8,75,0,9,247,80,7,5,0,8,87,0,8,23,192,8,0,83,7,51,0,8,119,0,8,55,0,9,207,81,7,15,0,8,103,0,8,39,0,9,175,0,8,7,0,8,135,0,8,71,0,9,239,80,7,9,0,8,95,0,8,31,0,9,159,84,7,99,0,8,127,0,8,63,0,9,223,82,7,27,0,8,111,0,8,47,0,9,191,0,8,15,0,8,143,0,8,79,0,9,255]),"fixed_td",w(-1,[80,
5,1,87,5,257,83,5,17,91,5,4097,81,5,5,89,5,1025,85,5,65,93,5,16385,80,5,3,88,5,513,84,5,33,92,5,8193,82,5,9,90,5,2049,86,5,129,192,5,24577,80,5,2,87,5,385,83,5,25,91,5,6145,81,5,7,89,5,1537,85,5,97,93,5,24577,80,5,4,88,5,769,84,5,49,92,5,12289,82,5,13,90,5,3073,86,5,193,192,5,24577]),"cplens",w(-1,[3,4,5,6,7,8,9,10,11,13,15,17,19,23,27,31,35,43,51,59,67,83,99,115,131,163,195,227,258,0,0]),"cplext",w(-1,[0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0,112,112]),"cpdist",w(-1,[1,2,3,4,5,7,
9,13,17,25,33,49,65,97,129,193,257,385,513,769,1025,1537,2049,3073,4097,6145,8193,12289,16385,24577]),"cpdext",w(-1,[0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),"BMAX",15);p("JU");c$=s(function(){this.len=this.mode=0;this.tree=null;this.dbits=this.lbits=this.dist=this.get=this.lit=this.need=this.tree_index=0;this.ltree=null;this.ltree_index=0;this.dtree=null;this.dtree_index=0;this.s=this.z=null;r(this,arguments)},JU,"InfCodes");m(c$,function(a,b){this.z=a;this.s=b},"JU.ZStream,JU.InfBlocks");
d(c$,"init",function(a,b,c,f,d,e){this.mode=0;this.lbits=a;this.dbits=b;this.ltree=c;this.ltree_index=f;this.dtree=d;this.dtree_index=e;this.tree=null},"~N,~N,~A,~N,~A,~N");d(c$,"proc",function(a){var b,c,f=0,d=0,e=0,g,h,j,e=this.z.next_in_index;g=this.z.avail_in;f=this.s.bitb;d=this.s.bitk;h=this.s.write;for(j=h<this.s.read?this.s.read-h-1:this.s.end-h;;)switch(this.mode){case 0:if(258<=j&&10<=g&&(this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=
e,this.s.write=h,a=this.inflate_fast(this.lbits,this.dbits,this.ltree,this.ltree_index,this.dtree,this.dtree_index,this.s,this.z),e=this.z.next_in_index,g=this.z.avail_in,f=this.s.bitb,d=this.s.bitk,h=this.s.write,j=h<this.s.read?this.s.read-h-1:this.s.end-h,0!=a)){this.mode=1==a?7:9;break}this.need=this.lbits;this.tree=this.ltree;this.tree_index=this.ltree_index;this.mode=1;case 1:for(b=this.need;d<b;){if(0!=g)a=0;else return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,
this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);g--;f|=(this.z.next_in[e++]&255)<<d;d+=8}b=3*(this.tree_index+(f&JU.InfCodes.inflate_mask[b]));f>>>=this.tree[b+1];d-=this.tree[b+1];c=this.tree[b];if(0==c){this.lit=this.tree[b+2];this.mode=6;break}if(0!=(c&16)){this.get=c&15;this.len=this.tree[b+2];this.mode=2;break}if(0==(c&64)){this.need=c;this.tree_index=F(b/3)+this.tree[b+2];break}if(0!=(c&32)){this.mode=7;break}this.mode=9;this.z.msg="invalid literal/length code";a=-3;this.s.bitb=
f;this.s.bitk=d;this.z.avail_in=g;this.z.total_in+=e-this.z.next_in_index;this.z.next_in_index=e;this.s.write=h;return this.s.inflate_flush(a);case 2:for(b=this.get;d<b;){if(0!=g)a=0;else return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);g--;f|=(this.z.next_in[e++]&255)<<d;d+=8}this.len+=f&JU.InfCodes.inflate_mask[b];f>>=b;d-=b;this.need=this.dbits;this.tree=this.dtree;this.tree_index=this.dtree_index;
this.mode=3;case 3:for(b=this.need;d<b;){if(0!=g)a=0;else return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);g--;f|=(this.z.next_in[e++]&255)<<d;d+=8}b=3*(this.tree_index+(f&JU.InfCodes.inflate_mask[b]));f>>=this.tree[b+1];d-=this.tree[b+1];c=this.tree[b];if(0!=(c&16)){this.get=c&15;this.dist=this.tree[b+2];this.mode=4;break}if(0==(c&64)){this.need=c;this.tree_index=F(b/3)+this.tree[b+2];break}this.mode=
9;this.z.msg="invalid distance code";a=-3;this.s.bitb=f;this.s.bitk=d;this.z.avail_in=g;this.z.total_in+=e-this.z.next_in_index;this.z.next_in_index=e;this.s.write=h;return this.s.inflate_flush(a);case 4:for(b=this.get;d<b;){if(0!=g)a=0;else return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);g--;f|=(this.z.next_in[e++]&255)<<d;d+=8}this.dist+=f&JU.InfCodes.inflate_mask[b];f>>=b;d-=b;this.mode=5;
case 5:for(b=h-this.dist;0>b;)b+=this.s.end;for(;0!=this.len;){if(0==j&&(h==this.s.end&&0!=this.s.read&&(h=0,j=h<this.s.read?this.s.read-h-1:this.s.end-h),0==j&&(this.s.write=h,a=this.s.inflate_flush(a),h=this.s.write,j=h<this.s.read?this.s.read-h-1:this.s.end-h,h==this.s.end&&0!=this.s.read&&(h=0,j=h<this.s.read?this.s.read-h-1:this.s.end-h),0==j)))return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);
this.s.window[h++]=this.s.window[b++];j--;b==this.s.end&&(b=0);this.len--}this.mode=0;break;case 6:if(0==j&&(h==this.s.end&&0!=this.s.read&&(h=0,j=h<this.s.read?this.s.read-h-1:this.s.end-h),0==j&&(this.s.write=h,a=this.s.inflate_flush(a),h=this.s.write,j=h<this.s.read?this.s.read-h-1:this.s.end-h,h==this.s.end&&0!=this.s.read&&(h=0,j=h<this.s.read?this.s.read-h-1:this.s.end-h),0==j)))return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=
e,this.s.write=h,this.s.inflate_flush(a);a=0;this.s.window[h++]=this.lit;j--;this.mode=0;break;case 7:7<d&&(d-=8,g++,e--);this.s.write=h;a=this.s.inflate_flush(a);h=this.s.write;if(this.s.read!=this.s.write)return this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);this.mode=8;case 8:return a=1,this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,
this.s.write=h,this.s.inflate_flush(a);case 9:return a=-3,this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a);default:return a=-2,this.s.bitb=f,this.s.bitk=d,this.z.avail_in=g,this.z.total_in+=e-this.z.next_in_index,this.z.next_in_index=e,this.s.write=h,this.s.inflate_flush(a)}},"~N");d(c$,"free",function(){},"JU.ZStream");d(c$,"inflate_fast",function(a,b,c,f,d,e,g,h){var j,n,m,u,p,q,s,r,t,v,w,y;q=h.next_in_index;
s=h.avail_in;u=g.bitb;p=g.bitk;r=g.write;t=r<g.read?g.read-r-1:g.end-r;a=JU.InfCodes.inflate_mask[a];v=JU.InfCodes.inflate_mask[b];do{for(;20>p;)s--,u|=(h.next_in[q++]&255)<<p,p+=8;j=u&a;n=c;m=f;y=3*(m+j);if(0==(b=n[y]))u>>=n[y+1],p-=n[y+1],g.window[r++]=n[y+2],t--;else{do{u>>=n[y+1];p-=n[y+1];if(0!=(b&16)){b&=15;w=n[y+2]+(u&JU.InfCodes.inflate_mask[b]);u>>=b;for(p-=b;15>p;)s--,u|=(h.next_in[q++]&255)<<p,p+=8;j=u&v;n=d;m=e;y=3*(m+j);b=n[y];do if(u>>=n[y+1],p-=n[y+1],0!=(b&16)){for(b&=15;p<b;)s--,
u|=(h.next_in[q++]&255)<<p,p+=8;j=n[y+2]+(u&JU.InfCodes.inflate_mask[b]);u>>=b;p-=b;t-=w;if(r>=j)j=r-j,0<r-j&&2>r-j?(g.window[r++]=g.window[j++],g.window[r++]=g.window[j++]):(System.arraycopy(g.window,j,g.window,r,2),r+=2,j+=2),w-=2;else{j=r-j;do j+=g.end;while(0>j);b=g.end-j;if(w>b){w-=b;if(0<r-j&&b>r-j){do g.window[r++]=g.window[j++];while(0!=--b)}else System.arraycopy(g.window,j,g.window,r,b),r+=b;j=0}}if(0<r-j&&w>r-j){do g.window[r++]=g.window[j++];while(0!=--w)}else System.arraycopy(g.window,
j,g.window,r,w),r+=w;break}else if(0==(b&64))j+=n[y+2],j+=u&JU.InfCodes.inflate_mask[b],y=3*(m+j),b=n[y];else return h.msg="invalid distance code",w=h.avail_in-s,w=p>>3<w?p>>3:w,s+=w,q-=w,p-=w<<3,g.bitb=u,g.bitk=p,h.avail_in=s,h.total_in+=q-h.next_in_index,h.next_in_index=q,g.write=r,-3;while(1);break}if(0==(b&64)){if(j+=n[y+2],j+=u&JU.InfCodes.inflate_mask[b],y=3*(m+j),0==(b=n[y])){u>>=n[y+1];p-=n[y+1];g.window[r++]=n[y+2];t--;break}}else{if(0!=(b&32))return w=h.avail_in-s,w=p>>3<w?p>>3:w,s+=w,q-=
w,p-=w<<3,g.bitb=u,g.bitk=p,h.avail_in=s,h.total_in+=q-h.next_in_index,h.next_in_index=q,g.write=r,1;h.msg="invalid literal/length code";w=h.avail_in-s;w=p>>3<w?p>>3:w;s+=w;q-=w;p-=w<<3;g.bitb=u;g.bitk=p;h.avail_in=s;h.total_in+=q-h.next_in_index;h.next_in_index=q;g.write=r;return-3}}while(1)}}while(258<=t&&10<=s);w=h.avail_in-s;w=p>>3<w?p>>3:w;q-=w;g.bitb=u;g.bitk=p-(w<<3);h.avail_in=s+w;h.total_in+=q-h.next_in_index;h.next_in_index=q;g.write=r;return 0},"~N,~N,~A,~N,~A,~N,JU.InfBlocks,JU.ZStream");
G(c$,"inflate_mask",w(-1,[0,1,3,7,15,31,63,127,255,511,1023,2047,4095,8191,16383,32767,65535]),"Z_OK",0,"Z_STREAM_END",1,"Z_STREAM_ERROR",-2,"Z_DATA_ERROR",-3,"START",0,"LEN",1,"LENEXT",2,"DIST",3,"DISTEXT",4,"COPY",5,"LIT",6,"WASH",7,"END",8,"BADCODE",9);q(["java.io.OutputStream"],"java.io.ByteArrayOutputStream",["java.lang.IllegalArgumentException","$.IndexOutOfBoundsException","$.OutOfMemoryError"],function(){c$=s(function(){this.buf=null;this.count=0;r(this,arguments)},java.io,"ByteArrayOutputStream",
java.io.OutputStream);m(c$,function(){this.construct(32)});m(c$,function(a){t(this,java.io.ByteArrayOutputStream,[]);if(0>a)throw new IllegalArgumentException("Negative initial size: "+a);this.buf=S(a,0)},"~N");d(c$,"ensureCapacity",function(a){0<a-this.buf.length&&this.grow(a)},"~N");d(c$,"grow",function(a){var b=this.buf.length<<1;0>b-a&&(b=a);if(0>b){if(0>a)throw new OutOfMemoryError;b=a}this.buf=java.io.ByteArrayOutputStream.arrayCopyByte(this.buf,b)},"~N");c$.arrayCopyByte=d(c$,"arrayCopyByte",
function(a,b){var c=S(b,0);System.arraycopy(a,0,c,0,a.length<b?a.length:b);return c},"~A,~N");e(c$,"writeByteAsInt",function(a){this.ensureCapacity(this.count+1);this.buf[this.count]=a;this.count+=1},"~N");d(c$,"write",function(a,b,c){if(0>b||b>a.length||0>c||0<b+c-a.length)throw new IndexOutOfBoundsException;this.ensureCapacity(this.count+c);System.arraycopy(a,b,this.buf,this.count,c);this.count+=c},"~A,~N,~N");d(c$,"writeTo",function(a){a.write(this.buf,0,this.count)},"java.io.OutputStream");d(c$,
"reset",function(){this.count=0});d(c$,"toByteArray",function(){return this.count==this.buf.length?this.buf:java.io.ByteArrayOutputStream.arrayCopyByte(this.buf,this.count)});d(c$,"size",function(){return this.count});e(c$,"toString",function(){return String.instantialize(this.buf,0,this.count)});e(c$,"close",function(){})});q(["java.io.Closeable","$.Flushable"],"java.io.OutputStream",["java.lang.IndexOutOfBoundsException","$.NullPointerException"],function(){c$=B(java.io,"OutputStream",null,[java.io.Closeable,
java.io.Flushable]);d(c$,"write",function(a,b,c){if(null==a)throw new NullPointerException;if(0>b||b>a.length||0>c||b+c>a.length||0>b+c)throw new IndexOutOfBoundsException;if(0!=c)for(var f=0;f<c;f++)this.writeByteAsInt(a[b+f])},"~A,~N,~N");e(c$,"flush",function(){});e(c$,"close",function(){})});p("java.util.zip");q(["java.io.IOException"],"java.util.zip.ZipException",null,function(){c$=B(java.util.zip,"ZipException",java.io.IOException)});p("MCview");q(["java.awt.Color"],"MCview.Atom",["java.lang.Float"],
function(){c$=s(function(){this.number=this.z=this.y=this.x=0;this.resName=this.name=null;this.resNumber=0;this.insCode=" ";this.resNumIns=null;this.type=0;this.chain=this.color=null;this.alignmentMapping=-1;this.tfactor=this.occupancy=this.atomIndex=0;this.isSelected=!1;r(this,arguments)},MCview,"Atom");J(c$,function(){this.color=java.awt.Color.lightGray});m(c$,function(a){this.atomIndex=Integer.parseInt(a.substring(6,11).trim());this.name=a.substring(12,15).trim();this.resName=a.substring(17,20);
this.chain=a.substring(21,22);this.resNumber=Integer.parseInt(a.substring(22,26).trim());this.resNumIns=a.substring(22,27).trim();this.insCode=a.substring(26,27).charAt(0);this.x=(new Float(a.substring(30,38).trim())).floatValue();this.y=(new Float(a.substring(38,46).trim())).floatValue();this.z=(new Float(a.substring(47,55).trim())).floatValue();var b=a.substring(54,60).trim();this.occupancy=0<b.length?(new Float(b)).floatValue():1;b=a.substring(60,66).trim();this.tfactor=0<b.length?(new Float(b)).floatValue():
1},"~S");m(c$,function(a,b,c){this.x=a;this.y=b;this.z=c},"~N,~N,~N")});p("MCview");q(["java.util.Vector"],"MCview.PDBChain","MCview.Bond $.Residue jalview.datamodel.AlignmentAnnotation $.Annotation $.Sequence $.SequenceFeature jalview.schemes.ResidueProperties java.awt.Color java.lang.StringBuilder".split(" "),function(){c$=s(function(){this.residues=this.atoms=this.bonds=this.id=null;this.offset=0;this.shadow=this.sequence=null;this.isNa=!1;this.isVisible=!0;this.seqend=this.seqstart=this.pdbend=
this.pdbstart=0;this.pdbid="";this.shadowMap=this.newline=null;r(this,arguments)},MCview,"PDBChain");J(c$,function(){this.bonds=new java.util.Vector;this.atoms=new java.util.Vector;this.residues=new java.util.Vector;this.newline=System.getProperty("line.separator")});m(c$,function(a,b){this.pdbid=a.toLowerCase();this.id=b},"~S,~S");d(c$,"setNewlineString",function(a){this.newline=a},"~S");d(c$,"getNewlineString",function(){return this.newline});d(c$,"print",function(){for(var a=new StringBuilder(256),
b,c=this.bonds.iterator();c.hasNext()&&((b=c.next())||1);)a.append(b.at1.resName).append(" ").append(b.at1.resNumber).append(" ").append(this.offset).append(this.newline);return a.toString()});d(c$,"makeExactMapping",function(a,b){for(var c=a.getSeq2Start()-2,f=b.getStart()+a.getSeq1Start()-3,d,e=this.atoms.iterator();e.hasNext()&&((d=e.next())||1);)d.alignmentMapping=-1;for(var g=0;g<a.astr1.length;g++)if("-"!=a.astr1.charAt(g)&&f++,"-"!=a.astr2.charAt(g)&&c++,a.astr1.charAt(g)==a.astr2.charAt(g))for(e=
this.residues.elementAt(c).atoms.iterator();e.hasNext()&&((d=e.next())||1);)d.alignmentMapping=f},"jalview.analysis.AlignSeq,jalview.datamodel.SequenceI");d(c$,"transferRESNUMFeatures",function(a,b){for(var c=a;null!=c&&null!=c.getDatasetSequence();)if(c=c.getDatasetSequence(),c===this.sequence)return null;null==b&&(b="IEA:jalview");for(var f=this.sequence.getSequenceFeatures(),d=0;d<f.length;d++)if(f[d].getFeatureGroup().equals(this.pdbid)){var e=new jalview.datamodel.SequenceFeature(f[d]);e.setBegin(1+
this.residues.elementAt(e.getBegin()-this.offset).atoms.elementAt(0).alignmentMapping);e.setEnd(1+this.residues.elementAt(e.getEnd()-this.offset).atoms.elementAt(0).alignmentMapping);e.setStatus(b+(null==e.getStatus()||0==e.getStatus().length?"":":"+e.getStatus()));0!=e.begin&&0!=e.end&&c.addSequenceFeature(e)}return f},"jalview.datamodel.SequenceI,~S");d(c$,"makeCaBondList",function(){for(var a=!1,b=0,c=0;c<this.residues.size()-1;c++){var f=this.residues.elementAt(c),d=this.residues.elementAt(c+
1),e=f.findAtom("CA"),g=d.findAtom("CA"),a=!1;null==e&&null==g&&(a=!0,e=f.findAtom("P"),g=d.findAtom("P"));null!=e&&null!=g?e.chain.equals(g.chain)&&(a&&b++,this.makeBond(e,g)):System.out.println("not found "+c)}0<this.residues.size()&&0.99<F(b/(this.residues.size()-1))&&(this.isNa=!0)});d(c$,"makeBond",function(a,b){this.bonds.addElement(new MCview.Bond(a,b))},"MCview.Atom,MCview.Atom");d(c$,"makeResidueList",function(a){var b=0,c,f=c=!1,d=new StringBuilder(256),e=new java.util.Vector,g=new java.util.Vector,
h,j=this.atoms.size()-1,n=-1;for(h=0;h<=j;h++){var m=n=this.atoms.elementAt(h).resNumber;0==h&&(this.offset=n);for(c=new java.util.Vector;n==m&&h<this.atoms.size();)c.add(this.atoms.elementAt(h)),h++,h<this.atoms.size()?n=this.atoms.elementAt(h).resNumber:n++;h--;this.residues.addElement(new MCview.Residue(c,n-1,b));m=this.residues.lastElement().atoms.get(0);c=new jalview.datamodel.SequenceFeature("RESNUM",m.resName+":"+m.resNumIns+" "+this.pdbid+this.id,"",this.offset+b,this.offset+b,this.pdbid);
e.addElement(c);g.addElement(new jalview.datamodel.Annotation(m.tfactor));if(null==(c=jalview.schemes.ResidueProperties.getAA3Hash().get(m.resName))){var u=m.resName.trim();c=2==u.length&&jalview.schemes.ResidueProperties.aaIndex[u.charCodeAt(0)]==jalview.schemes.ResidueProperties.aaIndex[68];m.name.equalsIgnoreCase("CA")||-1==jalview.schemes.ResidueProperties.nucleotideIndex[u.charCodeAt(c?1:0)]?d.append("X"):(f=!0,d.append(u.charAt(c?1:0)))}else f&&System.err.println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"),
d.append(jalview.schemes.ResidueProperties.aa[c.intValue()]);b++}1>this.id.length&&(this.id=" ");this.isNa=f;this.sequence=new jalview.datamodel.Sequence(this.id,d.toString(),this.offset,n-1);h=0;for(j=e.size();h<j;h++)this.sequence.addSequenceFeature(e.elementAt(h)),e.setElementAt(null,h);if(a){a=Array(g.size());h=b=0;for(j=a.length;h<j;h++)a[h]=g.elementAt(h),a[h].value>b&&(b=a[h].value),g.setElementAt(null,h);g=new jalview.datamodel.AlignmentAnnotation("Temperature Factor","Temperature Factor for "+
this.pdbid+this.id,a,0,b,2);g.setSequenceRef(this.sequence);this.sequence.addAlignmentAnnotation(g)}},"~B");d(c$,"setChargeColours",function(){for(var a,b=this.bonds.iterator();b.hasNext()&&((a=b.next())||1);)null!=a.at1&&null!=a.at2?(a.startCol=MCview.PDBChain.getChargeColour(a.at1.resName),a.endCol=MCview.PDBChain.getChargeColour(a.at2.resName)):(a.startCol=java.awt.Color.gray,a.endCol=java.awt.Color.gray)});c$.getChargeColour=d(c$,"getChargeColour",function(a){var b=java.awt.Color.lightGray;"ASP".equals(a)||
"GLU".equals(a)?b=java.awt.Color.red:"LYS".equals(a)||"ARG".equals(a)?b=java.awt.Color.blue:"CYS".equals(a)&&(b=java.awt.Color.yellow);return b},"~S");d(c$,"setChainColours",function(a){for(var b,c,f=this.bonds.iterator();f.hasNext()&&((c=f.next())||1);)try{b=jalview.schemes.ResidueProperties.aa3Hash.get(c.at1.resName).intValue(),c.startCol=a.findColour(jalview.schemes.ResidueProperties.aa[b].charAt(0)),b=jalview.schemes.ResidueProperties.aa3Hash.get(c.at2.resName).intValue(),c.endCol=a.findColour(jalview.schemes.ResidueProperties.aa[b].charAt(0))}catch(d){if(y(d,
Exception))c.startCol=java.awt.Color.gray,c.endCol=java.awt.Color.gray;else throw d;}},"jalview.schemes.ColourSchemeI");d(c$,"setChainColours",function(a){for(var b,c=this.bonds.iterator();c.hasNext()&&((b=c.next())||1);)b.startCol=a,b.endCol=a},"java.awt.Color");d(c$,"transferResidueAnnotation",function(a,b){var c=a.getSequence(),f=c;if(null!=c){for(;null!=f.getDatasetSequence();)f=f.getDatasetSequence();if(null!=this.shadow&&null!=this.shadow.getAnnotation())for(var d,e=0,g=this.shadow.getAnnotation();e<
g.length&&((d=g[e])||1);e++){var h=c.getAlignmentAnnotations(d.getCalcId(),d.label);if(null==h||0==h.size())d=new jalview.datamodel.AlignmentAnnotation(d),d.liftOver(this.sequence,this.shadowMap),d.liftOver(f,b),f.addAlignmentAnnotation(d)}else if(null!=this.sequence&&null!=this.sequence.getAnnotation()){e=0;for(g=this.sequence.getAnnotation();e<g.length&&((d=g[e])||1);e++)if(h=c.getAlignmentAnnotations(d.getCalcId(),d.label),null==h||0==h.size())d=new jalview.datamodel.AlignmentAnnotation(d),d.liftOver(f,
b)}}},"jalview.structure.StructureMapping,jalview.datamodel.Mapping");G(c$,"PDBFILEFEATURE","PDBFile","IEASTATUS","IEA:jalview")});p("MCview");q(["java.awt.Color"],"MCview.Bond",null,function(){c$=s(function(){this.at2=this.at1=this.endCol=this.startCol=this.end=this.start=null;r(this,arguments)},MCview,"Bond");J(c$,function(){this.endCol=this.startCol=java.awt.Color.lightGray});m(c$,function(a,b){this.start=Q(-1,[a.x,a.y,a.z]);this.end=Q(-1,[b.x,b.y,b.z]);this.startCol=a.color;this.endCol=b.color;
this.at1=a;this.at2=b},"MCview.Atom,MCview.Atom");d(c$,"translate",function(a,b,c){this.start[0]+=a;this.end[0]+=a;this.start[1]+=b;this.end[1]+=b;this.start[2]+=c;this.end[2]+=c},"~N,~N,~N")});p("MCview");c$=s(function(){this.atoms=null;this.count=this.number=0;r(this,arguments)},MCview,"Residue");m(c$,function(a,b,c){this.atoms=a;this.number=b;this.count=c},"java.util.Vector,~N,~N");d(c$,"findAtom",function(a){for(var b,c=this.atoms.iterator();c.hasNext()&&((b=c.next())||1);)if(b.name.equals(a))return b;
return null},"~S");p("jalview.structure");c$=s(function(){this.chain=this.pdbFile=null;this.atomIndex=this.pdbResNum=0;r(this,arguments)},jalview.structure,"AtomSpec");m(c$,function(a,b,c,f){this.pdbFile=a;this.chain=b;this.pdbResNum=c;this.atomIndex=f},"~S,~S,~N,~N");d(c$,"getPdbFile",function(){return this.pdbFile});d(c$,"getChain",function(){return this.chain});d(c$,"getPdbResNum",function(){return this.pdbResNum});d(c$,"getAtomIndex",function(){return this.atomIndex});e(c$,"toString",function(){return"pdbFile: "+
this.pdbFile+", chain: "+this.chain+", res: "+this.pdbResNum+", atom: "+this.atomIndex});p("jalview.structure");M(jalview.structure,"SecondaryStructureListener");p("jalview.structure");M(jalview.structure,"SequenceListener");p("jalview.structure");M(jalview.structure,"StructureListener");p("jalview.structure");q(null,"jalview.structure.StructureMapping",["jalview.datamodel.AlignmentAnnotation"],function(){c$=s(function(){this.mapping=this.pdbchain=this.pdbid=this.pdbfile=this.sequence=this.mappingDetails=
null;r(this,arguments)},jalview.structure,"StructureMapping");m(c$,function(a,b,c,f,d,e){this.sequence=a;this.pdbfile=b;this.pdbid=c;this.pdbchain=f;this.mapping=d;this.mappingDetails=e},"jalview.datamodel.SequenceI,~S,~S,~S,~A,~S");d(c$,"getSequence",function(){return this.sequence});d(c$,"getChain",function(){return this.pdbchain});d(c$,"getPdbId",function(){return this.pdbid});d(c$,"getAtomNum",function(a){return this.mapping.length>a?this.mapping[a][1]:0},"~N");d(c$,"getPDBResNum",function(a){return this.mapping.length>
a?this.mapping[a][0]:0},"~N");d(c$,"getSeqPos",function(a){for(var b=0;b<this.mapping.length;b++)if(this.mapping[b][0]==a)return b;return-1},"~N");d(c$,"transfer",function(a){a=new jalview.datamodel.AlignmentAnnotation(a);for(var b=this.sequence;null!=b.getDatasetSequence();)b=b.getDatasetSequence();a.remap(b,this.mapping,-1,-1,0);b.addAlignmentAnnotation(a);b!==this.sequence&&(a=new jalview.datamodel.AlignmentAnnotation(a),this.sequence.addAlignmentAnnotation(a));return a},"jalview.datamodel.AlignmentAnnotation")});
p("jalview.structure");M(jalview.structure,"VamsasListener");p("jalview.appletgui");q(["awt2swing.Panel","jalview.api.AlignmentViewPanel","java.awt.event.AdjustmentListener","awt2swing.Scrollbar"],"jalview.appletgui.AlignmentPanel","awt2swing.Frame jalview.analysis.AnnotationSorter jalview.appletgui.AnnotationLabels $.AnnotationPanel $.FeatureRenderer $.IdPanel $.IdwidthAdjuster $.PaintRefresher $.ScalePanel $.SeqPanel jalview.bin.JalviewLite jalview.structure.StructureSelectionManager java.awt.BorderLayout $.Color $.Dimension java.awt.event.ComponentAdapter java.beans.PropertyChangeListener".split(" "),
function(){c$=s(function(){this.alabels=this.annotationPanel=this.scalePanel=this.alignFrame=this.idwidthAdjuster=this.idPanel=this.seqPanel=this.overviewPanel=this.av=null;this.fastPaint=!0;this.vextent=this.hextent=0;this.apvscroll=this.annotationPanelHolder=this.hscrollFillerPanel=this.annotationSpaceFillerHolder=this.idSpaceFillerPanel1=this.idPanelHolder=this.scalePanelHolder=this.seqPanelHolder=this.hscroll=this.vscroll=this.sequenceHolderPanel=null;this.followingComplementScroll=!1;r(this,
arguments)},jalview.appletgui,"AlignmentPanel",awt2swing.Panel,[java.awt.event.AdjustmentListener,jalview.api.AlignmentViewPanel]);J(c$,function(){this.sequenceHolderPanel=new awt2swing.Panel;this.vscroll=new awt2swing.Scrollbar;this.hscroll=new awt2swing.Scrollbar;this.seqPanelHolder=new awt2swing.Panel;this.scalePanelHolder=new awt2swing.Panel;this.idPanelHolder=new awt2swing.Panel;this.idSpaceFillerPanel1=new awt2swing.Panel;this.annotationSpaceFillerHolder=new awt2swing.Panel;this.hscrollFillerPanel=
new awt2swing.Panel;this.annotationPanelHolder=new awt2swing.Panel;this.apvscroll=new awt2swing.Scrollbar});e(c$,"finalize",function(){this.annotationSpaceFillerHolder=this.annotationPanelHolder=this.annotationPanel=this.scalePanelHolder=this.scalePanel=this.sequenceHolderPanel=this.seqPanelHolder=this.seqPanel=this.av=this.alignFrame=null});m(c$,function(a,b){t(this,jalview.appletgui.AlignmentPanel,[]);this.setName("alignmentPanel");try{this.jbInit()}catch(c){if(y(c,Exception))c.printStackTrace();
else throw c;}this.alignFrame=a;this.av=b;this.seqPanel=new jalview.appletgui.SeqPanel(b,this);this.idPanel=new jalview.appletgui.IdPanel(b,this);this.scalePanel=new jalview.appletgui.ScalePanel(b,this);this.idwidthAdjuster=new jalview.appletgui.IdwidthAdjuster(this);this.annotationPanel=new jalview.appletgui.AnnotationPanel(this);this.annotationPanelHolder.add(this.annotationPanel,"Center");this.sequenceHolderPanel.add(this.annotationPanelHolder,"South");this.alabels=new jalview.appletgui.AnnotationLabels(this);
this.setAnnotationVisible(b.isShowAnnotation());this.idPanelHolder.add(this.idPanel,"Center");this.idSpaceFillerPanel1.add(this.idwidthAdjuster,"Center");this.annotationSpaceFillerHolder.add(this.alabels,"Center");this.scalePanelHolder.add(this.scalePanel,"Center");this.seqPanelHolder.add(this.seqPanel,"Center");this.fontChanged();this.setScrollValues(0,0);this.apvscroll.addAdjustmentListener(this);this.hscroll.addAdjustmentListener(this);this.vscroll.addAdjustmentListener(this);this.addComponentListener((H("jalview.appletgui.AlignmentPanel$1")?
0:jalview.appletgui.AlignmentPanel.$AlignmentPanel$1$(),C(jalview.appletgui.AlignmentPanel$1,this,T("av",b))));var f=this.calculateIdWidth();this.idPanel.idCanvas.setSize(f);this.hscrollFillerPanel.setSize(f.width,this.annotationPanel.getSize().height);this.idPanel.idCanvas.setSize(f.width,this.seqPanel.seqCanvas.getSize().height);this.annotationSpaceFillerHolder.setSize(f.width,this.annotationPanel.getSize().height);this.alabels.setSize(f.width,this.annotationPanel.getSize().height);b.addPropertyChangeListener((H("jalview.appletgui.AlignmentPanel$2")?
0:jalview.appletgui.AlignmentPanel.$AlignmentPanel$2$(),C(jalview.appletgui.AlignmentPanel$2,this,T("ap",this,"av",b))))},"jalview.appletgui.AlignFrame,jalview.appletgui.AlignViewport");e(c$,"getAlignViewport",function(){return this.av});d(c$,"getSequenceRenderer",function(){return this.seqPanel.seqCanvas.sr});e(c$,"getFeatureRenderer",function(){return this.seqPanel.seqCanvas.fr});e(c$,"cloneFeatureRenderer",function(){var a=new jalview.appletgui.FeatureRenderer(this.av);a.transferSettings(this.seqPanel.seqCanvas.fr);
return a});d(c$,"alignmentChanged",function(){this.av.alignmentChanged(this);null!=this.overviewPanel&&this.overviewPanel.updateOverviewImage();this.alignFrame.updateEditMenuBar();this.repaint()});d(c$,"fontChanged",function(){this.idPanel.idCanvas.image=null;var a=this.getFontMetrics(this.av.getFont());this.scalePanel.setSize(new java.awt.Dimension(10,this.av.getCharHeight()+a.getDescent()));this.idwidthAdjuster.setSize(new java.awt.Dimension(10,this.av.getCharHeight()+a.getDescent()));this.av.updateSequenceIdColours();
this.annotationPanel.image=null;var a=this.annotationPanel.adjustPanelHeight(!1),b=this.calculateIdWidth();b.setSize(b.width+4,this.seqPanel.seqCanvas.getSize().height);this.alabels.setSize(b.width+4,a);this.idPanel.idCanvas.setSize(b);this.hscrollFillerPanel.setSize(b);this.validateAnnotationDimensions(!1);this.annotationPanel.repaint();this.validate();this.repaint();null!=this.overviewPanel&&this.overviewPanel.updateOverviewImage()});d(c$,"setIdWidth",function(a,b){this.idPanel.idCanvas.setSize(a,
b);this.idPanelHolder.setSize(a,this.idPanelHolder.getSize().height);this.annotationSpaceFillerHolder.setSize(a,this.annotationSpaceFillerHolder.getSize().height);this.alabels.setSize(a,this.alabels.getSize().height);this.validate()},"~N,~N");d(c$,"calculateIdWidth",function(){null==this.av.nullFrame&&(this.av.nullFrame=new awt2swing.Frame,this.av.nullFrame.addNotify(),this.av.nullFrame.setFont(this.av.font));for(var a=this.av.nullFrame.getGraphics(),b=a.getFontMetrics(this.av.font),c=this.av.getAlignment(),
f=0,d=0,e;f<c.getHeight()&&null!=c.getSequenceAt(f);)e=c.getSequenceAt(f).getDisplayId(this.av.getShowJVSuffix()),b.stringWidth(e)>d&&(d=b.stringWidth(e)),f++;f=0;if(null!=c.getAlignmentAnnotation())for(b=a.getFontMetrics(this.av.nullFrame.getFont());f<c.getAlignmentAnnotation().length;)a=c.getAlignmentAnnotation()[f].label,b.stringWidth(a)>d&&(d=b.stringWidth(a)),f++;return new java.awt.Dimension(d,this.idPanel.idCanvas.getSize().height)});d(c$,"highlightSearchResults",function(a){this.scrollToPosition(a);
this.seqPanel.seqCanvas.highlightSearchResults(a)},"jalview.datamodel.SearchResults");d(c$,"scrollToPosition",function(a){return this.scrollToPosition(a,!0)},"jalview.datamodel.SearchResults");d(c$,"scrollToPosition",function(a,b){return this.scrollToPosition(a,b,!1)},"jalview.datamodel.SearchResults,~B");d(c$,"scrollToPosition",function(a,b,c){if(null!=a&&0<a.getSize()){var f=this.av.getAlignment(),d=f.findIndex(a);if(-1==d)return!1;var e=f.getSequenceAt(d),f=a.getResults(e,0,f.getWidth());if(null==
f)return jalview.bin.JalviewLite.debug&&System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+e.getStart()+","+e.getEnd()),!1;a=f[0];f=f[1];c&&(c=F((this.av.getEndRes()-this.av.getStartRes()+1)/2)-1,a=Math.max(a-c,0),f=Math.min(f+c,e.getEnd()-1));return 0>a||f==e.getEnd()?!1:this.scrollTo(a,f,d,!1,b)}return!0},"jalview.datamodel.SearchResults,~B,~B");d(c$,"scrollTo",function(a,b,c,f,d){var e,g,h,j,n=-1;if(this.av.hasHiddenColumns()){if(n=this.av.getColumnSelection().findColumnPosition(a),
b=this.av.getColumnSelection().findColumnPosition(b),n==b&&!f&&!this.av.getColumnSelection().isVisible(a))return!1}else n=a;this.av.getWrapAlignment()?this.scrollToWrappedVisible(n):(e=this.av.getStartRes())>=n?this.setScrollValues(n-1,c):(g=this.av.getEndRes())<=b?this.setScrollValues(e+1+b-g,c):(h=this.av.getStartSeq())>c?this.setScrollValues(this.av.getStartRes(),c):(j=this.av.getEndSeq())<=c&&this.setScrollValues(this.av.getStartRes(),h+c-j+1);d&&null!=this.overviewPanel&&this.overviewPanel.setBoxPosition();
this.paintAlignment(d);return!0},"~N,~N,~N,~B,~B");d(c$,"scrollToWrappedVisible",function(a){var b=this.seqPanel.seqCanvas.getWrappedCanvasWidth(this.seqPanel.seqCanvas.getSize().width);if(a<=this.av.getStartRes()||a>=this.av.getStartRes()+b)this.vscroll.setValue(F(a/b)),this.av.startRes=this.vscroll.getValue()*b},"~N");d(c$,"getOverviewPanel",function(){return this.overviewPanel});d(c$,"setOverviewPanel",function(a){this.overviewPanel=a},"jalview.appletgui.OverviewPanel");d(c$,"setAnnotationVisible",
function(a){this.av.getWrapAlignment()?(this.annotationSpaceFillerHolder.setVisible(!1),this.annotationPanelHolder.setVisible(!1)):(this.annotationSpaceFillerHolder.setVisible(a),this.annotationPanelHolder.setVisible(a));this.validate();this.repaint()},"~B");e(c$,"adjustAnnotationHeight",function(){0==this.alignFrame.getSize().height&&System.out.println("adjustAnnotationHeight frame size zero NEEDS FIXING");this.fontChanged();this.validateAnnotationDimensions(!0);this.apvscroll.addNotify();this.hscroll.addNotify();
this.validate();this.paintAlignment(!0)});d(c$,"validateAnnotationDimensions",function(a){var b=this.av.getCharHeight(),c=b*this.av.getAlignment().getHeight(),f=this.av.calcPanelHeight(),d=f,e=this.sequenceHolderPanel.getSize(),g=e.height-this.scalePanelHolder.getHeight();a?f+c>g&&(f=Math.min(f,g-2*b)):f=this.annotationPanelHolder.getSize().height;5>g-f&&(f=g);this.annotationPanel.setSize(new java.awt.Dimension(e.width,f));this.annotationPanelHolder.setSize(new java.awt.Dimension(e.width,f));this.seqPanel.seqCanvas.setSize(e.width,
this.seqPanel.seqCanvas.getSize().height);a=this.idPanel.getSize();this.alabels.setSize(new java.awt.Dimension(a.width,f));this.annotationSpaceFillerHolder.setSize(new java.awt.Dimension(a.width,f));a=this.apvscroll.getValue();a>d-f&&(a=0);this.apvscroll.setValues(a,f,0,d);this.annotationPanel.setScrollOffset(this.apvscroll.getValue(),!1);this.alabels.setScrollOffset(this.apvscroll.getValue(),!1)},"~B");d(c$,"setWrapAlignment",function(a){this.av.startSeq=0;this.av.startRes=0;this.scalePanelHolder.setVisible(!a);
this.hscroll.setVisible(!a);this.idwidthAdjuster.setVisible(!a);a?(this.annotationPanelHolder.setVisible(!1),this.annotationSpaceFillerHolder.setVisible(!1)):this.av.isShowAnnotation()&&(this.annotationPanelHolder.setVisible(!0),this.annotationSpaceFillerHolder.setVisible(!0));this.idSpaceFillerPanel1.setVisible(!a);this.fontChanged();this.validate();this.sequenceHolderPanel.validate();this.repaint()},"~B");d(c$,"scrollUp",function(a){if(a){if(1>this.vscroll.getValue())return!1;this.setScrollValues(this.hscroll.getValue(),
this.vscroll.getValue()-1)}else{if(this.vextent+this.vscroll.getValue()>=this.av.getAlignment().getHeight())return!1;this.setScrollValues(this.hscroll.getValue(),this.vscroll.getValue()+1)}this.repaint();return!0},"~B");d(c$,"scrollRight",function(a){if(a){if(this.hextent+this.hscroll.getValue()>=this.av.getAlignment().getWidth())return!1;this.setScrollValues(this.hscroll.getValue()+1,this.vscroll.getValue())}else{if(1>this.hscroll.getValue())return!1;this.setScrollValues(this.hscroll.getValue()-
1,this.vscroll.getValue())}this.repaint();return!0},"~B");d(c$,"setScrollValues",function(a,b){var c=this.av.getAlignment().getWidth(),f=this.av.getAlignment().getHeight();this.av.hasHiddenColumns()&&(c=this.av.getColumnSelection().findColumnPosition(c));0>a&&(a=0);this.hextent=F(this.seqPanel.seqCanvas.getSize().width/this.av.getCharWidth());this.vextent=F(this.seqPanel.seqCanvas.getSize().height/this.av.getCharHeight());this.hextent>c&&(this.hextent=c);this.vextent>f&&(this.vextent=f);this.hextent+
a>c&&(System.err.println("hextent was "+this.hextent+" and x was "+a),a=c-this.hextent);this.vextent+b>f&&(b=f-this.vextent);0>b&&(b=0);0>a&&(System.err.println("x was "+a),a=0);this.av.setStartSeq(b);var d=b+this.vextent;d>this.av.getAlignment().getHeight()&&(d=this.av.getAlignment().getHeight());this.av.setEndSeq(d);this.av.setStartRes(a);this.av.setEndRes(a+F(this.seqPanel.seqCanvas.getSize().width/this.av.getCharWidth())-1);this.hscroll.setValues(a,this.hextent,0,c);this.vscroll.setValues(b,this.vextent,
0,f);null!=this.overviewPanel&&this.overviewPanel.setBoxPosition();this.sendViewPosition()},"~N,~N");e(c$,"adjustmentValueChanged",function(a){if(null!=this.annotationPanel){var b=this.av.getStartRes(),c=this.av.getStartSeq();if(null==a||a.getSource()===this.apvscroll)this.annotationPanel.setScrollOffset(this.apvscroll.getValue(),!1),this.alabels.setScrollOffset(this.apvscroll.getValue(),!1);if(null==a||a.getSource()===this.hscroll){var f=this.hscroll.getValue();this.av.setStartRes(f);this.av.setEndRes(f+
F(this.seqPanel.seqCanvas.getSize().width/this.av.getCharWidth())-1)}if(null==a||a.getSource()===this.vscroll)a=this.vscroll.getValue(),this.av.getWrapAlignment()?(a=this.seqPanel.seqCanvas.getWrappedCanvasWidth(this.seqPanel.seqCanvas.getSize().width),this.av.setStartRes(this.vscroll.getValue()*a),this.av.setEndRes((this.vscroll.getValue()+1)*a)):(this.av.setStartSeq(a),this.av.setEndSeq(a+F(this.seqPanel.seqCanvas.getSize().height/this.av.getCharHeight())));null!=this.overviewPanel&&this.overviewPanel.setBoxPosition();
a=this.av.startRes-b;c=this.av.startSeq-c;this.av.getWrapAlignment()||!this.fastPaint||this.av.MAC?this.repaint():(a>this.av.endRes-this.av.startRes?a=this.av.endRes-this.av.startRes:a<this.av.startRes-this.av.endRes&&(a=this.av.startRes-this.av.endRes),this.idPanel.idCanvas.fastPaint(c),this.seqPanel.seqCanvas.fastPaint(a,c),this.scalePanel.repaint(),this.av.isShowAnnotation()&&this.annotationPanel.fastPaint(this.av.getStartRes()-b));this.sendViewPosition();this.isFollowingComplementScroll()?this.setFollowingComplementScroll(!1):
(b=this.getComplementPanel(),this.av.scrollComplementaryAlignment(b))}},"java.awt.event.AdjustmentEvent");d(c$,"getComplementPanel",function(){var a=null;if(null!=this.alignFrame){var b=this.alignFrame.getSplitFrame();null!=b&&(b=b.getComplement(this.alignFrame),null!=b&&(a=b.alignPanel))}return a});d(c$,"scrollToCentre",function(a,b){for(var c=a.getResultSequence(0),f=0,d=!1,e,g=this.av.getAlignment().getSequences().iterator();g.hasNext()&&((e=g.next())||1);){if(c===e.getDatasetSequence()){d=!0;
break}f++}d&&(f=Math.max(0,f-b),a.getResults().get(0).setSequence(this.av.getAlignment().getSequenceAt(f)),this.setFollowingComplementScroll(!0),this.scrollToPosition(a,!0,!0))},"jalview.datamodel.SearchResults,~N");d(c$,"sendViewPosition",function(){jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.av.applet).sendViewPosition(this,this.av.startRes,this.av.endRes,this.av.startSeq,this.av.endSeq)});e(c$,"paintAlignment",function(a){(new jalview.analysis.AnnotationSorter(this.getAlignment(),
this.av.isShowAutocalculatedAbove())).sort(this.getAlignment().getAlignmentAnnotation(),this.av.getSortAnnotationsBy());this.repaint();a&&(jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.av.applet).sequenceColoursChanged(this),null!=this.overviewPanel&&this.overviewPanel.updateOverviewImage())},"~B");e(c$,"paintComponent",function(){System.out.println("alignframe paintcomp");this.invalidate();var a=this.idPanel.idCanvas.getSize(),b=this.seqPanel.seqCanvas.getSize().height;
b!=a.height&&this.idPanel.idCanvas.setSize(a.width,b);this.av.getWrapAlignment()?(a=this.av.getAlignment().getWidth(),this.av.hasHiddenColumns()&&(a=this.av.getColumnSelection().findColumnPosition(a)-1),b=this.seqPanel.seqCanvas.getWrappedCanvasWidth(this.seqPanel.seqCanvas.getSize().width),0<b&&(a=F(a/b),this.vscroll.setMaximum(1+a),this.vscroll.setUnitIncrement(1),this.vscroll.setVisibleAmount(1))):this.setScrollValues(this.av.getStartRes(),this.av.getStartSeq())},"java.awt.Graphics");d(c$,"jbInit",
function(){this.setLayout(new java.awt.BorderLayout);this.sequenceHolderPanel.setLayout(new java.awt.BorderLayout);this.seqPanelHolder.setLayout(new java.awt.BorderLayout);this.scalePanelHolder.setBackground(java.awt.Color.white);this.scalePanelHolder.setLayout(new java.awt.BorderLayout);this.idPanelHolder.setLayout(new java.awt.BorderLayout);this.idSpaceFillerPanel1.setBackground(java.awt.Color.white);this.idSpaceFillerPanel1.setLayout(new java.awt.BorderLayout);this.annotationSpaceFillerHolder.setBackground(java.awt.Color.white);
this.annotationSpaceFillerHolder.setLayout(new java.awt.BorderLayout);this.hscroll.setOrientation(0);var a=new awt2swing.Panel;a.setLayout(new java.awt.BorderLayout);this.hscrollFillerPanel.setBackground(java.awt.Color.white);this.apvscroll.setOrientation(1);this.apvscroll.setVisible(!0);this.apvscroll.addAdjustmentListener(this);this.annotationPanelHolder.setBackground(java.awt.Color.white);this.annotationPanelHolder.setLayout(new java.awt.BorderLayout);this.annotationPanelHolder.add(this.apvscroll,
"East");a.setBackground(java.awt.Color.white);this.seqPanelHolder.setBackground(java.awt.Color.white);this.idPanelHolder.setBackground(java.awt.Color.white);this.sequenceHolderPanel.add(this.scalePanelHolder,"North");this.sequenceHolderPanel.add(this.seqPanelHolder,"Center");this.seqPanelHolder.add(this.vscroll,"East");this.add(this.idPanelHolder,"West");this.idPanelHolder.add(this.idSpaceFillerPanel1,"North");this.idPanelHolder.add(this.annotationSpaceFillerHolder,"South");this.add(a,"South");a.add(this.hscroll,
"Center");a.add(this.hscrollFillerPanel,"West");this.add(this.sequenceHolderPanel,"Center")});d(c$,"updateAnnotation",function(){this.updateAnnotation(!1)});d(c$,"updateAnnotation",function(a){this.updateAnnotation(a,!1)},"~B");d(c$,"updateAnnotation",function(a,b){this.av.updateGroupAnnotationSettings(a,b);this.adjustAnnotationHeight()},"~B,~B");e(c$,"getAlignment",function(){return this.av.getAlignment()});e(c$,"getViewName",function(){return this.getName()});e(c$,"getStructureSelectionManager",
function(){return jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.av.applet)});e(c$,"raiseOOMWarning",function(a,b){System.err.println("Out of memory whilst '"+a+"'");b.printStackTrace()},"~S,OutOfMemoryError");d(c$,"setFollowingComplementScroll",function(a){this.followingComplementScroll=a},"~B");d(c$,"isFollowingComplementScroll",function(){return this.followingComplementScroll});c$.$AlignmentPanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignmentPanel$1",
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c$.$AlignmentPanel$2$=function(){A(self.c$);c$=L(jalview.appletgui,"AlignmentPanel$2",null,java.beans.PropertyChangeListener);e(c$,"propertyChange",function(a){a.getPropertyName().equals("alignment")&&(jalview.appletgui.PaintRefresher.Refresh(this.f$.ap,this.f$.av.getSequenceSetId(),!0,!0),this.b$["jalview.appletgui.AlignmentPanel"].alignmentChanged())},"java.beans.PropertyChangeEvent");c$=z()}});p("jalview.api");q(["jalview.api.OOMHandlerI"],"jalview.api.AlignmentViewPanel",null,function(){M(jalview.api,
"AlignmentViewPanel",jalview.api.OOMHandlerI)});p("jalview.api");M(jalview.api,"OOMHandlerI");p("awt2swing");q(["javax.swing.JScrollBar"],"awt2swing.Scrollbar",null,function(){c$=B(awt2swing,"Scrollbar",javax.swing.JScrollBar);d(c$,"addChangeListener",function(a){this.addAdjustmentListener(a)},"javax.swing.event.ChangeListener");d(c$,"removeChangeListener",function(a){this.removeAdjustmentListener(a)},"javax.swing.event.ChangeListener")});p("javax.swing");q(["java.awt.Adjustable","javax.swing.JComponent",
"javax.swing.event.ChangeListener"],"javax.swing.JScrollBar","java.lang.IllegalArgumentException java.awt.Dimension java.awt.event.AdjustmentEvent $.AdjustmentListener javax.swing.BoundedRangeModel $.DefaultBoundedRangeModel $.UIManager".split(" "),function(){c$=s(function(){this.model=this.fwdAdjustmentEvents=null;this.blockIncrement=this.unitIncrement=this.orientation=0;H("javax.swing.JScrollBar.ModelListener")||javax.swing.JScrollBar.$JScrollBar$ModelListener$();r(this,arguments)},javax.swing,
"JScrollBar",javax.swing.JComponent,java.awt.Adjustable);J(c$,function(){this.fwdAdjustmentEvents=C(javax.swing.JScrollBar.ModelListener,this,null)});d(c$,"checkOrientation",function(a){switch(a){case 1:case 0:break;default:throw new IllegalArgumentException("orientation must be one of: VERTICAL, HORIZONTAL");}},"~N");m(c$,function(a,b,c,f,d){t(this,javax.swing.JScrollBar,[]);this.checkOrientation(a);this.unitIncrement=1;this.blockIncrement=0==c?1:c;this.orientation=a;this.model=new javax.swing.DefaultBoundedRangeModel(b,
c,f,d);this.model.addChangeListener(this.fwdAdjustmentEvents);this.setRequestFocusEnabled(!1);this.updateUI()},"~N,~N,~N,~N,~N");m(c$,function(a){this.construct(a,0,10,0,100)},"~N");m(c$,function(){this.construct(1)});e(c$,"getUI",function(){return this.ui});e(c$,"updateUI",function(){this.setUI(javax.swing.UIManager.getUI(this))});e(c$,"getUIClassID",function(){return"ScrollBarUI"});e(c$,"getOrientation",function(){return this.orientation});d(c$,"setOrientation",function(a){this.checkOrientation(a);
var b=this.orientation;this.orientation=a;this.firePropertyChangeInt("orientation",b,a);a!=b&&this.revalidate()},"~N");d(c$,"getModel",function(){return this.model});d(c$,"setModel",function(a){var b=this.model;null!=this.model&&this.model.removeChangeListener(this.fwdAdjustmentEvents);this.model=a;null!=this.model&&this.model.addChangeListener(this.fwdAdjustmentEvents);this.firePropertyChangeObject("model",b,this.model)},"javax.swing.BoundedRangeModel");d(c$,"getUnitIncrement",function(){return this.unitIncrement},
"~N");e(c$,"setUnitIncrement",function(a){var b=this.unitIncrement;this.unitIncrement=a;this.firePropertyChangeInt("unitIncrement",b,a)},"~N");d(c$,"getBlockIncrement",function(){return this.blockIncrement},"~N");e(c$,"setBlockIncrement",function(a){var b=this.blockIncrement;this.blockIncrement=a;this.firePropertyChangeInt("blockIncrement",b,a)},"~N");d(c$,"getUnitIncrement",function(){return this.unitIncrement});d(c$,"getBlockIncrement",function(){return this.blockIncrement});e(c$,"getValue",function(){return this.getModel().getValue()});
e(c$,"setValue",function(a){this.getModel().setValue(a)},"~N");e(c$,"getVisibleAmount",function(){return this.getModel().getExtent()});e(c$,"setVisibleAmount",function(a){this.getModel().setExtent(a)},"~N");e(c$,"getMinimum",function(){return this.getModel().getMinimum()});e(c$,"setMinimum",function(a){this.getModel().setMinimum(a)},"~N");e(c$,"getMaximum",function(){return this.getModel().getMaximum()});e(c$,"setMaximum",function(a){this.getModel().setMaximum(a)},"~N");d(c$,"getValueIsAdjusting",
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a)},"java.awt.event.AdjustmentListener");d(c$,"getAdjustmentListeners",function(){return this.listenerList.getListeners(java.awt.event.AdjustmentListener)});d(c$,"fireAdjustmentValueChanged",function(a,b,c){this.fireAdjustmentValueChanged(a,b,c,this.getValueIsAdjusting())},"~N,~N,~N");d(c$,"fireAdjustmentValueChanged",function(a,b,c,f){for(var d=this.listenerList.getListenerList(),e=null,g=d.length-2;0<=g;g-=2)d[g]===java.awt.event.AdjustmentListener&&(null==e&&(e=new java.awt.event.AdjustmentEvent(this,
a,b,c,f)),d[g+1].adjustmentValueChanged(e))},"~N,~N,~N,~B");e(c$,"getMinimumSize",function(){var a=this.getPreferredSize();return 1==this.orientation?new java.awt.Dimension(a.width,5):new java.awt.Dimension(5,a.height)});e(c$,"getMaximumSize",function(){var a=this.getPreferredSize();return 1==this.getOrientation()?new java.awt.Dimension(a.width,32767):new java.awt.Dimension(32767,a.height)});d(c$,"setEnabled",function(a){K(this,javax.swing.JScrollBar,"setEnabled",[a]);for(var b=this.getComponents(),
c=0;c<b.length;c++)b[c].setEnabled(a)},"~B");d(c$,"paramString",function(){var a=0==this.orientation?"HORIZONTAL":"VERTICAL";return K(this,javax.swing.JScrollBar,"paramString",[])+",blockIncrement="+this.blockIncrement+",orientation="+a+",unitIncrement="+this.unitIncrement});c$.$JScrollBar$ModelListener$=function(){A(self.c$);c$=s(function(){O(this,arguments);r(this,arguments)},javax.swing.JScrollBar,"ModelListener",null,javax.swing.event.ChangeListener);e(c$,"stateChanged",function(a){var b=a.getSource();
v(b,javax.swing.BoundedRangeModel)&&(a=b.getValue(),b=b.getValueIsAdjusting(),this.b$["javax.swing.JScrollBar"].fireAdjustmentValueChanged(601,5,a,b))},"javax.swing.event.ChangeEvent");c$=z()};G(c$,"$uiClassID","ScrollBarUI")});p("java.awt");c$=M(java.awt,"Adjustable");G(c$,"HORIZONTAL",0,"VERTICAL",1,"NO_ORIENTATION",2);p("java.awt.event");q(["java.awt.AWTEvent"],"java.awt.event.AdjustmentEvent",null,function(){c$=s(function(){this.adjustable=null;this.adjustmentType=this.value=0;this.isAdjusting=
!1;r(this,arguments)},java.awt.event,"AdjustmentEvent",java.awt.AWTEvent);m(c$,function(a,b,c,f){this.construct(a,b,c,f,!1)},"java.awt.Adjustable,~N,~N,~N");m(c$,function(a,b,c,f,d){t(this,java.awt.event.AdjustmentEvent,[a,b]);this.adjustable=a;this.adjustmentType=c;this.value=f;this.isAdjusting=d},"java.awt.Adjustable,~N,~N,~N,~B");d(c$,"getAdjustable",function(){return this.adjustable});d(c$,"getValue",function(){return this.value});d(c$,"getAdjustmentType",function(){return this.adjustmentType});
d(c$,"getValueIsAdjusting",function(){return this.isAdjusting});e(c$,"paramString",function(){var a;switch(this.id){case 601:a="ADJUSTMENT_VALUE_CHANGED";break;default:a="unknown type"}var b;switch(this.adjustmentType){case 1:b="UNIT_INCREMENT";break;case 2:b="UNIT_DECREMENT";break;case 4:b="BLOCK_INCREMENT";break;case 3:b="BLOCK_DECREMENT";break;case 5:b="TRACK";break;default:b="unknown type"}return a+",adjType="+b+",value="+this.value+",isAdjusting="+this.isAdjusting});G(c$,"ADJUSTMENT_FIRST",601,
"ADJUSTMENT_LAST",601,"ADJUSTMENT_VALUE_CHANGED",601,"UNIT_INCREMENT",1,"UNIT_DECREMENT",2,"BLOCK_DECREMENT",3,"BLOCK_INCREMENT",4,"TRACK",5)});p("jalview.appletgui");q(["awt2swing.Panel","java.awt.event.ActionListener","$.MouseListener","$.MouseMotionListener"],"jalview.appletgui.AnnotationLabels","awt2swing.Checkbox $.CheckboxMenuItem $.Frame $.MenuItem $.PopupMenu $.Util jalview.analysis.AlignmentUtils jalview.appletgui.AlignFrame $.CutAndPasteTransfer $.EditNameDialog $.PaintRefresher $.Tooltip jalview.bin.JalviewLite jalview.datamodel.AlignmentAnnotation $.SequenceGroup jalview.util.MessageManager $.ParseHtmlBodyAndLinks java.awt.Color $.Dimension $.FlowLayout java.awt.event.ItemListener java.lang.StringBuffer java.util.Arrays $.Collections $.Vector".split(" "),
function(){c$=s(function(){this.image=null;this.active=!1;this.av=this.ap=null;this.resizing=!1;this.scrollOffset=this.mouseX=this.oldY=0;this.selectedRow=-1;this.tooltip=null;this.resizePanel=this.hasHiddenRows=!1;this.dragEvent=null;this.dragCancelled=!1;r(this,arguments)},jalview.appletgui,"AnnotationLabels",awt2swing.Panel,[java.awt.event.ActionListener,java.awt.event.MouseListener,java.awt.event.MouseMotionListener]);m(c$,function(a){t(this,jalview.appletgui.AnnotationLabels,[]);this.ap=a;this.av=
a.av;this.setLayout(null);this.addMouseListener(this);this.addMouseMotionListener(this)},"jalview.appletgui.AlignmentPanel");m(c$,function(a){t(this,jalview.appletgui.AnnotationLabels,[]);this.av=a},"jalview.appletgui.AlignViewport");d(c$,"setScrollOffset",function(a,b){this.scrollOffset=a;b&&this.repaint()},"~N,~B");d(c$,"getSelectedRow",function(a){var b=-2,c=this.ap.av.getAlignment().getAlignmentAnnotation();if(null==c)return b;for(var f=0,d=0;d<c.length;d++)if(b=-1,c[d].visible&&(f+=c[d].height,
a<f)){b=d;break}return b},"~N");e(c$,"actionPerformed",function(a){var b=this.av.getAlignment().getAlignmentAnnotation();if(a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.ADDNEW)){b=new jalview.datamodel.AlignmentAnnotation("",null,Array(this.ap.av.getAlignment().getWidth()));if(!this.editLabelDescription(b))return;this.ap.av.getAlignment().addAnnotation(b);this.ap.av.getAlignment().setAnnotationIndex(b,0)}else if(a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.EDITNAME))this.editLabelDescription(b[this.selectedRow]);
else if(a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.HIDE))b[this.selectedRow].visible=!1;else if(a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.SHOWALL))for(a=0;a<b.length;a++)b[a].visible=null==b[a].annotations?!1:!0;else if(a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.OUTPUT_TEXT)){a=new jalview.appletgui.CutAndPasteTransfer(!1,this.ap.alignFrame);var c=new awt2swing.Frame;c.add(a);jalview.bin.JalviewLite.addFrame(c,this.ap.alignFrame.getTitle()+
" - "+b[this.selectedRow].label,500,100);a.setText(b[this.selectedRow].toString())}else a.getActionCommand().equals(jalview.appletgui.AnnotationLabels.COPYCONS_SEQ)&&(b=this.av.getConsensusSeq(),null!=b&&this.copy_annotseqtoclipboard(b));this.refresh()},"java.awt.event.ActionEvent");d(c$,"refresh",function(){this.ap.annotationPanel.adjustPanelHeight();this.setSize(this.getSize().width,this.ap.annotationPanel.getSize().height);this.ap.validate();this.ap.paintAlignment(!0)});d(c$,"editLabelDescription",
function(a){var b=new awt2swing.Checkbox('Fill Empty Gaps With "'+this.ap.av.getGapCharacter()+'"',a.padGaps),c=new jalview.appletgui.EditNameDialog(a.label,a.description,"      Annotation Label","Annotation Description",this.ap.alignFrame,"Edit Annotation Name / Description",500,180,!1),f=new awt2swing.Panel(new java.awt.FlowLayout);f.add(b);c.add(f);c.pack();c.setVisible(!0);return c.accept?(a.label=c.getName(),a.description=c.getDescription(),a.setPadGaps(b.getState(),this.av.getGapCharacter()),
this.repaint(),!0):!1},"jalview.datamodel.AlignmentAnnotation");e(c$,"mouseMoved",function(a){this.resizePanel=10>a.getY()&&14>a.getX();a=this.getSelectedRow(a.getY()+this.scrollOffset);-1<a?(a=new jalview.util.ParseHtmlBodyAndLinks(this.av.getAlignment().getAlignmentAnnotation()[a].getDescription(!0),!0,"\n"),null==this.tooltip?this.tooltip=new jalview.appletgui.Tooltip(a.getNonHtmlContent(),this):this.tooltip.setTip(a.getNonHtmlContent())):null!=this.tooltip&&this.tooltip.setTip("")},"java.awt.event.MouseEvent");
d(c$,"cancelDrag",function(){this.dragEvent=null;this.dragCancelled=!0});e(c$,"mouseDragged",function(a){if(!this.dragCancelled)if(this.dragEvent=a,this.resizePanel){var b=this.ap.annotationPanelHolder.getSize(),c=this.ap.annotationSpaceFillerHolder.getSize(),f=this.ap.seqPanelHolder.getSize();a=a.getY()-this.oldY;a/=this.ap.av.getCharHeight();a*=this.ap.av.getCharHeight();20<b.height-a&&20<f.height+a&&(this.ap.annotationPanel.setSize(b.width,b.height-a),this.setSize(new java.awt.Dimension(c.width,
b.height-a)),this.ap.annotationSpaceFillerHolder.setSize(new java.awt.Dimension(c.width,b.height-a)),this.ap.annotationPanelHolder.setSize(new java.awt.Dimension(b.width,b.height-a)),this.ap.apvscroll.setValues(this.ap.apvscroll.getValue(),b.height-a,0,this.av.calcPanelHeight()),f.height+=a,this.ap.seqPanelHolder.setPreferredSize(f),this.ap.setScrollValues(this.av.getStartRes(),this.av.getStartSeq()),this.ap.validate(),this.ap.addNotify())}else{if(0<(b=6-a.getY()))this.ap.apvscroll.setValue(this.ap.apvscroll.getValue()-
b),this.ap.adjustmentValueChanged(null);else if(0<(b=6-this.ap.annotationSpaceFillerHolder.getSize().height+a.getY()))this.ap.apvscroll.setValue(this.ap.apvscroll.getValue()+b),this.ap.adjustmentValueChanged(null);this.repaint()}},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){if(!this.resizePanel&&!this.dragCancelled){var b=this.selectedRow;a=this.getSelectedRow(a.getY()+this.scrollOffset);if(-1<b&&b!=a){var c=this.ap.av.getAlignment().getAlignmentAnnotation()[b];
-1==a&&(a=this.ap.av.getAlignment().getAlignmentAnnotation().length-1);var f=this.ap.av.getAlignment().getAlignmentAnnotation()[a];this.ap.av.getAlignment().getAlignmentAnnotation()[a]=c;this.ap.av.getAlignment().getAlignmentAnnotation()[b]=f}}this.resizePanel=!1;this.dragEvent=null;this.dragCancelled=!1;this.repaint();this.ap.annotationPanel.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(a){10>a.getY()&&14>a.getX()&&(this.resizePanel=!0,this.repaint())},"java.awt.event.MouseEvent");
e(c$,"mouseExited",function(){this.dragCancelled=!1;null==this.dragEvent?this.resizePanel=!1:this.resizePanel||(this.dragEvent=null);this.repaint()},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){this.oldY=a.getY();if(!this.resizePanel){this.dragCancelled=!1;this.selectedRow=this.getSelectedRow(a.getY()+this.scrollOffset);var b=this.ap.av.getAlignment().getAlignmentAnnotation();if(4==(a.getModifiers()&4)){var c=new awt2swing.PopupMenu(jalview.util.MessageManager.getString("label.annotations")),
f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.ADDNEW);f.addActionListener(this);c.add(f);if(0>this.selectedRow)this.hasHiddenRows&&(f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.SHOWALL),f.addActionListener(this),c.add(f)),this.add(c);else{f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.EDITNAME);f.addActionListener(this);c.add(f);f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.HIDE);f.addActionListener(this);c.add(f);if(this.selectedRow<b.length&&
null!=b[this.selectedRow].sequenceRef){var f=b[this.selectedRow].label,d=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.hide_all")+" "+f);d.addActionListener((H("jalview.appletgui.AnnotationLabels$1")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$1$(),C(jalview.appletgui.AnnotationLabels$1,this,T("label",f))));c.add(d)}this.hasHiddenRows&&(f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.SHOWALL),f.addActionListener(this),c.add(f));this.add(c);f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.OUTPUT_TEXT);
f.addActionListener(this);c.add(f);this.selectedRow<b.length&&(b[this.selectedRow].autoCalculated&&-1<b[this.selectedRow].label.indexOf("Consensus"))&&(c.addSeparator(),d=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.ignore_gaps_consensus"),null!=b[this.selectedRow].groupRef?b[this.selectedRow].groupRef.getIgnoreGapsConsensus():this.ap.av.isIgnoreGapsConsensus()),f=b[this.selectedRow],d.addItemListener((H("jalview.appletgui.AnnotationLabels$2")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$2$(),
C(jalview.appletgui.AnnotationLabels$2,this,T("aaa",f,"cbmi",d)))),c.add(d),null!=f.groupRef?(d=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_group_histogram"),b[this.selectedRow].groupRef.isShowConsensusHistogram()),d.addItemListener((H("jalview.appletgui.AnnotationLabels$3")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$3$(),C(jalview.appletgui.AnnotationLabels$3,this,T("aaa",f,"chist",d)))),c.add(d),d=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_group_logo"),
b[this.selectedRow].groupRef.isShowSequenceLogo()),d.addItemListener((H("jalview.appletgui.AnnotationLabels$4")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$4$(),C(jalview.appletgui.AnnotationLabels$4,this,T("aaa",f,"cprofl",d)))),c.add(d),b=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.normalise_group_logo"),b[this.selectedRow].groupRef.isNormaliseSequenceLogo()),b.addItemListener((H("jalview.appletgui.AnnotationLabels$5")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$5$(),
C(jalview.appletgui.AnnotationLabels$5,this,T("aaa",f,"cprofn",b))))):(d=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_histogram"),this.av.isShowConsensusHistogram()),d.addItemListener((H("jalview.appletgui.AnnotationLabels$6")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$6$(),C(jalview.appletgui.AnnotationLabels$6,this,T("chist",d)))),c.add(d),b=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.show_logo"),this.av.isShowSequenceLogo()),
b.addItemListener((H("jalview.appletgui.AnnotationLabels$7")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$7$(),C(jalview.appletgui.AnnotationLabels$7,this,T("cprof",b)))),c.add(b),b=new awt2swing.CheckboxMenuItem(jalview.util.MessageManager.getString("label.normalise_logo"),this.av.isNormaliseSequenceLogo()),b.addItemListener((H("jalview.appletgui.AnnotationLabels$8")?0:jalview.appletgui.AnnotationLabels.$AnnotationLabels$8$(),C(jalview.appletgui.AnnotationLabels$8,this,T("cprofn",b))))),
c.add(b),f=new awt2swing.MenuItem(jalview.appletgui.AnnotationLabels.COPYCONS_SEQ),f.addActionListener(this),c.add(f))}c.show(this,a.getX(),a.getY())}else-1<this.selectedRow&&this.selectedRow<b.length&&(null!=b[this.selectedRow].groupRef?2<=a.getClickCount()?(this.ap.seqPanel.ap.idPanel.highlightSearchResults(null),this.ap.av.setSelectionGroup(b[this.selectedRow].groupRef),this.ap.av.sendSelection(),this.ap.paintAlignment(!1),jalview.appletgui.PaintRefresher.Refresh(this.ap,this.ap.av.getSequenceSetId())):
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return a});d(c$,"setFont",function(a){K(this,javax.swing.JTextArea,"setFont",[a]);this.columnWidth=this.rowHeight=0},"java.awt.Font");d(c$,"paramString",function(){var a=this.wrap?"true":"false",b=this.word?"true":"false";return K(this,javax.swing.JTextArea,"paramString",[])+",colums="+this.columns+",columWidth="+this.columnWidth+",rows="+this.rows+",rowHeight="+this.rowHeight+",word="+b+",wrap="+a});d(c$,"getScrollableTracksViewportWidth",function(){return this.wrap?!0:K(this,javax.swing.JTextArea,
"getScrollableTracksViewportWidth",[])});d(c$,"getPreferredScrollableViewportSize",function(){var a=K(this,javax.swing.JTextArea,"getPreferredScrollableViewportSize",[]),a=null==a?new java.awt.Dimension(400,400):a,b=this.getInsets();a.width=0==this.columns?a.width:this.columns*this.getColumnWidth()+b.left+b.right;a.height=0==this.rows?a.height:this.rows*this.getRowHeight()+b.top+b.bottom;return a});e(c$,"getScrollableUnitIncrement",function(a,b){switch(b){case 1:return this.getRowHeight();case 0:return this.getColumnWidth();
default:throw new IllegalArgumentException("Invalid orientation: "+b);}},"java.awt.Rectangle,~N,~N");G(c$,"$uiClassID","TextAreaUI")});p("jalview.api");M(jalview.api,"ComplexAlignFile");p("jalview.appletgui");q(["awt2swing.Panel","java.awt.Dimension","java.util.ArrayList"],"jalview.appletgui.AppletJmol",null,function(){c$=s(function(){this.fileLoadingError=this._aps=this.ap=this.renderPanel=this.history=this.inputLine=this.scriptWindow=null;this.loadedInline=!1;this.jmb=this.fr=null;H("jalview.appletgui.AppletJmol.RenderPanel")||
jalview.appletgui.AppletJmol.$AppletJmol$RenderPanel$();r(this,arguments)},jalview.appletgui,"AppletJmol");J(c$,function(){this._aps=new java.util.ArrayList});m(c$,function(){},"jalview.datamodel.PDBEntry,~A,~O,jalview.appletgui.AlignmentPanel,~S");d(c$,"setJalviewColourScheme",function(){},"jalview.schemes.UserColourScheme");c$.$AppletJmol$RenderPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.currentSize=null;r(this,arguments)},jalview.appletgui.AppletJmol,"RenderPanel",awt2swing.Panel);
J(c$,function(){this.currentSize=new java.awt.Dimension});e(c$,"update",function(a){this.paint(a)},"java.awt.Graphics");d(c$,"PaintComponent",function(){this.currentSize=this.getSize()},"java.awt.Graphics");c$=z()}});p("jalview.appletgui");q(["java.awt.Dialog","java.awt.event.ActionListener","awt2swing.Button"],"jalview.appletgui.JVDialog",["awt2swing.Panel","java.awt.FlowLayout"],function(){c$=s(function(){this.cancel=this.ok=this.buttonPanel=this.ap=null;this.accept=!1;this.owner=null;r(this,arguments)},
jalview.appletgui,"JVDialog",java.awt.Dialog,java.awt.event.ActionListener);J(c$,function(){this.ok=new awt2swing.Button("Accept");this.cancel=new awt2swing.Button("Cancel")});m(c$,function(a,b,c,f,d){t(this,jalview.appletgui.JVDialog,[a,b,c]);this.owner=a;d+=a.getInsets().top+this.getInsets().bottom;this.setBounds(a.getBounds().x+F((a.getSize().width-f)/2),a.getBounds().y+F((a.getSize().height-d)/2),f,d)},"awt2swing.Frame,~S,~B,~N,~N");d(c$,"setMainPanel",function(a){this.add(a,"North");this.buttonPanel=
new awt2swing.Panel(new java.awt.FlowLayout);this.buttonPanel.add(this.ok);this.buttonPanel.add(this.cancel);this.ok.addActionListener(this);this.cancel.addActionListener(this);this.add(this.buttonPanel,"South");this.pack()},"awt2swing.Panel");e(c$,"actionPerformed",function(a){a.getSource()===this.ok&&(this.accept=!0);this.setVisible(!1)},"java.awt.event.ActionEvent")});p("jalview.appletgui");q(["jalview.appletgui.EmbmenuFrame"],"jalview.appletgui.SplitFrame","awt2swing.Panel jalview.analysis.AlignmentUtils jalview.bin.JalviewLite jalview.structure.StructureSelectionManager java.awt.BorderLayout $.Dimension $.GridLayout".split(" "),
function(){c$=s(function(){this.outermost=this.bottomFrame=this.topFrame=null;r(this,arguments)},jalview.appletgui,"SplitFrame",jalview.appletgui.EmbmenuFrame);m(c$,function(a,b){t(this,jalview.appletgui.SplitFrame,[]);this.topFrame=a;this.bottomFrame=b;this.init()},"jalview.appletgui.AlignFrame,jalview.appletgui.AlignFrame");d(c$,"init",function(){var a=ia(arguments);if(null!=a)return a.apply(this,arguments);this.constructSplit();var a=this.topFrame.viewport,b=this.bottomFrame.viewport,c=a.getAlignment(),
f=b.getAlignment(),d=c.isNucleotide()?a:f.isNucleotide()?b:null,f=!c.isNucleotide()?a:!f.isNucleotide()?b:null;if(jalview.analysis.AlignmentUtils.mapProteinToCdna(f.getAlignment(),d.getAlignment())){var e=jalview.structure.StructureSelectionManager.getStructureSelectionManager(a.applet);e.addMappings(f.getAlignment().getCodonFrames());a.setCodingComplement(b);e.addCommandListener(d);e.addCommandListener(f)}f.initComplementConsensus();a=c.isNucleotide()?this.bottomFrame.alignPanel:this.topFrame.alignPanel;
f.updateConsensus(a);this.adjustLayout()});d(c$,"constructSplit",function(){this.unsetMenuBar();this.outermost=new awt2swing.Panel(new java.awt.GridLayout(2,1));var a=new awt2swing.Panel,b=new awt2swing.Panel;this.outermost.add(a);this.outermost.add(b);this.addAlignFrameComponents(this.topFrame,a);this.addAlignFrameComponents(this.bottomFrame,b)});d(c$,"adjustLayout",function(){var a=this.topFrame.getAlignViewport().getAlignment().isNucleotide()?this.topFrame.viewport:this.bottomFrame.viewport,b=
a===this.topFrame.viewport?this.bottomFrame.viewport:this.topFrame.viewport,c=this.topFrame.alignPanel.idPanel.idCanvas.getWidth(),f=this.bottomFrame.alignPanel.idPanel.idCanvas.getWidth(),d=Math.max(c,f);c!=d&&(c=this.topFrame.alignPanel.idPanel.idCanvas.getSize(),this.topFrame.alignPanel.idPanel.idCanvas.setSize(new java.awt.Dimension(d,c.height)));f!=d&&(c=this.bottomFrame.alignPanel.idPanel.idCanvas.getSize(),this.bottomFrame.alignPanel.idPanel.idCanvas.setSize(new java.awt.Dimension(d,c.height)));
null!=b&&null!=a&&(f=b.getViewStyle(),d=f.isScaleProteinAsCdna()?3:1,f.setCharWidth(d*a.getViewStyle().getCharWidth()),b.setViewStyle(f))});d(c$,"addAlignFrameComponents",function(a,b){b.setLayout(new java.awt.BorderLayout);var c=a.makeEmbeddedPopupMenu(a.getJMenuBar(),!0,!1);b.add(c,"North");b.add(a.statusBar,"South");b.add(a.alignPanel,"Center");a.setSplitFrame(this)},"jalview.appletgui.AlignFrame,awt2swing.Panel");d(c$,"addToDisplay",function(a,b){this.createSplitFrameWindow(a,b);this.validate();
this.topFrame.alignPanel.adjustAnnotationHeight();this.topFrame.alignPanel.paintAlignment(!0);this.bottomFrame.alignPanel.adjustAnnotationHeight();this.bottomFrame.alignPanel.paintAlignment(!0)},"~B,jalview.bin.JalviewLite");d(c$,"createSplitFrameWindow",function(a,b){if(a)b.add(this.outermost),b.validate();else{this.add(this.outermost);var c=Math.max(this.topFrame.frameWidth,this.bottomFrame.frameWidth),f=this.topFrame.frameHeight+this.bottomFrame.frameHeight;jalview.bin.JalviewLite.addFrame(this,
this.getTitle(),c,f)}},"~B,jalview.bin.JalviewLite");d(c$,"getComplement",function(a){return this.topFrame===a?this.bottomFrame:this.bottomFrame===a?this.topFrame:null},"jalview.appletgui.AlignFrame")});p("java.awt");q(["java.awt.LayoutManager"],"java.awt.GridLayout",["java.lang.IllegalArgumentException","java.awt.Dimension"],function(){c$=s(function(){this.cols=this.rows=this.vgap=this.hgap=0;r(this,arguments)},java.awt,"GridLayout",null,[java.awt.LayoutManager,java.io.Serializable]);m(c$,function(){this.construct(1,
0,0,0)});m(c$,function(a,b){this.construct(a,b,0,0)},"~N,~N");m(c$,function(a,b,c,f){if(0==a&&0==b)throw new IllegalArgumentException("rows and cols cannot both be zero");this.rows=a;this.cols=b;this.hgap=c;this.vgap=f},"~N,~N,~N,~N");d(c$,"getRows",function(){return this.rows});d(c$,"setRows",function(a){if(0==a&&0==this.cols)throw new IllegalArgumentException("rows and cols cannot both be zero");this.rows=a},"~N");d(c$,"getColumns",function(){return this.cols});d(c$,"setColumns",function(a){if(0==
a&&0==this.rows)throw new IllegalArgumentException("rows and cols cannot both be zero");this.cols=a},"~N");d(c$,"getHgap",function(){return this.hgap});d(c$,"setHgap",function(a){this.hgap=a},"~N");d(c$,"getVgap",function(){return this.vgap});d(c$,"setVgap",function(a){this.vgap=a},"~N");e(c$,"addLayoutComponent",function(){},"~S,java.awt.Component");e(c$,"removeLayoutComponent",function(){},"java.awt.Component");e(c$,"preferredLayoutSize",function(a){var b=a.getInsets(),c=a.getComponentCount(),f=
this.rows,d=this.cols;0<f?d=F((c+f-1)/f):f=F((c+d-1)/d);for(var e=0,g=0,h=0;h<c;h++){var j=a.getComponent(h).getPreferredSize();e<j.width&&(e=j.width);g<j.height&&(g=j.height)}return new java.awt.Dimension(b.left+b.right+d*e+(d-1)*this.hgap,b.top+b.bottom+f*g+(f-1)*this.vgap)},"java.awt.Container");e(c$,"minimumLayoutSize",function(a){var b=a.getInsets(),c=a.getComponentCount(),f=this.rows,d=this.cols;0<f?d=F((c+f-1)/f):f=F((c+d-1)/d);for(var e=0,g=0,h=0;h<c;h++){var j=a.getComponent(h).getMinimumSize();
e<j.width&&(e=j.width);g<j.height&&(g=j.height)}return new java.awt.Dimension(b.left+b.right+d*e+(d-1)*this.hgap,b.top+b.bottom+f*g+(f-1)*this.vgap)},"java.awt.Container");e(c$,"layoutContainer",function(a){var b=a.getInsets(),c=a.getComponentCount(),f=this.rows,d=this.cols,e=a.getComponentOrientation().isLeftToRight();if(0!=c){0<f?d=F((c+f-1)/f):f=F((c+d-1)/d);var g=(d-1)*this.hgap,h=a.width-(b.left+b.right),j=F((h-g)/d),n=F((h-(j*d+g))/2),h=(f-1)*this.vgap,m=a.height-(b.top+b.bottom),g=F((m-h)/
f),h=F((m-(g*f+h))/2);if(e){e=0;for(n=b.left+n;e<d;e++,n+=j+this.hgap)for(var m=0,u=b.top+h;m<f;m++,u+=g+this.vgap){var p=m*d+e;p<c&&a.getComponent(p).setBounds(n,u,j,g)}}else{e=0;for(n=a.width-b.right-j-n;e<d;e++,n-=j+this.hgap){m=0;for(u=b.top+h;m<f;m++,u+=g+this.vgap)p=m*d+e,p<c&&a.getComponent(p).setBounds(n,u,j,g)}}}},"java.awt.Container");e(c$,"toString",function(){return this.getClass().getName()+"[hgap="+this.hgap+",vgap="+this.vgap+",rows="+this.rows+",cols="+this.cols+"]"})});p("jalview.io");
q(null,"jalview.io.AnnotationFile","jalview.analysis.Conservation jalview.datamodel.AlignmentAnnotation $.Annotation $.ColumnSelection $.GraphLine $.SequenceGroup jalview.io.AppletFormatAdapter jalview.jsdev.GenericFileAdapter jalview.schemes.ColourSchemeProperty $.ResidueProperties $.UserColourScheme jalview.util.Comparison $.Format java.awt.Color java.io.BufferedReader $.InputStreamReader $.StringReader java.lang.Boolean $.Float $.StringBuffer java.util.ArrayList $.BitSet $.Date $.Hashtable $.StringTokenizer $.Vector".split(" "),
function(){c$=s(function(){this.text=this.newline=null;H("jalview.io.AnnotationFile.ViewDef")||jalview.io.AnnotationFile.$AnnotationFile$ViewDef$();this.refSeqId=this.refSeq=null;this.nlinesread=0;this.lastread="";r(this,arguments)},jalview.io,"AnnotationFile");J(c$,function(){this.newline=System.getProperty("line.separator")});m(c$,function(){this.init()});d(c$,"setNewlineString",function(a){this.newline=a;this.init()},"~S");d(c$,"getNewlineString",function(){return this.newline});d(c$,"init",function(){this.text=
new StringBuffer("JALVIEW_ANNOTATION"+this.newline+"# Created: "+new java.util.Date+this.newline+this.newline);this.refSeqId=this.refSeq=null});d(c$,"printAnnotations",function(a,b,c){return this.printAnnotations(a,b,c,null,null,null)},"~A,java.util.List,java.util.Hashtable");d(c$,"printAnnotations",function(a,b,c,f,d,e){null!=e&&(null!=e.viewname&&this.text.append("VIEW_DEF\t"+e.viewname+"\n"),null==b&&(b=e.visibleGroups),null==f&&(f=e.hiddencols));null!=d&&d.hasSeqrep()&&this.text.append("VIEW_SETREF\t"+
d.getSeqrep().getName()+"\n");if(null!=f&&f.hasHiddenColumns()){this.text.append("VIEW_HIDECOLS\t");var g=!1,h;for(f=f.getHiddenColumns().iterator();f.hasNext()&&((h=f.next())||1);)g?this.text.append(","):g=!0,this.text.append(""+h[0]),this.text.append("-"),this.text.append(""+h[1]);this.text.append("\n")}if(null!=a){var j=!0,n;f=h=null;var m=new StringBuffer,u=new StringBuffer;d=new StringBuffer;var p=new java.util.Hashtable;e=new java.util.Hashtable;for(var q=new java.util.BitSet,s,r=0;r<a.length;r++)if(n=
a[r],n.visible||n.hasScore()||-1<n.graphGroup&&q.get(n.graphGroup)){s=null;j=!0;this.writeSequence_Ref(h,n.sequenceRef);h=n.sequenceRef;this.writeGroup_Ref(f,n.groupRef);f=n.groupRef;for(var t=n.hasIcons,v=n.hasText,w=n.$hasScore,y=!1,z=0;null!=n.annotations&&z<n.annotations.length&&(!t||!v||!w);z++)null!=n.annotations[z]&&(v=(new Boolean(v|(null!=n.annotations[z].displayCharacter&&0<n.annotations[z].displayCharacter.length&&!n.annotations[z].displayCharacter.equals(" ")))).valueOf(),t=(new Boolean(t|
(0!=n.annotations[z].secondaryStructure.charCodeAt(0)&&" "!=n.annotations[z].secondaryStructure))).valueOf(),w=(new Boolean(w|!Float.isNaN(n.annotations[z].value))).valueOf(),y=(new Boolean(y|(null!=n.annotations[z].description&&0<n.annotations[z].description.length))).valueOf());0==n.graph?(this.text.append("NO_GRAPH\t"),w=!1):(1==n.graph?(this.text.append("BAR_GRAPH\t"),t=!1):2==n.graph&&(t=!1,this.text.append("LINE_GRAPH\t")),null!=n.getThreshold()&&(u.append("GRAPHLINE\t"),u.append(n.label),u.append("\t"),
u.append(n.getThreshold().value),u.append("\t"),u.append(n.getThreshold().label),u.append("\t"),u.append(jalview.util.Format.getHexString(n.getThreshold().colour)),u.append(this.newline)),-1<n.graphGroup&&(q.set(n.graphGroup),g=new Integer(n.graphGroup),p.containsKey(g)?p.put(g,p.get(g)+"\t"+n.label):(e.put(g,E(-1,[h,f])),p.put(g,n.label))));this.text.append(n.label+"\t");null!=n.description&&this.text.append(n.description+"\t");for(z=0;null!=n.annotations&&z<n.annotations.length;z++)null!=h&&jalview.util.Comparison.isGap(h.getCharAt(z))||
(null!=n.annotations[z]&&(g="",t&&(this.text.append(g)," "!=n.annotations[z].secondaryStructure&&this.text.append(n.annotations[z].secondaryStructure),g=","),w&&(Float.isNaN(n.annotations[z].value)?(System.err.println("Skipping NaN - not valid value."),this.text.append(g+0)):this.text.append(g+n.annotations[z].value),g=","),v&&(null!=n.annotations[z].displayCharacter&&0<n.annotations[z].displayCharacter.length&&!n.annotations[z].displayCharacter.equals(" "))&&(this.text.append(g+n.annotations[z].displayCharacter),
g=","),y&&(null!=n.annotations[z].description&&0<n.annotations[z].description.length&&!n.annotations[z].description.equals(n.annotations[z].displayCharacter))&&(this.text.append(g+n.annotations[z].description),g=","),null!=s&&!s.equals(n.annotations[z].colour)&&(j=!1),s=n.annotations[z].colour,null!=n.annotations[z].colour&&n.annotations[z].colour!==java.awt.Color.black&&this.text.append(g+"["+jalview.util.Format.getHexString(n.annotations[z].colour)+"]")),this.text.append("|"));n.hasScore()&&this.text.append("\t"+
n.score);this.text.append(this.newline);null!=s&&(s!==java.awt.Color.black&&j)&&(m.append("COLOUR\t"),m.append(n.label),m.append("\t"),m.append(jalview.util.Format.getHexString(s)),m.append(this.newline));if(n.scaleColLabel||n.showAllColLabels||n.centreColLabels)d.append("ROWPROPERTIES\t"),d.append(n.label),d.append("\tscaletofit="),d.append(n.scaleColLabel),d.append("\tshowalllabs="),d.append(n.showAllColLabels),d.append("\tcentrelabs="),d.append(n.centreColLabels),d.append(this.newline);0<u.length()&&
(this.text.append(u.toString()),u.setLength(0))}this.text.append(this.newline);this.text.append(m.toString());if(0<p.size()){a=h;for(var g=f,A,p=p.entrySet().iterator();p.hasNext()&&((A=p.next())||1);)j=e.get(A.getKey()),this.writeSequence_Ref(h,j[0]),h=j[0],this.writeGroup_Ref(f,j[1]),f=j[1],this.text.append("COMBINE\t"),this.text.append(A.getValue()),this.text.append(this.newline);this.writeSequence_Ref(h,a);this.writeGroup_Ref(f,g)}this.text.append(d.toString())}null!=b&&this.printGroups(b);if(null!=
c){this.text.append(this.newline);this.text.append(this.newline);this.text.append("ALIGNMENT");for(b=c.keys();b.hasMoreElements();)g=b.nextElement().toString(),this.text.append("\t"),this.text.append(g),this.text.append("="),this.text.append(c.get(g))}return this.text.toString()},"~A,java.util.List,java.util.Hashtable,jalview.datamodel.ColumnSelection,jalview.datamodel.AlignmentI,jalview.io.AnnotationFile.ViewDef");d(c$,"writeGroup_Ref",function(a,b){return null==b?(null!=a&&(this.text.append(this.newline),
this.text.append("GROUP_REF\t"),this.text.append("ALIGNMENT"),this.text.append(this.newline)),!0):null==a||a!==b?(this.text.append(this.newline),this.text.append("GROUP_REF\t"),this.text.append(b.getName()),this.text.append(this.newline),!0):!1},"jalview.datamodel.SequenceGroup,jalview.datamodel.SequenceGroup");d(c$,"writeSequence_Ref",function(a,b){if(null==b){if(null!=a)return this.text.append(this.newline),this.text.append("SEQUENCE_REF\t"),this.text.append("ALIGNMENT"),this.text.append(this.newline),
!0}else if(null==a||a!==b)return this.text.append(this.newline),this.text.append("SEQUENCE_REF\t"),this.text.append(b.getName()),this.text.append(this.newline),!0;return!1},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");d(c$,"printGroups",function(a){var b=null,c;for(a=a.iterator();a.hasNext()&&((c=a.next())||1);){c.hasSeqrep()?(b=c.getSeqrep(),this.text.append("SEQUENCE_REF\t"),this.text.append(b.getName()),this.text.append(this.newline),this.text.append("SEQUENCE_GROUP\t"),this.text.append(c.getName()),
this.text.append("\t"),this.text.append(""+b.findPosition(c.getStartRes())),this.text.append("\t"),this.text.append(b.findPosition(c.getEndRes())),this.text.append("\t"),this.text.append("-1\t")):(this.text.append("SEQUENCE_GROUP\t"+c.getName()+"\t"+(c.getStartRes()+1)+"\t"+(c.getEndRes()+1)+"\t-1\t"),b=null);for(var f=0;f<c.getSize();f++)this.text.append(c.getSequenceAt(f).getName()),this.text.append("\t");this.text.append(this.newline);this.text.append("PROPERTIES\t");this.text.append(c.getName());
this.text.append("\t");null!=c.getDescription()&&(this.text.append("description="),this.text.append(c.getDescription()),this.text.append("\t"));null!=c.cs&&(this.text.append("colour="),this.text.append(jalview.schemes.ColourSchemeProperty.getColourName(c.cs)),this.text.append("\t"),0!=c.cs.getThreshold()&&(this.text.append("pidThreshold="),this.text.append(c.cs.getThreshold())),c.cs.conservationApplied()&&(this.text.append("consThreshold="),this.text.append(c.cs.getConservationInc()),this.text.append("\t")));
this.text.append("outlineColour=");this.text.append(jalview.util.Format.getHexString(c.getOutlineColour()));this.text.append("\t");this.text.append("displayBoxes=");this.text.append(c.getDisplayBoxes());this.text.append("\t");this.text.append("displayText=");this.text.append(c.getDisplayText());this.text.append("\t");this.text.append("colourText=");this.text.append(c.getColourText());this.text.append("\t");this.text.append("showUnconserved=");this.text.append(c.getShowNonconserved());this.text.append("\t");
c.textColour!==java.awt.Color.black&&(this.text.append("textCol1="),this.text.append(jalview.util.Format.getHexString(c.textColour)),this.text.append("\t"));c.textColour2!==java.awt.Color.white&&(this.text.append("textCol2="),this.text.append(jalview.util.Format.getHexString(c.textColour2)),this.text.append("\t"));0!=c.thresholdTextColour&&(this.text.append("textColThreshold="),this.text.append(c.thresholdTextColour),this.text.append("\t"));null!=c.idColour&&(this.text.append("idColour="),this.text.append(jalview.util.Format.getHexString(c.idColour)),
this.text.append("\t"));c.isHidereps()&&this.text.append("hide=true\t");c.isHideCols()&&this.text.append("hidecols=true\t");null!=b&&(this.text.append(this.newline),this.text.append("SEQUENCE_REF"));this.text.append(this.newline);this.text.append(this.newline)}},"java.util.List");d(c$,"annotateAlignmentView",function(a,b,c){var f=a.getColumnSelection();null==f&&(f=new jalview.datamodel.ColumnSelection);(b=this.readAnnotationFile(a.getAlignment(),f,b,c))&&(f.hasSelectedColumns()||f.hasHiddenColumns())&&
a.setColumnSelection(f);return b},"jalview.api.AlignViewportI,~S,~S");d(c$,"readAnnotationFile",function(a,b,c){return this.readAnnotationFile(a,null,b,c)},"jalview.datamodel.AlignmentI,~S,~S");d(c$,"readAnnotationFile",function(a,b,c,f){var d=null;try{if(f.equals(jalview.io.AppletFormatAdapter.FILE))d=jalview.jsdev.GenericFileAdapter.getReader(c,!1);else if(f.equals(jalview.io.AppletFormatAdapter.URL))d=jalview.jsdev.GenericFileAdapter.getReader(c,!0);else if(f.equals(jalview.io.AppletFormatAdapter.PASTE))d=
new java.io.BufferedReader(new java.io.StringReader(c));else if(f.equals(jalview.io.AppletFormatAdapter.CLASSLOADER)){var e=this.getClass().getResourceAsStream("/"+c);null!=e&&(d=new java.io.BufferedReader(new java.io.InputStreamReader(e)))}if(null!=d)return this.parseAnnotationFrom(a,b,d)}catch(g){if(y(g,Exception))g.printStackTrace(),System.out.println("Problem reading annotation file: "+g),0<this.nlinesread&&System.out.println("Last read line "+this.nlinesread+": '"+this.lastread+"' (first 80 chars) ...");
else throw g;}return!1},"jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,~S,~S");d(c$,"parseAnnotationFrom",function(a,b,c){this.nlinesread=0;var f=new java.util.ArrayList,d=new java.util.ArrayList,e=!1,g=null,h=new java.util.Hashtable,j=new java.util.Hashtable,n,m,u,p,q,s,r=1,t=0;if(null!=a.getAlignmentAnnotation()&&(t=a.getAlignmentAnnotation().length,0<t))for(var v=a.getAlignmentAnnotation(),w=0;w<v.length;w++)v[w].autoCalculated&&j.put(this.autoAnnotsKey(v[w],v[w].sequenceRef,null==
v[w].groupRef?null:v[w].groupRef.getName()),new Integer(1));var v=a.getWidth(),z,A;n=null;for(w=!1;null!=(n=c.readLine());)if(this.nlinesread++,this.lastread=String.instantialize(n),0!=n.indexOf("#")&&-1<n.indexOf("JALVIEW_ANNOTATION")){w=!0;break}if(!w)return c.close(),!1;for(;null!=(n=c.readLine());)if(this.nlinesread++,this.lastread=String.instantialize(n),!(0==n.indexOf("#")||-1<n.indexOf("JALVIEW_ANNOTATION")||0==n.length))if(z=new java.util.StringTokenizer(n,"\t"),p=z.nextToken(),p.equalsIgnoreCase("COLOUR"))this.colourAnnotations(a,
z.nextToken(),z.nextToken()),e=!0;else if(p.equalsIgnoreCase(jalview.io.AnnotationFile.COMBINE))f.add(E(-1,[z,this.refSeq,g])),e=!0;else if(p.equalsIgnoreCase("ROWPROPERTIES"))this.addRowProperties(a,z),e=!0;else if(p.equalsIgnoreCase(jalview.io.AnnotationFile.GRAPHLINE))d.add(E(-1,[jalview.io.AnnotationFile.GRAPHLINE,z,this.refSeq,g])),e=!0;else if(p.equalsIgnoreCase("SEQUENCE_REF"))if(z.hasMoreTokens()){this.refSeq=a.findName(this.refSeqId=z.nextToken());null==this.refSeq&&(this.refSeqId=null);
try{r=Integer.parseInt(z.nextToken()),1>r&&(r=1,System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile"))}catch(B){if(y(B,Exception))r=1;else throw B;}}else this.refSeqId=this.refSeq=null;else if(p.equalsIgnoreCase("GROUP_REF"))g=null,z.hasMoreTokens()&&(g=z.nextToken(),1>g.length?g=null:null==h.get(g)&&h.put(g,new java.util.Vector));else if(p.equalsIgnoreCase("SEQUENCE_GROUP"))this.addGroup(a,z),e=!0;else if(p.equalsIgnoreCase("PROPERTIES"))this.addProperties(a,z),e=!0;else if(p.equalsIgnoreCase("BELOW_ALIGNMENT"))this.setBelowAlignment(a,
z),e=!0;else if(p.equalsIgnoreCase("ALIGNMENT"))this.addAlignmentDetails(a,z),e=!0;else if(p.equalsIgnoreCase("VIEW_SETREF"))null!=this.refSeq&&a.setSeqrep(this.refSeq),e=!0;else if(p.equalsIgnoreCase("VIEW_HIDECOLS"))z.hasMoreTokens()&&(null==b&&(b=new jalview.datamodel.ColumnSelection),this.parseHideCols(b,z.nextToken())),e=!0;else if(p.equalsIgnoreCase("HIDE_INSERTIONS"))e=null==this.refSeq?a.getSeqrep():this.refSeq,null==e&&(e=a.getSequenceAt(0)),null!=e&&(null==b?System.err.println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "+
n):b.hideInsertionsFor(e)),e=!0;else{q=jalview.datamodel.AlignmentAnnotation.getGraphValueFromString(p);m=z.nextToken();s=0;A=Array(v);u=null;w=NaN;if(z.hasMoreTokens()){n=z.nextToken();-1==n.indexOf("|")&&(u=n,z.hasMoreTokens()&&(n=z.nextToken()));z.hasMoreTokens()&&(w=Float.$valueOf(z.nextToken()).floatValue());z=new java.util.StringTokenizer(n,"|",!0);n=!0;for(var C=1==z.countTokens();z.hasMoreElements()&&s<v;){p=z.nextToken().trim();if(C)try{w=Float.$valueOf(p).floatValue();break}catch(F){if(!y(F,
NumberFormatException))throw F;}p.equals("|")?(n&&s++,n=!0):(A[s++]=this.parseAnnotation(p,q),n=!1)}}n=new jalview.datamodel.AlignmentAnnotation(m,u,0==s?null:A,0,0,q);n.score=w;if(!j.containsKey(this.autoAnnotsKey(n,this.refSeq,g))){if(null!=this.refSeq){n.belowAlignment=!1;e=this.refSeq;do w=new jalview.datamodel.AlignmentAnnotation(n),n.createSequenceMapping(e,r,!1),n.adjustForAlignment(),e.addAlignmentAnnotation(n),a.addAnnotation(n),a.setAnnotationIndex(n,a.getAlignmentAnnotation().length-t-
1),null!=g&&h.get(g).addElement(n),n=w;while(null!=this.refSeqId&&null!=(e=a.findName(e,this.refSeqId,!0)))}else a.addAnnotation(n),a.setAnnotationIndex(n,a.getAlignmentAnnotation().length-t-1),null!=g&&h.get(g).addElement(n);e=!0}}b=new java.util.Hashtable;for(c=h.keys();c.hasMoreElements();){for(var g=c.nextElement(),j=!1,H,r=a.getGroups().iterator();r.hasNext()&&((H=r.next())||1);)if(H.getName().equals(g))if(j)System.err.println("Ignoring 1:many group reference mappings for group name '"+g+"'");
else if(j=!0,t=h.get(g),b.put(g,H),null!=t&&0<t.size()){v=null;w=0;for(n=t.size();w<n;w++)v=t.elementAt(w),v.groupRef=H}h.get(g).removeAllElements()}for(var G,d=d.iterator();d.hasNext()&&((G=d.next())||1);)G[0]===jalview.io.AnnotationFile.GRAPHLINE&&this.addLine(a,G[1],G[2],null==G[3]?null:b.get(G[3]));G=0;for(var I,f=f.iterator();f.hasNext()&&((I=f.next())||1);)this.combineAnnotations(a,++G,I[0],I[1],null==I[2]?null:b.get(I[2]));return e},"jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,java.io.BufferedReader");
d(c$,"parseHideCols",function(a,b){for(var c=new java.util.StringTokenizer(b,",");c.hasMoreTokens();){var f=c.nextToken().trim(),d,e=f.indexOf("-");-1==e?(d=e=Integer.parseInt(f),0<=d&&a.hideColumns(d,e)):(d=Integer.parseInt(f.substring(0,e)),e=e<f.length-1?Integer.parseInt(f.substring(e+1)):d,0<d&&e>=d&&a.hideColumns(d,e))}},"jalview.datamodel.ColumnSelection,~S");d(c$,"autoAnnotsKey",function(a,b){return a.graph+"\t"+a.label+"\t"+a.description+"\t"+(null!=b?b.getDisplayId(!0):"")},"jalview.datamodel.AlignmentAnnotation,jalview.datamodel.SequenceI,~S");
d(c$,"parseAnnotation",function(a,b){var c=0==b,f=null,d=null,e=" ",g=0,h=!1,j=!1,n=null,m=a.indexOf("["),u=a.indexOf("]");-1<m&&-1<u&&(n=(new jalview.schemes.UserColourScheme).getColourFromString(a.substring(m+1,u)),0<m&&","==a.charAt(m-1)&&m--,a=a.substring(0,m)+a.substring(u+1));for(var m=new java.util.StringTokenizer(a,",",!0),p=!1,q=0;m.hasMoreTokens();)if(q++,u=m.nextToken().trim(),u.equals(","))!p&&(h&&!j)&&(j=!0,d=" "),p=!1;else{p=!0;if(h)1==u.length&&(d=u);else try{d=u;g=(new Float(u)).floatValue();
h=!0;continue}catch(s){if(!y(s,NumberFormatException))throw s;}if(c&&(u.equals("H")||u.equals("E")||u.equals("S")||u.equals(" ")))e=u.charAt(0),d.equals(u.substring(0,1))&&(d="");else if(null==f||h&&2<q)f=u}null!=d&&(null!=f&&1==f.length)&&(1<d.length?(c=d,d=f,f=c):d.equals(f)&&(f=null));f=new jalview.datamodel.Annotation(d,f,e,g);f.colour=n;return f},"~S,~N");d(c$,"colourAnnotations",function(a,b,c){c=new jalview.schemes.UserColourScheme(c);for(var f,d=0;d<a.getAlignmentAnnotation().length;d++)if(a.getAlignmentAnnotation()[d].label.equalsIgnoreCase(b)){f=
a.getAlignmentAnnotation()[d].annotations;for(var e=0;e<f.length;e++)null!=f[e]&&(f[e].colour=c.findColour("A"))}},"jalview.datamodel.AlignmentI,~S,~S");d(c$,"combineAnnotations",function(a,b,c,f,d){var e=c.nextToken(),g=0;if(null!=a.getAlignmentAnnotation()){for(var h=0;h<a.getAlignmentAnnotation().length;h++){var j=a.getAlignmentAnnotation()[h];j.graphGroup>g&&(g=j.graphGroup+1);if(j.sequenceRef===f&&j.groupRef===d&&j.label.equalsIgnoreCase(e)){-1<j.graphGroup?g=j.graphGroup:(g<=b&&(g=b+1),j.graphGroup=
g);break}}for(;c.hasMoreTokens();){e=c.nextToken();for(h=0;h<a.getAlignmentAnnotation().length;h++)if(j=a.getAlignmentAnnotation()[h],j.sequenceRef===f&&j.groupRef===d&&j.label.equalsIgnoreCase(e)){j.graphGroup=g;break}}}else System.err.println("Couldn't combine annotations. None are added to alignment yet!")},"jalview.datamodel.AlignmentI,~N,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup");d(c$,"addLine",function(a,b,c,f){var d=b.nextToken();a=a.getAlignmentAnnotation();
var e=(new Float(b.nextToken())).floatValue(),g=b.hasMoreTokens()?b.nextToken():null,h=null;b.hasMoreTokens()&&(h=(new jalview.schemes.UserColourScheme(b.nextToken())).findColour("A"));if(null!=a)for(b=0;b<a.length;b++)a[b].label.equalsIgnoreCase(d)&&((null==c||a[b].sequenceRef===c)&&(null==f||a[b].groupRef===f))&&a[b].setThreshold(new jalview.datamodel.GraphLine(e,g,h))},"jalview.datamodel.AlignmentI,java.util.StringTokenizer,jalview.datamodel.SequenceI,jalview.datamodel.SequenceGroup");d(c$,"addGroup",
function(a,b){var c=new jalview.datamodel.SequenceGroup;c.setName(b.nextToken());var f="";try{f=b.nextToken(),0<f.length&&!f.startsWith("*")?c.setStartRes(Integer.parseInt(f)-1):c.setStartRes(0),f=b.nextToken(),0<f.length&&!f.startsWith("*")?c.setEndRes(Integer.parseInt(f)-1):c.setEndRes(a.getWidth()-1)}catch(d){if(y(d,Exception))System.err.println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"+f+"' - assuming alignment width for group."),c.setStartRes(0),
c.setEndRes(a.getWidth()-1);else throw d;}f=b.nextToken();if(f.equals("-1"))for(;b.hasMoreElements();)c.addSequence(a.findName(b.nextToken()),!1);else for(f=new java.util.StringTokenizer(f,",");f.hasMoreTokens();){var e=f.nextToken();if(e.equals("*"))for(e=0;e<a.getHeight();e++)c.addSequence(a.getSequenceAt(e),!1);else if(0<=e.indexOf("-")){var g=new java.util.StringTokenizer(e,"-"),e=Integer.parseInt(g.nextToken()),g=Integer.parseInt(g.nextToken());if(g>e)for(;e<=g;e++)c.addSequence(a.getSequenceAt(e-
1),!1)}else c.addSequence(a.getSequenceAt(Integer.parseInt(e)-1),!1)}null!=this.refSeq&&(c.setStartRes(this.refSeq.findIndex(c.getStartRes()+1)-1),c.setEndRes(this.refSeq.findIndex(c.getEndRes()+1)-1),c.setSeqrep(this.refSeq));0<c.getSize()&&a.addGroup(c)},"jalview.datamodel.AlignmentI,java.util.StringTokenizer");d(c$,"addRowProperties",function(a,b){for(var c=b.nextToken(),f,d,e=!1,g=!1,h=!1;b.hasMoreTokens();)if(f=b.nextToken(),d=f.substring(0,f.indexOf("=")),f=f.substring(f.indexOf("=")+1),d.equalsIgnoreCase("scaletofit")&&
(e=Boolean.$valueOf(f).booleanValue()),d.equalsIgnoreCase("showalllabs")&&(h=Boolean.$valueOf(f).booleanValue()),d.equalsIgnoreCase("centrelabs")&&(g=Boolean.$valueOf(f).booleanValue()),d=a.getAlignmentAnnotation(),null!=d)for(f=0;f<d.length;f++)d[f].label.equalsIgnoreCase(c)&&(d[f].centreColLabels=g,d[f].scaleColLabel=e,d[f].showAllColLabels=h)},"jalview.datamodel.AlignmentI,java.util.StringTokenizer");d(c$,"addProperties",function(a,b){if(null!=a.getGroups()){for(var c=b.nextToken(),f=null,d,e=
a.getGroups().iterator();e.hasNext()&&((d=e.next())||1)&&!(f=d).getName().equals(c);)f=null;if(null!=f){c=f.cs;for(f.cs=null;b.hasMoreTokens();)e=b.nextToken(),d=e.substring(0,e.indexOf("=")),e=e.substring(e.indexOf("=")+1),d.equalsIgnoreCase("description")?f.setDescription(e):d.equalsIgnoreCase("colour")?f.cs=jalview.schemes.ColourSchemeProperty.getColour(a,e):d.equalsIgnoreCase("pidThreshold")?f.cs.setThreshold(Integer.parseInt(e),!0):d.equalsIgnoreCase("consThreshold")?(f.cs.setConservationInc(Integer.parseInt(e)),
d=new jalview.analysis.Conservation("Group",jalview.schemes.ResidueProperties.propHash,3,f.getSequences(null),f.getStartRes(),f.getEndRes()+1),d.calculate(),d.verdict(!1,25),f.cs.setConservation(d)):d.equalsIgnoreCase("outlineColour")?f.setOutlineColour((new jalview.schemes.UserColourScheme(e)).findColour("A")):d.equalsIgnoreCase("displayBoxes")?f.setDisplayBoxes(Boolean.$valueOf(e).booleanValue()):d.equalsIgnoreCase("showUnconserved")?f.setShowNonconserved(Boolean.$valueOf(e).booleanValue()):d.equalsIgnoreCase("displayText")?
f.setDisplayText(Boolean.$valueOf(e).booleanValue()):d.equalsIgnoreCase("colourText")?f.setColourText(Boolean.$valueOf(e).booleanValue()):d.equalsIgnoreCase("textCol1")?f.textColour=(new jalview.schemes.UserColourScheme(e)).findColour("A"):d.equalsIgnoreCase("textCol2")?f.textColour2=(new jalview.schemes.UserColourScheme(e)).findColour("A"):d.equalsIgnoreCase("textColThreshold")?f.thresholdTextColour=Integer.parseInt(e):d.equalsIgnoreCase("idColour")?f.setIdColour((c=new jalview.schemes.UserColourScheme(e)).findColour("A")):
d.equalsIgnoreCase("hide")?f.setHidereps(!0):d.equalsIgnoreCase("hidecols")&&f.setHideCols(!0),f.recalcConservation();null==f.cs&&(f.cs=c)}}},"jalview.datamodel.AlignmentI,java.util.StringTokenizer");d(c$,"setBelowAlignment",function(a,b){var c,f,d=a.getAlignmentAnnotation();for(null==d&&System.err.print("Warning - no annotation to set below for sequence associated annotation:");b.hasMoreTokens();)if(c=b.nextToken(),null==d)System.err.print(" "+c);else for(var e=0;e<a.getAlignmentAnnotation().length;e++)f=
a.getAlignmentAnnotation()[e],f.sequenceRef===this.refSeq&&f.label.equals(c)&&(f.belowAlignment=!0);null==d&&System.err.print("\n")},"jalview.datamodel.AlignmentI,java.util.StringTokenizer");d(c$,"addAlignmentDetails",function(a,b){for(var c,f;b.hasMoreTokens();)c=b.nextToken(),f=c.substring(0,c.indexOf("=")),c=c.substring(c.indexOf("=")+1),a.setProperty(f,c)},"jalview.datamodel.AlignmentI,java.util.StringTokenizer");d(c$,"printCSVAnnotations",function(a){for(var b=new StringBuffer,c=0;c<a.length;c++){var f=
a[c].toString(),d=0;do{var e=f.indexOf("\n",d);b.append(a[c].label);b.append(",");e>d?b.append(f.substring(d,e+1)):(b.append(f.substring(d)),b.append(this.newline));d=e+1}while(0<d)}return b.toString()},"~A");d(c$,"printAnnotationsForView",function(a){return this.printAnnotations(a.isShowAnnotation()?a.getAlignment().getAlignmentAnnotation():null,a.getAlignment().getGroups(),a.getAlignment().getProperties(),a.getColumnSelection(),a.getAlignment(),null)},"jalview.api.AlignViewportI");d(c$,"printAnnotationsForAlignment",
function(a){return this.printAnnotations(a.getAlignmentAnnotation(),a.getGroups(),a.getProperties(),null,a,null)},"jalview.datamodel.AlignmentI");c$.$AnnotationFile$ViewDef$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.hiddenRepSeqs=this.visibleGroups=this.hiddencols=this.hidseqs=this.viewname=null;r(this,arguments)},jalview.io.AnnotationFile,"ViewDef");m(c$,function(a,b,c,d){this.viewname=a;this.hidseqs=b;this.hiddencols=c;this.hiddenRepSeqs=d},"~S,jalview.datamodel.HiddenSequences,jalview.datamodel.ColumnSelection,java.util.Hashtable");
c$=z()};G(c$,"GRAPHLINE","GRAPHLINE","COMBINE","COMBINE")});p("jalview.io");q(["jalview.io.FileParse","jalview.jsdev.RegExp"],"jalview.io.NewickFile","jalview.datamodel.SequenceNode jalview.util.MessageManager java.io.BufferedReader $.IOException java.lang.Float $.StringBuffer java.util.StringTokenizer".split(" "),function(){c$=s(function(){this.root=null;this.ReplaceUnderscores=this.RootHasDistance=this.$HasDistances=this.$HasBootstrap=!1;this.printRootInfo=!0;this.NodeSafeName=null;this.QuoteChar=
"'";r(this,arguments)},jalview.io,"NewickFile",jalview.io.FileParse);J(c$,function(){this.NodeSafeName=E(-1,[jalview.jsdev.RegExp.perlCode("m/[\\[,:'()]/"),jalview.jsdev.RegExp.perlCode("s/'/''/"),jalview.jsdev.RegExp.perlCode("s/\\/w/_/")])});m(c$,function(a){t(this,jalview.io.NewickFile,[a,"Paste"])},"~S");m(c$,function(a){t(this,jalview.io.NewickFile,[]);this.root=a},"jalview.datamodel.SequenceNode");m(c$,function(a,b){t(this,jalview.io.NewickFile,[]);this.$HasBootstrap=b;this.root=a},"jalview.datamodel.SequenceNode,~B");
m(c$,function(a,b,c){t(this,jalview.io.NewickFile,[]);this.root=a;this.$HasBootstrap=b;this.$HasDistances=c},"jalview.datamodel.SequenceNode,~B,~B");m(c$,function(a,b,c,d){t(this,jalview.io.NewickFile,[]);this.root=a;this.$HasBootstrap=b;this.$HasDistances=c;this.RootHasDistance=d},"jalview.datamodel.SequenceNode,~B,~B,~B");d(c$,"ErrorStringrange",function(a,b,c,d,e){return(null==a?"":a)+b+" at position "+d+" ( "+e.substring(0>d-c?0:d-c,d+c>e.length?e.length:d+c)+" )\n"},"~S,~S,~N,~N,~S");d(c$,"HasBootstrap",
function(){return this.$HasBootstrap});d(c$,"HasDistances",function(){return this.$HasDistances});d(c$,"HasRootDistance",function(){return this.RootHasDistance});d(c$,"parse",function(){for(var a,b=new StringBuffer;null!=(a=this.nextLine());)b.append(a);a=b.toString();this.root=new jalview.datamodel.SequenceNode;for(var b=null,c=this.root,d=-1,e=0,k=null,g=null,h=null,j=0.001,n=-1,m=!1,u=jalview.jsdev.RegExp.newRegex(["[(\\['),;]"]),p=0,q=e,s=!1;u.searchFrom(a,e)&&null==k;){var r=u.matchedFrom(),
t;switch(t=a.charAt(r)){case "(":if(m){k=this.ErrorStringrange(k,"Unexpected '('",7,r,a);continue}d++;null==c.right()?(c.setRight(new jalview.datamodel.SequenceNode(null,c,null,0.001,-1,!1)),c=c.right()):(null!=c.left()&&(g=new jalview.datamodel.SequenceNode(null,c,null,0,0,!0),g.SetChildren(c.left(),c.right()),c.setRight(g)),c.setLeft(new jalview.datamodel.SequenceNode(null,c,null,0.001,-1,!1)),c=c.left());null==b&&(b=c);g=null;j=0.001;n=-1;break;case "'":e=jalview.jsdev.RegExp.newRegex(["'([^']|'')+'"]);
e.searchFrom(a,r)?(p=e.stringMatched().length,g=String.instantialize(e.stringMatched().substring(1,p-1)),g=jalview.jsdev.RegExp.perlCode("s/''/'/").replaceAll(g),p=r+p+1,s=!0):k=this.ErrorStringrange(k,"Unterminated quotes for nodename",7,r,a);break;default:";"==t&&-1!=d&&(k=this.ErrorStringrange(k,"Wayward semicolon (depth="+d+")",7,r,a));if("["==t)if(e=jalview.jsdev.RegExp.newRegex(["]"]),e.searchFrom(a,r)){p=e.matchedFrom()+1;this.warningMessage="Tree file contained comments which may confuse input algorithm.";
break}else k=this.ErrorStringrange(k,"Unterminated comment",3,r,a);for(e=a.substring(q,r);-1<e.indexOf("]");){t=e.indexOf("[");var v=e.indexOf("]"),h=e.substring(t+1,v),e=e.substring(0,t)+e.substring(v+1)}var v=jalview.jsdev.RegExp.newRegex(["\\b([^' :;\\](),]+)"]),w=jalview.jsdev.RegExp.newRegex(["\\s*([0-9+]+)\\s*:"]);t=jalview.jsdev.RegExp.newRegex([":([-0-9Ee.+]+)"]);if(!s&&v.search(e)&&(0==v.matchedFromI(1)||":"!=e.charAt(v.matchedFromI(1)-1)))null==g?g=this.ReplaceUnderscores?v.stringMatchedI(1).$replace("_",
" "):v.stringMatchedI(1):k=this.ErrorStringrange(k,"File has broken algorithm - overwritten nodename",10,r,a);if(w.search(e)&&(w.stringMatchedI(1).equals(v.stringMatchedI(1))&&(g=null),null==g||0==g.length||w.matchedFromI(1)>v.matchedFromI(1)+v.stringMatched().length))try{n=(new Integer(w.stringMatchedI(1))).intValue(),this.$HasBootstrap=!0}catch(z){if(y(z,Exception))k=this.ErrorStringrange(k,"Can't parse bootstrap value",4,q+w.matchedFrom(),a);else throw z;}s=!1;if(t.search(e))try{j=(new Float(t.stringMatchedI(1))).floatValue(),
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p("awt2swing");q(["javax.swing.JTextField"],"awt2swing.TextField",["java.awt.event.TextEvent","javax.swing.event.DocumentListener"],function(){c$=B(awt2swing,"TextField",javax.swing.JTextField);d(c$,"addTextListener",function(a){this.getDocument().addDocumentListener((H("awt2swing.TextField$1")?0:awt2swing.TextField.$TextField$1$(),C(awt2swing.TextField$1,this,T("textListener",a))))},"java.awt.event.TextListener");c$.$TextField$1$=function(){A(self.c$);c$=L(awt2swing,"TextField$1",null,javax.swing.event.DocumentListener);
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c}var e="";null!=this.av.getColumnSelection()&&(0<this.av.getColumnSelection().size()&&null!=c[this.av.getColumnSelection().getMin()])&&(e=c[this.av.getColumnSelection().getMin()].displayCharacter);if(a.getActionCommand().equals("Remove Annotation"))for(a=0;a<this.av.getColumnSelection().size();a++)c[this.av.getColumnSelection().columnAt(a)]=null;else if(a.getActionCommand().equals("Label")){e=this.enterLabel(e,"Enter Label");if(null==e)return;0<e.length&&!b[this.activeRow].hasText&&(b[this.activeRow].hasText=
!0);for(a=0;a<this.av.getColumnSelection().size();a++){var k=this.av.getColumnSelection().columnAt(a);this.av.getColumnSelection().isVisible(k)&&(null==c[k]&&(c[k]=new jalview.datamodel.Annotation(e,""," ",0)),c[k].displayCharacter=e)}}else if(a.getActionCommand().equals("Colour")){d=(new jalview.appletgui.UserDefinedColours(this,java.awt.Color.black,this.ap.alignFrame)).getColor();for(a=0;a<this.av.getColumnSelection().size();a++)k=this.av.getColumnSelection().columnAt(a),this.av.getColumnSelection().isVisible(k)&&
(null==c[k]&&(c[k]=new jalview.datamodel.Annotation("",""," ",0)),c[k].colour=d)}else{d=String.fromCharCode(0);e="\u03b1";a.getActionCommand().equals("Helix")?d="H":a.getActionCommand().equals("Sheet")?(d="E",e="\u03b2"):a.getActionCommand().equals("RNA Helix")&&(d="S",e="\u03c3");b[this.activeRow].hasIcons||(b[this.activeRow].hasIcons=!0);e=this.enterLabel(e,"Enter Label");if(null==e)return;0<e.length&&!b[this.activeRow].hasText&&(b[this.activeRow].hasText=!0,a.getActionCommand().equals("RNA Helix")&&
(b[this.activeRow].showAllColLabels=!0));for(a=0;a<this.av.getColumnSelection().size();a++)k=this.av.getColumnSelection().columnAt(a),this.av.getColumnSelection().isVisible(k)&&(null==c[k]&&(c[k]=new jalview.datamodel.Annotation(e,"",d,0)),c[k].secondaryStructure="S"!=d?d:0==e.length?" ":e.charAt(0),c[k].displayCharacter=e)}this.av.getAlignment().validateAnnotation(b[this.activeRow]);this.ap.alignmentChanged();this.adjustPanelHeight();this.repaint()}},"java.awt.event.ActionEvent");d(c$,"enterLabel",
function(a,b){var c=new jalview.appletgui.EditNameDialog(a,null,b,null,this.ap.alignFrame,"Enter Label",400,200,!0);return c.accept?c.getName():null},"~S,~S");e(c$,"mousePressed",function(a){var b=this.av.getAlignment().getAlignmentAnnotation();if(null!=b){var c=-this.scrollOffset;this.activeRow=-1;for(var d=0;d<b.length;d++)if(b[d].visible&&(c+=b[d].height),a.getY()<c){b[d].editable?this.activeRow=d:0<b[d].graph&&(this.graphStretch=d,this.graphStretchY=a.getY());break}4==(a.getModifiers()&4)&&-1!=
this.activeRow?null!=this.av.getColumnSelection()&&(b=new awt2swing.PopupMenu(jalview.util.MessageManager.getString("label.structure_type")),!0==this.av.getAlignment().isNucleotide()?c=new awt2swing.MenuItem("RNA Helix"):(c=new awt2swing.MenuItem("Helix"),c.addActionListener(this),b.add(c),c=new awt2swing.MenuItem("Sheet")),c.addActionListener(this),b.add(c),c=new awt2swing.MenuItem("Label"),c.addActionListener(this),b.add(c),c=new awt2swing.MenuItem("Colour"),c.addActionListener(this),b.add(c),c=
new awt2swing.MenuItem("Remove Annotation"),c.addActionListener(this),b.add(c),this.ap.alignFrame.add(b),b.show(this,a.getX(),a.getY())):this.ap.scalePanel.mousePressed(a)}},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){this.graphStretchY=this.graphStretch=-1;this.mouseDragging=!1;this.needValidating&&(this.ap.validate(),this.needValidating=!1);this.ap.scalePanel.mouseReleased(a)},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseDragged",
function(a){-1<this.graphStretch?(this.av.getAlignment().getAlignmentAnnotation()[this.graphStretch].graphHeight+=this.graphStretchY-a.getY(),0>this.av.getAlignment().getAlignmentAnnotation()[this.graphStretch].graphHeight&&(this.av.getAlignment().getAlignmentAnnotation()[this.graphStretch].graphHeight=0),this.graphStretchY=a.getY(),this.av.calcPanelHeight(),this.needValidating=!0,this.ap.paintAlignment(!0)):this.ap.scalePanel.mouseDragged(a)},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(a){var b=
this.av.getAlignment().getAlignmentAnnotation();if(null!=b){for(var c=-1,d=-this.scrollOffset,e=0;e<b.length;e++)if(b[e].visible&&(d+=b[e].height),a.getY()<d){c=e;break}a=F(a.getX()/this.av.getCharWidth())+this.av.getStartRes();this.av.hasHiddenColumns()&&(a=this.av.getColumnSelection().adjustForHiddenColumns(a));-1<c&&(a<b[c].annotations.length&&null!=b[c].annotations[a])&&(d=new StringBuffer("Sequence position "+(a+1)),null!=b[c].annotations[a].description&&d.append("  "+b[c].annotations[a].description),
this.ap.alignFrame.setStatus(d.toString()))}},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(a){this.ap.scalePanel.mouseEntered(a)},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(a){this.ap.scalePanel.mouseExited(a)},"java.awt.event.MouseEvent");d(c$,"adjustPanelHeight",function(){return this.adjustPanelHeight(!0)});d(c$,"adjustPanelHeight",function(a){var b=this.av.calcPanelHeight();this.setSize(new java.awt.Dimension(this.getSize().width,b));a&&this.repaint();return b},"~B");
d(c$,"addEditableColumn",function(){if(-1==this.activeRow){var a=this.av.getAlignment().getAlignmentAnnotation();if(null!=a)for(var b=0;b<a.length;b++)if(a[b].editable){this.activeRow=b;break}}},"~N");e(c$,"paintComponent",function(a){if(!this.av.getWrapAlignment()&&this.av.isShowAnnotation()){var b=this.getSize();this.imgWidth=b.width;if(!(1>this.imgWidth||1>b.height)){if(null==this.image||this.imgWidth!=this.image.getWidth(this)||b.height!=this.image.getHeight(this))this.image=this.createImage(this.imgWidth,
b.height),this.gg=this.image.getGraphics(),this.gg.setFont(this.av.getFont()),this.fm=this.gg.getFontMetrics(),this.$fastPaint=!1;this.$fastPaint?(a.drawImage(this.image,0,0,this),this.$fastPaint=!1):(this.gg.setColor(java.awt.Color.white),this.gg.fillRect(0,0,this.getSize().width,this.getSize().height),this.drawComponent(this.gg,this.av.startRes,this.av.endRes+1),a.drawImage(this.image,0,0,this))}}},"java.awt.Graphics");d(c$,"fastPaint",function(a){if(!(0==a||null==this.av.getAlignment().getAlignmentAnnotation()||
1>this.av.getAlignment().getAlignmentAnnotation().length)){this.gg.copyArea(0,0,this.imgWidth,this.getSize().height,-a*this.av.getCharWidth(),0);var b=this.av.startRes,c=this.av.endRes+1,d=0;0<a?(d=(c-b-a)*this.av.getCharWidth(),b=c-a):0>a&&(c=b-a);this.gg.translate(d,0);this.drawComponent(this.gg,b,c);this.gg.translate(-d,0);this.$fastPaint=!0}this.repaint()},"~N");d(c$,"drawComponent",function(a,b,c){var d=this.av.getFont();a.setFont(d);a.setColor(java.awt.Color.white);a.fillRect(0,0,(c-b)*this.av.getCharWidth(),
this.getSize().height);null==this.fm&&(this.fm=a.getFontMetrics());null==this.av.getAlignment().getAlignmentAnnotation()||1>this.av.getAlignment().getAlignmentAnnotation().length?(a.setColor(java.awt.Color.white),a.fillRect(0,0,this.getSize().width,this.getSize().height),a.setColor(java.awt.Color.black),this.av.validCharWidth&&awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.alignment_has_no_annotations"),20,15)):(a.translate(0,-this.scrollOffset),this.renderer.drawComponent(this,
this.av,a,this.activeRow,b,c),a.translate(0,+this.scrollOffset))},"java.awt.Graphics,~N,~N");d(c$,"setScrollOffset",function(a,b){this.scrollOffset=a;b&&this.repaint()},"~N,~B");d(c$,"getFontMetrics",function(){return this.fm});e(c$,"getFadedImage",function(){return this.image});e(c$,"getFadedImageWidth",function(){return this.imgWidth});e(c$,"getVisibleVRange",function(){if(null!=this.ap&&null!=this.ap.alabels){var a=-this.ap.alabels.scrollOffset,b=a+this.ap.annotationPanelHolder.getHeight();this.$bounds[0]=
a;this.$bounds[1]=b;return this.$bounds}return null});G(c$,"GRAPH_HEIGHT",40)});p("jalview.renderer");q(["java.awt.image.ImageObserver"],"jalview.renderer.AwtRenderPanelI",null,function(){M(jalview.renderer,"AwtRenderPanelI",java.awt.image.ImageObserver)});p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ActionListener $.AdjustmentListener $.FocusListener awt2swing.Button $.Label $.Scrollbar $.TextField java.awt.GridLayout java.util.Vector".split(" "),"jalview.appletgui.UserDefinedColours",
"awt2swing.Frame jalview.appletgui.AnnotationColourChooser $.FeatureColourChooser $.FeatureRenderer $.FeatureSettings jalview.bin.JalviewLite jalview.schemes.ResidueProperties $.UserColourScheme jalview.util.MessageManager java.awt.Color $.Dialog $.Font $.Rectangle java.awt.event.MouseAdapter java.lang.Error".split(" "),function(){c$=s(function(){this.originalColour=this.originalLabel=this.caller=this.dialog=this.jmol=this.frame=this.oldColourScheme=this.oldColours=this.selectedButton=this.seqGroup=
this.ap=null;this.B=this.G=this.R=0;this.target=this.bText=this.bScroller=this.label5=this.gText=this.gScroller=this.label4=this.rText=this.label1=this.rScroller=this.cancelButton=this.applyButton=this.okButton=this.okcancelPanel=this.gridLayout=this.buttonPanel=null;r(this,arguments)},jalview.appletgui,"UserDefinedColours",awt2swing.Panel,[java.awt.event.ActionListener,java.awt.event.AdjustmentListener,java.awt.event.FocusListener]);J(c$,function(){this.oldColours=new java.util.Vector;this.buttonPanel=
new awt2swing.Panel;this.gridLayout=new java.awt.GridLayout;this.okcancelPanel=new awt2swing.Panel;this.okButton=new awt2swing.Button;this.applyButton=new awt2swing.Button;this.cancelButton=new awt2swing.Button;this.rScroller=new awt2swing.Scrollbar;this.label1=new awt2swing.Label;this.rText=new awt2swing.TextField;this.label4=new awt2swing.Label;this.gScroller=new awt2swing.Scrollbar;this.gText=new awt2swing.TextField;this.label5=new awt2swing.Label;this.bScroller=new awt2swing.Scrollbar;this.bText=
new awt2swing.TextField;this.target=new awt2swing.Panel});d(c$,"loadDefaultColours",function(){return null});m(c$,function(a,b){t(this,jalview.appletgui.UserDefinedColours,[]);this.ap=a;this.seqGroup=b;this.oldColourScheme=null!=this.seqGroup?this.seqGroup.cs:a.av.getGlobalColourScheme();this.init()},"jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceGroup");m(c$,function(a){t(this,jalview.appletgui.UserDefinedColours,[]);this.jmol=a;this.init()},"jalview.appletgui.AppletJmol");m(c$,function(a,
b){t(this,jalview.appletgui.UserDefinedColours,[]);this.caller=a;this.originalColour=a.colourPanel.getBackground();this.originalLabel="Feature Colour";this.setForDialog("Select Feature Colour",b);this.setTargetColour(a.colourPanel.getBackground());this.dialog.setVisible(!0)},"jalview.appletgui.FeatureRenderer,awt2swing.Frame");m(c$,function(a,b,c){this.construct(a,b,c,"Select Colour")},"java.awt.Component,java.awt.Color,awt2swing.Frame");m(c$,function(a,b,c,d){t(this,jalview.appletgui.UserDefinedColours,
[]);this.caller=a;this.originalColour=b;this.originalLabel=d;this.setForDialog(d,c);this.setTargetColour(b);this.dialog.setVisible(!0)},"java.awt.Component,java.awt.Color,awt2swing.Frame,~S");m(c$,function(a,b,c){this.construct(a,b,c,c)},"~O,~S,java.awt.Color");m(c$,function(a,b,c){this.construct(a,b,c,c.getMaxColor())},"jalview.appletgui.FeatureSettings,~S,jalview.schemes.GraduatedColor");m(c$,function(a,b,c,d){t(this,jalview.appletgui.UserDefinedColours,[]);this.caller=a;this.originalColour=c;this.originalLabel=
b;this.init();this.remove(this.buttonPanel);this.setTargetColour(d);this.okcancelPanel.setBounds(new java.awt.Rectangle(0,113,400,35));this.frame.setTitle(jalview.util.MessageManager.getString("label.user_defined_colours")+" - "+b);this.frame.setSize(420,200)},"~O,~S,~O,java.awt.Color");d(c$,"setForDialog",function(a,b){this.init();this.frame.setVisible(!1);this.remove(this.buttonPanel);if(v(b,awt2swing.Frame))this.dialog=new java.awt.Dialog(b,a,!0);else throw Error(jalview.util.MessageManager.getString("label.error_unsupported_owwner_user_colour_scheme"));
this.dialog.add(this);this.setSize(400,123);this.okcancelPanel.setBounds(new java.awt.Rectangle(0,123,400,35));var c=160+b.getInsets().top+this.getInsets().bottom;this.dialog.setBounds(b.getBounds().x+F((b.getSize().width-400)/2),b.getBounds().y+F((b.getSize().height-c)/2),400,c)},"~S,java.awt.Container");e(c$,"actionPerformed",function(a){a=a.getSource();a===this.okButton?this.okButton_actionPerformed():a===this.applyButton?this.applyButton_actionPerformed():a===this.cancelButton?this.cancelButton_actionPerformed():
a===this.rText?this.rText_actionPerformed():a===this.gText?this.gText_actionPerformed():a===this.bText&&this.bText_actionPerformed()},"java.awt.event.ActionEvent");e(c$,"adjustmentValueChanged",function(a){a.getSource()===this.rScroller?this.rScroller_adjustmentValueChanged():a.getSource()===this.gScroller?this.gScroller_adjustmentValueChanged():a.getSource()===this.bScroller&&this.bScroller_adjustmentValueChanged()},"java.awt.event.AdjustmentEvent");d(c$,"init",function(){try{this.jbInit()}catch(a){if(y(a,
Exception))a.printStackTrace();else throw a;}this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("label.user_defined_colours"),420,345);null!=this.seqGroup&&this.frame.setTitle(this.frame.getTitle()+" ("+this.seqGroup.getName()+")");for(var b=0;20>b;b++)this.makeButton(jalview.schemes.ResidueProperties.aa2Triplet.get(jalview.schemes.ResidueProperties.aa[b])+"",jalview.schemes.ResidueProperties.aa[b]);this.makeButton("B",
"B");this.makeButton("Z","Z");this.makeButton("X","X");this.makeButton("Gap","'.','-',' '");this.validate()});d(c$,"rText_actionPerformed",function(){try{var a=Integer.parseInt(this.rText.getText());this.rScroller.setValue(a);this.rScroller_adjustmentValueChanged()}catch(b){if(!y(b,NumberFormatException))throw b;}});d(c$,"gText_actionPerformed",function(){try{var a=Integer.parseInt(this.gText.getText());this.gScroller.setValue(a);this.gScroller_adjustmentValueChanged()}catch(b){if(!y(b,NumberFormatException))throw b;
}});d(c$,"bText_actionPerformed",function(){try{var a=Integer.parseInt(this.bText.getText());this.bScroller.setValue(a);this.bScroller_adjustmentValueChanged()}catch(b){if(!y(b,NumberFormatException))throw b;}});d(c$,"rScroller_adjustmentValueChanged",function(){this.R=this.rScroller.getValue();this.rText.setText(this.R+"");this.colourChanged()});d(c$,"gScroller_adjustmentValueChanged",function(){this.G=this.gScroller.getValue();this.gText.setText(this.G+"");this.colourChanged()});d(c$,"bScroller_adjustmentValueChanged",
function(){this.B=this.bScroller.getValue();this.bText.setText(this.B+"");this.colourChanged()});d(c$,"colourChanged",function(){var a=new java.awt.Color(this.R,this.G,this.B);this.target.setBackground(a);this.target.repaint();null!=this.selectedButton&&(this.selectedButton.setBackground(a),this.selectedButton.repaint())});d(c$,"setTargetColour",function(a){this.R=a.getRed();this.G=a.getGreen();this.B=a.getBlue();this.rScroller.setValue(this.R);this.gScroller.setValue(this.G);this.bScroller.setValue(this.B);
this.rText.setText(this.R+"");this.gText.setText(this.G+"");this.bText.setText(this.B+"");this.colourChanged()},"java.awt.Color");d(c$,"colourButtonPressed",function(a){this.selectedButton=a.getSource();this.setTargetColour(this.selectedButton.getBackground())},"java.awt.event.MouseEvent");d(c$,"makeButton",function(a,b){var c=new awt2swing.Button,d=java.awt.Color.white;if(null!=this.oldColourScheme)try{d=this.oldColourScheme.findColourSeq(b.charAt(0),-1,null)}catch(e){if(!y(e,Exception))throw e;
}c.setBackground(d);this.oldColours.addElement(d);c.setLabel(a);c.setForeground(d.darker().darker().darker());c.setFont(new java.awt.Font("Verdana",1,10));c.addMouseListener((H("jalview.appletgui.UserDefinedColours$1")?0:jalview.appletgui.UserDefinedColours.$UserDefinedColours$1$(),C(jalview.appletgui.UserDefinedColours$1,this,null)));this.buttonPanel.add(c,null)},"~S,~S");d(c$,"okButton_actionPerformed",function(){this.applyButton_actionPerformed();null!=this.dialog&&this.dialog.setVisible(!1);this.frame.setVisible(!1)});
d(c$,"getColor",function(){return new java.awt.Color(this.R,this.G,this.B)});d(c$,"applyButton_actionPerformed",function(){if(null!=this.caller)v(this.caller,jalview.appletgui.FeatureSettings)?this.caller.setUserColour(this.originalLabel,this.getColor()):v(this.caller,jalview.appletgui.AnnotationColourChooser)?this.originalLabel.equals("Min Colour")?this.caller.minColour_actionPerformed(this.getColor()):this.caller.maxColour_actionPerformed(this.getColor()):v(this.caller,jalview.appletgui.FeatureRenderer)?
this.caller.colourPanel.updateColor(this.getColor()):v(this.caller,jalview.appletgui.FeatureColourChooser)&&(-1<this.originalLabel.indexOf("inimum")?this.caller.minColour_actionPerformed(this.getColor()):this.caller.maxColour_actionPerformed(this.getColor()));else{for(var a=Array(24),b=0;24>b;b++){var c=this.buttonPanel.getComponent(b);a[b]=c.getBackground()}a=new jalview.schemes.UserColourScheme(a);null!=this.ap&&a.setThreshold(0,this.ap.av.isIgnoreGapsConsensus());null!=this.ap?(null!=this.seqGroup?
this.seqGroup.cs=a:this.ap.av.setGlobalColourScheme(a),this.ap.seqPanel.seqCanvas.img=null,this.ap.paintAlignment(!0)):null!=this.jmol&&this.jmol.setJalviewColourScheme(a)}});d(c$,"cancelButton_actionPerformed",function(){if(null!=this.caller)v(this.caller,jalview.appletgui.FeatureSettings)?this.caller.setUserColour(this.originalLabel,this.originalColour):v(this.caller,jalview.appletgui.AnnotationColourChooser)?this.originalLabel.equals("Min Colour")?this.caller.minColour_actionPerformed(this.originalColour):
this.caller.maxColour_actionPerformed(this.originalColour):v(this.caller,jalview.appletgui.FeatureRenderer)?this.caller.colourPanel.updateColor(this.originalColour):v(this.caller,jalview.appletgui.FeatureColourChooser)&&(-1<this.originalLabel.indexOf("inimum")?this.caller.minColour_actionPerformed(this.originalColour):this.caller.maxColour_actionPerformed(this.originalColour)),null!=this.dialog&&this.dialog.setVisible(!1);else{for(var a=Array(24),b=0;24>b;b++)a[b]=this.oldColours.elementAt(b),this.buttonPanel.getComponent(b).setBackground(a[b]);
a=new jalview.schemes.UserColourScheme(a);null!=this.ap?(null!=this.seqGroup?this.seqGroup.cs=a:this.ap.av.setGlobalColourScheme(a),this.ap.paintAlignment(!0)):null!=this.jmol&&this.jmol.setJalviewColourScheme(a)}this.frame.setVisible(!1)});d(c$,"jbInit",function(){this.setLayout(null);this.buttonPanel.setLayout(this.gridLayout);this.gridLayout.setColumns(6);this.gridLayout.setRows(4);this.okButton.setFont(new java.awt.Font("Verdana",0,11));this.okButton.setLabel(jalview.util.MessageManager.getString("action.ok"));
this.okButton.addActionListener(this);this.applyButton.setFont(new java.awt.Font("Verdana",0,11));this.applyButton.setLabel(jalview.util.MessageManager.getString("action.apply"));this.applyButton.addActionListener(this);this.cancelButton.setFont(new java.awt.Font("Verdana",0,11));this.cancelButton.setLabel(jalview.util.MessageManager.getString("action.cancel"));this.cancelButton.addActionListener(this);this.setBackground(new java.awt.Color(212,208,223));this.okcancelPanel.setBounds(new java.awt.Rectangle(0,
265,400,35));this.buttonPanel.setBounds(new java.awt.Rectangle(0,123,400,142));this.rScroller.setMaximum(256);this.rScroller.setMinimum(0);this.rScroller.setOrientation(0);this.rScroller.setUnitIncrement(1);this.rScroller.setVisibleAmount(1);this.rScroller.setBounds(new java.awt.Rectangle(36,27,119,19));this.rScroller.addAdjustmentListener(this);this.label1.setAlignment(4);this.label1.setText("R");this.label1.setBounds(new java.awt.Rectangle(19,30,16,15));this.rText.setFont(new java.awt.Font("Dialog",
0,10));this.rText.setText("0        ");this.rText.setBounds(new java.awt.Rectangle(156,27,53,19));this.rText.addActionListener(this);this.rText.addFocusListener(this);this.label4.setAlignment(4);this.label4.setText("G");this.label4.setBounds(new java.awt.Rectangle(15,56,20,15));this.gScroller.setMaximum(256);this.gScroller.setMinimum(0);this.gScroller.setOrientation(0);this.gScroller.setUnitIncrement(1);this.gScroller.setVisibleAmount(1);this.gScroller.setBounds(new java.awt.Rectangle(35,52,120,20));
this.gScroller.addAdjustmentListener(this);this.gText.setFont(new java.awt.Font("Dialog",0,10));this.gText.setText("0        ");this.gText.setBounds(new java.awt.Rectangle(156,52,53,20));this.gText.addActionListener(this);this.gText.addFocusListener(this);this.label5.setAlignment(4);this.label5.setText("B");this.label5.setBounds(new java.awt.Rectangle(14,82,20,15));this.bScroller.setMaximum(256);this.bScroller.setMinimum(0);this.bScroller.setOrientation(0);this.bScroller.setUnitIncrement(1);this.bScroller.setVisibleAmount(1);
this.bScroller.setBounds(new java.awt.Rectangle(35,78,120,20));this.bScroller.addAdjustmentListener(this);this.bText.setFont(new java.awt.Font("Dialog",0,10));this.bText.setText("0        ");this.bText.setBounds(new java.awt.Rectangle(157,78,52,20));this.bText.addActionListener(this);this.bText.addFocusListener(this);this.target.setBackground(java.awt.Color.black);this.target.setBounds(new java.awt.Rectangle(229,26,134,79));this.add(this.okcancelPanel,null);this.okcancelPanel.add(this.okButton,null);
this.okcancelPanel.add(this.applyButton,null);this.okcancelPanel.add(this.cancelButton,null);this.add(this.rText);this.add(this.gText);this.add(this.bText);this.add(this.buttonPanel,null);this.add(this.target,null);this.add(this.gScroller);this.add(this.rScroller);this.add(this.bScroller);this.add(this.label5);this.add(this.label4);this.add(this.label1)});e(c$,"focusGained",function(){},"java.awt.event.FocusEvent");e(c$,"focusLost",function(a){a=a.getComponent();a===this.rText?this.rText_actionPerformed():
a===this.gText?this.gText_actionPerformed():a===this.bText&&this.bText_actionPerformed()},"java.awt.event.FocusEvent");c$.$UserDefinedColours$1$=function(){A(self.c$);c$=L(jalview.appletgui,"UserDefinedColours$1",java.awt.event.MouseAdapter);e(c$,"mousePressed",function(a){this.b$["jalview.appletgui.UserDefinedColours"].colourButtonPressed(a)},"java.awt.event.MouseEvent");c$=z()}});p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ActionListener $.AdjustmentListener $.ItemListener $.MouseListener awt2swing.Button $.Checkbox $.Choice $.Scrollbar $.TextField java.awt.BorderLayout $.FlowLayout".split(" "),
"jalview.appletgui.AnnotationColourChooser","awt2swing.Frame jalview.appletgui.UserDefinedColours jalview.bin.JalviewLite jalview.datamodel.GraphLine jalview.schemes.AnnotationColourGradient $.ColourSchemeI jalview.util.MessageManager java.awt.Color $.Dimension $.Font java.lang.Error $.Float java.util.Hashtable $.Vector".split(" "),function(){c$=s(function(){this.currentAnnotation=this.oldgroupColours=this.oldcs=this.ap=this.av=this.frame=null;this.adjusting=!1;this.thresholdIsMin=this.borderLayout1=
this.currentColours=this.thresholdValue=this.slider=this.jPanel3=this.flowLayout1=this.threshold=this.jPanel2=this.jPanel1=this.defColours=this.cancel=this.ok=this.maxColour=this.minColour=this.annotations=null;r(this,arguments)},jalview.appletgui,"AnnotationColourChooser",awt2swing.Panel,[java.awt.event.ActionListener,java.awt.event.AdjustmentListener,java.awt.event.ItemListener,java.awt.event.MouseListener]);J(c$,function(){this.annotations=new awt2swing.Choice;this.minColour=new awt2swing.Button;
this.maxColour=new awt2swing.Button;this.ok=new awt2swing.Button;this.cancel=new awt2swing.Button;this.defColours=new awt2swing.Button;this.jPanel1=new awt2swing.Panel;this.jPanel2=new awt2swing.Panel;this.threshold=new awt2swing.Choice;this.flowLayout1=new java.awt.FlowLayout;this.jPanel3=new awt2swing.Panel;this.slider=new awt2swing.Scrollbar(0);this.thresholdValue=new awt2swing.TextField(20);this.currentColours=new awt2swing.Checkbox;this.borderLayout1=new java.awt.BorderLayout;this.thresholdIsMin=
new awt2swing.Checkbox});m(c$,function(a,b){t(this,jalview.appletgui.AnnotationColourChooser,[]);try{this.jbInit()}catch(c){if(!y(c,Exception))throw c;}this.oldcs=a.getGlobalColourScheme();if(null!=a.getAlignment().getGroups()){this.oldgroupColours=new java.util.Hashtable;for(var d,e=b.av.getAlignment().getGroups().iterator();e.hasNext()&&((d=e.next())||1);)null!=d.cs?this.oldgroupColours.put(d,d.cs):this.oldgroupColours.put(d,"null")}this.av=a;this.ap=b;this.slider.addAdjustmentListener(this);this.slider.addMouseListener(this);
if(null!=a.getAlignment().getAlignmentAnnotation()){this.setDefaultMinMax();this.adjusting=!0;v(this.oldcs,jalview.schemes.AnnotationColourGradient)&&(d=this.oldcs,this.currentColours.setState(d.isPredefinedColours()||null!=d.getBaseColour()),!d.isPredefinedColours()&&null==d.getBaseColour()&&(this.minColour.setBackground(d.getMinColour()),this.maxColour.setBackground(d.getMaxColour())));d=new java.util.Vector;for(var e=1,k=0;k<a.getAlignment().getAlignmentAnnotation().length;k++){var g=a.getAlignment().getAlignmentAnnotation()[k].label;
d.contains(g)?d.addElement(g+"_"+e++):d.addElement(g)}for(k=0;k<d.size();k++)this.annotations.addItem(d.elementAt(k).toString());this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_no_thereshold"));this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_above_thereshold"));this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_below_thereshold"));if(v(this.oldcs,jalview.schemes.AnnotationColourGradient)){d=
this.oldcs;this.annotations.select(d.getAnnotation());switch(d.getAboveThreshold()){case -1:this.threshold.select(new Integer(0));break;case 1:this.threshold.select(new Integer(1));break;case 0:this.threshold.select(new Integer(1));break;default:throw Error(jalview.util.MessageManager.getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));}this.thresholdIsMin.setState(d.thresholdIsMinMax);this.thresholdValue.setText(""+d.getAnnotationThreshold())}this.adjusting=!1;
this.changeColour();this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("label.colour_by_annotation"),560,175);this.validate()}},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");d(c$,"setDefaultMinMax",function(){this.minColour.setBackground(this.av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MIN",java.awt.Color.orange));this.maxColour.setBackground(this.av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MAX",
java.awt.Color.red))});m(c$,function(){t(this,jalview.appletgui.AnnotationColourChooser,[]);try{this.jbInit()}catch(a){if(y(a,Exception))a.printStackTrace();else throw a;}});d(c$,"jbInit",function(){this.minColour.setFont(new java.awt.Font("Verdana",0,11));this.minColour.setLabel(jalview.util.MessageManager.getString("label.min_colour"));this.minColour.addActionListener(this);this.maxColour.setFont(new java.awt.Font("Verdana",0,11));this.maxColour.setLabel(jalview.util.MessageManager.getString("label.max_colour"));
this.maxColour.addActionListener(this);this.thresholdIsMin.addItemListener(this);this.ok.setLabel(jalview.util.MessageManager.getString("action.ok"));this.ok.addActionListener(this);this.cancel.setLabel(jalview.util.MessageManager.getString("action.cancel"));this.cancel.addActionListener(this);this.defColours.setLabel(jalview.util.MessageManager.getString("action.set_defaults"));this.defColours.addActionListener(this);this.annotations.addItemListener(this);this.thresholdValue.addActionListener(this);
this.slider.setBackground(java.awt.Color.white);this.slider.setPreferredSize(new java.awt.Dimension(193,21));this.slider.setEnabled(!1);this.thresholdValue.setPreferredSize(new java.awt.Dimension(79,22));this.thresholdValue.setEnabled(!1);this.thresholdValue.setColumns(5);this.currentColours.setFont(new java.awt.Font("Verdana",0,11));this.currentColours.setLabel(jalview.util.MessageManager.getString("label.use_original_colours"));this.currentColours.addItemListener(this);this.thresholdIsMin.setBackground(java.awt.Color.white);
this.thresholdIsMin.setLabel(jalview.util.MessageManager.getString("label.threshold_minmax"));this.setLayout(this.borderLayout1);this.jPanel1.setBackground(java.awt.Color.white);this.jPanel2.setLayout(new java.awt.FlowLayout);this.jPanel2.setBackground(java.awt.Color.white);this.threshold.addItemListener(this);this.jPanel3.setLayout(new java.awt.FlowLayout);this.jPanel3.setBackground(java.awt.Color.white);var a=new awt2swing.Panel;a.setLayout(new java.awt.BorderLayout);a.setBackground(java.awt.Color.white);
this.jPanel1.add(this.ok);this.jPanel1.add(this.cancel);this.jPanel2.add(this.annotations);this.jPanel2.add(this.currentColours);this.jPanel2.add(this.minColour);this.jPanel2.add(this.maxColour);a.add(this.thresholdIsMin,"West");a.add(this.slider,"Center");a.add(this.thresholdValue,"East");var b=new awt2swing.Panel;b.setLayout(new java.awt.BorderLayout);b.setBackground(java.awt.Color.white);b.add(this.jPanel2,"North");b.add(this.threshold,"West");this.jPanel3.add(this.defColours);b.add(this.jPanel3,
"East");b.add(a,"South");this.add(b,"Center");this.add(this.jPanel1,"South")});e(c$,"actionPerformed",function(a){if(a.getSource()===this.thresholdValue)try{var b=(new Float(this.thresholdValue.getText())).floatValue();this.slider.setValue(I(1E3*b));this.adjustmentValueChanged(null)}catch(c){if(!y(c,NumberFormatException))throw c;}else a.getSource()===this.minColour?this.minColour_actionPerformed(null):a.getSource()===this.maxColour?this.maxColour_actionPerformed(null):a.getSource()===this.defColours?
this.defColour_actionPerformed():a.getSource()===this.ok?(this.changeColour(),this.frame.setVisible(!1)):a.getSource()===this.cancel?(this.reset(),this.ap.paintAlignment(!0),this.frame.setVisible(!1)):this.changeColour()},"java.awt.event.ActionEvent");e(c$,"itemStateChanged",function(a){a.getSource()===this.currentColours&&(this.currentColours.getState()&&this.reset(),this.maxColour.setEnabled(!this.currentColours.getState()),this.minColour.setEnabled(!this.currentColours.getState()));this.changeColour()},
"java.awt.event.ItemEvent");e(c$,"adjustmentValueChanged",function(){this.adjusting||(this.thresholdValue.setText(this.slider.getValue()/1E3+""),this.currentColours.getState()&&!v(this.av.getGlobalColourScheme(),jalview.schemes.AnnotationColourGradient)&&this.changeColour(),this.currentAnnotation.threshold.value=this.slider.getValue()/1E3,this.ap.paintAlignment(!1))},"java.awt.event.AdjustmentEvent");d(c$,"minColour_actionPerformed",function(a){null!=a?(this.minColour.setBackground(a),this.minColour.repaint(),
this.changeColour()):new jalview.appletgui.UserDefinedColours(this,"Min Colour",this.minColour.getBackground())},"java.awt.Color");d(c$,"maxColour_actionPerformed",function(a){null!=a?(this.maxColour.setBackground(a),this.maxColour.repaint(),this.changeColour()):new jalview.appletgui.UserDefinedColours(this,"Max Colour",this.maxColour.getBackground())},"java.awt.Color");d(c$,"defColour_actionPerformed",function(){this.setDefaultMinMax();this.minColour.repaint();this.maxColour.repaint();this.changeColour()});
d(c$,"changeColour",function(){if(!this.adjusting){this.currentAnnotation=this.av.getAlignment().getAlignmentAnnotation()[this.annotations.getSelectedIndex()];var a=-1;1==this.threshold.getSelectedIndex()?a=1:2==this.threshold.getSelectedIndex()&&(a=0);this.slider.setEnabled(!0);this.thresholdValue.setEnabled(!0);this.thresholdIsMin.setEnabled(!0);-1==a?(this.slider.setEnabled(!1),this.thresholdValue.setEnabled(!1),this.thresholdIsMin.setEnabled(!1),this.thresholdValue.setText("")):-1!=a&&null==this.currentAnnotation.threshold&&
this.currentAnnotation.setThreshold(new jalview.datamodel.GraphLine((this.currentAnnotation.graphMax-this.currentAnnotation.graphMin)/2,"Threshold",java.awt.Color.black));-1!=a&&(this.adjusting=!0,this.slider.setMinimum(I(1E3*this.currentAnnotation.graphMin)),this.slider.setMaximum(I(1E3*this.currentAnnotation.graphMax)),this.slider.setValue(I(1E3*this.currentAnnotation.threshold.value)),this.thresholdValue.setText(this.currentAnnotation.threshold.value+""),this.slider.setEnabled(!0),this.thresholdValue.setEnabled(!0),
this.adjusting=!1);var b=null,b=this.currentColours.getState()?new jalview.schemes.AnnotationColourGradient(this.currentAnnotation,this.av.getGlobalColourScheme(),a):new jalview.schemes.AnnotationColourGradient(this.currentAnnotation,this.minColour.getBackground(),this.maxColour.getBackground(),a);0==this.currentAnnotation.graphMin&&0==this.currentAnnotation.graphMax&&b.setPredefinedColours(!0);b.thresholdIsMinMax=this.thresholdIsMin.getState();this.av.setGlobalColourScheme(b);if(null!=this.av.getAlignment().getGroups())for(var c,
b=this.ap.av.getAlignment().getGroups().iterator();b.hasNext()&&((c=b.next())||1);)null!=c.cs&&(c.cs=this.currentColours.getState()?new jalview.schemes.AnnotationColourGradient(this.currentAnnotation,c.cs,a):new jalview.schemes.AnnotationColourGradient(this.currentAnnotation,this.minColour.getBackground(),this.maxColour.getBackground(),a));this.ap.alignmentChanged();this.ap.paintAlignment(!0)}});d(c$,"reset",function(){this.av.setGlobalColourScheme(this.oldcs);if(null!=this.av.getAlignment().getGroups())for(var a,
b=this.ap.av.getAlignment().getGroups().iterator();b.hasNext()&&((a=b.next())||1);){var c=this.oldgroupColours.get(a);a.cs=v(c,jalview.schemes.ColourSchemeI)?c:null}this.ap.paintAlignment(!0)});e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){this.ap.paintAlignment(!0)},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},
"java.awt.event.MouseEvent")});p("awt2swing");q(["javax.swing.JComboBox"],"awt2swing.Choice",null,function(){c$=B(awt2swing,"Choice",javax.swing.JComboBox);d(c$,"select",function(a){this.setSelectedItem(a)},"~O")});p("javax.swing");q("java.awt.ItemSelectable java.awt.event.ActionListener javax.swing.ActionPropertyChangeListener $.JComponent javax.swing.event.ListDataListener javax.swing.JPopupMenu".split(" "),"javax.swing.JComboBox","java.lang.IllegalArgumentException $.RuntimeException java.awt.Component $.EventQueue java.awt.event.ActionEvent $.InputEvent $.ItemEvent $.ItemListener javax.swing.AbstractAction $.DefaultComboBoxModel $.MutableComboBoxModel $.SwingUtilities $.UIManager javax.swing.event.AncestorListener $.PopupMenuEvent $.PopupMenuListener".split(" "),
function(){c$=s(function(){this.editor=this.renderer=this.dataModel=null;this.maximumRowCount=8;this.$isEditable=!1;this.keySelectionManager=null;this.actionCommand="comboBoxChanged";this.lightWeightPopupEnabled=!1;this.prototypeDisplayValue=this.selectedItemReminder=null;this.selectingItem=this.firingActionEvent=!1;this.actionPropertyChangeListener=this.$action=null;H("javax.swing.JComboBox.DefaultKeySelectionManager")||javax.swing.JComboBox.$JComboBox$DefaultKeySelectionManager$();r(this,arguments)},
javax.swing,"JComboBox",javax.swing.JComponent,[java.awt.ItemSelectable,javax.swing.event.ListDataListener,java.awt.event.ActionListener]);J(c$,function(){this.lightWeightPopupEnabled=javax.swing.JPopupMenu.getDefaultLightWeightPopupEnabled()});m(c$,function(a){t(this,javax.swing.JComboBox);this.setModel(a);this.init()},"javax.swing.ComboBoxModel");m(c$,function(a){t(this,javax.swing.JComboBox);this.setModel(new javax.swing.DefaultComboBoxModel(a));this.init()},"~A");m(c$,function(a){t(this,javax.swing.JComboBox);
this.setModel(new javax.swing.DefaultComboBoxModel(a));this.init()},"java.util.Vector");m(c$,function(){t(this,javax.swing.JComboBox);this.setModel(new javax.swing.DefaultComboBoxModel);this.init()});d(c$,"init",function(){this.installAncestorListener();this.setUIProperty("opaque",new Boolean(!0));this.updateUI()});d(c$,"installAncestorListener",function(){this.addAncestorListener((H("javax.swing.JComboBox$1")?0:javax.swing.JComboBox.$JComboBox$1$(),C(javax.swing.JComboBox$1,this,null)))});e(c$,"updateUI",
function(){this.setUI(javax.swing.UIManager.getUI(this));var a=this.getRenderer();v(a,java.awt.Component)&&javax.swing.SwingUtilities.updateComponentTreeUI(a)});e(c$,"getUIClassID",function(){return"ComboBoxUI"});e(c$,"getUI",function(){return this.ui});d(c$,"setModel",function(a){var b=this.dataModel;null!=b&&b.removeListDataListener(this);this.dataModel=a;this.dataModel.addListDataListener(this);this.selectedItemReminder=this.dataModel.getSelectedItem();this.firePropertyChangeObject("model",b,this.dataModel)},
"javax.swing.ComboBoxModel");d(c$,"getModel",function(){return this.dataModel});d(c$,"setLightWeightPopupEnabled",function(a){var b=this.lightWeightPopupEnabled;this.lightWeightPopupEnabled=a;this.firePropertyChangeBool("lightWeightPopupEnabled",b,this.lightWeightPopupEnabled)},"~B");d(c$,"isLightWeightPopupEnabled",function(){return this.lightWeightPopupEnabled});d(c$,"setEditable",function(a){var b=this.$isEditable;this.$isEditable=a;this.firePropertyChangeBool("editable",b,this.$isEditable)},"~B");
d(c$,"isEditable",function(){return this.$isEditable});d(c$,"setMaximumRowCount",function(a){var b=this.maximumRowCount;this.maximumRowCount=a;this.firePropertyChangeInt("maximumRowCount",b,this.maximumRowCount)},"~N");d(c$,"getMaximumRowCount",function(){return this.maximumRowCount});d(c$,"setRenderer",function(a){var b=this.renderer;this.renderer=a;this.firePropertyChangeObject("renderer",b,this.renderer);this.invalidate()},"javax.swing.ListCellRenderer");d(c$,"getRenderer",function(){return this.renderer});
d(c$,"setEditor",function(a){var b=this.editor;null!=this.editor&&this.editor.removeActionListener(this);this.editor=a;null!=this.editor&&this.editor.addActionListener(this);this.firePropertyChangeObject("editor",b,this.editor)},"javax.swing.ComboBoxEditor");d(c$,"getEditor",function(){return this.editor});d(c$,"setSelectedItem",function(a){var b=this.selectedItemReminder,c=a;if(null==b||!b.equals(a)){if(null!=a&&!this.isEditable()){for(var b=!1,d=0;d<this.dataModel.getSize();d++){var e=this.dataModel.getElementAt(d);
if(a.equals(e)){b=!0;c=e;break}}if(!b)return}this.selectingItem=!0;this.dataModel.setSelectedItem(c);this.selectingItem=!1;this.selectedItemReminder!==this.dataModel.getSelectedItem()&&this.selectedItemChanged()}this.fireActionEvent()},"~O");d(c$,"getSelectedItem",function(){return this.dataModel.getSelectedItem()});d(c$,"setSelectedIndex",function(a){var b=this.dataModel.getSize();if(-1==a)this.setSelectedItem(null);else{if(-1>a||a>=b)throw new IllegalArgumentException("setSelectedIndex: "+a+" out of bounds");
this.setSelectedItem(this.dataModel.getElementAt(a))}},"~N");d(c$,"getSelectedIndex",function(){var a=this.dataModel.getSelectedItem(),b,c,d;b=0;for(c=this.dataModel.getSize();b<c;b++)if(d=this.dataModel.getElementAt(b),null!=d&&d.equals(a))return b;return-1});d(c$,"getPrototypeDisplayValue",function(){return this.prototypeDisplayValue});d(c$,"setPrototypeDisplayValue",function(a){var b=this.prototypeDisplayValue;this.prototypeDisplayValue=a;this.firePropertyChangeObject("prototypeDisplayValue",b,
a)},"~O");d(c$,"addItem",function(a){this.checkMutableComboBoxModel();this.dataModel.addElement(a)},"~O");d(c$,"insertItemAt",function(a,b){this.checkMutableComboBoxModel();this.dataModel.insertElementAt(a,b)},"~O,~N");d(c$,"removeItem",function(a){this.checkMutableComboBoxModel();this.dataModel.removeElement(a)},"~O");d(c$,"removeItemAt",function(a){this.checkMutableComboBoxModel();this.dataModel.removeElementAt(a)},"~N");d(c$,"removeAllItems",function(){this.checkMutableComboBoxModel();var a=this.dataModel,
b=a.getSize();if(v(a,javax.swing.DefaultComboBoxModel))a.removeAllElements();else for(var c=0;c<b;++c){var d=a.getElementAt(0);a.removeElement(d)}this.selectedItemReminder=null;this.isEditable()&&this.editor.setItem(null)});d(c$,"checkMutableComboBoxModel",function(){if(!v(this.dataModel,javax.swing.MutableComboBoxModel))throw new RuntimeException("Cannot use this method with a non-Mutable data model.");});d(c$,"showPopup",function(){this.setPopupVisible(!0)});d(c$,"hidePopup",function(){this.setPopupVisible(!1)});
d(c$,"setPopupVisible",function(a){this.getUI().setPopupVisible(this,a)},"~B");d(c$,"isPopupVisible",function(){return this.getUI().isPopupVisible(this)});e(c$,"addItemListener",function(a){this.listenerList.add(java.awt.event.ItemListener,a)},"java.awt.event.ItemListener");e(c$,"removeItemListener",function(a){this.listenerList.remove(java.awt.event.ItemListener,a)},"java.awt.event.ItemListener");d(c$,"getItemListeners",function(){return this.listenerList.getListeners(java.awt.event.ItemListener)});
d(c$,"addActionListener",function(a){this.listenerList.add(java.awt.event.ActionListener,a)},"java.awt.event.ActionListener");d(c$,"removeActionListener",function(a){null!=a&&this.getAction()===a?this.setAction(null):this.listenerList.remove(java.awt.event.ActionListener,a)},"java.awt.event.ActionListener");d(c$,"getActionListeners",function(){return this.listenerList.getListeners(java.awt.event.ActionListener)});d(c$,"addPopupMenuListener",function(a){this.listenerList.add(javax.swing.event.PopupMenuListener,
a)},"javax.swing.event.PopupMenuListener");d(c$,"removePopupMenuListener",function(a){this.listenerList.remove(javax.swing.event.PopupMenuListener,a)},"javax.swing.event.PopupMenuListener");d(c$,"getPopupMenuListeners",function(){return this.listenerList.getListeners(javax.swing.event.PopupMenuListener)});d(c$,"firePopupMenuWillBecomeVisible",function(){for(var a=this.listenerList.getListenerList(),b=null,c=a.length-2;0<=c;c-=2)a[c]===javax.swing.event.PopupMenuListener&&(null==b&&(b=new javax.swing.event.PopupMenuEvent(this)),
a[c+1].popupMenuWillBecomeVisible(b))});d(c$,"firePopupMenuWillBecomeInvisible",function(){for(var a=this.listenerList.getListenerList(),b=null,c=a.length-2;0<=c;c-=2)a[c]===javax.swing.event.PopupMenuListener&&(null==b&&(b=new javax.swing.event.PopupMenuEvent(this)),a[c+1].popupMenuWillBecomeInvisible(b))});d(c$,"firePopupMenuCanceled",function(){for(var a=this.listenerList.getListenerList(),b=null,c=a.length-2;0<=c;c-=2)a[c]===javax.swing.event.PopupMenuListener&&(null==b&&(b=new javax.swing.event.PopupMenuEvent(this)),
a[c+1].popupMenuCanceled(b))});d(c$,"setActionCommand",function(a){this.actionCommand=a},"~S");d(c$,"getActionCommand",function(){return this.actionCommand});d(c$,"setAction",function(a){var b=this.getAction();if(null==this.$action||!this.$action.equals(a))this.$action=a,null!=b&&(this.removeActionListener(b),b.removePropertyChangeListener(this.actionPropertyChangeListener),this.actionPropertyChangeListener=null),this.configurePropertiesFromAction(this.$action),null!=this.$action&&(this.isListener(java.awt.event.ActionListener,
this.$action)||this.addActionListener(this.$action),this.actionPropertyChangeListener=this.createActionPropertyChangeListener(this.$action),this.$action.addPropertyChangeListener(this.actionPropertyChangeListener)),this.firePropertyChangeObject("action",b,this.$action)},"javax.swing.Action");d(c$,"isListener",function(a,b){for(var c=!1,d=this.listenerList.getListenerList(),e=d.length-2;0<=e;e-=2)d[e]===a&&d[e+1]===b&&(c=!0);return c},"Class,java.awt.event.ActionListener");d(c$,"getAction",function(){return this.$action});
d(c$,"configurePropertiesFromAction",function(a){javax.swing.AbstractAction.setEnabledFromAction(this,a);javax.swing.AbstractAction.setToolTipTextFromAction(this,a);this.setActionCommandFromAction(a)},"javax.swing.Action");d(c$,"createActionPropertyChangeListener",function(a){return new javax.swing.JComboBox.ComboBoxActionPropertyChangeListener(this,a)},"javax.swing.Action");d(c$,"actionPropertyChanged",function(a,b){"ActionCommandKey"===b?this.setActionCommandFromAction(a):"enabled"===b?javax.swing.AbstractAction.setEnabledFromAction(this,
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p("javax.swing");q(["javax.swing.ListModel"],"javax.swing.ComboBoxModel",null,function(){M(javax.swing,"ComboBoxModel",javax.swing.ListModel)});p("jalview.schemes");q(["jalview.schemes.FollowerColourScheme"],"jalview.schemes.AnnotationColourGradient","jalview.datamodel.AlignmentI $.GraphLine jalview.renderer.AnnotationRenderer jalview.schemes.ColourSchemeProperty jalview.util.Comparison java.awt.Color java.util.IdentityHashMap".split(" "),function(){c$=s(function(){this.annotation=null;this.aboveAnnotationThreshold=
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m(c$,function(){this.construct(!1)});m(c$,function(a){this.debugRedraw=a},"~B");d(c$,"drawStemAnnot",function(a,b,c,d,e,k,g,h,j,n){a.setColor(jalview.renderer.AnnotationRenderer.STEM_COLOUR);var m=F(c/this.charWidth)+g;g=c;d*=this.charWidth;jalview.jsdev.RegExp.newRegex(["(\\))"]);var p=0==h||null==b[h-1]?" ":b[h-1].secondaryStructure,m=0==m||null==b[m-1]||p!=b[m-1].secondaryStructure;b=!j||!n||null==b[h]||p!=b[h].secondaryStructure;0<h&&jalview.schemes.ResidueProperties.isCloseParenRNA(p)?(m&&(a.fillPolygon(w(-1,
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null!=c?(this.sOffset=c[0],this.visHeight=c[1],this.useClip=0==this.visHeight?!1:this.canClip):this.useClip=!1;this.updateFromAlignViewport(b)},"jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI");d(c$,"updateFromAlignViewport",function(a){this.charWidth=a.getCharWidth();this.endRes=a.getEndRes();this.charHeight=a.getCharHeight();this.hasHiddenColumns=a.hasHiddenColumns();this.validCharWidth=a.isValidCharWidth();this.av_renderHistogram=a.isShowConsensusHistogram();this.av_renderProfile=
a.isShowSequenceLogo();this.av_normaliseProfile=a.isNormaliseSequenceLogo();this.profcolour=a.getGlobalColourScheme();null==this.profcolour&&(this.profcolour=a.getAlignment().isNucleotide()?new jalview.schemes.NucleotideColourScheme:new jalview.schemes.ZappoColourScheme);this.columnSelection=a.getColumnSelection();this.hconsensus=a.getSequenceConsensusHash();this.complementConsensus=a.getComplementConsensusHash();this.hStrucConsensus=a.getRnaStructureConsensusHash();this.av_ignoreGapsConsensus=a.isIgnoreGapsConsensus()},
"jalview.api.AlignViewportI");d(c$,"getProfileFor",function(a,b){if(a.autoCalculated&&(a.label.startsWith("Consensus")||a.label.startsWith("cDNA Consensus"))){var c=a.label.startsWith("cDNA Consensus");if(null!=a.groupRef&&null!=a.groupRef.consensusData&&a.groupRef.isShowSequenceLogo())return jalview.analysis.AAFrequency.extractProfile(a.groupRef.consensusData[b],a.groupRef.getIgnoreGapsConsensus());if(null==a.groupRef&&null==a.sequenceRef)return c?jalview.analysis.AAFrequency.extractCdnaProfile(this.complementConsensus[b],
this.av_ignoreGapsConsensus):jalview.analysis.AAFrequency.extractProfile(this.hconsensus[b],this.av_ignoreGapsConsensus)}else if(a.autoCalculated&&a.label.startsWith("StrucConsensus")&&null==a.groupRef&&null==a.sequenceRef&&null!=this.hStrucConsensus&&this.hStrucConsensus.length>b)return jalview.analysis.StructureFrequency.extractProfile(this.hStrucConsensus[b],this.av_ignoreGapsConsensus);return null},"jalview.datamodel.AlignmentAnnotation,~N");d(c$,"drawComponent",function(a,b,c,d,e,k){var g=System.currentTimeMillis(),
h=!1;this.updateFromAwtRenderPanel(a,b);this.fm=c.getFontMetrics();a=b.getAlignment().getAlignmentAnnotation();if(null==a)return!1;var j=0,n=0,m=0,p,q,s=0,r=!1,t=!1,v=!1;b.isCentreColumnLabels();for(var w=!1,y=b.getAlignmentConsensusAnnotation(),z=b.getAlignmentStrucConsensusAnnotation(),A=b.getComplementConsensusAnnotation(),B=!0,E=!0,C=!1,F=this.rna,H=new java.util.BitSet,G=0,J=1,K=c.getFont(),L=0,M=0,N=0,O=0,Q=!1,T=!1,S=0;S<a.length;S++){var P=a[S],F=P.isRNA();null!=P.groupRef&&P===P.groupRef.getConsensus()?
(B=P.groupRef.isShowConsensusHistogram(),E=P.groupRef.isShowSequenceLogo(),C=P.groupRef.isNormaliseSequenceLogo()):P===y||P===z||P===A?(B=this.av_renderHistogram,E=this.av_renderProfile,C=this.av_normaliseProfile):B=!0;var V=P.annotations;if(P.visible){v=P.showAllColLabels;w=P.scaleColLabel;p=" ";q=0;if(!this.useClip||n-this.charHeight<this.visHeight&&n+P.height+2*this.charHeight>=this.sOffset){Q||(Q=!0,L=n,M=S);N=n;O=S;if(0<P.graph){if(-1<P.graphGroup&&H.get(P.graphGroup))continue;n+=P.height;P.hasText&&
(s=this.charHeight-this.fm.getDescent(),n-=this.charHeight)}else s=P.hasText?this.charHeight-this.fm.getDescent():0;if(P.autoCalculated&&b.isCalculationInProgress(P)){n+=this.charHeight;h=!0;c.drawImage(this.fadedImage,0,n-P.height,this.imgWidth,n,0,n-P.height,this.imgWidth,n,this.annotationPanel);c.setColor(java.awt.Color.black);continue}for(j=0==e?0:-1;j<k-e;){if(this.hasHiddenColumns){if(m=this.columnSelection.adjustForHiddenColumns(e+j),m>V.length-1)break}else m=e+j;var R=(r=null==V||V.length<=
m||null==V[m]?!1:!0)?V[m].displayCharacter:null;if(-1<j){if(d==S&&(c.setColor(java.awt.Color.red),null!=this.columnSelection))for(G=0;G<this.columnSelection.size();G++)this.columnSelection.columnAt(G)==m&&c.fillRect(j*this.charWidth,n,this.charWidth,this.charHeight);P.getInvalidStrucPos()>j?(c.setColor(java.awt.Color.orange),c.fillRect(j*this.charWidth,n,this.charWidth,this.charHeight)):P.getInvalidStrucPos()==j&&(c.setColor(java.awt.Color.orange.darker()),c.fillRect(j*this.charWidth,n,this.charWidth,
this.charHeight));this.validCharWidth&&(r&&null!=R&&0<R.length)&&(G=this.fm.charsWidth(R.toCharArray(),0,R.length),w&&G>this.charWidth&&(J=this.charWidth,J/=G,c.setFont(K.deriveFont(java.awt.geom.AffineTransform.getScaleInstance(J,1))),G=this.charWidth),G=I((this.charWidth-G)/2),null==V[m].colour?c.setColor(java.awt.Color.black):c.setColor(V[m].colour),0==m||0<P.graph?awt2swing.Util.drawString(c,R,j*this.charWidth+G,n+s):(null==V[m-1]||v||!R.equals(V[m-1].displayCharacter)||2>R.length&&" "==V[m].secondaryStructure)&&
awt2swing.Util.drawString(c,R,j*this.charWidth+G,n+s),c.setFont(K))}if(P.hasIcons&&(G=r?V[m].secondaryStructure:"-","("==G&&-1<R.indexOf(")")&&(G=")"),"["==G&&-1<R.indexOf("]")&&(G="]"),"{"==G&&-1<R.indexOf("}")&&(G="}"),"<"==G&&-1<R.indexOf("<")&&(G=">"),65<=G.charCodeAt(0)&&-1<R.indexOf(G.charCodeAt(0)+32)&&(G=String.fromCharCode(G.charCodeAt(0)+32)),!r||G!=p)){if(-1<j)switch(p){case "(":case ")":this.drawStemAnnot(c,V,q,j,n,s,e,m,r,t);break;case "H":if(!F){this.drawHelixAnnot(c,V,q,j,n,s,e,m,r,
t);break}case "E":if(!F){this.drawSheetAnnot(c,V,q,j,n,s,e,m,r,t);break}case "{":case "}":case "[":case "]":case ">":case "<":case "A":case "a":case "B":case "b":case "C":case "c":case "D":case "d":case "e":case "F":case "f":case "G":case "g":case "h":case "I":case "i":case "J":case "j":case "K":case "k":case "L":case "l":case "M":case "m":case "N":case "n":case "O":case "o":case "P":case "p":case "Q":case "q":case "R":case "r":case "S":case "s":case "T":case "t":case "U":case "u":case "V":case "v":case "W":case "w":case "X":case "x":case "Y":case "y":case "Z":case "z":p=
this.getNotCanonicalColor(p);this.drawNotCanonicalAnnot(c,p,V,q,j,n,s,e,m,r,t);break;default:c.setColor(java.awt.Color.gray),c.fillRect(q,n+6+s,j*this.charWidth-q,2)}p=r?G:" ";-1<j&&(q=j*this.charWidth)}m++;j++}m>=V.length?(m=V.length-1,t=!1):t=!0;r=null==V||V.length<=m||null==V[m]?!1:!0;if(P.hasIcons)switch(p){case "H":if(!F){this.drawHelixAnnot(c,V,q,j,n,s,e,m,r,t);break}case "E":if(!F){this.drawSheetAnnot(c,V,q,j,n,s,e,m,r,t);break}case "(":case ")":this.drawStemAnnot(c,V,q,j,n,s,e,m,r,t);break;
case "{":case "}":case "[":case "]":case ">":case "<":case "A":case "a":case "B":case "b":case "C":case "c":case "D":case "d":case "e":case "F":case "f":case "G":case "g":case "h":case "I":case "i":case "J":case "j":case "K":case "k":case "L":case "l":case "M":case "m":case "N":case "n":case "O":case "o":case "P":case "p":case "Q":case "q":case "R":case "r":case "T":case "t":case "U":case "u":case "V":case "v":case "W":case "w":case "X":case "x":case "Y":case "y":case "Z":case "z":p=this.getNotCanonicalColor(p);
this.drawNotCanonicalAnnot(c,p,V,q,j,n,s,e,m,r,t);break;default:this.drawGlyphLine(c,V,q,j,n,s,e,m,r,t)}if(0<P.graph&&0<P.graphHeight)if(2==P.graph)if(-1<P.graphGroup&&!H.get(P.graphGroup)){j=-999999;q=9999999;for(r=0;r<a.length;r++)a[r].graphGroup==P.graphGroup&&(a[r]!==P&&(a[r].visible=!1),a[r].graphMax>j&&(j=a[r].graphMax),a[r].graphMin<q&&(q=a[r].graphMin));for(r=0;r<a.length;r++)a[r].graphGroup==P.graphGroup&&this.drawLineGraph(c,a[r],a[r].annotations,e,k,n,q,j,P.graphHeight);H.set(P.graphGroup)}else this.drawLineGraph(c,
P,V,e,k,n,P.graphMin,P.graphMax,P.graphHeight);else 1==P.graph&&this.drawBarGraph(c,P,V,e,k,P.graphMin,P.graphMax,n,B,E,C)}else Q&&!T&&(T=!0);0<P.graph&&P.hasText&&(n+=this.charHeight);0==P.graph&&(n+=a[S].height)}}this.debugRedraw&&(this.canClip&&(Q&&System.err.println("Start clip at : "+L+" (index "+M+")"),T&&System.err.println("End clip at : "+N+" (index "+O+")")),System.err.println("Annotation Rendering time:"+(System.currentTimeMillis()-g)));return!h},"jalview.renderer.AwtRenderPanelI,jalview.api.AlignViewportI,java.awt.Graphics,~N,~N,~N");
d(c$,"drawGlyphLine",function(a,b,c,d,e,k){a.setColor(jalview.renderer.AnnotationRenderer.GLYPHLINE_COLOR);a.fillRect(c,e+6+k,d*this.charWidth-c,2)},"java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B");d(c$,"drawSheetAnnot",function(a,b,c,d,e,k,g,h,j,n){a.setColor(jalview.renderer.AnnotationRenderer.SHEET_COLOUR);!n||!j||null==b||null==b[h]||"E"!=b[h].secondaryStructure?(a.fillRect(c,e+4+k,d*this.charWidth-c-4,7),a.fillPolygon(w(-1,[d*this.charWidth-4,d*this.charWidth-4,d*this.charWidth]),w(-1,[e+k,e+
14+k,e+7+k]),3)):a.fillRect(c,e+4+k,(d+1)*this.charWidth-c,7)},"java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B");d(c$,"drawHelixAnnot",function(a,b,c,d,e,k,g,h,j){a.setColor(jalview.renderer.AnnotationRenderer.HELIX_COLOUR);g=F(c/this.charWidth)+g;var n=c,m=d*this.charWidth;if(this.MAC)d=F(this.charWidth/2),a.fillRoundRect(c,e+4+k,m-n,8,8,8),0==g||(null==b[g-1]||"H"!=b[g-1].secondaryStructure)||a.fillRoundRect(c,e+4+k,m-n-d+1,8,0,0),j&&!(null==b[h]||"H"!=b[h].secondaryStructure)&&a.fillRoundRect(c+
d,e+4+k,m-n-d+1,8,0,0);else{if(0==g||null==b[g-1]||"H"!=b[g-1].secondaryStructure)a.fillArc(c,e+4+k,this.charWidth,8,90,180),n+=F(this.charWidth/2);if(!j||null==b[h]||"H"!=b[h].secondaryStructure)a.fillArc(d*this.charWidth-this.charWidth,e+4+k,this.charWidth,8,270,180),m-=F(this.charWidth/2);a.fillRect(n,e+4+k,m-n,8)}},"java.awt.Graphics,~A,~N,~N,~N,~N,~N,~N,~B,~B");d(c$,"drawLineGraph",function(a,b,c,d,e,k,g,h,j){if(!(d>c.length)){var n=0;e<this.endRes&&e++;e=Math.min(e,c.length);0==d&&n++;var m=
k,p=k;h-=g;0>g&&(p=k-I((0-g/h)*j));a.setColor(java.awt.Color.gray);a.drawLine(n-this.charWidth,p,(e-d+1)*this.charWidth,p);e=Math.min(e,c.length);for(var q=c.length-1;n<e-d;){p=d+n;this.hasHiddenColumns&&(p=this.columnSelection.adjustForHiddenColumns(p));if(p>q)break;null==c[p]||null==c[p-1]||(null==c[p].colour?a.setColor(java.awt.Color.black):a.setColor(c[p].colour),m=k-I((c[p-1].value-g)/h*j),p=k-I((c[p].value-g)/h*j),a.drawLine(n*this.charWidth-F(this.charWidth/2),m,n*this.charWidth+F(this.charWidth/
2),p));n++}null!=b.threshold&&(a.setColor(b.threshold.colour),a.setStroke(new java.awt.BasicStroke(1,2,1,3,Q(-1,[5,3]),0)),p=I(k-(b.threshold.value-g)/h*j),a.drawLine(0,p,(e-d)*this.charWidth,p),a.setStroke(new java.awt.BasicStroke))}},"java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~N");d(c$,"drawBarGraph",function(a,b,c,d,e,k,g,h,j,n,m){if(!(d>c.length)){var p=a.getFont();e=Math.min(e,c.length);var q=0,s=h,r=h;g-=k;0>k&&(r=h-I((0-k/g)*b.graphHeight));a.setColor(java.awt.Color.gray);
a.drawLine(q,r,(e-d)*this.charWidth,r);for(var t,v=c.length-1;q<e-d;){t=d+q;this.hasHiddenColumns&&(t=this.columnSelection.adjustForHiddenColumns(t));if(t>v)break;if(null!=c[t]&&(null==c[t].colour?a.setColor(java.awt.Color.black):a.setColor(c[t].colour),s=h-I((c[t].value-k)/g*b.graphHeight),j&&(0<s-r?a.fillRect(q*this.charWidth,r,this.charWidth,s-r):a.fillRect(q*this.charWidth,s,this.charWidth,r-s)),n)){var w=this.getProfileFor(b,t);if(null!=w&&0!=w[2]){var y=1==w[0],z=2==w[0],A=m?h-b.graphHeight:
s,s=m?b.graphHeight:r-s,B,E,C;C=N(y?2:z?3:1,"\x00");B=a.getFontMetrics(p).getLineMetrics("Q",a);var G=1/(m?w[2]:100);B.getAscent();for(var H=0,J=3,K=0;K<w[1];)y?(C[0]=String.fromCharCode(w[J++]),C[1]=String.fromCharCode(w[J++])):z?C=jalview.analysis.CodingUtils.decodeCodon(w[J++]):C[0]=String.fromCharCode(w[J++]),E=this.charWidth,E/=this.fm.charsWidth(C,0,C.length),A+=H,H=s*G*w[J++],B=p.getLineMetrics(C,0,1,a.getFontMetrics().getFontRenderContext()),a.setFont(p.deriveFont(java.awt.geom.AffineTransform.getScaleInstance(E,
H/B.getAscent()))),B=a.getFontMetrics().getLineMetrics(C,0,1,a),E=null,z?(E=jalview.schemes.ResidueProperties.codonTranslate(String.instantialize(C)),E=this.profcolour.findColourSeq(E.charAt(0),t,null)):E=this.profcolour.findColourSeq(C[0],t,null),a.setColor(E===java.awt.Color.white?java.awt.Color.lightGray:E),B=A+(H-B.getDescent()-B.getBaselineOffsets()[B.getBaselineIndex()]),a.drawChars(C,0,C.length,q*this.charWidth,F(B)),K++;a.setFont(p)}}q++}null!=b.threshold&&(a.setColor(b.threshold.colour),
a.setStroke(new java.awt.BasicStroke(1,2,1,3,Q(-1,[5,3]),0)),r=I(h-(b.threshold.value-k)/g*b.graphHeight),a.drawLine(0,r,(e-d)*this.charWidth,r),a.setStroke(new java.awt.BasicStroke))}},"java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N,~N,~B,~B,~B");d(c$,"drawGraph",function(a,b,c,d,e,k,g){g=Math.min(g,c.length);a.setColor(java.awt.Color.white);a.fillRect(0,0,d,e);a.setColor(new java.awt.Color(0,0,180));d=0;for(var h=k;h<g;h++)null!=c[h]&&(null==c[h].colour?a.setColor(java.awt.Color.black):
a.setColor(c[h].colour),k=I(c[h].value/b.graphMax*e),k>e&&(k=e),a.fillRect(d,e-k,this.charWidth,k)),d+=this.charWidth},"java.awt.Graphics,jalview.datamodel.AlignmentAnnotation,~A,~N,~N,~N,~N");d(c$,"getNotCanonicalColor",function(a){switch(a){case "{":case "}":return new java.awt.Color(255,125,5);case "[":case "]":return new java.awt.Color(245,115,10);case ">":case "<":return new java.awt.Color(235,135,15);case "A":case "a":return new java.awt.Color(225,105,20);case "B":case "b":return new java.awt.Color(215,
145,30);case "C":case "c":return new java.awt.Color(205,95,35);case "D":case "d":return new java.awt.Color(195,155,45);case "E":case "e":return new java.awt.Color(185,85,55);case "F":case "f":return new java.awt.Color(175,165,65);case "G":case "g":return new java.awt.Color(170,75,75);case "H":case "h":return new java.awt.Color(160,175,85);case "I":case "i":return new java.awt.Color(150,65,95);case "J":case "j":return new java.awt.Color(140,185,105);case "K":case "k":return new java.awt.Color(130,
55,110);case "L":case "l":return new java.awt.Color(120,195,120);case "M":case "m":return new java.awt.Color(110,45,130);case "N":case "n":return new java.awt.Color(100,205,140);case "O":case "o":return new java.awt.Color(90,35,150);case "P":case "p":return new java.awt.Color(85,215,160);case "Q":case "q":return new java.awt.Color(75,25,170);case "R":case "r":return new java.awt.Color(65,225,180);case "S":case "s":return new java.awt.Color(55,15,185);case "T":case "t":return new java.awt.Color(45,
235,195);case "U":case "u":return new java.awt.Color(35,5,205);case "V":case "v":return new java.awt.Color(25,245,215);case "W":case "w":return new java.awt.Color(15,0,225);case "X":case "x":return new java.awt.Color(10,255,235);case "Y":case "y":return new java.awt.Color(5,150,245);case "Z":case "z":return new java.awt.Color(0,80,255);default:return System.out.println("This is not a interaction : "+a),null}},"~S");c$.GLYPHLINE_COLOR=c$.prototype.GLYPHLINE_COLOR=java.awt.Color.gray;c$.SHEET_COLOUR=
c$.prototype.SHEET_COLOUR=java.awt.Color.green;c$.HELIX_COLOUR=c$.prototype.HELIX_COLOUR=java.awt.Color.red;c$.STEM_COLOUR=c$.prototype.STEM_COLOUR=java.awt.Color.blue});p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ActionListener $.AdjustmentListener $.ItemListener $.MouseListener awt2swing.Checkbox $.Choice $.Scrollbar $.TextField".split(" "),"jalview.appletgui.FeatureColourChooser","awt2swing.Label jalview.appletgui.JVDialog $.PaintRefresher $.UserDefinedColours jalview.datamodel.GraphLine jalview.schemes.GraduatedColor jalview.util.MessageManager java.awt.Color $.Dimension $.FlowLayout $.Font $.GridLayout java.awt.event.ActionEvent java.lang.Float".split(" "),
function(){c$=s(function(){this.oldgroupColours=this.oldcs=this.cs=this.fs=this.fr=this.owner=this.frame=null;this.adjusting=!1;this.max=this.min=0;this.threshline=this.colourFromLabel=this.thresholdIsMin=this.thresholdValue=this.slider=this.jPanel4=this.jPanel3=this.threshold=this.jPanel2=this.jPanel1=this.maxColour=this.minColour=this.af=this.type=null;r(this,arguments)},jalview.appletgui,"FeatureColourChooser",awt2swing.Panel,[java.awt.event.ActionListener,java.awt.event.AdjustmentListener,java.awt.event.ItemListener,
java.awt.event.MouseListener]);J(c$,function(){this.minColour=new awt2swing.Panel;this.maxColour=new awt2swing.Panel;this.jPanel1=new awt2swing.Panel;this.jPanel2=new awt2swing.Panel;this.threshold=new awt2swing.Choice;this.jPanel3=new awt2swing.Panel;this.jPanel4=new awt2swing.Panel;this.slider=new awt2swing.Scrollbar(0);this.thresholdValue=new awt2swing.TextField(20);this.thresholdIsMin=new awt2swing.Checkbox;this.colourFromLabel=new awt2swing.Checkbox});m(c$,function(a,b){t(this,jalview.appletgui.FeatureColourChooser,
[]);this.af=a;this.init(a.getSeqcanvas().getFeatureRenderer(),b)},"jalview.appletgui.AlignFrame,~S");m(c$,function(a,b){t(this,jalview.appletgui.FeatureColourChooser,[]);this.fs=a;this.init(a.fr,b)},"jalview.appletgui.FeatureSettings,~S");d(c$,"init",function(a,b){this.type=b;this.fr=a;var c=this.fr.getMinMax().get(b)[0];this.min=c[0];this.max=c[1];this.oldcs=this.fr.getFeatureColours().get(b);if(v(this.oldcs,jalview.schemes.GraduatedColor))this.cs=new jalview.schemes.GraduatedColor(this.oldcs,this.min,
this.max);else{var d=java.awt.Color.black;v(this.oldcs,java.awt.Color)&&(d=this.oldcs);this.cs=new jalview.schemes.GraduatedColor(java.awt.Color.white,d,c[0],c[1])}this.minColour.setBackground(this.cs.getMinColor());this.maxColour.setBackground(this.cs.getMaxColor());this.minColour.setForeground(this.cs.getMinColor());this.maxColour.setForeground(this.cs.getMaxColor());this.colourFromLabel.setState(this.cs.isColourByLabel());this.adjusting=!0;try{this.jbInit()}catch(e){if(!y(e,Exception))throw e;
}this.threshold.select(new Integer(-1==this.cs.getThreshType()?0:1==this.cs.getThreshType()?1:2));this.adjusting=!1;this.changeColour();this.colourFromLabel.addItemListener(this);this.slider.addAdjustmentListener(this);this.slider.addMouseListener(this);this.owner=null!=this.af?this.af:this.fs.frame;this.frame=new jalview.appletgui.JVDialog(this.owner,jalview.util.MessageManager.formatMessage("label.graduated_color_for_params",E(-1,[b])),!0,480,248);this.frame.setMainPanel(this);this.validate();this.frame.setVisible(!0);
this.frame.accept?this.changeColour():(this.reset(),jalview.appletgui.PaintRefresher.Refresh(this,this.fr.getViewport().getSequenceSetId()),this.frame.setVisible(!1))},"jalview.appletgui.FeatureRenderer,~S");m(c$,function(){t(this,jalview.appletgui.FeatureColourChooser,[]);try{this.jbInit()}catch(a){if(y(a,Exception))a.printStackTrace();else throw a;}});d(c$,"jbInit",function(){var a=new awt2swing.Label(jalview.util.MessageManager.getString("label.min")),b=new awt2swing.Label(jalview.util.MessageManager.getString("label.max"));
a.setFont(new java.awt.Font("Verdana",0,11));b.setFont(new java.awt.Font("Verdana",0,11));this.minColour.setBounds(0,0,40,27);this.maxColour.setBounds(0,0,40,27);this.minColour.addMouseListener(this);this.maxColour.setFont(new java.awt.Font("Verdana",0,11));this.maxColour.addMouseListener(this);this.thresholdIsMin.addItemListener(this);this.setLayout(new java.awt.GridLayout(4,1));this.jPanel1.setLayout(new java.awt.FlowLayout);this.jPanel2.setLayout(new java.awt.FlowLayout);this.jPanel3.setLayout(new java.awt.GridLayout(1,
1));this.jPanel4.setLayout(new java.awt.FlowLayout);this.jPanel1.setBackground(java.awt.Color.white);this.jPanel2.setBackground(java.awt.Color.white);this.jPanel4.setBackground(java.awt.Color.white);this.threshold.addItemListener(this);this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_no_thereshold"));this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_above_thereshold"));this.threshold.addItem(jalview.util.MessageManager.getString("label.threshold_feature_below_thereshold"));
this.thresholdValue.addActionListener(this);this.slider.setBackground(java.awt.Color.white);this.slider.setEnabled(!1);this.slider.setSize(new java.awt.Dimension(93,21));this.thresholdValue.setEnabled(!1);this.thresholdValue.setSize(new java.awt.Dimension(79,22));this.thresholdValue.setColumns(5);this.jPanel3.setBackground(java.awt.Color.white);this.colourFromLabel.setFont(new java.awt.Font("Verdana",0,11));this.colourFromLabel.setLabel(jalview.util.MessageManager.getString("label.colour_by_label"));
this.colourFromLabel.setSize(new java.awt.Dimension(139,22));this.thresholdIsMin.setBackground(java.awt.Color.white);this.thresholdIsMin.setLabel(jalview.util.MessageManager.getString("label.threshold_minmax"));this.thresholdIsMin.setSize(new java.awt.Dimension(135,23));this.jPanel1.add(a);this.jPanel1.add(this.minColour);this.jPanel1.add(b);this.jPanel1.add(this.maxColour);this.jPanel1.add(this.colourFromLabel);this.jPanel2.add(this.threshold);this.jPanel3.add(this.slider);this.jPanel4.add(this.thresholdValue);
this.jPanel4.add(this.thresholdIsMin);this.add(this.jPanel1);this.add(this.jPanel2);this.add(this.jPanel3);this.add(this.jPanel4)});e(c$,"actionPerformed",function(a){if(a.getSource()===this.thresholdValue)try{var b=(new Float(this.thresholdValue.getText())).floatValue();this.slider.setValue(I(1E3*b));this.adjustmentValueChanged(null)}catch(c){if(!y(c,NumberFormatException))throw c;}else a.getSource()===this.minColour?this.minColour_actionPerformed(null):a.getSource()===this.maxColour?this.maxColour_actionPerformed(null):
this.changeColour()},"java.awt.event.ActionEvent");e(c$,"itemStateChanged",function(){this.maxColour.setEnabled(!this.colourFromLabel.getState());this.minColour.setEnabled(!this.colourFromLabel.getState());this.changeColour()},"java.awt.event.ItemEvent");e(c$,"adjustmentValueChanged",function(){this.adjusting||(this.thresholdValue.setText(this.slider.getValue()/1E3+""),this.valueChanged())},"java.awt.event.AdjustmentEvent");d(c$,"valueChanged",function(){this.threshline.value=this.slider.getValue()/
1E3;this.cs.setThresh(this.threshline.value);this.changeColour();jalview.appletgui.PaintRefresher.Refresh(this,this.fr.getViewport().getSequenceSetId())});d(c$,"minColour_actionPerformed",function(a){null==a?new jalview.appletgui.UserDefinedColours(this,this.minColour.getBackground(),this.owner,jalview.util.MessageManager.getString("label.select_colour_minimum_value")):(this.minColour.setBackground(a),this.minColour.setForeground(a),this.minColour.repaint(),this.changeColour())},"java.awt.Color");
d(c$,"maxColour_actionPerformed",function(a){null==a?new jalview.appletgui.UserDefinedColours(this,this.maxColour.getBackground(),this.owner,jalview.util.MessageManager.getString("label.select_colour_maximum_value")):(this.maxColour.setBackground(a),this.maxColour.setForeground(a),this.maxColour.repaint(),this.changeColour())},"java.awt.Color");d(c$,"changeColour",function(){if(!this.adjusting){var a=-1;1==this.threshold.getSelectedIndex()?a=1:2==this.threshold.getSelectedIndex()&&(a=0);this.slider.setEnabled(!0);
this.thresholdValue.setEnabled(!0);var b=new jalview.schemes.GraduatedColor(this.minColour.getBackground(),this.maxColour.getBackground(),this.min,this.max);b.setColourByLabel(this.colourFromLabel.getState());this.maxColour.setEnabled(!this.colourFromLabel.getState());this.minColour.setEnabled(!this.colourFromLabel.getState());-1==a?(this.slider.setEnabled(!1),this.thresholdValue.setEnabled(!1),this.thresholdValue.setText("")):-1!=a&&null==this.threshline&&(this.threshline=new jalview.datamodel.GraphLine((this.max-
this.min)/2,"Threshold",java.awt.Color.black));-1!=a&&(this.adjusting=!0,b.setThresh(this.threshline.value),this.slider.setMinimum(I(1E3*this.min)),this.slider.setMaximum(I(1E3*this.max)),this.slider.setValue(I(1E3*this.threshline.value)),this.thresholdValue.setText(this.threshline.value+""),this.slider.setEnabled(!0),this.thresholdValue.setEnabled(!0),this.adjusting=!1);b.setThreshType(a);this.thresholdIsMin.getState()&&-1!=a&&(b=1==a?new jalview.schemes.GraduatedColor(b,this.threshline.value,this.max):
new jalview.schemes.GraduatedColor(b,this.min,this.threshline.value));this.fr.setColour(this.type,b);this.cs=b;jalview.appletgui.PaintRefresher.Refresh(this,this.fr.getViewport().getSequenceSetId())}});d(c$,"reset",function(){this.fr.setColour(this.type,this.oldcs);jalview.appletgui.PaintRefresher.Refresh(this,this.fr.getViewport().getSequenceSetId())});e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",
function(a){a.getSource()===this.minColour||a.getSource()===this.maxColour?this.actionPerformed(new java.awt.event.ActionEvent(a.getSource(),1,"Clicked")):jalview.appletgui.PaintRefresher.Refresh(this,this.fr.getViewport().getSequenceSetId())},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent")});p("jalview.schemes");q(null,"jalview.schemes.GraduatedColor",["jalview.schemes.UserColourScheme","java.awt.Color",
"java.lang.Float"],function(){c$=s(function(){this.thresholdState=-1;this.thrsh=this.range=this.base=this.db=this.dg=this.dr=this.lb=this.lg=this.lr=0;this.tolow=!1;this.autoScale=!0;this.ucs=null;this.colourByLabel=!1;r(this,arguments)},jalview.schemes,"GraduatedColor");m(c$,function(a,b,c,d){this.thrsh=NaN;this.tolow=c>=d;this.lr=a.getRed()/255;this.lg=a.getGreen()/255;this.lb=a.getBlue()/255;this.dr=b.getRed()/255-this.lr;this.dg=b.getGreen()/255-this.lg;this.db=b.getBlue()/255-this.lb;this.tolow?
(this.base=d,this.range=c-d):(this.base=c,this.range=d-c)},"java.awt.Color,java.awt.Color,~N,~N");m(c$,function(a){this.lr=a.lr;this.lg=a.lg;this.lb=a.lb;this.dr=a.dr;this.dg=a.dg;this.db=a.db;this.base=a.base;this.range=a.range;this.tolow=a.tolow;this.thresholdState=a.thresholdState;this.thrsh=a.thrsh;this.autoScale=a.autoScale;this.colourByLabel=a.colourByLabel},"jalview.schemes.GraduatedColor");m(c$,function(a,b,c){this.construct(a);this.updateBounds(b,c)},"jalview.schemes.GraduatedColor,~N,~N");
d(c$,"getMinColor",function(){return new java.awt.Color(this.lr,this.lg,this.lb)});d(c$,"getMaxColor",function(){return new java.awt.Color(this.lr+this.dr,this.lg+this.dg,this.lb+this.db)});d(c$,"getTolow",function(){return this.tolow});d(c$,"setTolow",function(a){this.tolow=a},"~B");d(c$,"isColored",function(a){a=a.getScore();if(Float.isNaN(a)||-1==this.thresholdState||Float.isNaN(this.thrsh))return!0;var b=1==this.thresholdState;return a<=this.thrsh?!b:b},"jalview.datamodel.SequenceFeature");d(c$,
"isColourByLabel",function(){return this.colourByLabel});d(c$,"setColourByLabel",function(a){this.colourByLabel=a},"~B");d(c$,"findColor",function(a){if(this.colourByLabel)return null==this.ucs&&(this.ucs=new jalview.schemes.UserColourScheme),this.ucs.createColourFromName(a.getDescription());if(0==this.range)return this.getMaxColor();a=a.getScore();if(Float.isNaN(a))return this.getMinColor();a=(a-this.base)/this.range;this.tolow&&(a=-a);0>a&&(a=0);1<a&&(a=1);return new java.awt.Color(this.lr+a*this.dr,
this.lg+a*this.dg,this.lb+a*this.db)},"jalview.datamodel.SequenceFeature");d(c$,"setThresh",function(a){this.thrsh=a},"~N");d(c$,"getThresh",function(){return this.thrsh});d(c$,"setThreshType",function(a){this.thresholdState=a},"~N");d(c$,"getThreshType",function(){return this.thresholdState});d(c$,"getMax",function(){return this.tolow?this.base:this.base+this.range});d(c$,"getMin",function(){return this.tolow?this.base+this.range:this.base});d(c$,"isAutoScale",function(){return this.autoScale});
d(c$,"setAutoScaled",function(a){this.autoScale=a},"~B");d(c$,"updateBounds",function(a,b){b<a?(this.base=b,this.range=a-b,this.tolow=!0):(this.base=a,this.range=b-a,this.tolow=!1)},"~N,~N")});p("jalview.appletgui");q(["awt2swing.Panel","jalview.renderer.seqfeatures.FeatureRenderer"],"jalview.appletgui.FeatureRenderer","awt2swing.Button $.Choice $.Label $.ScrollPane $.TextArea $.TextField $.Util jalview.appletgui.FeatureColourChooser $.JVDialog $.UserDefinedColours jalview.datamodel.SearchResults jalview.io.FeaturesFile jalview.schemes.GraduatedColor $.UserColourScheme jalview.util.MessageManager java.awt.BorderLayout $.Color $.Font $.GridLayout java.awt.event.ActionListener $.ItemListener $.MouseAdapter java.lang.Error".split(" "),
function(){c$=s(function(){this.featureLinks=null;this.featureIndex=0;this.deleteFeature=!1;this.colourPanel=null;H("jalview.appletgui.FeatureRenderer.FeatureColourPanel")||jalview.appletgui.FeatureRenderer.$FeatureRenderer$FeatureColourPanel$();r(this,arguments)},jalview.appletgui,"FeatureRenderer",jalview.renderer.seqfeatures.FeatureRenderer);m(c$,function(a){t(this,jalview.appletgui.FeatureRenderer);this.av=a;this.setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"))},
"jalview.viewmodel.AlignmentViewport");d(c$,"amendFeatures",function(a,b,c,d){var e=new awt2swing.Panel(new java.awt.BorderLayout),k=new awt2swing.TextField(16),g=new awt2swing.TextField(16),h=new awt2swing.TextArea(3,35),j=new awt2swing.TextField(8),n=new awt2swing.TextField(8),m,p=new awt2swing.Button("Delete");this.deleteFeature=!1;this.colourPanel=C(jalview.appletgui.FeatureRenderer.FeatureColourPanel,this,null);this.colourPanel.setSize(110,15);var q=new awt2swing.Panel(new java.awt.GridLayout(3,
1));this.featureIndex=0;var s;if(!c&&1<b.length){q=new awt2swing.Panel(new java.awt.GridLayout(4,1));s=new awt2swing.Panel;s.add(new awt2swing.Label("Select Feature: "));m=new awt2swing.Choice;for(var r=0;r<b.length;r++){var t=b[r].getType()+"/"+b[r].getBegin()+"-"+b[r].getEnd();null!=b[r].getFeatureGroup()&&(t+=" ("+b[r].getFeatureGroup()+")");m.addItem(t)}s.add(m);m.addItemListener((H("jalview.appletgui.FeatureRenderer$1")?0:jalview.appletgui.FeatureRenderer.$FeatureRenderer$1$(),C(jalview.appletgui.FeatureRenderer$1,
this,T("overlaps",m,"name",k,"features",b,"description",h,"source",g,"start",j,"end",n,"sequences",a,"ap",d))));q.add(s)}s=new awt2swing.Panel;q.add(s);s.add(new awt2swing.Label("Name: ",4));s.add(k);s=new awt2swing.Panel;q.add(s);s.add(new awt2swing.Label("Group: ",4));s.add(g);s=new awt2swing.Panel;q.add(s);s.add(new awt2swing.Label("Colour: ",4));s.add(this.colourPanel);e.add(q,"North");q=new awt2swing.Panel;q.add(new awt2swing.Label("Description: ",4));q.add((new awt2swing.ScrollPane).add(h));
c||(e.add(q,"South"),q=new awt2swing.Panel,q.add(new awt2swing.Label(" Start:",4)),q.add(j),q.add(new awt2swing.Label("  End:",4)),q.add(n));e.add(q,"Center");null==jalview.appletgui.FeatureRenderer.lastFeatureAdded&&(jalview.appletgui.FeatureRenderer.lastFeatureAdded=null!=b[0].type?b[0].type:"feature_1");null==jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded&&(null!=b[0].featureGroup?jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded=b[0].featureGroup:jalview.appletgui.FeatureRenderer.lastFeatureAdded=
"Jalview");r=c?jalview.util.MessageManager.getString("label.create_new_sequence_features"):jalview.util.MessageManager.formatMessage("label.amend_delete_features",E(-1,[a[0].getName()]));r=new jalview.appletgui.JVDialog(d.alignFrame,r,!0,385,240);r.setMainPanel(e);c?(k.setText(jalview.appletgui.FeatureRenderer.lastFeatureAdded),g.setText(jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded)):(r.ok.setLabel(jalview.util.MessageManager.getString("label.amend")),r.buttonPanel.add(p,1),p.addActionListener((H("jalview.appletgui.FeatureRenderer$2")?
0:jalview.appletgui.FeatureRenderer.$FeatureRenderer$2$(),C(jalview.appletgui.FeatureRenderer$2,this,T("dialog",r)))),k.setText(b[0].getType()),g.setText(b[0].getFeatureGroup()));j.setText(b[0].getBegin()+"");n.setText(b[0].getEnd()+"");h.setText(b[0].getDescription());null==this.getColour(k.getText())&&(new jalview.schemes.UserColourScheme).createColourFromName(k.getText());e=this.getFeatureStyle(k.getText());this.colourPanel.updateColor(e);r.setResizable(!0);this.colourPanel.addMouseListener((H("jalview.appletgui.FeatureRenderer$3")?
0:jalview.appletgui.FeatureRenderer.$FeatureRenderer$3$(),C(jalview.appletgui.FeatureRenderer$3,this,T("fr",this,"ap",d,"name",k,"dialog",r))));r.setVisible(!0);e=new jalview.io.FeaturesFile;r.accept&&(this.lastSeq=null,jalview.appletgui.FeatureRenderer.lastFeatureAdded=k.getText().trim(),jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded=g.getText().trim(),jalview.appletgui.FeatureRenderer.lastDescriptionAdded=h.getText().$replace("\n"," "));null!=jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded&&
1>jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded.length&&(jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded=null);if(c)if(r.accept&&0<k.getText().length){for(r=0;r<a.length;r++)b[r].type=jalview.appletgui.FeatureRenderer.lastFeatureAdded,b[r].featureGroup=jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded,b[r].description=jalview.appletgui.FeatureRenderer.lastDescriptionAdded,a[r].addSequenceFeature(b[r]),e.parseDescriptionHTML(b[r],!1);a=this.colourPanel.getBackground();null!=
jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded&&this.setGroupVisibility(jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded,!0);this.setColour(jalview.appletgui.FeatureRenderer.lastFeatureAdded,a);this.setVisible(jalview.appletgui.FeatureRenderer.lastFeatureAdded);this.findAllFeatures(!1)}else return!1;else{b=b[this.featureIndex];if(r.accept){b.type=jalview.appletgui.FeatureRenderer.lastFeatureAdded;b.featureGroup=jalview.appletgui.FeatureRenderer.lastFeatureGroupAdded;b.description=
jalview.appletgui.FeatureRenderer.lastDescriptionAdded;this.colourPanel.isGcol||this.setColour(b.type,this.colourPanel.getBackground());try{b.begin=Integer.parseInt(j.getText()),b.end=Integer.parseInt(n.getText())}catch(v){if(!y(v,NumberFormatException))throw v;}e.parseDescriptionHTML(b,!1);this.setVisible(jalview.appletgui.FeatureRenderer.lastFeatureAdded)}this.deleteFeature&&a[0].deleteFeature(b)}null!=this.av.featureSettings&&this.av.featureSettings.refreshTable();d.paintAlignment(!0);return!0},
"~A,~A,~B,jalview.appletgui.AlignmentPanel");c$.$FeatureRenderer$FeatureColourPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.label="";this.maxCol=null;this.isGcol=this.isColourByLabel=!1;r(this,arguments)},jalview.appletgui.FeatureRenderer,"FeatureColourPanel",awt2swing.Panel);d(c$,"updateColor",function(a){var b=null,c=null,d="";if(v(a,java.awt.Color))this.isGcol=!1,b=a,c=null;else if(v(a,jalview.schemes.GraduatedColor))this.isGcol=!0,c=a,b=null;else throw Error(jalview.util.MessageManager.getString("error.invalid_colour_for_mycheckbox"));
null!=b?this.setBackground(a=b):(-1!=c.getThreshType()&&(d+=" "+(1==c.getThreshType()?"(>)":"(<)")),(this.isColourByLabel=c.isColourByLabel())?(this.setBackground(a=java.awt.Color.white),d+=" (by Label)"):(this.setBackground(a=c.getMinColor()),this.maxCol=c.getMaxColor()));this.label=d;this.setBackground(a);this.repaint()},"~O");m(c$,function(){t(this,jalview.appletgui.FeatureRenderer.FeatureColourPanel,[null])});d(c$,"PaintComponent",function(a){var b=this.getSize();this.isGcol&&(this.isColourByLabel?
(a.setColor(java.awt.Color.white),a.fillRect(F(b.width/2),0,F(b.width/2),b.height),a.setColor(java.awt.Color.black),b=new java.awt.Font("Verdana",0,10),a.setFont(b),awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.label"),0,0)):(a.setColor(this.maxCol),a.fillRect(F(b.width/2),0,F(b.width/2),b.height)))},"java.awt.Graphics");c$=z()};c$.$FeatureRenderer$1$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureRenderer$1",null,java.awt.event.ItemListener);e(c$,"itemStateChanged",
function(){var a=this.f$.overlaps.getSelectedIndex();if(-1!=a){this.b$["jalview.appletgui.FeatureRenderer"].featureIndex=a;this.f$.name.setText(this.f$.features[a].getType());this.f$.description.setText(this.f$.features[a].getDescription());this.f$.source.setText(this.f$.features[a].getFeatureGroup());this.f$.start.setText(this.f$.features[a].getBegin()+"");this.f$.end.setText(this.f$.features[a].getEnd()+"");var b=new jalview.datamodel.SearchResults;b.addResult(this.f$.sequences[0],this.f$.features[a].getBegin(),
this.f$.features[a].getEnd());this.f$.ap.seqPanel.seqCanvas.highlightSearchResults(b)}a=this.b$["jalview.appletgui.FeatureRenderer"].getFeatureStyle(this.f$.name.getText());null==a&&(a=(new jalview.schemes.UserColourScheme).createColourFromName(this.f$.name.getText()));this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.updateColor(a)},"java.awt.event.ItemEvent");c$=z()};c$.$FeatureRenderer$2$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureRenderer$2",null,java.awt.event.ActionListener);
e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.FeatureRenderer"].deleteFeature=!0;this.f$.dialog.setVisible(!1)},"java.awt.event.ActionEvent");c$=z()};c$.$FeatureRenderer$3$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureRenderer$3",java.awt.event.MouseAdapter);e(c$,"mousePressed",function(){this.b$["jalview.appletgui.FeatureRenderer"].colourPanel.isGcol?(new jalview.appletgui.FeatureColourChooser(this.f$.ap.alignFrame,this.f$.name.getText()),this.f$.dialog.transferFocus()):new jalview.appletgui.UserDefinedColours(this.f$.fr,
this.f$.ap.alignFrame)},"java.awt.event.MouseEvent");c$=z()};G(c$,"lastFeatureAdded",null,"lastFeatureGroupAdded",null,"lastDescriptionAdded",null)});p("jalview.renderer.seqfeatures");q(["jalview.viewmodel.seqfeatures.FeatureRendererModel"],"jalview.renderer.seqfeatures.FeatureRenderer","awt2swing.Util jalview.util.Comparison java.awt.AlphaComposite $.Color java.awt.image.BufferedImage java.lang.Float".split(" "),function(){c$=s(function(){this.fm=null;this.charOffset=0;this.offscreenRender=!1;this.lastSeq=
null;this.s="\x00";this.av_charWidth=this.av_charHeight=this.i=0;this.av_isShowSeqFeatureHeight=this.av_validCharWidth=!1;this.lastSequenceFeatures=this.offscreenImage=null;this.epos=this.spos=this.sfindex=this.sfSize=0;this.transparencyAvailable=!0;r(this,arguments)},jalview.renderer.seqfeatures,"FeatureRenderer",jalview.viewmodel.seqfeatures.FeatureRendererModel);d(c$,"updateAvConfig",function(){this.av_charHeight=this.av.getCharHeight();this.av_charWidth=this.av.getCharWidth();this.av_validCharWidth=
this.av.isValidCharWidth();this.av_isShowSeqFeatureHeight=this.av.isShowSequenceFeaturesHeight()});d(c$,"renderFeature",function(a,b,c,d,e,k,g,h){this.updateAvConfig();if(c<=g&&d>=k){c<k&&(c=k);d>=g&&(d=g);g=h+this.av_charHeight-F(this.av_charHeight/5);for(this.i=c;this.i<=d;this.i++)this.s=b.getCharAt(this.i),jalview.util.Comparison.isGap(this.s)||(a.setColor(e),a.fillRect((this.i-k)*this.av_charWidth,h,this.av_charWidth,this.av_charHeight),!this.offscreenRender&&this.av_validCharWidth&&(a.setColor(java.awt.Color.white),
this.charOffset=F((this.av_charWidth-this.fm.charWidth(this.s))/2),awt2swing.Util.drawString(a,String.valueOf(this.s),this.charOffset+this.av_charWidth*(this.i-k),g)))}},"java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N");d(c$,"renderScoreFeature",function(a,b,c,d,e,k,g,h,j){this.updateAvConfig();if(c<=g&&d>=k){c<k&&(c=k);d>=g&&(d=g);g=h+this.av_charHeight-F(this.av_charHeight/5);var n=0,m=this.av_charHeight;0!=j[0]?128>j[1]?(m=F(this.av_charHeight*(128-j[1])/512),n=this.av_charHeight-
F(m/2)):(n=F(this.av_charHeight/2),m=F(this.av_charHeight*(j[1]-128)/512)):(m=F(this.av_charHeight*j[1]/255),n=this.av_charHeight-m);for(this.i=c;this.i<=d;this.i++)this.s=b.getCharAt(this.i),jalview.util.Comparison.isGap(this.s)||(a.setColor(e),c=(this.i-k)*this.av_charWidth,a.drawRect(c,h,this.av_charWidth,this.av_charHeight),a.fillRect(c,h+n,this.av_charWidth,m),!this.offscreenRender&&this.av_validCharWidth&&(a.setColor(java.awt.Color.black),this.charOffset=F((this.av_charWidth-this.fm.charWidth(this.s))/
2),awt2swing.Util.drawString(a,String.valueOf(this.s),this.charOffset+this.av_charWidth*(this.i-k),g)))}},"java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,java.awt.Color,~N,~N,~N,~A");d(c$,"findFeatureColour",function(a,b,c){return new java.awt.Color(this.findFeatureColour(a.getRGB(),b,c))},"java.awt.Color,jalview.datamodel.SequenceI,~N");d(c$,"findFeatureColour",function(a,b,c){if(!this.av.isShowSequenceFeatures())return a;var d=b.getSequenceFeatures();b!==this.lastSeq?(this.lastSeq=b,this.lastSequenceFeatures=
d,null!=this.lastSequenceFeatures&&(this.sfSize=this.lastSequenceFeatures.length)):this.lastSequenceFeatures!==d&&(this.lastSequenceFeatures=d,null!=this.lastSequenceFeatures&&(this.sfSize=this.lastSequenceFeatures.length));if(null==this.lastSequenceFeatures||0==this.sfSize)return a;if(jalview.util.Comparison.isGap(this.lastSeq.getCharAt(c)))return java.awt.Color.white.getRGB();1!=this.transparency&&null==this.offscreenImage&&(this.offscreenImage=new java.awt.image.BufferedImage(1,1,2));this.currentColour=
null;this.offscreenRender=!0;if(null!=this.offscreenImage)return this.offscreenImage.setRGB(0,0,a),this.drawSequence(this.offscreenImage.getGraphics(),this.lastSeq,c,c,0),this.offscreenImage.getRGB(0,0);this.drawSequence(null,this.lastSeq,this.lastSeq.findPosition(c),-1,-1);return null==this.currentColour?a:this.currentColour.intValue()},"~N,jalview.datamodel.SequenceI,~N");d(c$,"drawSequence",function(a,b,c,d,e){var k=b.getSequenceFeatures();if(!(null==k||0==k.length)){null!=a&&(this.fm=a.getFontMetrics());
this.updateFeatures();if(null==this.lastSeq||b!==this.lastSeq||k!==this.lastSequenceFeatures)this.lastSeq=b,this.lastSequenceFeatures=k;1!=this.transparency&&null!=a&&a.setComposite(java.awt.AlphaComposite.getInstance(3,this.transparency));this.offscreenRender||(this.spos=this.lastSeq.findPosition(c),this.epos=this.lastSeq.findPosition(d));this.sfSize=this.lastSequenceFeatures.length;for(var g=0;g<this.renderOrder.length;g++)if(k=this.renderOrder[g],null!=k&&this.showFeatureOfType(k))for(this.sfindex=
0;this.sfindex<this.sfSize;this.sfindex++){var h=this.lastSequenceFeatures[this.sfindex];if(h.type.equals(k)&&!(null!=this.featureGroups&&null!=h.featureGroup&&0!=h.featureGroup.length&&this.featureGroups.containsKey(h.featureGroup)&&!this.featureGroups.get(h.featureGroup).booleanValue())&&(this.offscreenRender||!(h.getBegin()>this.epos||h.getEnd()<this.spos)))this.offscreenRender&&null==this.offscreenImage?h.begin<=c&&h.end>=c&&(this.currentColour=new Integer(this.getColour(h).getRGB())):h.type.equals("disulfide bond")?
(this.renderFeature(a,b,b.findIndex(h.begin)-1,b.findIndex(h.begin)-1,this.getColour(h),c,d,e),this.renderFeature(a,b,b.findIndex(h.end)-1,b.findIndex(h.end)-1,this.getColour(h),c,d,e)):this.showFeature(h)&&(this.av_isShowSeqFeatureHeight&&!Float.isNaN(h.score)?this.renderScoreFeature(a,b,b.findIndex(h.begin)-1,b.findIndex(h.end)-1,this.getColour(h),c,d,e,this.normaliseScore(h)):this.renderFeature(a,b,b.findIndex(h.begin)-1,b.findIndex(h.end)-1,this.getColour(h),c,d,e))}1!=this.transparency&&(null!=
a&&this.transparencyAvailable)&&a.setComposite(java.awt.AlphaComposite.getInstance(3,1))}},"java.awt.Graphics,jalview.datamodel.SequenceI,~N,~N,~N");d(c$,"setTransparencyAvailable",function(a){this.transparencyAvailable=a},"~B");e(c$,"isTransparencyAvailable",function(){return this.transparencyAvailable});e(c$,"featuresAdded",function(){this.lastSeq=null;this.findAllFeatures()})});p("jalview.viewmodel.seqfeatures");q(["jalview.api.FeatureRenderer","java.beans.PropertyChangeSupport","java.lang.Boolean",
"java.util.Hashtable","java.util.concurrent.ConcurrentHashMap"],"jalview.viewmodel.seqfeatures.FeatureRendererModel","jalview.schemes.GraduatedColor $.UserColourScheme jalview.util.QuickSort jalview.viewmodel.seqfeatures.FeatureRendererSettings $.FeaturesDisplayed java.awt.Color java.lang.Error $.Float java.util.ArrayList $.Arrays".split(" "),function(){c$=s(function(){this.transparency=1;this.minmax=this.av=this.changeSupport=this.renderOrder=this.currentColour=this.featureGroups=this.featureColours=
null;this.findingFeatures=this.newFeatureAdded=!1;this.featureOrder=this.firing=null;r(this,arguments)},jalview.viewmodel.seqfeatures,"FeatureRendererModel",null,jalview.api.FeatureRenderer);J(c$,function(){this.featureColours=new java.util.concurrent.ConcurrentHashMap;this.featureGroups=new java.util.concurrent.ConcurrentHashMap;this.changeSupport=new java.beans.PropertyChangeSupport(this);this.minmax=new java.util.Hashtable;this.firing=Boolean.FALSE});e(c$,"getViewport",function(){return this.av});
d(c$,"getSettings",function(){return new jalview.viewmodel.seqfeatures.FeatureRendererSettings(this)});d(c$,"transferSettings",function(a){this.renderOrder=a.renderOrder;this.featureGroups=a.featureGroups;this.featureColours=a.featureColours;this.transparency=a.transparency;this.featureOrder=a.featureOrder},"jalview.viewmodel.seqfeatures.FeatureRendererSettings");d(c$,"transferSettings",function(a){var b=new jalview.viewmodel.seqfeatures.FeatureRendererSettings(a);this.renderOrder=b.renderOrder;this.featureGroups=
b.featureGroups;this.featureColours=b.featureColours;this.transparency=b.transparency;this.featureOrder=b.featureOrder;if(null!=this.av&&this.av!==a.getViewport()&&null!=a.getFeaturesDisplayed())if(b=this.getFeaturesDisplayed(),null==b)this.setFeaturesDisplayedFrom(a.getFeaturesDisplayed());else{b.clear();for(a=a.getFeaturesDisplayed().getVisibleFeatures();a.hasNext();)b.setVisible(a.next())}},"jalview.api.FeatureRenderer");d(c$,"setFeaturesDisplayedFrom",function(a){this.av.setFeaturesDisplayed(new jalview.viewmodel.seqfeatures.FeaturesDisplayed(a))},
"jalview.api.FeaturesDisplayedI");e(c$,"setVisible",function(a){var b=this.av.getFeaturesDisplayed();null==b&&this.av.setFeaturesDisplayed(b=new jalview.viewmodel.seqfeatures.FeaturesDisplayed);b.isRegistered(a)||this.pushFeatureType(java.util.Arrays.asList(E(-1,[a])));b.setVisible(a)},"~S");e(c$,"setAllVisible",function(a){var b=this.av.getFeaturesDisplayed();null==b&&this.av.setFeaturesDisplayed(b=new jalview.viewmodel.seqfeatures.FeaturesDisplayed);for(var c=new java.util.ArrayList,d,e=a.iterator();e.hasNext()&&
((d=e.next())||1);)b.isRegistered(d)||c.add(d);0<c.size()&&this.pushFeatureType(c);b.setAllVisible(a)},"java.util.List");d(c$,"pushFeatureType",function(a){var b=a.size(),c=Array((null==this.renderOrder?0:this.renderOrder.length)+b);a.toArray(c);null!=this.renderOrder&&(System.arraycopy(c,0,c,this.renderOrder.length,b),System.arraycopy(this.renderOrder,0,c,0,this.renderOrder.length));this.renderOrder=c},"java.util.List");d(c$,"getMinMax",function(){return this.minmax});d(c$,"normaliseScore",function(a){var b=
this.minmax.get(a.type)[0],c=S(-1,[0,255]);null!=b&&(0!=c[0]||0>b[0]?(c[0]=1,c[1]=fa(F(128)+127*(a.score/b[1]))):c[1]=Clazz_floatToByte(F(255)*(a.score/b[1])));return c},"jalview.datamodel.SequenceFeature");d(c$,"updateFeatures",function(){if(null==this.av.getFeaturesDisplayed()||null==this.renderOrder||this.newFeatureAdded)if(this.findAllFeatures(),1>this.av.getFeaturesDisplayed().getVisibleFeatureCount())return!1;return!0});d(c$,"findAllFeatures",function(){this.firing.equals(Boolean.FALSE)&&(this.firing=
Boolean.TRUE,this.findAllFeatures(!0),this.changeSupport.firePropertyChange("changeSupport",null,null),this.firing=Boolean.FALSE)});e(c$,"findFeaturesAtRes",function(a,b){var c=new java.util.ArrayList,d=a.getSequenceFeatures();if(null!=d)for(var e=0;e<d.length;e++)this.av.areFeaturesDisplayed()&&this.av.getFeaturesDisplayed().isVisible(d[e].getType())&&(null!=d[e].featureGroup&&null!=this.featureGroups&&this.featureGroups.containsKey(d[e].featureGroup)&&!this.featureGroups.get(d[e].featureGroup).booleanValue()||
d[e].getBegin()<=b&&d[e].getEnd()>=b&&c.add(d[e]));return c},"jalview.datamodel.SequenceI,~N");d(c$,"findAllFeatures",function(a){this.newFeatureAdded=!1;if(this.findingFeatures)this.newFeatureAdded=!0;else{this.findingFeatures=!0;null==this.av.getFeaturesDisplayed()&&this.av.setFeaturesDisplayed(new jalview.viewmodel.seqfeatures.FeaturesDisplayed);var b=this.av.getFeaturesDisplayed(),c=new java.util.ArrayList,d=new java.util.ArrayList;if(null!=this.renderOrder)for(var e=0;e<this.renderOrder.length;e++)null!=
this.renderOrder[e]&&d.add(this.renderOrder[e]);null==this.minmax&&(this.minmax=new java.util.Hashtable);for(var k=this.av.getAlignment(),e=0;e<k.getHeight();e++){var g=k.getSequenceAt(e).getSequenceFeatures();if(null!=g)for(var h=0;h<g.length;){if(!b.isRegistered(g[h].getType())){var j=g[h].getFeatureGroup();if(null!=j){var n=this.featureGroups.get(j);null==n&&(n=Boolean.$valueOf(a),this.featureGroups.put(j,n));if(!n.booleanValue()){h++;continue}}!(0==g[h].begin&&0==g[h].end)&&(a&&!d.contains(g[h].getType()))&&
(b.setVisible(g[h].getType()),this.setOrder(g[h].getType(),0))}c.contains(g[h].getType())||c.add(g[h].getType());Float.isNaN(g[h].score)||(j=1<=g[h].getBegin()?0:1,n=this.minmax.get(g[h].getType()),null==n&&(n=E(-1,[null,null]),this.minmax.put(g[h].getType(),n)),null==n[j]?n[j]=Q(-1,[g[h].score,g[h].score]):(n[j][0]>g[h].score&&(n[j][0]=g[h].score),n[j][1]<g[h].score&&(n[j][1]=g[h].score)));h++}}this.updateRenderOrder(c);this.findingFeatures=!1}},"~B");d(c$,"updateRenderOrder",function(a){a=new java.util.ArrayList(a);
var b=this.renderOrder;this.renderOrder=Array(a.size());var c,d=null,e=null==this.featureOrder,k=0;if(null!=b&&0<b.length)for(var g=0;g<b.length;g++)null!=b[g]&&(e&&this.setOrder(b[g],1-(1+g)/b.length),a.contains(b[g])&&(this.renderOrder[k++]=b[g],a.remove(b[g]),null!=this.minmax&&(c=this.minmax.get(b[g]),null!=c&&(d=this.featureColours.get(b[g]),null!=d&&(v(d,jalview.schemes.GraduatedColor)&&d.isAutoScale())&&d.updateBounds(c[0][0],c[0][1])))));if(0!=a.size()){for(var g=b=a.size()-1,h=!1,j=Array(a.size()),
n=Q(a.size(),0),m,p=a.iterator();p.hasNext()&&((m=p.next())||1);){j[b]=m;null!=this.minmax&&(c=this.minmax.get(j[b]),null!=c&&(d=this.featureColours.get(j[b]),null!=d&&(v(d,jalview.schemes.GraduatedColor)&&d.isAutoScale())&&d.updateBounds(c[0][0],c[0][1])));if(e||!this.featureOrder.containsKey(j[b]))c=e?a.size():this.featureOrder.size(),this.setOrder(j[b],b/c);n[b]=2-this.featureOrder.get(j[b]).floatValue();b<g&&(h=h||n[b]>n[b+1]);b--}1<g&&h&&jalview.util.QuickSort.sortFloatObject(n,j);System.arraycopy(j,
0,this.renderOrder,k,j.length)}},"java.util.List");e(c$,"getFeatureStyle",function(a){var b=this.featureColours.get(a);null==b&&(b=(new jalview.schemes.UserColourScheme).createColourFromName(a),this.featureColours.put(a,b));return b},"~S");d(c$,"getColour",function(a){var b=this.getFeatureStyle(a);if(v(b,java.awt.Color))return b;if(v(b,jalview.schemes.GraduatedColor))return b.getMaxColor();throw Error("Implementation Error: Unrecognised render object "+b.getClass()+" for features of type "+a);},"~S");
d(c$,"getColour",function(a){var b=this.getFeatureStyle(a.getType());if(v(b,java.awt.Color))return b;if(v(b,jalview.schemes.GraduatedColor))return b.findColor(a);throw Error("Implementation Error: Unrecognised render object "+b.getClass()+" for features of type "+a.getType());},"jalview.datamodel.SequenceFeature");d(c$,"showFeature",function(a){var b=this.getFeatureStyle(a.type);return v(b,jalview.schemes.GraduatedColor)?b.isColored(a):!0},"jalview.datamodel.SequenceFeature");d(c$,"showFeatureOfType",
function(a){return this.av.getFeaturesDisplayed().isVisible(a)},"~S");e(c$,"setColour",function(a,b){this.featureColours.put(a,b)},"~S,~O");d(c$,"setTransparency",function(a){this.transparency=a},"~N");d(c$,"getTransparency",function(){return this.transparency});d(c$,"setOrder",function(a,b){null==this.featureOrder&&(this.featureOrder=new java.util.Hashtable);this.featureOrder.put(a,new Float(b));return b},"~S,~N");d(c$,"getOrder",function(a){return null!=this.featureOrder&&this.featureOrder.containsKey(a)?
this.featureOrder.get(a).floatValue():-1},"~S");e(c$,"getFeatureColours",function(){return new java.util.concurrent.ConcurrentHashMap(this.featureColours)});d(c$,"setFeaturePriority",function(a){this.setFeaturePriority(a,!0)},"~A");d(c$,"setFeaturePriority",function(a,b){var c=null;b?null!=(c=this.av.getFeaturesDisplayed())?this.av.getFeaturesDisplayed().clear():this.av.setFeaturesDisplayed(c=new jalview.viewmodel.seqfeatures.FeaturesDisplayed):c=this.av.getFeaturesDisplayed();if(null!=a&&(this.renderOrder=
Array(a.length),0<a.length))for(var d=0;d<a.length;d++){var e=a[d][0].toString();this.setColour(e,a[d][1]);a[d][2].booleanValue()&&c.setVisible(e);this.renderOrder[a.length-d-1]=e}},"~A,~B");d(c$,"addPropertyChangeListener",function(a){this.changeSupport.addPropertyChangeListener(a)},"java.beans.PropertyChangeListener");d(c$,"removePropertyChangeListener",function(a){this.changeSupport.removePropertyChangeListener(a)},"java.beans.PropertyChangeListener");d(c$,"getAllFeatureColours",function(){return this.featureColours.keySet()});
d(c$,"clearRenderOrder",function(){this.renderOrder=null});d(c$,"hasRenderOrder",function(){return null!=this.renderOrder});d(c$,"getRenderOrder",function(){return null==this.renderOrder?java.util.Arrays.asList(E(-1,[])):java.util.Arrays.asList(this.renderOrder)});d(c$,"getFeatureGroupsSize",function(){return null!=this.featureGroups?0:this.featureGroups.size()});e(c$,"getFeatureGroups",function(){return null==this.featureGroups?java.util.Arrays.asList([]):java.util.Arrays.asList(this.featureGroups.keySet().toArray([]))});
d(c$,"checkGroupVisibility",function(a,b){return this.featureGroups.containsKey(a)?this.featureGroups.get(a).booleanValue():b?(this.featureGroups.put(a,new Boolean(!0)),!0):!1},"~S,~B");e(c$,"getGroups",function(a){if(null!=this.featureGroups){for(var b=new java.util.ArrayList,c,d=this.featureGroups.keySet().iterator();d.hasNext()&&((c=d.next())||1);)this.featureGroups.get(c).booleanValue()==a&&b.add(c);return b}return null},"~B");d(c$,"setGroupVisibility",function(a,b){this.featureGroups.put(a,new Boolean(b))},
"~S,~B");d(c$,"setGroupVisibility",function(a,b){if(null!=a&&0<a.size()&&null!=this.featureGroups)for(var c=!1,d,e=a.iterator();e.hasNext()&&((d=e.next())||1);){var k=this.featureGroups.get(d);this.featureGroups.put(d,new Boolean(b));null!=k&&(c=c||b!=k.booleanValue())}},"java.util.List,~B");e(c$,"getDisplayedFeatureCols",function(){var a=new java.util.Hashtable;if(null==this.getViewport().getFeaturesDisplayed())return a;for(var b=this.getViewport().getFeaturesDisplayed().getVisibleFeatures();b.hasNext();){var c=
b.next();a.put(c,this.getColour(c))}return a});d(c$,"getFeaturesDisplayed",function(){return this.av.getFeaturesDisplayed()});e(c$,"getDisplayedFeatureTypes",function(){var a=null,a=this.getRenderOrder().toArray([]),b=this.av.getFeaturesDisplayed();if(null!=b)for(var c=0;c<a.length;c++)b.isVisible(a[c])||(a[c]=null);return a});e(c$,"getDisplayedFeatureGroups",function(){for(var a=null,b=new java.util.ArrayList,c=this.getFeatureGroups().iterator(),d=!1;c.hasNext();)if(a=c.next(),this.checkGroupVisibility(a,
!1)&&(d=!0,b.add(a)),d)a=Array(b.size()),b.toArray(a);else return null;return a})});p("jalview.api");M(jalview.api,"FeatureRenderer");p("java.util.concurrent");q(["java.util.AbstractMap","$.AbstractSet","$.Iterator","$.Map","$.MapEntry"],"java.util.concurrent.ConcurrentHashMap","java.lang.IllegalArgumentException $.IllegalStateException java.util.AbstractCollection $.Arrays $.ConcurrentModificationException java.util.MapEntry.Type java.util.NoSuchElementException".split(" "),function(){c$=s(function(){this.elementCount=
0;this.elementData=null;this.modCount=this.threshold=this.loadFactor=0;r(this,arguments)},java.util.concurrent,"ConcurrentHashMap",java.util.AbstractMap,[java.util.Map,Cloneable,java.io.Serializable]);d(c$,"newElementArray",function(a){return Array(a)},"~N");m(c$,function(){this.construct(16)});m(c$,function(a){t(this,java.util.concurrent.ConcurrentHashMap,[]);if(0<=a)this.elementCount=0,this.elementData=this.newElementArray(0==a?1:a),this.loadFactor=0.75,this.computeMaxSize();else throw new IllegalArgumentException;
},"~N");m(c$,function(a,b){t(this,java.util.concurrent.ConcurrentHashMap,[]);if(0<=a&&0<b)this.elementCount=0,this.elementData=this.newElementArray(0==a?1:a),this.loadFactor=b,this.computeMaxSize();else throw new IllegalArgumentException;},"~N,~N");m(c$,function(a){this.construct(6>a.size()?11:2*a.size());K(this,java.util.concurrent.ConcurrentHashMap,"putAll",[a])},"java.util.Map");e(c$,"clear",function(){0<this.elementCount&&(this.elementCount=0,java.util.Arrays.fill(this.elementData,null),this.modCount++)});
d(c$,"clone",function(){return this.cloneHM()});d(c$,"cloneHM",function(){try{var a=this.cloneAM();a.elementData=this.newElementArray(this.elementData.length);for(var b,c=0;c<this.elementData.length;c++)if(null!=(b=this.elementData[c]))a.elementData[c]=b.clone();return a}catch(d){if(v(d,CloneNotSupportedException))return null;throw d;}});d(c$,"computeMaxSize",($fz=function(){this.threshold=Math.round(this.elementData.length*this.loadFactor)},$fz.isPrivate=!0,$fz));e(c$,"containsKey",function(a){return null!=
this.getEntry(a)},"~O");d(c$,"keysEqual",function(a,b){return(null==a?0:a.hashCode())!=b.origKeyHash?!1:null==a&&null==b.key?!0:a.equals(b.key)},"~O,java.util.concurrent.ConcurrentHashMap.Entry");e(c$,"containsValue",function(a){if(null!=a)for(var b=this.elementData.length;0<=--b;)for(var c=this.elementData[b];null!=c;){if(a.equals(c.value))return!0;c=c.next}else for(b=this.elementData.length;0<=--b;)for(c=this.elementData[b];null!=c;){if(null==c.value)return!0;c=c.next}return!1},"~O");e(c$,"entrySet",
function(){return new java.util.concurrent.ConcurrentHashMap.ConcurrentHashMapEntrySet(this)});e(c$,"get",function(a){a=this.getEntry(a);return null!=a?a.value:null},"~O");d(c$,"getEntry",function(a){var b=this.getModuloHash(a);return this.findEntry(a,b)},"~O");d(c$,"getModuloHash",function(a){return null==a?0:(a.hashCode()&2147483647)%this.elementData.length},"~O");d(c$,"findEntry",function(a,b){var c;c=this.elementData[b];if(null!=a)for(;null!=c&&!this.keysEqual(a,c);)c=c.next;else for(;null!=c&&
null!=c.key;)c=c.next;return c},"~O,~N");e(c$,"isEmpty",function(){return 0==this.elementCount});e(c$,"keySet",function(){null==this.$keySet&&(this.$keySet=(H("java.util.concurrent.ConcurrentHashMap$1")?0:java.util.concurrent.ConcurrentHashMap.$ConcurrentHashMap$1$(),C(java.util.concurrent.ConcurrentHashMap$1,this,null)));return this.$keySet});e(c$,"put",function(a,b){var c=this.getModuloHash(a),d=this.findEntry(a,c);if(null==d)return this.modCount++,++this.elementCount>this.threshold&&(this.rehash(),
c=null==a?0:(a.hashCode()&2147483647)%this.elementData.length),this.createEntry(a,c,b),null;c=d.value;d.value=b;return c},"~O,~O");d(c$,"createEntry",function(a,b,c){a=new java.util.concurrent.ConcurrentHashMap.Entry(a,c);a.next=this.elementData[b];return this.elementData[b]=a},"~O,~N,~O");d(c$,"putAll",function(a){if(!a.isEmpty()){var b=this.elementCount+a.size();b>this.threshold&&this.rehash(b);this.putAllHM(a)}},"java.util.Map");d(c$,"rehash",function(a){a=0==a?1:a<<1;for(var b=this.newElementArray(a),
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c);)d=c,c=c.next}else for(c=this.elementData[0];null!=c&&null!=c.key;)d=c,c=c.next;if(null==c)return null;null==d?this.elementData[b]=c.next:d.next=c.next;this.modCount++;this.elementCount--;return c},"~O");e(c$,"size",function(){return this.elementCount});e(c$,"values",function(){null==this.valuesCollection&&(this.valuesCollection=(H("java.util.concurrent.ConcurrentHashMap$2")?0:java.util.concurrent.ConcurrentHashMap.$ConcurrentHashMap$2$(),C(java.util.concurrent.ConcurrentHashMap$2,this,null)));
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m(c$,function(a,b,c,d,e){t(this,java.awt.image.DirectColorModel,[java.awt.color.ColorSpace.getInstance(1E3),a,b,c,d,e,!1,0==e?1:3,java.awt.image.ColorModel.getDefaultTransferType(a)])},"~N,~N,~N,~N,~N");m(c$,function(a,b,c,d,e,k,g,h){t(this,java.awt.image.DirectColorModel,[a,b,c,d,e,k,g,0==k?1:3,h])},"java.awt.color.ColorSpace,~N,~N,~N,~N,~N,~B,~N");d(c$,"getRedMask",function(){return this.maskArray[0]});d(c$,"getGreenMask",function(){return this.maskArray[1]});d(c$,"getBlueMask",function(){return this.maskArray[2]});
d(c$,"getAlphaMask",function(){return this.supportsAlpha?this.maskArray[3]:0});d(c$,"getDefaultRGBComponents",function(a){a=this.getComponents(a,null,0);a=this.getNormalizedComponents(a,0,null,0);return this.colorSpace.toRGB(a)},"~N");d(c$,"getsRGBComponentFromsRGB",function(a,b){var c=(a&this.maskArray[b])>>>this.maskOffsets[b];if(this.$isAlphaPremultiplied)var d=(a&this.maskArray[3])>>>this.maskOffsets[3],c=0==d?0:I(255*c*this.scaleFactors[b]/(d*this.scaleFactors[3])+0.5);else 1!=this.scaleFactors[b]&&
(c=I(c*this.scaleFactors[b]+0.5));return c},"~N,~N");d(c$,"getsRGBComponentFromLinearRGB",function(a,b){var c=(a&this.maskArray[b])>>>this.maskOffsets[b];if(this.$isAlphaPremultiplied)var d=(1<<this.lRGBprecision)-1,e=(a&this.maskArray[3])>>>this.maskOffsets[3],c=0==e?0:I(c*this.scaleFactors[b]*d/(e*this.scaleFactors[3])+0.5);else this.nBits[b]!=this.lRGBprecision&&(c=16==this.lRGBprecision?I(257*c*this.scaleFactors[b]+0.5):I(c*this.scaleFactors[b]+0.5));return this.tosRGB8LUT[c]&255},"~N,~N");d(c$,
"getRed",function(a){if(this.is_sRGB)return this.getsRGBComponentFromsRGB(a,0);if(this.is_LinearRGB)return this.getsRGBComponentFromLinearRGB(a,0);a=this.getDefaultRGBComponents(a);return I(255*a[0]+0.5)},"~N");d(c$,"getGreen",function(a){if(this.is_sRGB)return this.getsRGBComponentFromsRGB(a,1);if(this.is_LinearRGB)return this.getsRGBComponentFromLinearRGB(a,1);a=this.getDefaultRGBComponents(a);return I(255*a[1]+0.5)},"~N");d(c$,"getBlue",function(a){if(this.is_sRGB)return this.getsRGBComponentFromsRGB(a,
2);if(this.is_LinearRGB)return this.getsRGBComponentFromLinearRGB(a,2);a=this.getDefaultRGBComponents(a);return I(255*a[2]+0.5)},"~N");d(c$,"getAlpha",function(a){if(!this.supportsAlpha)return 255;a=(a&this.maskArray[3])>>>this.maskOffsets[3];1!=this.scaleFactors[3]&&(a=I(a*this.scaleFactors[3]+0.5));return a},"~N");d(c$,"getRGB",function(a){if(this.is_sRGB||this.is_LinearRGB)return this.getAlpha(a)<<24|this.getRed(a)<<16|this.getGreen(a)<<8|this.getBlue(a)<<0;var b=this.getDefaultRGBComponents(a);
return this.getAlpha(a)<<24|I(255*b[0]+0.5)<<16|I(255*b[1]+0.5)<<8|I(255*b[2]+0.5)<<0},"~N");d(c$,"getRed",function(a){var b=0;switch(this.transferType){case 0:b=a[0]&255;break;case 3:b=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+this.transferType);}return this.getRed(b)},"~O");d(c$,"getGreen",function(a){var b=0;switch(this.transferType){case 0:b=a[0]&255;break;case 3:b=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+
this.transferType);}return this.getGreen(b)},"~O");d(c$,"getBlue",function(a){var b=0;switch(this.transferType){case 0:b=a[0]&255;break;case 3:b=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+this.transferType);}return this.getBlue(b)},"~O");d(c$,"getAlpha",function(a){var b=0;switch(this.transferType){case 0:b=a[0]&255;break;case 3:b=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+
this.transferType);}return this.getAlpha(b)},"~O");d(c$,"getRGB",function(a){var b=0;switch(this.transferType){case 0:b=a[0]&255;break;case 3:b=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+this.transferType);}return this.getRGB(b)},"~O");d(c$,"getDataElements",function(a,b){var c=null;3==this.transferType&&null!=b?(c=b,c[0]=0):c=w(1,0);var d=java.awt.image.ColorModel.getRGBdefault();if(this===d||this.equals(d))return c[0]=a,c;
var e,k,g;e=a>>16&255;k=a>>8&255;g=a&255;if(this.is_sRGB||this.is_LinearRGB){var h,j;this.is_LinearRGB?8==this.lRGBprecision?(e=this.fromsRGB8LUT8[e]&255,k=this.fromsRGB8LUT8[k]&255,g=this.fromsRGB8LUT8[g]&255,h=8,j=0.003921569):(e=this.fromsRGB8LUT16[e]&65535,k=this.fromsRGB8LUT16[k]&65535,g=this.fromsRGB8LUT16[g]&65535,h=16,j=1.5259022E-5):(h=8,j=0.003921569);this.supportsAlpha&&(d=a>>24&255,this.$isAlphaPremultiplied&&(j*=0.003921569*d,h=-1),8!=this.nBits[3]&&(d=I(0.003921569*d*((1<<this.nBits[3])-
1)+0.5),d>(1<<this.nBits[3])-1&&(d=(1<<this.nBits[3])-1)),c[0]=d<<this.maskOffsets[3]);this.nBits[0]!=h&&(e=I(e*j*((1<<this.nBits[0])-1)+0.5));this.nBits[1]!=h&&(k=I(k*j*((1<<this.nBits[1])-1)+0.5));this.nBits[2]!=h&&(g=I(g*j*((1<<this.nBits[2])-1)+0.5))}else{h=Q(3,0);j=0.003921569;h[0]=e*j;h[1]=k*j;h[2]=g*j;h=this.colorSpace.fromRGB(h);if(this.supportsAlpha){d=a>>24&255;if(this.$isAlphaPremultiplied){j*=d;for(e=0;3>e;e++)h[e]*=j}8!=this.nBits[3]&&(d=I(0.003921569*d*((1<<this.nBits[3])-1)+0.5),d>
(1<<this.nBits[3])-1&&(d=(1<<this.nBits[3])-1));c[0]=d<<this.maskOffsets[3]}e=I(h[0]*((1<<this.nBits[0])-1)+0.5);k=I(h[1]*((1<<this.nBits[1])-1)+0.5);g=I(h[2]*((1<<this.nBits[2])-1)+0.5)}23<this.maxBits&&(e>(1<<this.nBits[0])-1&&(e=(1<<this.nBits[0])-1),k>(1<<this.nBits[1])-1&&(k=(1<<this.nBits[1])-1),g>(1<<this.nBits[2])-1&&(g=(1<<this.nBits[2])-1));c[0]|=e<<this.maskOffsets[0]|k<<this.maskOffsets[1]|g<<this.maskOffsets[2];switch(this.transferType){case 0:return d=null==b?S(1,0):b,d[0]=255&c[0],
d;case 3:return c}throw new UnsupportedOperationException("This method has not been implemented for transferType "+this.transferType);},"~N,~O");d(c$,"getComponents",function(a,b,c){null==b&&(b=w(c+this.numComponents,0));for(var d=0;d<this.numComponents;d++)b[c+d]=(a&this.maskArray[d])>>>this.maskOffsets[d];return b},"~N,~A,~N");d(c$,"getComponents",function(a,b,c){var d=0;switch(this.transferType){case 0:d=a[0]&255;break;case 3:d=a[0];break;default:throw new UnsupportedOperationException("This method has not been implemented for transferType "+
this.transferType);}return this.getComponents(d,b,c)},"~O,~A,~N");e(c$,"createCompatibleWritableRaster",function(a,b){if(0>=a||0>=b)throw new IllegalArgumentException("Width ("+a+") and height ("+b+") cannot be <= 0");var c;this.supportsAlpha?(c=w(4,0),c[3]=this.alpha_mask):c=w(3,0);c[0]=this.red_mask;c[1]=this.green_mask;c[2]=this.blue_mask;return 8<this.pixel_bits?java.awt.image.Raster.createPackedRaster(3,a,b,c,null):java.awt.image.Raster.createPackedRaster(0,a,b,c,null)},"~N,~N");d(c$,"getDataElement",
function(a,b){for(var c=0,d=0;d<this.numComponents;d++)c|=a[b+d]<<this.maskOffsets[d]&this.maskArray[d];return c},"~A,~N");d(c$,"getDataElements",function(a,b,c){for(var d=0,e=0;e<this.numComponents;e++)d|=a[b+e]<<this.maskOffsets[e]&this.maskArray[e];switch(this.transferType){case 0:return v(c,Array)?(a=c,a[0]=d&255):a=S(-1,[d&255]),a;case 3:return v(c,Array)?(a=c,a[0]=d):a=w(-1,[d]),a;default:throw new ClassCastException("This method has not been implemented for transferType "+this.transferType);
}},"~A,~N,~O");e(c$,"toString",function(){return String.instantialize("DirectColorModel: rmask="+Integer.toHexString(this.red_mask)+" gmask="+Integer.toHexString(this.green_mask)+" bmask="+Integer.toHexString(this.blue_mask)+" amask="+Integer.toHexString(this.alpha_mask))})});p("java.awt.image");q(["java.awt.image.ColorModel"],"java.awt.image.PackedColorModel",["java.lang.IllegalArgumentException"],function(){c$=s(function(){this.scaleFactors=this.maskOffsets=this.maskArray=null;r(this,arguments)},
java.awt.image,"PackedColorModel",java.awt.image.ColorModel);m(c$,function(a,b,c,d,e,k,g){t(this,java.awt.image.PackedColorModel,[b,java.awt.image.PackedColorModel.createBitsArray(c,d),a,0==d?!1:!0,e,k,g]);if(1>b||32<b)throw new IllegalArgumentException("Number of bits must be between 1 and 32.");this.maskArray=w(this.numComponents,0);this.maskOffsets=w(this.numComponents,0);this.scaleFactors=Q(this.numComponents,0);for(b=0;b<this.numColorComponents;b++)this.DecomposeMask(c[b],b,a.getName(b));0!=
d&&(this.DecomposeMask(d,this.numColorComponents,"alpha"),1==this.nBits[this.numComponents-1]&&(this.transparency=2))},"java.awt.color.ColorSpace,~N,~A,~N,~B,~N,~N");m(c$,function(a,b,c,d,e,k,g,h,j){t(this,java.awt.image.PackedColorModel,[b,java.awt.image.PackedColorModel.createBitsArray(c,d,e,k),a,0==k?!1:!0,g,h,j]);if(5!=a.getType())throw new IllegalArgumentException("ColorSpace must be TYPE_RGB.");this.maskArray=w(this.numComponents,0);this.maskOffsets=w(this.numComponents,0);this.scaleFactors=
Q(this.numComponents,0);this.DecomposeMask(c,0,"red");this.DecomposeMask(d,1,"green");this.DecomposeMask(e,2,"blue");0!=k&&(this.DecomposeMask(k,3,"alpha"),1==this.nBits[3]&&(this.transparency=2))},"java.awt.color.ColorSpace,~N,~N,~N,~N,~N,~B,~N,~N");d(c$,"getMask",function(a){return this.maskArray[a]},"~N");d(c$,"getMasks",function(){return this.maskArray.clone()});d(c$,"DecomposeMask",function(a,b,c){var d=0,e=this.nBits[b];this.maskArray[b]=a;if(0!=a)for(;0==(a&1);)a>>>=1,d++;if(d+e>this.pixel_bits)throw new IllegalArgumentException(c+
" mask "+Integer.toHexString(this.maskArray[b])+" overflows pixel (expecting "+this.pixel_bits+" bits");this.maskOffsets[b]=d;this.scaleFactors[b]=0==e?256:255/((1<<e)-1)},"~N,~N,~S");d(c$,"equals",function(a){if(!v(a,java.awt.image.PackedColorModel)||!K(this,java.awt.image.PackedColorModel,"equals",[a]))return!1;var b=a.getNumComponents();if(b!=this.numComponents)return!1;for(var c=0;c<b;c++)if(this.maskArray[c]!=a.getMask(c))return!1;return!0},"~O");c$.createBitsArray=d(c$,"createBitsArray",function(a,
b){for(var c=a.length,d=w(c+(0==b?0:1),0),e=0;e<c;e++)if(d[e]=java.awt.image.PackedColorModel.countBits(a[e]),0>d[e])throw new IllegalArgumentException("Noncontiguous color mask ("+Integer.toHexString(a[e])+"at index "+e);if(0!=b&&(d[c]=java.awt.image.PackedColorModel.countBits(b),0>d[c]))throw new IllegalArgumentException("Noncontiguous alpha mask ("+Integer.toHexString(b));return d},"~A,~N");c$.createBitsArray=d(c$,"createBitsArray",function(a,b,c,d){var e=w(3+(0==d?0:1),0);e[0]=java.awt.image.PackedColorModel.countBits(a);
e[1]=java.awt.image.PackedColorModel.countBits(b);e[2]=java.awt.image.PackedColorModel.countBits(c);if(0>e[0])throw new IllegalArgumentException("Noncontiguous red mask ("+Integer.toHexString(a));if(0>e[1])throw new IllegalArgumentException("Noncontiguous green mask ("+Integer.toHexString(b));if(0>e[2])throw new IllegalArgumentException("Noncontiguous blue mask ("+Integer.toHexString(c));if(0!=d&&(e[3]=java.awt.image.PackedColorModel.countBits(d),0>e[3]))throw new IllegalArgumentException("Noncontiguous alpha mask ("+
Integer.toHexString(d));return e},"~N,~N,~N,~N");c$.countBits=d(c$,"countBits",function(a){var b=0;if(0!=a){for(;0==(a&1);)a>>>=1;for(;1==(a&1);)a>>>=1,b++}return 0!=a?-1:b},"~N")});p("java.awt.image");q(["java.awt.image.MultiPixelPackedSampleModel","$.SinglePixelPackedSampleModel"],"java.awt.image.Raster","java.lang.IllegalArgumentException $.NullPointerException java.awt.Point $.Rectangle java.awt.image.DataBuffer $.DataBufferByte $.DataBufferInt $.RasterFormatException swingjs.api.Interface".split(" "),
function(){c$=s(function(){this.dataBuffer=this.sampleModel=null;this.numDataElements=this.numBands=this.sampleModelTranslateY=this.sampleModelTranslateX=this.height=this.width=this.minY=this.minX=0;this.parent=null;r(this,arguments)},java.awt.image,"Raster");c$.createPackedRaster=d(c$,"createPackedRaster",function(a,b,c,d,e){switch(a){case 0:a=new java.awt.image.DataBufferByte(b*c);break;case 3:a=new java.awt.image.DataBufferInt(b*c);break;default:throw new IllegalArgumentException("Unsupported data type "+
a);}return java.awt.image.Raster.createPackedRaster(a,b,c,b,d,e)},"~N,~N,~N,~A,java.awt.Point");c$.createPackedRaster=d(c$,"createPackedRaster",function(a,b,c,d,e,k){if(0>=d)throw new IllegalArgumentException("Number of bands ("+d+") must be greater than 0");if(0>=e)throw new IllegalArgumentException("Bits per band ("+e+") must be greater than 0");if(1!=d){var g=w(d,0),h=(1<<e)-1,j=(d-1)*e;if(j+e>java.awt.image.DataBuffer.getDataTypeSize(a))throw new IllegalArgumentException("bitsPerBand("+e+") * bands is  greater than data type size.");
switch(a){case 0:case 3:break;default:throw new IllegalArgumentException("Unsupported data type "+a);}for(var n=0;n<d;n++)g[n]=h<<j,j-=e;return java.awt.image.Raster.createPackedRaster(a,b,c,g,k)}switch(a){case 0:a=new java.awt.image.DataBufferByte(F(Math.ceil(b/F(8/e)))*c);break;case 3:a=new java.awt.image.DataBufferInt(F(Math.ceil(b/F(32/e)))*c);break;default:throw new IllegalArgumentException("Unsupported data type "+a);}return java.awt.image.Raster.createPackedRaster(a,b,c,e,k)},"~N,~N,~N,~N,~N,java.awt.Point");
c$.createPackedRaster=d(c$,"createPackedRaster",function(a,b,c,d,e,k){if(null==a)throw new NullPointerException("DataBuffer cannot be null");null==k&&(k=new java.awt.Point(0,0));var g=a.getDataType();b=new java.awt.image.SinglePixelPackedSampleModel(g,b,c,d,e);switch(g){case 0:case 3:break;default:throw new IllegalArgumentException("Unsupported data type "+g);}g=swingjs.api.Interface.getInstance("jssun.awt.image."+(0==g?"Byte":"Integer")+"InterleavedRaster",!0);g.setParams(b,a,k);return g},"java.awt.image.DataBuffer,~N,~N,~N,~A,java.awt.Point");
c$.createPackedRaster=d(c$,"createPackedRaster",function(a,b,c,d,e){if(null==a)throw new NullPointerException("DataBuffer cannot be null");null==e&&(e=new java.awt.Point(0,0));var k=a.getDataType();if(0!=k&&3!=k)throw new IllegalArgumentException("Unsupported data type "+k);if(1!=a.getNumBanks())throw new java.awt.image.RasterFormatException("DataBuffer for packed Rasters must only have 1 bank.");b=new java.awt.image.MultiPixelPackedSampleModel(k,b,c,d);return 0==k&&(1==d||2==d||4==d)?new jssun.awt.image.BytePackedRaster(b,
a,e):new jssun.awt.image.SunWritableRaster(b,a,e)},"java.awt.image.DataBuffer,~N,~N,~N,java.awt.Point");c$.createRaster=d(c$,"createRaster",function(a,b,c){if(null==a||null==b)throw new NullPointerException("SampleModel and DataBuffer cannot be null");null==c&&(c=new java.awt.Point(0,0));var d=a.getDataType();return v(a,java.awt.image.MultiPixelPackedSampleModel)&&0==d&&8>a.getSampleSize(0)?new jssun.awt.image.BytePackedRaster(a,b,c):new java.awt.image.Raster(a,b,c)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Point");
c$.createWritableRaster=d(c$,"createWritableRaster",function(a,b){null==b&&(b=new java.awt.Point(0,0));return java.awt.image.Raster.createWritableRaster(a,a.createDataBuffer(),b)},"java.awt.image.SampleModel,java.awt.Point");c$.createWritableRaster=d(c$,"createWritableRaster",function(a,b,c){if(null==a||null==b)throw new NullPointerException("SampleModel and DataBuffer cannot be null");null==c&&(c=new java.awt.Point(0,0));var d=a.getDataType();return v(a,java.awt.image.MultiPixelPackedSampleModel)&&
0==d&&8>a.getSampleSize(0)?new jssun.awt.image.BytePackedRaster(a,b,c):new jssun.awt.image.SunWritableRaster(a,b,c)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Point");m(c$,function(a,b){this.setRaster(a,a.createDataBuffer(),new java.awt.Rectangle(b.x,b.y,a.getWidth(),a.getHeight()),b,null)},"java.awt.image.SampleModel,java.awt.Point");m(c$,function(a,b,c){this.setRaster(a,b,new java.awt.Rectangle(c.x,c.y,a.getWidth(),a.getHeight()),c,null)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Point");
m(c$,function(){});m(c$,function(a,b,c,d,e){this.setRaster(a,b,c,d,e)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");d(c$,"setRaster",function(a,b,c,d,e){if(null==a||null==b||null==c||null==d)throw new NullPointerException("SampleModel, dataBuffer, aRegion and sampleModelTranslate cannot be null");this.sampleModel=a;this.dataBuffer=b;this.minX=c.x;this.minY=c.y;this.width=c.width;this.height=c.height;if(0>=this.width||0>=this.height)throw new java.awt.image.RasterFormatException("negative or zero "+
(0>=this.width?"width":"height"));if(this.minX+this.width<this.minX)throw new java.awt.image.RasterFormatException("overflow condition for X coordinates of Raster");if(this.minY+this.height<this.minY)throw new java.awt.image.RasterFormatException("overflow condition for Y coordinates of Raster");this.sampleModelTranslateX=d.x;this.sampleModelTranslateY=d.y;this.numBands=a.getNumBands();this.numDataElements=a.getNumDataElements();this.parent=e},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");
d(c$,"getParent",function(){return this.parent});d(c$,"getSampleModelTranslateX",function(){return this.sampleModelTranslateX});d(c$,"getSampleModelTranslateY",function(){return this.sampleModelTranslateY});d(c$,"createCompatibleWritableRaster",function(){return new jssun.awt.image.SunWritableRaster(this.sampleModel,new java.awt.Point(0,0))});d(c$,"createCompatibleWritableRaster",function(a,b){if(0>=a||0>=b)throw new java.awt.image.RasterFormatException("negative "+(0>=a?"width":"height"));var c=
this.sampleModel.createCompatibleSampleModel(a,b);return new jssun.awt.image.SunWritableRaster(c,new java.awt.Point(0,0))},"~N,~N");d(c$,"createCompatibleWritableRaster",function(a){if(null==a)throw new NullPointerException("Rect cannot be null");return this.createCompatibleWritableRaster(a.x,a.y,a.width,a.height)},"java.awt.Rectangle");d(c$,"createCompatibleWritableRaster",function(a,b,c,d){return this.createCompatibleWritableRaster(c,d).createWritableChild(0,0,c,d,a,b,null)},"~N,~N,~N,~N");d(c$,
"createTranslatedChild",function(a,b){return this.createChild(this.minX,this.minY,this.width,this.height,a,b,null)},"~N,~N");d(c$,"createChild",function(a,b,c,d,e,k,g){if(a<this.minX)throw new java.awt.image.RasterFormatException("parentX lies outside raster");if(b<this.minY)throw new java.awt.image.RasterFormatException("parentY lies outside raster");if(a+c<a||a+c>this.width+this.minX)throw new java.awt.image.RasterFormatException("(parentX + width) is outside raster");if(b+d<b||b+d>this.height+
this.minY)throw new java.awt.image.RasterFormatException("(parentY + height) is outside raster");g=null==g?this.sampleModel:this.sampleModel.createSubsetSampleModel(g);a=e-a;b=k-b;return new java.awt.image.Raster(g,this.getDataBuffer(),new java.awt.Rectangle(e,k,c,d),new java.awt.Point(this.sampleModelTranslateX+a,this.sampleModelTranslateY+b),this)},"~N,~N,~N,~N,~N,~N,~A");d(c$,"getBounds",function(){return new java.awt.Rectangle(this.minX,this.minY,this.width,this.height)});d(c$,"getMinX",function(){return this.minX});
d(c$,"getMinY",function(){return this.minY});d(c$,"getWidth",function(){return this.width});d(c$,"getHeight",function(){return this.height});d(c$,"getNumBands",function(){return this.numBands});d(c$,"getNumDataElements",function(){return this.sampleModel.getNumDataElements()});d(c$,"getTransferType",function(){return this.sampleModel.getTransferType()});d(c$,"getDataBuffer",function(){return this.dataBuffer});d(c$,"getSampleModel",function(){return this.sampleModel});d(c$,"getDataElements",function(a,
b,c){return this.sampleModel.getDataElements(a-this.sampleModelTranslateX,b-this.sampleModelTranslateY,c,this.dataBuffer)},"~N,~N,~O");d(c$,"getDataElements",function(a,b,c,d,e){return this.sampleModel.getDataElements(a-this.sampleModelTranslateX,b-this.sampleModelTranslateY,c,d,e,this.dataBuffer)},"~N,~N,~N,~N,~O");d(c$,"getPixel",function(a,b,c){return this.sampleModel.getPixel(a-this.sampleModelTranslateX,b-this.sampleModelTranslateY,c,this.dataBuffer)},"~N,~N,~A");d(c$,"getPixel",function(a,b,
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function(){c$=s(function(){this.scanlineStride=this.dataBitOffset=this.dataElementSize=this.pixelsPerDataElement=this.bitMask=this.pixelBitStride=0;r(this,arguments)},java.awt.image,"MultiPixelPackedSampleModel",java.awt.image.SampleModel);m(c$,function(a,b,c,d){this.construct(a,b,c,d,F((b*d+java.awt.image.DataBuffer.getDataTypeSize(a)-1)/java.awt.image.DataBuffer.getDataTypeSize(a)),0);if(0!=a&&3!=a)throw new IllegalArgumentException("Unsupported data type "+a);},"~N,~N,~N,~N");m(c$,function(a,b,
c,d,e,k){t(this,java.awt.image.MultiPixelPackedSampleModel,[a,b,c,1]);if(0!=a&&3!=a)throw new IllegalArgumentException("Unsupported data type "+a);this.dataType=a;this.pixelBitStride=d;this.scanlineStride=e;this.dataBitOffset=k;this.dataElementSize=java.awt.image.DataBuffer.getDataTypeSize(a);this.pixelsPerDataElement=F(this.dataElementSize/d);if(this.pixelsPerDataElement*d!=this.dataElementSize)throw new java.awt.image.RasterFormatException("MultiPixelPackedSampleModel does not allow pixels to span data element boundaries");
this.bitMask=(1<<d)-1},"~N,~N,~N,~N,~N,~N");e(c$,"createCompatibleSampleModel",function(a,b){return new java.awt.image.MultiPixelPackedSampleModel(this.dataType,a,b,this.pixelBitStride)},"~N,~N");e(c$,"createDataBuffer",function(){var a=null,b=this.scanlineStride*this.height;switch(this.dataType){case 0:a=new java.awt.image.DataBufferByte(b+F((this.dataBitOffset+7)/8));break;case 3:a=new java.awt.image.DataBufferInt(b+F((this.dataBitOffset+31)/32))}return a});e(c$,"getNumDataElements",function(){return 1});
d(c$,"getSampleSize",function(){return w(-1,[this.pixelBitStride])});d(c$,"getSampleSize",function(){return this.pixelBitStride},"~N");d(c$,"getOffset",function(a,b){var c=b*this.scanlineStride;return c+=F((a*this.pixelBitStride+this.dataBitOffset)/this.dataElementSize)},"~N,~N");d(c$,"getBitOffset",function(a){return(a*this.pixelBitStride+this.dataBitOffset)%this.dataElementSize},"~N");d(c$,"getScanlineStride",function(){return this.scanlineStride});d(c$,"getPixelBitStride",function(){return this.pixelBitStride});
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a*this.pixelBitStride;return d.getElem(b*this.scanlineStride+F(a/this.dataElementSize))>>this.dataElementSize-(a&this.dataElementSize-1)-this.pixelBitStride&this.bitMask},"~N,~N,~N,java.awt.image.DataBuffer");d(c$,"setSample",function(a,b,c,d,e){if(0>a||0>b||a>=this.width||b>=this.height||0!=c)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");a=this.dataBitOffset+a*this.pixelBitStride;b=b*this.scanlineStride+F(a/this.dataElementSize);a=this.dataElementSize-(a&this.dataElementSize-
1)-this.pixelBitStride;c=e.getElem(b);c&=~(this.bitMask<<a);c|=(d&this.bitMask)<<a;e.setElem(b,c)},"~N,~N,~N,~N,java.awt.image.DataBuffer");d(c$,"getDataElements",function(a,b,c,d){if(0>a||0>b||a>=this.width||b>=this.height)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");var e=this.getTransferType();a=this.dataBitOffset+a*this.pixelBitStride;var k=this.dataElementSize-(a&this.dataElementSize-1)-this.pixelBitStride,g=0;switch(e){case 0:c=null==c?S(1,0):c;g=d.getElem(b*this.scanlineStride+
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b>>this.dataElementSize-(a&this.dataElementSize-1)-this.pixelBitStride&this.bitMask;return c},"~N,~N,~A,java.awt.image.DataBuffer");d(c$,"setDataElements",function(a,b,c,d){if(0>a||0>b||a>=this.width||b>=this.height)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");var e=this.getTransferType();a=this.dataBitOffset+a*this.pixelBitStride;b=b*this.scanlineStride+F(a/this.dataElementSize);a=this.dataElementSize-(a&this.dataElementSize-1)-this.pixelBitStride;var k=d.getElem(b),k=k&
~(this.bitMask<<a);switch(e){case 0:k|=(c[0]&255&this.bitMask)<<a;d.setElem(b,k);break;case 3:k|=(c[0]&this.bitMask)<<a,d.setElem(b,k)}},"~N,~N,~O,java.awt.image.DataBuffer");d(c$,"setPixel",function(a,b,c,d){if(0>a||0>b||a>=this.width||b>=this.height)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");a=this.dataBitOffset+a*this.pixelBitStride;b=b*this.scanlineStride+F(a/this.dataElementSize);a=this.dataElementSize-(a&this.dataElementSize-1)-this.pixelBitStride;var e=d.getElem(b),
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a.scanlineStride},"~O");e(c$,"hashCode",function(){var a=0,a=this.width,a=a<<8^this.height,a=a<<8,a=a^this.numBands,a=a<<8,a=a^this.dataType,a=a<<8,a=a^this.pixelBitStride,a=a<<8,a=a^this.bitMask,a=a<<8,a=a^this.pixelsPerDataElement,a=a<<8,a=a^this.dataElementSize,a=a<<8,a=a^this.dataBitOffset,a=a<<8;return a^=this.scanlineStride})});p("java.awt.image");q(null,"java.awt.image.SampleModel",["java.lang.IllegalArgumentException"],function(){c$=s(function(){this.dataType=this.numBands=this.height=this.width=
0;r(this,arguments)},java.awt.image,"SampleModel");m(c$,function(a,b,c,d){var e=b*c;if(0>=b||0>=c)throw new IllegalArgumentException("Width ("+b+") and height ("+c+") must be > 0");if(2147483647<=e)throw new IllegalArgumentException("Dimensions (width="+b+" height="+c+") are too large");if(0>a||3<a&&32!=a)throw new IllegalArgumentException("Unsupported dataType: "+a);if(0>=d)throw new IllegalArgumentException("Number of bands must be > 0");this.dataType=a;this.width=b;this.height=c;this.numBands=
d},"~N,~N,~N,~N");d(c$,"getWidth",function(){return this.width});d(c$,"getHeight",function(){return this.height});d(c$,"getNumBands",function(){return this.numBands});d(c$,"getDataType",function(){return this.dataType});d(c$,"getTransferType",function(){return this.dataType});d(c$,"getPixel",function(a,b,c,d){c=null!=c?c:w(this.numBands,0);for(var e=0;e<this.numBands;e++)c[e]=this.getSample(a,b,e,d);return c},"~N,~N,~A,java.awt.image.DataBuffer");d(c$,"getDataElements",function(a,b,c,d,e,k){var g=
this.getTransferType(),h=this.getNumDataElements(),j=0,n=null;switch(g){case 0:var m,p;p=null==e?S(h*c*d,0):e;for(e=b;e<b+d;e++)for(g=a;g<a+c;g++){m=n=this.getDataElements(g,e,n,k);for(var q=0;q<h;q++)p[j++]=m[q]}e=p;break;case 2:m=null==e?ga(h*c*d,0):e;for(e=b;e<b+d;e++)for(g=a;g<a+c;g++){p=n=this.getDataElements(g,e,n,k);for(q=0;q<h;q++)m[j++]=p[q]}e=m;break;case 3:m=null==e?w(h*c*d,0):e;for(e=b;e<b+d;e++)for(g=a;g<a+c;g++){p=n=this.getDataElements(g,e,n,k);for(q=0;q<h;q++)m[j++]=p[q]}e=m}return e},
"~N,~N,~N,~N,~O,java.awt.image.DataBuffer");d(c$,"setDataElements",function(a,b,c,d,e,k){var g=0,h=this.getTransferType(),j=this.getNumDataElements();switch(h){case 0:for(var n=S(j,0),h=b;h<b+d;h++)for(var m=a;m<a+c;m++){for(var p=0;p<j;p++)n[p]=e[g++];this.setDataElements(m,h,n,k)}break;case 3:n=w(j,0);for(h=b;h<b+d;h++)for(m=a;m<a+c;m++){for(p=0;p<j;p++)n[p]=e[g++];this.setDataElements(m,h,n,k)}}},"~N,~N,~N,~N,~O,java.awt.image.DataBuffer");d(c$,"getPixels",function(a,b,c,d,e,k){var g=0;e=null!=
e?e:w(this.numBands*c*d,0);for(var h=b;h<d+b;h++)for(var j=a;j<c+a;j++)for(var n=0;n<this.numBands;n++)e[g++]=this.getSample(j,h,n,k);return e},"~N,~N,~N,~N,~A,java.awt.image.DataBuffer");d(c$,"getSampleFloat",function(a,b,c,d){return this.getSample(a,b,c,d)},"~N,~N,~N,java.awt.image.DataBuffer");d(c$,"getSampleDouble",function(a,b,c,d){return this.getSample(a,b,c,d)},"~N,~N,~N,java.awt.image.DataBuffer");d(c$,"getSamples",function(a,b,c,d,e,k,g){var h=0;k=null!=k?k:w(c*d,0);for(var j=b;j<d+b;j++)for(var n=
a;n<c+a;n++)k[h++]=this.getSample(n,j,e,g);return k},"~N,~N,~N,~N,~N,~A,java.awt.image.DataBuffer");d(c$,"setPixel",function(a,b,c,d){for(var e=0;e<this.numBands;e++)this.setSample(a,b,e,c[e],d)},"~N,~N,~A,java.awt.image.DataBuffer");d(c$,"setPixel",function(a,b,c,d){for(var e=0;e<this.numBands;e++)this.setSample(a,b,e,c[e],d)},"~N,~N,~A,java.awt.image.DataBuffer");d(c$,"setPixels",function(a,b,c,d,e,k){for(var g=0,h=b;h<b+d;h++)for(var j=a;j<a+c;j++)for(var n=0;n<this.numBands;n++)this.setSample(j,
h,n,e[g++],k)},"~N,~N,~N,~N,~A,java.awt.image.DataBuffer");d(c$,"setSamples",function(a,b,c,d,e,k,g){for(var h=0,j=b;j<b+d;j++)for(var n=a;n<a+c;n++)this.setSample(n,j,e,k[h++],g)},"~N,~N,~N,~N,~N,~A,java.awt.image.DataBuffer")});p("java.awt.image");q(null,"java.awt.image.DataBuffer",["java.lang.ArrayIndexOutOfBoundsException","$.IllegalArgumentException","jssun.java2d.StateTrackable","$.StateTrackableDelegate"],function(){c$=s(function(){this.size=this.offset=this.banks=this.dataType=0;this.theTrackable=
this.offsets=null;r(this,arguments)},java.awt.image,"DataBuffer");c$.getDataTypeSize=d(c$,"getDataTypeSize",function(a){if(0>a||3<a)throw new IllegalArgumentException("Unknown data type "+a);return java.awt.image.DataBuffer.dataTypeSize[a]},"~N");m(c$,function(a,b){this.construct(jssun.java2d.StateTrackable.State.UNTRACKABLE,a,b)},"~N,~N");m(c$,function(a,b,c){this.theTrackable=jssun.java2d.StateTrackableDelegate.createInstance(a);this.dataType=b;this.banks=1;this.size=c;this.offset=0;this.offsets=
w(1,0)},"jssun.java2d.StateTrackable.State,~N,~N");m(c$,function(a,b,c){this.construct(jssun.java2d.StateTrackable.State.UNTRACKABLE,a,b,c)},"~N,~N,~N");m(c$,function(a,b,c,d){this.theTrackable=jssun.java2d.StateTrackableDelegate.createInstance(a);this.dataType=b;this.banks=d;this.size=c;this.offset=0;this.offsets=w(this.banks,0)},"jssun.java2d.StateTrackable.State,~N,~N,~N");m(c$,function(a,b,c,d){this.construct(jssun.java2d.StateTrackable.State.UNTRACKABLE,a,b,c,d)},"~N,~N,~N,~N");m(c$,function(a,
b,c,d,e){this.theTrackable=jssun.java2d.StateTrackableDelegate.createInstance(a);this.dataType=b;this.banks=d;this.size=c;this.offset=e;this.offsets=w(d,0);for(a=0;a<d;a++)this.offsets[a]=e},"jssun.java2d.StateTrackable.State,~N,~N,~N,~N");m(c$,function(a,b,c,d){this.construct(jssun.java2d.StateTrackable.State.UNTRACKABLE,a,b,c,d)},"~N,~N,~N,~A");m(c$,function(a,b,c,d,e){if(d!=e.length)throw new ArrayIndexOutOfBoundsException("Number of banks does not match number of bank offsets");this.theTrackable=
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"setElem",function(a,b){this.setElem(0,a,b)},"~N,~N");d(c$,"getElemFloat",function(a){return this.getElem(a)},"~N");d(c$,"getElemFloat",function(a,b){return this.getElem(a,b)},"~N,~N");d(c$,"setElemFloat",function(a,b){this.setElem(a,I(b))},"~N,~N");d(c$,"setElemFloat",function(a,b,c){this.setElem(a,b,I(c))},"~N,~N,~N");d(c$,"getElemDouble",function(a){return this.getElem(a)},"~N");d(c$,"getElemDouble",function(a,b){return this.getElem(a,b)},"~N,~N");d(c$,"setElemDouble",function(a,b){this.setElem(a,
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null,jssun.java2d.StateTrackable);c$.createInstance=d(c$,"createInstance",function(a){switch(a){case jssun.java2d.StateTrackable.State.UNTRACKABLE:return jssun.java2d.StateTrackableDelegate.UNTRACKABLE_DELEGATE;case jssun.java2d.StateTrackable.State.STABLE:return new jssun.java2d.StateTrackableDelegate(jssun.java2d.StateTrackable.State.STABLE);case jssun.java2d.StateTrackable.State.DYNAMIC:return new jssun.java2d.StateTrackableDelegate(jssun.java2d.StateTrackable.State.DYNAMIC);case jssun.java2d.StateTrackable.State.IMMUTABLE:return jssun.java2d.StateTrackableDelegate.IMMUTABLE_DELEGATE;
default:throw new InternalError("unknown state");}},"jssun.java2d.StateTrackable.State");m(c$,function(a){this.theState=a},"jssun.java2d.StateTrackable.State");e(c$,"getState",function(){return this.theState});e(c$,"getStateTracker",function(){var a=this.theTracker;if(null==a){switch(this.theState){case jssun.java2d.StateTrackable.State.IMMUTABLE:a=jssun.java2d.StateTracker.ALWAYS_CURRENT;break;case jssun.java2d.StateTrackable.State.STABLE:a=(H("jssun.java2d.StateTrackableDelegate$1")?0:jssun.java2d.StateTrackableDelegate.$StateTrackableDelegate$1$(),
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this.theTracker=null});d(c$,"setUntrackable",function(){if(this.theState===jssun.java2d.StateTrackable.State.IMMUTABLE)throw new IllegalStateException("IMMUTABLE objects cannot become UNTRACKABLE");this.theState=jssun.java2d.StateTrackable.State.UNTRACKABLE;this.theTracker=null});d(c$,"addDynamicAgent",function(){if(this.theState===jssun.java2d.StateTrackable.State.IMMUTABLE)throw new IllegalStateException("Cannot change state from IMMUTABLE");++this.numDynamicAgents;this.theState===jssun.java2d.StateTrackable.State.STABLE&&
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c,d,e,k,this.dataBuffer)},"~N,~N,~N,~N,~N,~A");d(c$,"setSamples",function(a,b,c,d,e,k){this.sampleModel.setSamples(a-this.sampleModelTranslateX,b-this.sampleModelTranslateY,c,d,e,k,this.dataBuffer)},"~N,~N,~N,~N,~N,~A");d(c$,"setSamples",function(a,b,c,d,e,k){this.sampleModel.setSamples(a-this.sampleModelTranslateX,b-this.sampleModelTranslateY,c,d,e,k,this.dataBuffer)},"~N,~N,~N,~N,~N,~A")});p("jssun.java2d.loops");q(null,"jssun.java2d.loops.CompositeType",["java.lang.InternalError"],function(){c$=
s(function(){this.uniqueID=0;this.next=this.desc=null;r(this,arguments)},jssun.java2d.loops,"CompositeType");d(c$,"deriveSubType",function(a){return new jssun.java2d.loops.CompositeType(this,a)},"~S");c$.forAlphaComposite=d(c$,"forAlphaComposite",function(a){switch(a.getRule()){case 1:return jssun.java2d.loops.CompositeType.Clear;case 2:return 1<=a.getAlpha()?jssun.java2d.loops.CompositeType.SrcNoEa:jssun.java2d.loops.CompositeType.Src;case 9:return jssun.java2d.loops.CompositeType.Dst;case 3:return 1<=
a.getAlpha()?jssun.java2d.loops.CompositeType.SrcOverNoEa:jssun.java2d.loops.CompositeType.SrcOver;case 4:return jssun.java2d.loops.CompositeType.DstOver;case 5:return jssun.java2d.loops.CompositeType.SrcIn;case 6:return jssun.java2d.loops.CompositeType.DstIn;case 7:return jssun.java2d.loops.CompositeType.SrcOut;case 8:return jssun.java2d.loops.CompositeType.DstOut;case 10:return jssun.java2d.loops.CompositeType.SrcAtop;case 11:return jssun.java2d.loops.CompositeType.DstAtop;case 12:return jssun.java2d.loops.CompositeType.AlphaXor;
default:throw new InternalError("Unrecognized alpha rule");}},"java.awt.AlphaComposite");m(c$,function(a,b){this.next=a;this.desc=b;this.uniqueID=jssun.java2d.loops.CompositeType.makeUniqueID()},"jssun.java2d.loops.CompositeType,~S");c$.makeUniqueID=d(c$,"makeUniqueID",function(){if(255<jssun.java2d.loops.CompositeType.unusedUID)throw new InternalError("composite type id overflow");return jssun.java2d.loops.CompositeType.unusedUID++});d(c$,"getUniqueID",function(){return this.uniqueID});d(c$,"getDescriptor",
function(){return this.desc});d(c$,"getSuperType",function(){return this.next});e(c$,"hashCode",function(){return this.desc.hashCode()});d(c$,"isDerivedFrom",function(a){var b=this;do{if(b.desc===a.desc)return!0;b=b.next}while(null!=b);return!1},"jssun.java2d.loops.CompositeType");e(c$,"equals",function(a){return v(a,jssun.java2d.loops.CompositeType)?a.uniqueID==this.uniqueID:!1},"~O");e(c$,"toString",function(){return this.desc});G(c$,"DESC_ANY","Any CompositeContext","DESC_XOR","XOR mode","DESC_CLEAR",
"Porter-Duff Clear","DESC_SRC","Porter-Duff Src","DESC_DST","Porter-Duff Dst","DESC_SRC_OVER","Porter-Duff Src Over Dst","DESC_DST_OVER","Porter-Duff Dst Over Src","DESC_SRC_IN","Porter-Duff Src In Dst","DESC_DST_IN","Porter-Duff Dst In Src","DESC_SRC_OUT","Porter-Duff Src HeldOutBy Dst","DESC_DST_OUT","Porter-Duff Dst HeldOutBy Src","DESC_SRC_ATOP","Porter-Duff Src Atop Dst","DESC_DST_ATOP","Porter-Duff Dst Atop Src","DESC_ALPHA_XOR","Porter-Duff Xor","DESC_SRC_NO_EA","Porter-Duff Src, No Extra Alpha",
"DESC_SRC_OVER_NO_EA","Porter-Duff SrcOverDst, No Extra Alpha","DESC_ANY_ALPHA","Any AlphaComposite Rule");c$.Any=c$.prototype.Any=new jssun.java2d.loops.CompositeType(null,"Any CompositeContext");c$.General=c$.prototype.General=jssun.java2d.loops.CompositeType.Any;c$.AnyAlpha=c$.prototype.AnyAlpha=jssun.java2d.loops.CompositeType.General.deriveSubType("Any AlphaComposite Rule");c$.Xor=c$.prototype.Xor=jssun.java2d.loops.CompositeType.General.deriveSubType("XOR mode");c$.Clear=c$.prototype.Clear=
jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Clear");c$.Src=c$.prototype.Src=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Src");c$.Dst=c$.prototype.Dst=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Dst");c$.SrcOver=c$.prototype.SrcOver=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Src Over Dst");c$.DstOver=c$.prototype.DstOver=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Dst Over Src");
c$.SrcIn=c$.prototype.SrcIn=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Src In Dst");c$.DstIn=c$.prototype.DstIn=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Dst In Src");c$.SrcOut=c$.prototype.SrcOut=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Src HeldOutBy Dst");c$.DstOut=c$.prototype.DstOut=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Dst HeldOutBy Src");c$.SrcAtop=c$.prototype.SrcAtop=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Src Atop Dst");
c$.DstAtop=c$.prototype.DstAtop=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Dst Atop Src");c$.AlphaXor=c$.prototype.AlphaXor=jssun.java2d.loops.CompositeType.AnyAlpha.deriveSubType("Porter-Duff Xor");c$.SrcNoEa=c$.prototype.SrcNoEa=jssun.java2d.loops.CompositeType.Src.deriveSubType("Porter-Duff Src, No Extra Alpha");c$.SrcOverNoEa=c$.prototype.SrcOverNoEa=jssun.java2d.loops.CompositeType.SrcOver.deriveSubType("Porter-Duff SrcOverDst, No Extra Alpha");G(c$,"unusedUID",1)});
p("awt2swing");q(["javax.swing.JScrollPane"],"awt2swing.ScrollPane",null,function(){c$=B(awt2swing,"ScrollPane",javax.swing.JScrollPane)});p("javax.swing");q(["javax.swing.JComponent","$.JScrollBar","$.ScrollPaneConstants","javax.swing.plaf.UIResource"],"javax.swing.JScrollPane","java.lang.Boolean $.ClassCastException $.IllegalArgumentException java.awt.Point $.Rectangle javax.swing.JViewport $.ScrollPaneLayout $.Scrollable $.SwingUtilities $.UIManager".split(" "),function(){c$=s(function(){this.viewportBorder=
null;this.verticalScrollBarPolicy=20;this.horizontalScrollBarPolicy=30;this.upperRight=this.upperLeft=this.lowerRight=this.lowerLeft=this.columnHeader=this.rowHeader=this.horizontalScrollBar=this.verticalScrollBar=this.viewport=null;this.wheelScrollState=!0;H("javax.swing.JScrollPane.ScrollBar")||javax.swing.JScrollPane.$JScrollPane$ScrollBar$();r(this,arguments)},javax.swing,"JScrollPane",javax.swing.JComponent,javax.swing.ScrollPaneConstants);m(c$,function(a,b,c){t(this,javax.swing.JScrollPane,
[]);this.setLayout(new javax.swing.ScrollPaneLayout.UIResource);this.setVerticalScrollBarPolicy(b);this.setHorizontalScrollBarPolicy(c);this.setViewport(this.createViewport());this.setVerticalScrollBar(this.createVerticalScrollBar());this.setHorizontalScrollBar(this.createHorizontalScrollBar());null!=a&&this.setViewportView(a);this.setUIProperty("opaque",new Boolean(!0));this.updateUI();this.getComponentOrientation().isLeftToRight()||this.viewport.setViewPosition(new java.awt.Point(2147483647,0))},
"java.awt.Component,~N,~N");m(c$,function(a){this.construct(a,20,30)},"java.awt.Component");m(c$,function(a,b){this.construct(null,a,b)},"~N,~N");m(c$,function(){this.construct(null,20,30)});e(c$,"getUI",function(){return this.ui});e(c$,"updateUI",function(){this.setUI(javax.swing.UIManager.getUI(this))});e(c$,"getUIClassID",function(){return"ScrollPaneUI"});d(c$,"setLayout",function(a){if(v(a,javax.swing.ScrollPaneLayout))K(this,javax.swing.JScrollPane,"setLayout",[a]),a.syncWithScrollPane(this);
else if(null==a)K(this,javax.swing.JScrollPane,"setLayout",[a]);else throw new ClassCastException("layout of JScrollPane must be a ScrollPaneLayout");},"java.awt.LayoutManager");e(c$,"isValidateRoot",function(){return!0});d(c$,"getVerticalScrollBarPolicy",function(){return this.verticalScrollBarPolicy});d(c$,"setVerticalScrollBarPolicy",function(a){switch(a){case 20:case 21:case 22:break;default:throw new IllegalArgumentException("invalid verticalScrollBarPolicy");}var b=this.verticalScrollBarPolicy;
this.verticalScrollBarPolicy=a;this.firePropertyChangeInt("verticalScrollBarPolicy",b,a);this.revalidate();this.repaint()},"~N");d(c$,"getHorizontalScrollBarPolicy",function(){return this.horizontalScrollBarPolicy});d(c$,"setHorizontalScrollBarPolicy",function(a){switch(a){case 30:case 31:case 32:break;default:throw new IllegalArgumentException("invalid horizontalScrollBarPolicy");}var b=this.horizontalScrollBarPolicy;this.horizontalScrollBarPolicy=a;this.firePropertyChangeInt("horizontalScrollBarPolicy",
b,a);this.revalidate();this.repaint()},"~N");d(c$,"getViewportBorder",function(){return this.viewportBorder});d(c$,"setViewportBorder",function(a){var b=this.viewportBorder;this.viewportBorder=a;this.firePropertyChangeObject("viewportBorder",b,a)},"javax.swing.border.Border");d(c$,"getViewportBorderBounds",function(){var a=new java.awt.Rectangle(this.getSize()),b=this.getInsets();a.x=b.left;a.y=b.top;a.width-=b.left+b.right;a.height-=b.top+b.bottom;var b=javax.swing.SwingUtilities.isLeftToRight(this),
c=this.getColumnHeader();null!=c&&c.isVisible()&&(c=c.getHeight(),a.y+=c,a.height-=c);c=this.getRowHeader();null!=c&&c.isVisible()&&(c=c.getWidth(),b&&(a.x+=c),a.width-=c);c=this.getVerticalScrollBar();null!=c&&c.isVisible()&&(c=c.getWidth(),b||(a.x+=c),a.width-=c);b=this.getHorizontalScrollBar();null!=b&&b.isVisible()&&(a.height-=b.getHeight());return a});d(c$,"createHorizontalScrollBar",function(){return C(javax.swing.JScrollPane.ScrollBar,this,null,0)});d(c$,"getHorizontalScrollBar",function(){return this.horizontalScrollBar});
d(c$,"setHorizontalScrollBar",function(a){var b=this.getHorizontalScrollBar();this.horizontalScrollBar=a;null!=a?this.add(a,"HORIZONTAL_SCROLLBAR"):null!=b&&this.remove(b);this.firePropertyChangeObject("horizontalScrollBar",b,a);this.revalidate();this.repaint()},"javax.swing.JScrollBar");d(c$,"createVerticalScrollBar",function(){return C(javax.swing.JScrollPane.ScrollBar,this,null,1)});d(c$,"getVerticalScrollBar",function(){return this.verticalScrollBar});d(c$,"setVerticalScrollBar",function(a){var b=
this.getVerticalScrollBar();this.verticalScrollBar=a;this.add(a,"VERTICAL_SCROLLBAR");this.firePropertyChangeObject("verticalScrollBar",b,a);this.revalidate();this.repaint()},"javax.swing.JScrollBar");d(c$,"createViewport",function(){return new javax.swing.JViewport});d(c$,"getViewport",function(){return this.viewport});d(c$,"setViewport",function(a){var b=this.getViewport();this.viewport=a;null!=a?this.add(a,"VIEWPORT"):null!=b&&this.remove(b);this.firePropertyChangeObject("viewport",b,a);this.revalidate();
this.repaint()},"javax.swing.JViewport");d(c$,"setViewportView",function(a){null==this.getViewport()&&this.setViewport(this.createViewport());this.getViewport().setView(a)},"java.awt.Component");d(c$,"getRowHeader",function(){return this.rowHeader});d(c$,"setRowHeader",function(a){var b=this.getRowHeader();this.rowHeader=a;null!=a?this.add(a,"ROW_HEADER"):null!=b&&this.remove(b);this.firePropertyChangeObject("rowHeader",b,a);this.revalidate();this.repaint()},"javax.swing.JViewport");d(c$,"setRowHeaderView",
function(a){null==this.getRowHeader()&&this.setRowHeader(this.createViewport());this.getRowHeader().setView(a)},"java.awt.Component");d(c$,"getColumnHeader",function(){return this.columnHeader});d(c$,"setColumnHeader",function(a){var b=this.getColumnHeader();this.columnHeader=a;null!=a?this.add(a,"COLUMN_HEADER"):null!=b&&this.remove(b);this.firePropertyChangeObject("columnHeader",b,a);this.revalidate();this.repaint()},"javax.swing.JViewport");d(c$,"setColumnHeaderView",function(a){null==this.getColumnHeader()&&
this.setColumnHeader(this.createViewport());this.getColumnHeader().setView(a)},"java.awt.Component");d(c$,"getCorner",function(a){var b=this.getComponentOrientation().isLeftToRight();a.equals("LOWER_LEADING_CORNER")?a=b?"LOWER_LEFT_CORNER":"LOWER_RIGHT_CORNER":a.equals("LOWER_TRAILING_CORNER")?a=b?"LOWER_RIGHT_CORNER":"LOWER_LEFT_CORNER":a.equals("UPPER_LEADING_CORNER")?a=b?"UPPER_LEFT_CORNER":"UPPER_RIGHT_CORNER":a.equals("UPPER_TRAILING_CORNER")&&(a=b?"UPPER_RIGHT_CORNER":"UPPER_LEFT_CORNER");return a.equals("LOWER_LEFT_CORNER")?
this.lowerLeft:a.equals("LOWER_RIGHT_CORNER")?this.lowerRight:a.equals("UPPER_LEFT_CORNER")?this.upperLeft:a.equals("UPPER_RIGHT_CORNER")?this.upperRight:null},"~S");d(c$,"setCorner",function(a,b){var c;c=this.getComponentOrientation().isLeftToRight();a.equals("LOWER_LEADING_CORNER")?a=c?"LOWER_LEFT_CORNER":"LOWER_RIGHT_CORNER":a.equals("LOWER_TRAILING_CORNER")?a=c?"LOWER_RIGHT_CORNER":"LOWER_LEFT_CORNER":a.equals("UPPER_LEADING_CORNER")?a=c?"UPPER_LEFT_CORNER":"UPPER_RIGHT_CORNER":a.equals("UPPER_TRAILING_CORNER")&&
(a=c?"UPPER_RIGHT_CORNER":"UPPER_LEFT_CORNER");if(a.equals("LOWER_LEFT_CORNER"))c=this.lowerLeft,this.lowerLeft=b;else if(a.equals("LOWER_RIGHT_CORNER"))c=this.lowerRight,this.lowerRight=b;else if(a.equals("UPPER_LEFT_CORNER"))c=this.upperLeft,this.upperLeft=b;else if(a.equals("UPPER_RIGHT_CORNER"))c=this.upperRight,this.upperRight=b;else throw new IllegalArgumentException("invalid corner key");null!=c&&this.remove(c);null!=b&&this.add(b,a);this.firePropertyChangeObject(a,c,b);this.revalidate();this.repaint()},
"~S,java.awt.Component");d(c$,"setComponentOrientation",function(a){K(this,javax.swing.JScrollPane,"setComponentOrientation",[a]);null!=this.verticalScrollBar&&this.verticalScrollBar.setComponentOrientation(a);null!=this.horizontalScrollBar&&this.horizontalScrollBar.setComponentOrientation(a)},"java.awt.ComponentOrientation");d(c$,"isWheelScrollingEnabled",function(){return this.wheelScrollState});d(c$,"setWheelScrollingEnabled",function(a){var b=this.wheelScrollState;this.wheelScrollState=a;this.firePropertyChangeBool("wheelScrollingEnabled",
b,a)},"~B");d(c$,"paramString",function(){var a=null!=this.viewportBorder?this.viewportBorder.toString():"",b=null!=this.viewport?this.viewport.toString():"",c;c=20==this.verticalScrollBarPolicy?"VERTICAL_SCROLLBAR_AS_NEEDED":21==this.verticalScrollBarPolicy?"VERTICAL_SCROLLBAR_NEVER":22==this.verticalScrollBarPolicy?"VERTICAL_SCROLLBAR_ALWAYS":"";var d;d=30==this.horizontalScrollBarPolicy?"HORIZONTAL_SCROLLBAR_AS_NEEDED":31==this.horizontalScrollBarPolicy?"HORIZONTAL_SCROLLBAR_NEVER":32==this.horizontalScrollBarPolicy?
"HORIZONTAL_SCROLLBAR_ALWAYS":"";var e=null!=this.horizontalScrollBar?this.horizontalScrollBar.toString():"",k=null!=this.verticalScrollBar?this.verticalScrollBar.toString():"",g=null!=this.columnHeader?this.columnHeader.toString():"",h=null!=this.rowHeader?this.rowHeader.toString():"",j=null!=this.lowerLeft?this.lowerLeft.toString():"",n=null!=this.lowerRight?this.lowerRight.toString():"",m=null!=this.upperLeft?this.upperLeft.toString():"",p=null!=this.upperRight?this.upperRight.toString():"";return K(this,
javax.swing.JScrollPane,"paramString",[])+",columnHeader="+g+",horizontalScrollBar="+e+",horizontalScrollBarPolicy="+d+",lowerLeft="+j+",lowerRight="+n+",rowHeader="+h+",upperLeft="+m+",upperRight="+p+",verticalScrollBar="+k+",verticalScrollBarPolicy="+c+",viewport="+b+",viewportBorder="+a});c$.$JScrollPane$ScrollBar$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.blockIncrementSet=this.unitIncrementSet=!1;r(this,arguments)},javax.swing.JScrollPane,"ScrollBar",javax.swing.JScrollBar,
javax.swing.plaf.UIResource);m(c$,function(a){t(this,javax.swing.JScrollPane.ScrollBar,[a]);this.putClientProperty("JScrollBar.fastWheelScrolling",Boolean.TRUE)},"~N");d(c$,"setUnitIncrement",function(a){this.unitIncrementSet=!0;this.putClientProperty("JScrollBar.fastWheelScrolling",null);K(this,javax.swing.JScrollPane.ScrollBar,"setUnitIncrement",[a])},"~N");d(c$,"getUnitIncrement",function(a){var b=this.b$["javax.swing.JScrollPane"].getViewport();if(!this.unitIncrementSet&&null!=b&&v(b.getView(),
javax.swing.Scrollable)){var c=b.getView(),b=b.getViewRect();return c.getScrollableUnitIncrement(b,this.getOrientation(),a)}return K(this,javax.swing.JScrollPane.ScrollBar,"getUnitIncrement",[a])},"~N");d(c$,"setBlockIncrement",function(a){this.blockIncrementSet=!0;this.putClientProperty("JScrollBar.fastWheelScrolling",null);K(this,javax.swing.JScrollPane.ScrollBar,"setBlockIncrement",[a])},"~N");d(c$,"getBlockIncrement",function(a){var b=this.b$["javax.swing.JScrollPane"].getViewport();if(this.blockIncrementSet||
null==b)return K(this,javax.swing.JScrollPane.ScrollBar,"getBlockIncrement",[a]);if(v(b.getView(),javax.swing.Scrollable)){var c=b.getView(),b=b.getViewRect();return c.getScrollableBlockIncrement(b,this.getOrientation(),a)}return 1==this.getOrientation()?b.getExtentSize().height:b.getExtentSize().width},"~N");c$=z()};G(c$,"$uiClassID","ScrollPaneUI")});p("javax.swing");c$=M(javax.swing,"ScrollPaneConstants");G(c$,"VIEWPORT","VIEWPORT","VERTICAL_SCROLLBAR","VERTICAL_SCROLLBAR","HORIZONTAL_SCROLLBAR",
"HORIZONTAL_SCROLLBAR","ROW_HEADER","ROW_HEADER","COLUMN_HEADER","COLUMN_HEADER","LOWER_LEFT_CORNER","LOWER_LEFT_CORNER","LOWER_RIGHT_CORNER","LOWER_RIGHT_CORNER","UPPER_LEFT_CORNER","UPPER_LEFT_CORNER","UPPER_RIGHT_CORNER","UPPER_RIGHT_CORNER","LOWER_LEADING_CORNER","LOWER_LEADING_CORNER","LOWER_TRAILING_CORNER","LOWER_TRAILING_CORNER","UPPER_LEADING_CORNER","UPPER_LEADING_CORNER","UPPER_TRAILING_CORNER","UPPER_TRAILING_CORNER","VERTICAL_SCROLLBAR_POLICY","VERTICAL_SCROLLBAR_POLICY","HORIZONTAL_SCROLLBAR_POLICY",
"HORIZONTAL_SCROLLBAR_POLICY","VERTICAL_SCROLLBAR_AS_NEEDED",20,"VERTICAL_SCROLLBAR_NEVER",21,"VERTICAL_SCROLLBAR_ALWAYS",22,"HORIZONTAL_SCROLLBAR_AS_NEEDED",30,"HORIZONTAL_SCROLLBAR_NEVER",31,"HORIZONTAL_SCROLLBAR_ALWAYS",32);p("javax.swing");q(["java.awt.LayoutManager","javax.swing.ScrollPaneConstants","javax.swing.plaf.UIResource"],"javax.swing.ScrollPaneLayout","java.lang.IllegalArgumentException java.awt.Dimension $.Insets $.Rectangle javax.swing.Scrollable $.SwingUtilities $.UIManager".split(" "),
function(){c$=s(function(){this.upperRight=this.upperLeft=this.lowerRight=this.lowerLeft=this.colHead=this.rowHead=this.hsb=this.vsb=this.viewport=null;this.vsbPolicy=20;this.hsbPolicy=30;r(this,arguments)},javax.swing,"ScrollPaneLayout",null,[java.awt.LayoutManager,javax.swing.ScrollPaneConstants]);d(c$,"syncWithScrollPane",function(a){this.viewport=a.getViewport();this.vsb=a.getVerticalScrollBar();this.hsb=a.getHorizontalScrollBar();this.rowHead=a.getRowHeader();this.colHead=a.getColumnHeader();
this.lowerLeft=a.getCorner("LOWER_LEFT_CORNER");this.lowerRight=a.getCorner("LOWER_RIGHT_CORNER");this.upperLeft=a.getCorner("UPPER_LEFT_CORNER");this.upperRight=a.getCorner("UPPER_RIGHT_CORNER");this.vsbPolicy=a.getVerticalScrollBarPolicy();this.hsbPolicy=a.getHorizontalScrollBarPolicy()},"javax.swing.JScrollPane");d(c$,"addSingletonComponent",function(a,b){null!=a&&a!==b&&a.getParent().remove(a);return b},"java.awt.Component,java.awt.Component");e(c$,"addLayoutComponent",function(a,b){if(a.equals("VIEWPORT"))this.viewport=
this.addSingletonComponent(this.viewport,b);else if(a.equals("VERTICAL_SCROLLBAR"))this.vsb=this.addSingletonComponent(this.vsb,b);else if(a.equals("HORIZONTAL_SCROLLBAR"))this.hsb=this.addSingletonComponent(this.hsb,b);else if(a.equals("ROW_HEADER"))this.rowHead=this.addSingletonComponent(this.rowHead,b);else if(a.equals("COLUMN_HEADER"))this.colHead=this.addSingletonComponent(this.colHead,b);else if(a.equals("LOWER_LEFT_CORNER"))this.lowerLeft=this.addSingletonComponent(this.lowerLeft,b);else if(a.equals("LOWER_RIGHT_CORNER"))this.lowerRight=
this.addSingletonComponent(this.lowerRight,b);else if(a.equals("UPPER_LEFT_CORNER"))this.upperLeft=this.addSingletonComponent(this.upperLeft,b);else if(a.equals("UPPER_RIGHT_CORNER"))this.upperRight=this.addSingletonComponent(this.upperRight,b);else throw new IllegalArgumentException("invalid layout key "+a);},"~S,java.awt.Component");e(c$,"removeLayoutComponent",function(a){a===this.viewport?this.viewport=null:a===this.vsb?this.vsb=null:a===this.hsb?this.hsb=null:a===this.rowHead?this.rowHead=null:
a===this.colHead?this.colHead=null:a===this.lowerLeft?this.lowerLeft=null:a===this.lowerRight?this.lowerRight=null:a===this.upperLeft?this.upperLeft=null:a===this.upperRight&&(this.upperRight=null)},"java.awt.Component");d(c$,"getVerticalScrollBarPolicy",function(){return this.vsbPolicy});d(c$,"setVerticalScrollBarPolicy",function(a){switch(a){case 20:case 21:case 22:this.vsbPolicy=a;break;default:throw new IllegalArgumentException("invalid verticalScrollBarPolicy");}},"~N");d(c$,"getHorizontalScrollBarPolicy",
function(){return this.hsbPolicy});d(c$,"setHorizontalScrollBarPolicy",function(a){switch(a){case 30:case 31:case 32:this.hsbPolicy=a;break;default:throw new IllegalArgumentException("invalid horizontalScrollBarPolicy");}},"~N");d(c$,"getViewport",function(){return this.viewport});d(c$,"getHorizontalScrollBar",function(){return this.hsb});d(c$,"getVerticalScrollBar",function(){return this.vsb});d(c$,"getRowHeader",function(){return this.rowHead});d(c$,"getColumnHeader",function(){return this.colHead});
d(c$,"getCorner",function(a){return a.equals("LOWER_LEFT_CORNER")?this.lowerLeft:a.equals("LOWER_RIGHT_CORNER")?this.lowerRight:a.equals("UPPER_LEFT_CORNER")?this.upperLeft:a.equals("UPPER_RIGHT_CORNER")?this.upperRight:null},"~S");e(c$,"preferredLayoutSize",function(a){this.vsbPolicy=a.getVerticalScrollBarPolicy();this.hsbPolicy=a.getHorizontalScrollBarPolicy();var b=a.getInsets(),c=b.left+b.right,b=b.top+b.bottom,d=null,e=null,k=null;null!=this.viewport&&(d=this.viewport.getPreferredSize(),k=this.viewport.getView(),
e=null!=k?k.getPreferredSize():new java.awt.Dimension(0,0));null!=d&&(c+=d.width,b+=d.height);var g=a.getViewportBorder();null!=g&&(a=g.getBorderInsets(a),c+=a.left+a.right,b+=a.top+a.bottom);null!=this.rowHead&&this.rowHead.isVisible()&&(c+=this.rowHead.getPreferredSize().width);null!=this.colHead&&this.colHead.isVisible()&&(b+=this.colHead.getPreferredSize().height);null!=this.vsb&&21!=this.vsbPolicy&&(22==this.vsbPolicy?c+=this.vsb.getPreferredSize().width:null!=e&&null!=d&&(a=!0,v(k,javax.swing.Scrollable)&&
(a=!k.getScrollableTracksViewportHeight()),a&&e.height>d.height&&(c+=this.vsb.getPreferredSize().width)));null!=this.hsb&&31!=this.hsbPolicy&&(32==this.hsbPolicy?b+=this.hsb.getPreferredSize().height:null!=e&&null!=d&&(a=!0,v(k,javax.swing.Scrollable)&&(a=!k.getScrollableTracksViewportWidth()),a&&e.width>d.width&&(b+=this.hsb.getPreferredSize().height)));return new java.awt.Dimension(c,b)},"java.awt.Container");e(c$,"minimumLayoutSize",function(a){this.vsbPolicy=a.getVerticalScrollBarPolicy();this.hsbPolicy=
a.getHorizontalScrollBarPolicy();var b=a.getInsets(),c=b.left+b.right,b=b.top+b.bottom;if(null!=this.viewport)var d=this.viewport.getMinimumSize(),c=c+d.width,b=b+d.height;d=a.getViewportBorder();null!=d&&(a=d.getBorderInsets(a),c+=a.left+a.right,b+=a.top+a.bottom);null!=this.rowHead&&this.rowHead.isVisible()&&(d=this.rowHead.getMinimumSize(),c+=d.width,b=Math.max(b,d.height));null!=this.colHead&&this.colHead.isVisible()&&(d=this.colHead.getMinimumSize(),c=Math.max(c,d.width),b+=d.height);null!=this.vsb&&
21!=this.vsbPolicy&&(d=this.vsb.getMinimumSize(),c+=d.width,b=Math.max(b,d.height));null!=this.hsb&&31!=this.hsbPolicy&&(d=this.hsb.getMinimumSize(),c=Math.max(c,d.width),b+=d.height);return new java.awt.Dimension(c,b)},"java.awt.Container");e(c$,"layoutContainer",function(a){this.vsbPolicy=a.getVerticalScrollBarPolicy();this.hsbPolicy=a.getHorizontalScrollBarPolicy();var b=a.getBounds();b.x=b.y=0;var c=a.getInsets();b.x=c.left;b.y=c.top;b.width-=c.left+c.right;b.height-=c.top+c.bottom;var c=javax.swing.SwingUtilities.isLeftToRight(a),
d=new java.awt.Rectangle(0,b.y,0,0);if(null!=this.colHead&&this.colHead.isVisible()){var e=Math.min(b.height,this.colHead.getPreferredSize().height);d.height=e;b.y+=e;b.height-=e}e=new java.awt.Rectangle(0,0,0,0);if(null!=this.rowHead&&this.rowHead.isVisible()){var k=Math.min(b.width,this.rowHead.getPreferredSize().width);e.width=k;b.width-=k;c?(e.x=b.x,b.x+=k):e.x=b.x+b.width}k=a.getViewportBorder();null!=k?(a=k.getBorderInsets(a),b.x+=a.left,b.y+=a.top,b.width-=a.left+a.right,b.height-=a.top+a.bottom):
a=new java.awt.Insets(0,0,0,0);var g=null!=this.viewport?this.viewport.getView():null,k=null!=g?g.getPreferredSize():new java.awt.Dimension(0,0),h=null!=this.viewport?this.viewport.toViewCoordinates(b.getSize()):new java.awt.Dimension(0,0),j=!1,n=!1,m=0>b.width||0>b.height,p;!m&&v(g,javax.swing.Scrollable)?(p=g,j=p.getScrollableTracksViewportWidth(),n=p.getScrollableTracksViewportHeight()):p=null;var g=new java.awt.Rectangle(0,b.y-a.top,0,0),q;q=m?!1:22==this.vsbPolicy?!0:21==this.vsbPolicy?!1:!n&&
k.height>h.height;null!=this.vsb&&q&&(this.adjustForVSB(!0,b,g,a,c),h=this.viewport.toViewCoordinates(b.getSize()));var r=new java.awt.Rectangle(b.x-a.left,0,0,0),m=m?!1:32==this.hsbPolicy?!0:31==this.hsbPolicy?!1:!j&&k.width>h.width;null!=this.hsb&&m&&(this.adjustForHSB(!0,b,r,a),null!=this.vsb&&(!q&&21!=this.vsbPolicy)&&(h=this.viewport.toViewCoordinates(b.getSize()),(q=k.height>h.height)&&this.adjustForVSB(!0,b,g,a,c)));if(null!=this.viewport&&(this.viewport.setBounds(b),null!=p)){var h=this.viewport.toViewCoordinates(b.getSize()),
s=m,t=q,j=p.getScrollableTracksViewportWidth(),n=p.getScrollableTracksViewportHeight();null!=this.vsb&&20==this.vsbPolicy&&(n=!n&&k.height>h.height,n!=q&&(q=n,this.adjustForVSB(q,b,g,a,c),h=this.viewport.toViewCoordinates(b.getSize())));null!=this.hsb&&30==this.hsbPolicy&&(h=!j&&k.width>h.width,h!=m&&(m=h,this.adjustForHSB(m,b,r,a),null!=this.vsb&&(!q&&21!=this.vsbPolicy)&&(h=this.viewport.toViewCoordinates(b.getSize()),(q=k.height>h.height)&&this.adjustForVSB(!0,b,g,a,c))));(s!=m||t!=q)&&this.viewport.setBounds(b)}g.height=
b.height+a.top+a.bottom;r.width=b.width+a.left+a.right;e.height=b.height+a.top+a.bottom;e.y=b.y-a.top;d.width=b.width+a.left+a.right;d.x=b.x-a.left;null!=this.rowHead&&this.rowHead.setBounds(e);null!=this.colHead&&this.colHead.setBounds(d);if(null!=this.vsb)if(q){if(null!=this.colHead&&javax.swing.UIManager.getBoolean("ScrollPane.fillUpperCorner")&&(c&&null==this.upperRight||!c&&null==this.upperLeft))g.y=d.y,g.height+=d.height;this.vsb.setVisible(!0);this.vsb.setBounds(g)}else this.vsb.setVisible(!1);
if(null!=this.hsb)if(m){if(null!=this.rowHead&&javax.swing.UIManager.getBoolean("ScrollPane.fillLowerCorner")&&(c&&null==this.lowerLeft||!c&&null==this.lowerRight))c&&(r.x=e.x),r.width+=e.width;this.hsb.setVisible(!0);this.hsb.setBounds(r)}else this.hsb.setVisible(!1);null!=this.lowerLeft&&this.lowerLeft.setBounds(c?e.x:g.x,r.y,c?e.width:g.width,r.height);null!=this.lowerRight&&this.lowerRight.setBounds(c?g.x:e.x,r.y,c?g.width:e.width,r.height);null!=this.upperLeft&&this.upperLeft.setBounds(c?e.x:
g.x,d.y,c?e.width:g.width,d.height);null!=this.upperRight&&this.upperRight.setBounds(c?g.x:e.x,d.y,c?g.width:e.width,d.height)},"java.awt.Container");d(c$,"adjustForVSB",function(a,b,c,d,e){var k=c.width;a?(a=Math.max(0,Math.min(this.vsb.getPreferredSize().width,b.width)),b.width-=a,c.width=a,e?c.x=b.x+b.width+d.right:(c.x=b.x-d.left,b.x+=a)):b.width+=k},"~B,java.awt.Rectangle,java.awt.Rectangle,java.awt.Insets,~B");d(c$,"adjustForHSB",function(a,b,c,d){var e=c.height;a?(a=Math.max(0,Math.min(b.height,
this.hsb.getPreferredSize().height)),b.height-=a,c.y=b.y+b.height+d.bottom,c.height=a):b.height+=e},"~B,java.awt.Rectangle,java.awt.Rectangle,java.awt.Insets");d(c$,"getViewportBorderBounds",function(a){return a.getViewportBorderBounds()},"javax.swing.JScrollPane");A(self.c$);c$=B(javax.swing.ScrollPaneLayout,"UIResource",javax.swing.ScrollPaneLayout,javax.swing.plaf.UIResource);c$=z()});p("jalview.io");q(["jalview.io.AlignFile","java.lang.Enum","$.Exception"],"jalview.io.FeaturesFile","jalview.analysis.SequenceIdMatcher jalview.datamodel.AlignedCodonFrame $.SequenceDummy $.SequenceFeature jalview.jsdev.GenericFileAdapter jalview.schemes.GraduatedColor $.UserColourScheme jalview.util.Format $.MapList $.ParseHtmlBodyAndLinks java.awt.Color java.lang.Float $.StringBuffer java.util.ArrayList $.Arrays $.HashMap $.Hashtable $.StringTokenizer $.Vector".split(" "),
function(){c$=s(function(){this.doGffSource=!0;this.gffversion=0;H("jalview.io.FeaturesFile.InvalidGFF3FieldException")||jalview.io.FeaturesFile.$FeaturesFile$InvalidGFF3FieldException$();this.matcher=this.lastmatchedAl=null;r(this,arguments)},jalview.io,"FeaturesFile",jalview.io.AlignFile);m(c$,function(){t(this,jalview.io.FeaturesFile,[])});d(c$,"parse",function(a,b,c){return this.parse(a,b,null,c,!1)},"jalview.datamodel.AlignmentI,java.util.Hashtable,~B");d(c$,"parse",function(a,b,c,d){return this.parse(a,
b,null,c,d)},"jalview.datamodel.AlignmentI,java.util.Map,~B,~B");d(c$,"parse",function(a,b,c,d){return this.parse(a,b,c,d,!1)},"jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B");d(c$,"parse",function(a,b,c,d,e){var k=null;try{for(var g=null,h=new java.util.ArrayList,j,n,m=null,p,q,r,s,t,v,w=null,z=null,A=new java.util.Hashtable,B=!0,E=new java.util.HashMap;null!=(k=this.nextLine());)if(k.startsWith("#"))k.startsWith("##")&&(this.processGffPragma(k,E,a,h),k="");else if(t=new java.util.StringTokenizer(k,
"\t"),1==t.countTokens()&&k.trim().equalsIgnoreCase("GFF"))B=!0;else if(1<t.countTokens()&&4>t.countTokens())if(B=!1,j=t.nextToken(),j.equalsIgnoreCase("startgroup"))w=t.nextToken(),t.hasMoreElements()&&(z=t.nextToken(),c.put(w,z));else if(j.equalsIgnoreCase("endgroup"))t.nextToken(),z=w=null;else{var C=null,F=t.nextToken();if(-1<F.indexOf("|")||F.trim().equalsIgnoreCase("label")){var G=new java.util.StringTokenizer(F,"|",!0),H=1.4E-45,I=3.4028235E38,J=!1,K=G.nextToken();if("|"===K){System.err.println("Expected either 'label' or a colour specification in the line: "+
k);continue}var L=null;0==K.toLowerCase().indexOf("label")&&(J=!0,K=G.hasMoreTokens()?G.nextToken():null,K=G.hasMoreTokens()?G.nextToken():null);var M=null,N,O;if(null!=K){K.equals("|")?K="":G.nextToken();L=G.nextToken();L.equals("|")?L="":G.nextToken();M=G.nextToken();G.nextToken();0!=M.toLowerCase().indexOf("abso")?(N=M,M=null):(N=G.nextToken(),G.nextToken());O=G.nextToken();G.hasMoreTokens()&&G.nextToken();try{0<N.length&&(H=(new Float(N)).floatValue())}catch(Q){if(y(Q,Exception))System.err.println("Couldn't parse the minimum value for graduated colour for type ("+
F+") - did you misspell 'auto' for the optional automatic colour switch ?"),Q.printStackTrace();else throw Q;}try{0<O.length&&(I=(new Float(O)).floatValue())}catch(R){if(y(R,Exception))System.err.println("Couldn't parse the maximum value for graduated colour for type ("+F+")"),R.printStackTrace();else throw R;}}else K="FFFFFF",L="000000";try{C=new jalview.schemes.GraduatedColor((new jalview.schemes.UserColourScheme(K)).findColour("A"),(new jalview.schemes.UserColourScheme(L)).findColour("A"),H,I)}catch(S){if(y(S,
Exception))System.err.println("Couldn't parse the graduated colour scheme ("+F+")"),S.printStackTrace();else throw S;}if(null!=C){C.setColourByLabel(J);C.setAutoScaled(null==M);I=H=null;G.hasMoreTokens()&&(H=G.nextToken(),H.toLowerCase().startsWith("below")?C.setThreshType(0):H.toLowerCase().startsWith("above")?C.setThreshType(1):(C.setThreshType(-1),H.toLowerCase().startsWith("no")||System.err.println("Ignoring unrecognised threshold type : "+H)));if(-1!=C.getThreshType())try{G.nextToken(),I=G.nextToken(),
C.setThresh((new Float(I)).floatValue())}catch(P){if(y(P,Exception))System.err.println("Couldn't parse threshold value as a float: ("+I+")"),P.printStackTrace();else throw P;}if(G.hasMoreTokens()){for(System.err.println("Ignoring additional tokens in parameters in graduated colour specification\n");G.hasMoreTokens();)System.err.println("|"+G.nextToken());System.err.println("\n")}}}else var T=new jalview.schemes.UserColourScheme(F),C=T.findColour("A");null!=C&&b.put(j,C);if(t.hasMoreElements()){var U=
t.nextToken();A.put(j,U);null==c&&(c=new java.util.Hashtable);c.put(j,U)}}else for(C="";t.hasMoreElements();){if(B&&(C=m=t.nextToken(),g=this.findName(a,C,e,h),null!=g)){n=t.nextToken();H=null;this.doGffSource&&-1==n.indexOf(" ")&&(H=String.instantialize(n));j=t.nextToken();try{var W=t.nextToken();q=0==W.length||W.equals("-")?0:Integer.parseInt(W)}catch(X){if(y(X,NumberFormatException))q=0;else throw X;}try{W=t.nextToken(),r=0==W.length||W.equals("-")?0:Integer.parseInt(W)}catch(Y){if(y(Y,NumberFormatException))r=
0;else throw Y;}0==r&&(q=0);try{s=(new Float(t.nextToken())).floatValue()}catch(Z){if(y(Z,NumberFormatException))s=0;else throw Z;}v=new jalview.datamodel.SequenceFeature(j,n,q,r,s,H);try{v.setValue("STRAND",t.nextToken()),v.setValue("FRAME",t.nextToken())}catch($){if(!y($,Exception))throw $;}if(t.hasMoreTokens()){for(var ba=new StringBuffer,H=!1;t.hasMoreTokens();)ba.append((H?"\t":"")+t.nextElement()),H=!0;v.setValue("ATTRIBUTES",ba.toString())}if(this.processOrAddSeqFeature(a,h,g,v,B,e))for(;null!=
(g=a.findName(g,C,!0));)g.addSequenceFeature(new jalview.datamodel.SequenceFeature(v));break}n=B&&null==g?m:t.nextToken();if(!t.hasMoreTokens())return System.err.println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up."),!1;m=t.nextToken();if(m.equals("ID_NOT_SPECIFIED")){C=null;try{p=Integer.parseInt(t.nextToken()),g=a.getSequenceAt(p)}catch(ca){if(y(ca,NumberFormatException))g=null;else throw ca;}}else g=this.findName(a,C=m,e,null),t.nextToken();if(null==
g){System.out.println("Sequence not found: "+k);break}q=Integer.parseInt(t.nextToken());r=Integer.parseInt(t.nextToken());j=t.nextToken();b.containsKey(j)||(T=new jalview.schemes.UserColourScheme(j),b.put(j,T.findColour("A")));v=new jalview.datamodel.SequenceFeature(j,n,"",q,r,w);if(t.hasMoreTokens()){try{s=(new Float(t.nextToken())).floatValue()}catch(da){if(y(da,NumberFormatException))s=0;else throw da;}v.setScore(s)}null!=z&&d&&(v.addLink(z),v.description+="%LINK%");A.containsKey(j)&&d&&(v.addLink(A.get(j).toString()),
v.description+="%LINK%");this.parseDescriptionHTML(v,d);for(g.addSequenceFeature(v);null!=C&&null!=(g=a.findName(g,C,!1));)g.addSequenceFeature(new jalview.datamodel.SequenceFeature(v));B=!1}this.resetMatcher()}catch(aa){if(y(aa,Exception))return this.warningMessage=(null==this.warningMessage?"":this.warningMessage)+"Parsing error at\n"+k,System.out.println("Error parsing feature file: "+aa+"\n"+k),aa.printStackTrace(System.err),this.resetMatcher(),!1;throw aa;}return!0},"jalview.datamodel.AlignmentI,java.util.Map,java.util.Map,~B,~B");
d(c$,"processGffPragma",function(a,b,c,d){b=a.indexOf(" ");var e=-1==b?a.substring(2).trim():a.substring(2,b),e=jalview.io.FeaturesFile.GFFPRAGMA.get(e.toLowerCase());if(null!=e)switch(e){case jalview.io.FeaturesFile.GffPragmas.gff_version:this.gffversion=Integer.parseInt(a.substring(b+1));break;case jalview.io.FeaturesFile.GffPragmas.feature_ontology:break;case jalview.io.FeaturesFile.GffPragmas.attribute_ontology:break;case jalview.io.FeaturesFile.GffPragmas.source_ontology:break;case jalview.io.FeaturesFile.GffPragmas.species_build:break;
case jalview.io.FeaturesFile.GffPragmas.hash:break;case jalview.io.FeaturesFile.GffPragmas.fasta:this.process_as_fasta(c,d);break;default:System.err.println("Ignoring unknown pragma:\n"+a)}},"~S,java.util.Map,jalview.datamodel.AlignmentI,java.util.ArrayList");d(c$,"process_as_fasta",function(a,b){try{this.mark()}catch(c){if(!y(c,java.io.IOException))throw c;}for(var d=jalview.jsdev.GenericFileAdapter.getFile("FastaFile",[]).getSeqs(),e=new jalview.analysis.SequenceIdMatcher(b),k=0,g=d.size();k<g;k++){var h=
e.findIdMatch(d.get(k));if(null!=h){var j=d.get(k);v(h,jalview.datamodel.SequenceDummy)&&(h.become(j),d.set(k,h))}}for(var n,d=d.iterator();d.hasNext()&&((n=d.next())||1);)a.addSequence(n)},"jalview.datamodel.AlignmentI,java.util.List");d(c$,"processOrAddSeqFeature",function(a,b,c,d,e,k){var g=d.getValue("ATTRIBUTES"),h=!0;if(e&&null!=g){e=8;for(var j,n=0,g=g.$plit("\t");n<g.length&&((j=g[n])||1);n++)if(!(null==j||0==j.trim().length)){e++;for(var m=new java.util.HashMap,p,q=0,r=j.trim().$plit(";");q<
r.length&&((p=r[q])||1);q++)if(p=p.trim(),0!=p.length){var s=p.indexOf("="),t=p.indexOf(" "),v=null,w=null;-1<t&&(-1==s||t<s)?(v=p.substring(0,t),w=p.substring(t+1)):-1<s&&(-1==t||s<t)?(v=p.substring(0,s),w=p.substring(s+1)):v=p;null!=v&&(s=m.get(v),null==s&&(s=new java.util.ArrayList,m.put(v,s)),null!=w&&s.add(w.trim()))}try{h=(new Boolean(h&this.processGffKey(m,e,c,d,a,b,k))).valueOf()}catch(z){if(y(z,jalview.io.FeaturesFile.InvalidGFF3FieldException))System.err.println(z);else throw z;}}}h&&c.addSequenceFeature(d);
return h},"jalview.datamodel.AlignmentI,java.util.List,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,~B,~B");d(c$,"processGffKey",function(a,b,c,d,e,k,g){if(d.getType().equals("similarity")){b=d.getStrand();k=this.findNames(e,k,g,a.get(d="Query"));if(null==k||1!=k.size())throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,d,a,"Expecting exactly one sequence in Query field (got "+a.get(d)+")");if(a.containsKey(d="Align"))return g=new jalview.datamodel.AlignedCodonFrame,
a=this.constructCodonMappingFromAlign(a,d,b),g.addMap(c,k.get(0),a),e.addCodonFrame(g),!1}return!0},"java.util.Map,~N,jalview.datamodel.SequenceI,jalview.datamodel.SequenceFeature,jalview.datamodel.AlignmentI,java.util.List,~B");d(c$,"constructCodonMappingFromAlign",function(a,b,c){if(0==c)throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,b,a,"Invalid strand for a codon mapping (cannot be 0)");for(var d=new java.util.ArrayList,e=new java.util.ArrayList,k=0,g=0,h,j=a.get(b).iterator();j.hasNext()&&
((h=j.next())||1);){for(var n=new java.util.ArrayList,m=new java.util.StringTokenizer(h," ");m.hasMoreTokens();){var p=m.nextToken();try{n.add(new Integer(p))}catch(q){if(y(q,NumberFormatException))throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,b,a,"Invalid number in field "+p);throw q;}}if(3!=n.size())throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,b,a,"Invalid number of fields for this attribute ("+n.size()+")");d.add(new Integer(n.get(0).intValue()));d.add(new Integer(n.get(0).intValue()+
c*n.get(2).intValue()));n.get(1).equals(new Integer(k))&&0<g?(k+=n.get(2).intValue()/3,g=n.get(2).intValue()%3,e.set(e.size()-1,new Integer(k))):(e.add(n.get(1)),k=n.get(1).intValue()+n.get(2).intValue()/3,g=n.get(2).intValue()%3,e.add(new Integer(k)))}if(1==d.size()%2)throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,b,a,"Couldn't parse the DNA alignment range correctly");if(1==e.size()%2)throw C(jalview.io.FeaturesFile.InvalidGFF3FieldException,this,null,b,a,"Couldn't parse the protein alignment range correctly");
a=w(d.size(),0);b=w(e.size(),0);c=0;for(var r,d=d.iterator();d.hasNext()&&((r=d.next())||1);)a[c++]=r.intValue();c=0;for(d=e.iterator();d.hasNext()&&((r=d.next())||1);)b[c++]=r.intValue();return new jalview.util.MapList(a,b,3,1)},"java.util.Map,~S,~N");d(c$,"findNames",function(a,b,c,d){var e=new java.util.ArrayList,k;for(d=d.iterator();d.hasNext()&&((k=d.next())||1);){var g=this.findName(a,k,c,b);null!=g&&e.add(g)}return e},"jalview.datamodel.AlignmentI,java.util.List,~B,java.util.List");d(c$,"resetMatcher",
function(){this.matcher=this.lastmatchedAl=null});d(c$,"findName",function(a,b,c,d){var e=null;if(c)this.lastmatchedAl!==a&&(this.matcher=new jalview.analysis.SequenceIdMatcher((this.lastmatchedAl=a).getSequencesArray()),null!=d&&this.matcher.addAll(d)),e=this.matcher.findIdMatch(b);else if(e=a.findName(b,!0),null==e&&null!=d){var k;for(a=d.iterator();a.hasNext()&&((k=a.next())||1);)if(b.equals(k.getName()))return k}null==e&&null!=d&&(e=new jalview.datamodel.SequenceDummy(b),c&&this.matcher.addAll(java.util.Arrays.asList(E(-1,
[e]))),d.add(e));return e},"jalview.datamodel.AlignmentI,~S,~B,java.util.List");d(c$,"parseDescriptionHTML",function(a,b){if(null!=a.getDescription()){var c=new jalview.util.ParseHtmlBodyAndLinks(a.getDescription(),b,this.newline);a.description=b?c.getNonHtmlContent():a.description;for(var d,c=c.getLinks().iterator();c.hasNext()&&((d=c.next())||1);)a.addLink(d)}},"jalview.datamodel.SequenceFeature,~B");d(c$,"printJalviewFormat",function(a,b){return this.printJalviewFormat(a,b,!0,!0)},"~A,java.util.Map");
d(c$,"printJalviewFormat",function(a,b,c,d){var e=new StringBuffer,k,g=!1;if(c&&!d&&(null==b||1>b.size()))return"No Features Visible";if(null!=b&&c){k=b.keySet().iterator();for(var h,j;k.hasNext();){h=k.next().toString();if(v(b.get(h),jalview.schemes.GraduatedColor)){var n=b.get(h);j=(n.isColourByLabel()?"label|":"")+jalview.util.Format.getHexString(n.getMinColor())+"|"+jalview.util.Format.getHexString(n.getMaxColor())+(n.isAutoScale()?"|":"|abso|")+n.getMin()+"|"+n.getMax()+"|";-1!=n.getThreshType()?
(0==n.getThreshType()?j+="below":(1!=n.getThreshType()&&System.err.println("WARNING: Unsupported threshold type ("+n.getThreshType()+") : Assuming 'above'"),j+="above"),j+="|"+n.getThresh()):j+="none"}else j=v(b.get(h),java.awt.Color)?jalview.util.Format.getHexString(b.get(h)):jalview.util.Format.getHexString(new java.awt.Color(Integer.parseInt(b.get(h).toString())));e.append(h);e.append("\t");e.append(j);e.append(this.newline)}}h=new java.util.Vector;j=0;for(var m=!1,n=0;n<a.length;n++)if(k=a[n].getSequenceFeatures(),
null!=k)for(var p=0;p<k.length;p++)m=0==k[p].begin&&0==k[p].end,!d&&m||!m&&c&&!b.containsKey(k[p].type)||null!=k[p].featureGroup&&!h.contains(k[p].featureGroup)&&h.addElement(k[p].featureGroup);var q=null;do{0<h.size()&&j<h.size()?(q=h.elementAt(j).toString(),e.append(this.newline),e.append("STARTGROUP\t"),e.append(q),e.append(this.newline)):q=null;for(n=0;n<a.length;n++)if(k=a[n].getSequenceFeatures(),null!=k)for(p=0;p<k.length;p++)if(m=0==k[p].begin&&0==k[p].end,!(!d&&m||!m&&c&&!b.containsKey(k[p].type)))if(!(null!=
q&&(null==k[p].featureGroup||!k[p].featureGroup.equals(q)))&&!(null==q&&null!=k[p].featureGroup)){g=!0;if(null==k[p].description||k[p].description.equals(""))e.append(k[p].type+"\t");else{null!=k[p].links&&-1==k[p].getDescription().indexOf("<html>")&&e.append("<html>");e.append(k[p].description+" ");if(null!=k[p].links){for(m=0;m<k[p].links.size();m++){var r=k[p].links.elementAt(m).toString(),s=r.substring(r.indexOf("|")+1),r=r.substring(0,r.indexOf("|"));-1==k[p].description.indexOf(s)&&e.append('<a href="'+
s+'">'+r+"</a>")}-1==k[p].getDescription().indexOf("</html>")&&e.append("</html>")}e.append("\t")}e.append(a[n].getName());e.append("\t-1\t");e.append(""+k[p].begin);e.append("\t");e.append(""+k[p].end);e.append("\t");e.append(k[p].type);Float.isNaN(k[p].score)||(e.append("\t"),e.append(k[p].score));e.append(this.newline)}if(null!=q)e.append("ENDGROUP\t"),e.append(q),e.append(this.newline),j++;else break}while(j<h.size()+1);return!g?"No Features Visible":e.toString()},"~A,java.util.Map,~B,~B");d(c$,
"printGFFFormat",function(a,b){return this.printGFFFormat(a,b,!0,!0)},"~A,java.util.Map");d(c$,"printGFFFormat",function(a,b,c,d){for(var e=new StringBuffer,k,g,h=0;h<a.length;h++)if(null!=a[h].getSequenceFeatures()){k=a[h].getSequenceFeatures();for(var j=0;j<k.length;j++)g=0==k[j].begin&&0==k[j].end,!d&&g||!g&&c&&!b.containsKey(k[j].type)||(g=k[j].featureGroup,null==g&&(g=k[j].getDescription()),e.append(a[h].getName()),e.append("\t"),e.append(g),e.append("\t"),e.append(k[j].type),e.append("\t"),
e.append(""+k[j].begin),e.append("\t"),e.append(""+k[j].end),e.append("\t"),e.append(k[j].score),e.append("\t"),null!=k[j].getValue("STRAND")?(e.append(k[j].getValue("STRAND")),e.append("\t")):e.append(".\t"),null!=k[j].getValue("FRAME")?e.append(k[j].getValue("FRAME")):e.append("."),null!=k[j].getValue("ATTRIBUTES")&&e.append(k[j].getValue("ATTRIBUTES")),e.append(this.newline))}return e.toString()},"~A,java.util.Map,~B,~B");d(c$,"parse",function(){});e(c$,"print",function(){return"USE printGFFFormat() or printJalviewFormat()"});
c$.$FeaturesFile$InvalidGFF3FieldException$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.value=this.field=null;r(this,arguments)},jalview.io.FeaturesFile,"InvalidGFF3FieldException",Exception);m(c$,function(a,b,c){t(this,jalview.io.FeaturesFile.InvalidGFF3FieldException,[c+" (Field was "+a+" and value was "+b.get(a).toString()]);this.field=a;this.value=b.get(a).toString()},"~S,java.util.Map,~S");c$=z()};A(self.c$);c$=B(jalview.io.FeaturesFile,"GffPragmas",Enum);R(c$,"gff_version",
0,[]);R(c$,"sequence_region",1,[]);R(c$,"feature_ontology",2,[]);R(c$,"attribute_ontology",3,[]);R(c$,"source_ontology",4,[]);R(c$,"species_build",5,[]);R(c$,"fasta",6,[]);R(c$,"hash",7,[]);c$=z();G(c$,"GFFPRAGMA",null);jalview.io.FeaturesFile.GFFPRAGMA=new java.util.HashMap;jalview.io.FeaturesFile.GFFPRAGMA.put("sequence-region",jalview.io.FeaturesFile.GffPragmas.sequence_region);jalview.io.FeaturesFile.GFFPRAGMA.put("feature-ontology",jalview.io.FeaturesFile.GffPragmas.feature_ontology);jalview.io.FeaturesFile.GFFPRAGMA.put("#",
jalview.io.FeaturesFile.GffPragmas.hash);jalview.io.FeaturesFile.GFFPRAGMA.put("fasta",jalview.io.FeaturesFile.GffPragmas.fasta);jalview.io.FeaturesFile.GFFPRAGMA.put("species-build",jalview.io.FeaturesFile.GffPragmas.species_build);jalview.io.FeaturesFile.GFFPRAGMA.put("source-ontology",jalview.io.FeaturesFile.GffPragmas.source_ontology);jalview.io.FeaturesFile.GFFPRAGMA.put("attribute-ontology",jalview.io.FeaturesFile.GffPragmas.attribute_ontology)});p("jalview.datamodel");q(["jalview.datamodel.Sequence",
"$.SequenceI"],"jalview.datamodel.SequenceDummy",null,function(){c$=s(function(){this.dummy=!0;r(this,arguments)},jalview.datamodel,"SequenceDummy",jalview.datamodel.Sequence,jalview.datamodel.SequenceI);m(c$,function(a){t(this,jalview.datamodel.SequenceDummy,[a,"THISAPLACEHOLDER"])},"~S");d(c$,"become",function(a){this.initSeqFrom(a,null);this.dummy=!1},"jalview.datamodel.SequenceI");d(c$,"isDummy",function(){return this.dummy})});p("java.awt.event");q(["java.awt.event.MouseListener","$.MouseMotionListener",
"$.MouseWheelListener"],"java.awt.event.MouseAdapter",null,function(){c$=B(java.awt.event,"MouseAdapter",null,[java.awt.event.MouseListener,java.awt.event.MouseWheelListener,java.awt.event.MouseMotionListener]);e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");
e(c$,"mouseWheelMoved",function(){},"java.awt.event.MouseWheelEvent");e(c$,"mouseDragged",function(){},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(){},"java.awt.event.MouseEvent")});p("jalview.appletgui");q("awt2swing.Checkbox $.Panel jalview.api.FeatureSettingsControllerI java.awt.event.ActionListener $.AdjustmentListener $.ItemListener $.MouseListener $.MouseMotionListener".split(" "),"jalview.appletgui.FeatureSettings","awt2swing.Button $.Frame $.Label $.MenuItem $.PopupMenu $.ScrollPane $.Scrollbar $.Util jalview.appletgui.FeatureColourChooser $.UserDefinedColours jalview.bin.JalviewLite jalview.schemes.GraduatedColor jalview.util.MessageManager java.awt.BorderLayout $.Color $.Font $.GridLayout $.Toolkit java.awt.event.WindowAdapter java.lang.Boolean $.Error java.util.Vector".split(" "),
function(){c$=s(function(){this.selectedCheck=this.groupItemListener=this.transparency=this.linkImage=this.scrollPane=this.featurePanel=this.groupPanel=this.frame=this.av=this.ap=this.fr=null;this.dragging=!1;H("jalview.appletgui.FeatureSettings.MyCheckbox")||jalview.appletgui.FeatureSettings.$FeatureSettings$MyCheckbox$();r(this,arguments)},jalview.appletgui,"FeatureSettings",awt2swing.Panel,[java.awt.event.ItemListener,java.awt.event.MouseListener,java.awt.event.MouseMotionListener,java.awt.event.ActionListener,
java.awt.event.AdjustmentListener,jalview.api.FeatureSettingsControllerI]);J(c$,function(){this.featurePanel=new awt2swing.Panel;this.groupItemListener=(H("jalview.appletgui.FeatureSettings$1")?0:jalview.appletgui.FeatureSettings.$FeatureSettings$1$(),C(jalview.appletgui.FeatureSettings$1,this,null))});m(c$,function(a){t(this,jalview.appletgui.FeatureSettings,[]);this.ap=a;this.av=a.av;a.av.featureSettings=this;this.fr=a.seqPanel.seqCanvas.getFeatureRenderer();this.transparency=new awt2swing.Scrollbar(0,
100-I(100*this.fr.getTransparency()),1,1,100);this.fr.isTransparencyAvailable()?this.transparency.addAdjustmentListener(this):this.transparency.setEnabled(!1);a=this.getClass().getResource("/images/link.gif");null!=a&&(this.linkImage=java.awt.Toolkit.getDefaultToolkit().getImage(a));(this.av.isShowSequenceFeatures()||!this.fr.hasRenderOrder())&&this.fr.findAllFeatures(!0);this.discoverAllFeatureData();this.setLayout(new java.awt.BorderLayout);this.scrollPane=new awt2swing.ScrollPane;this.scrollPane.add(this.featurePanel);
null!=this.fr.getAllFeatureColours()&&0<this.fr.getAllFeatureColours().size()&&this.add(this.scrollPane,"Center");var b=new awt2swing.Button("Invert Selection");b.addActionListener(this);a=new awt2swing.Panel(new java.awt.GridLayout(2,1,5,10));a.add(b);b=new awt2swing.Panel(new java.awt.BorderLayout);this.fr.isTransparencyAvailable()?(b.add(this.transparency,"Center"),b.add(new awt2swing.Label("Transparency"),"East")):b.add(new awt2swing.Label("Transparency not available in this web browser"),"Center");
a.add(b,"South");this.add(a,"South");null!=this.groupPanel&&(this.groupPanel.setLayout(new java.awt.GridLayout(F(this.fr.getFeatureGroupsSize()/4)+1,4)),this.groupPanel.validate(),this.add(this.groupPanel,"North"));this.frame=new awt2swing.Frame;this.frame.add(this);this.frame.addWindowListener((H("jalview.appletgui.FeatureSettings$2")?0:jalview.appletgui.FeatureSettings.$FeatureSettings$2$(),C(jalview.appletgui.FeatureSettings$2,this,T("me",this))));a=50*this.featurePanel.getComponentCount()+60;
a=Math.max(200,a);a=Math.min(400,a);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("label.feature_settings"),300,a)},"jalview.appletgui.AlignmentPanel");d(c$,"PaintComponent",function(a){a.setColor(java.awt.Color.black);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.no_features_added_to_this_alignment"),10,20);awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.features_can_be_added_from_searches_1"),10,40);awt2swing.Util.drawString(a,
jalview.util.MessageManager.getString("label.features_can_be_added_from_searches_2"),10,60)},"java.awt.Graphics");d(c$,"popupSort",function(a,b,c,d){var e=a.type,k=this.fr.getFeatureStyle(e),g=new awt2swing.PopupMenu(jalview.util.MessageManager.formatMessage("label.settings_for_type",E(-1,[e]))),h=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.sort_by_score"));g.add(h);h.addActionListener((H("jalview.appletgui.FeatureSettings$3")?0:jalview.appletgui.FeatureSettings.$FeatureSettings$3$(),
C(jalview.appletgui.FeatureSettings$3,this,T("me",this,"type",e))));h=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.sort_by_density"));h.addActionListener((H("jalview.appletgui.FeatureSettings$4")?0:jalview.appletgui.FeatureSettings.$FeatureSettings$4$(),C(jalview.appletgui.FeatureSettings$4,this,T("me",this,"type",e))));g.add(h);null!=b&&(b=b.get(e),null!=b&&null!=b[0]&&(b=new awt2swing.MenuItem(v(k,java.awt.Color)?"Graduated Colour":"Single Colour"),g.add(b),b.addActionListener((H("jalview.appletgui.FeatureSettings$5")?
0:jalview.appletgui.FeatureSettings.$FeatureSettings$5$(),C(jalview.appletgui.FeatureSettings$5,this,T("typeCol",k,"me",this,"type",e,"check",a))))));this.featurePanel.add(g);g.show(this.featurePanel,c,d)},"jalview.appletgui.FeatureSettings.MyCheckbox,java.util.Hashtable,~N,~N");e(c$,"discoverAllFeatureData",function(){null!=this.fr.getAllFeatureColours()&&0<this.fr.getAllFeatureColours().size()&&this.rebuildGroups();this.resetTable(!1)});d(c$,"rebuildGroups",function(){var a=!1;null==this.groupPanel?
this.groupPanel=new awt2swing.Panel:(a=!0,this.groupPanel.removeAll());for(var b,c=this.fr.getFeatureGroups().iterator();c.hasNext()&&((b=c.next())||1);){var d=this.fr.checkGroupVisibility(b,!1),e=C(jalview.appletgui.FeatureSettings.MyCheckbox,this,null,b,d,null!=this.fr.featureLinks&&this.fr.featureLinks.containsKey(b));e.addMouseListener(this);e.setFont(new java.awt.Font("Serif",1,12));e.addItemListener(this.groupItemListener);e.setVisible(d);this.groupPanel.add(e)}a&&this.groupPanel.validate()});
d(c$,"resetTable",function(a){for(var b,c=null,d=new java.util.Vector,e=this.av.getAlignment(),k=0;k<e.getHeight();k++)if(null!=e.getSequenceAt(k).getSequenceFeatures()){b=e.getSequenceAt(k).getSequenceFeatures();for(var g=0;g<b.length;){c=b[g].featureGroup;if(null==c||this.fr.checkGroupVisibility(c,!0))c=b[g].getType(),d.contains(c)||d.addElement(c);g++}}b=this.featurePanel.getComponentCount();for(k=0;k<b;k++)e=this.featurePanel.getComponents(),e=e[k],d.contains(e.type)||(this.featurePanel.remove(k),
b--,k--);if(null!=this.fr.getRenderOrder()){k=this.fr.getRenderOrder();for(b=k.size()-1;-1<b;b--)e=k.get(b),d.contains(e)&&(d.removeElement(e),this.addCheck(!1,e))}for(d=d.elements();d.hasMoreElements();)this.addCheck(a,d.nextElement().toString());this.featurePanel.setLayout(new java.awt.GridLayout(this.featurePanel.getComponentCount(),1,10,5));this.featurePanel.validate();null!=this.scrollPane&&this.scrollPane.validate();this.itemStateChanged(null)},"~B");d(c$,"addCheck",function(a,b){var c,d=this.featurePanel.getComponents(),
e;c=!0;for(var k=0;k<this.featurePanel.getComponentCount();k++)if(e=d[k],e.type.equals(b)){c=!1;break}if(c){c=!1;if(a||this.av.getFeaturesDisplayed().isVisible(b))c=!0;e=C(jalview.appletgui.FeatureSettings.MyCheckbox,this,null,b,c,null!=this.fr.featureLinks&&this.fr.featureLinks.containsKey(b),this.fr.getFeatureStyle(b));e.addMouseListener(this);e.addMouseMotionListener(this);e.addItemListener(this);a?this.featurePanel.add(e,0):this.featurePanel.add(e)}},"~B,~S");e(c$,"actionPerformed",function(){for(var a=
0;a<this.featurePanel.getComponentCount();a++){var b=this.featurePanel.getComponent(a);b.setState(!b.getState())}this.selectionChanged()},"java.awt.event.ActionEvent");e(c$,"itemStateChanged",function(){this.selectionChanged()},"java.awt.event.ItemEvent");d(c$,"selectionChanged",function(){for(var a=this.featurePanel.getComponents(),b=a.length,c=E(b,3,null),d=0,e=0;e<b;e++){var k=a[e];c[d][0]=k.type;c[d][1]=this.fr.getFeatureStyle(k.type);c[d][2]=new Boolean(k.getState());d++}a=E(d,3,null);System.arraycopy(c,
0,a,0,d);this.fr.setFeaturePriority(a);this.ap.paintAlignment(!0)});e(c$,"mousePressed",function(a){this.selectedCheck=a.getSource();null!=this.fr.featureLinks&&this.fr.featureLinks.containsKey(this.selectedCheck.type)&&a.getX()>this.selectedCheck.stringWidth+20&&a.consume()},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){a.getSource().getParent()===this.featurePanel&&(this.dragging=!0)},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){if(a.getSource().getParent()===this.featurePanel){var b=
null,c=null,b=a.getY()+a.getComponent().getLocation().y,b=b>this.featurePanel.getSize().height?this.featurePanel.getComponent(this.featurePanel.getComponentCount()-1):0>b?this.featurePanel.getComponent(0):this.featurePanel.getComponentAt(a.getX(),a.getY()+a.getComponent().getLocation().y);null!=b&&v(b,awt2swing.Checkbox)&&(c=b);if(null!=this.selectedCheck&&null!=c&&this.selectedCheck!==c){a=-1;for(b=0;b<this.featurePanel.getComponentCount();b++)if(c===this.featurePanel.getComponent(b)){a=b;break}this.featurePanel.remove(this.selectedCheck);
this.featurePanel.add(this.selectedCheck,a);this.featurePanel.validate();this.itemStateChanged(null)}}},"java.awt.event.MouseEvent");d(c$,"setUserColour",function(a,b){if(v(b,java.awt.Color)||v(b,jalview.schemes.GraduatedColor))this.fr.setColour(a,b);else throw Error(jalview.util.MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));this.refreshTable()},"~S,~O");d(c$,"refreshTable",function(){this.featurePanel.removeAll();this.resetTable(!1);this.ap.paintAlignment(!0)});
e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(a){var b=a.getSource();0!=(a.getModifiers()&4)&&this.popupSort(b,this.fr.getMinMax(),a.getX(),a.getY());if(null!=this.fr.featureLinks&&this.fr.featureLinks.containsKey(b.type)&&a.getX()>b.stringWidth+20){a.consume();var c=this.fr.featureLinks.get(b.type).toString();this.ap.alignFrame.showURL(c.substring(c.indexOf("|")+1),c.substring(0,c.indexOf("|")))}b.getParent()===
this.featurePanel&&1<a.getClickCount()&&(a=this.fr.getFeatureStyle(b.type),v(a,java.awt.Color)?new jalview.appletgui.UserDefinedColours(this,b.type,a):(new jalview.appletgui.FeatureColourChooser(this,b.type),b.updateColor(this.fr.getFeatureStyle(b.type))))},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(){},"java.awt.event.MouseEvent");e(c$,"adjustmentValueChanged",function(){this.fr.setTransparency((100-this.transparency.getValue())/100);this.ap.seqPanel.seqCanvas.repaint()},"java.awt.event.AdjustmentEvent");
c$.$FeatureSettings$MyCheckbox$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.type=null;this.stringWidth=0;this.hasLink=!1;this.col=this.gcol=null;r(this,arguments)},jalview.appletgui.FeatureSettings,"MyCheckbox",awt2swing.Checkbox);d(c$,"updateColor",function(a){if(v(a,java.awt.Color))this.col=a,this.gcol=null;else if(v(a,jalview.schemes.GraduatedColor))this.gcol=a,this.col=null;else throw Error(jalview.util.MessageManager.getString("error.invalid_colour_for_mycheckbox"));null!=this.col?
this.setBackground(this.col):(a=this.type,-1!=this.gcol.getThreshType()&&(a+=" "+(1==this.gcol.getThreshType()?"(>)":"(<)")),this.gcol.isColourByLabel()?(this.setBackground(java.awt.Color.white),a+=" (by Label)"):this.setBackground(this.gcol.getMinColor()),this.setLabel(a));this.repaint()},"~O");m(c$,function(a,b,c){t(this,jalview.appletgui.FeatureSettings.MyCheckbox,[a,b]);this.type=a;this.stringWidth=this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFontMetrics(this.b$["jalview.appletgui.FeatureSettings"].av.nullFrame.getFont()).stringWidth(a);
this.hasLink=c},"~S,~B,~B");m(c$,function(a,b,c,d){this.construct(a,b,c);this.updateColor(d)},"~S,~B,~B,~O");d(c$,"PaintComponent",function(a){var b=this.getSize();if(null!=this.gcol){if(this.gcol.isColourByLabel())a.setColor(java.awt.Color.white);else{var c=this.gcol.getMaxColor();a.setColor(c)}a.fillRect(F(b.width/2),0,F(b.width/2),b.height)}this.hasLink&&a.drawImage(this.b$["jalview.appletgui.FeatureSettings"].linkImage,this.stringWidth+25,F((this.getSize().height-this.b$["jalview.appletgui.FeatureSettings"].linkImage.getHeight(this))/
2),this)},"java.awt.Graphics");c$=z()};c$.$FeatureSettings$1$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureSettings$1",null,java.awt.event.ItemListener);e(c$,"itemStateChanged",function(a){a=a.getSource();this.b$["jalview.appletgui.FeatureSettings"].fr.setGroupVisibility(a.getLabel(),a.getState());this.b$["jalview.appletgui.FeatureSettings"].ap.seqPanel.seqCanvas.repaint();null!=this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel&&this.b$["jalview.appletgui.FeatureSettings"].ap.overviewPanel.updateOverviewImage();
this.b$["jalview.appletgui.FeatureSettings"].resetTable(!0)},"java.awt.event.ItemEvent");c$=z()};c$.$FeatureSettings$2$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureSettings$2",java.awt.event.WindowAdapter);e(c$,"windowClosing",function(){this.f$.me.av.featureSettings===this.f$.me&&(this.f$.me.av.featureSettings=null,this.f$.me.ap=null,this.f$.me.av=null)},"java.awt.event.WindowEvent");c$=z()};c$.$FeatureSettings$3$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureSettings$3",null,java.awt.event.ActionListener);
e(c$,"actionPerformed",function(){this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureScore(E(-1,[this.f$.type]))},"java.awt.event.ActionEvent");c$=z()};c$.$FeatureSettings$4$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureSettings$4",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.f$.me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(E(-1,[this.f$.type]))},"java.awt.event.ActionEvent");c$=z()};c$.$FeatureSettings$5$=function(){A(self.c$);c$=L(jalview.appletgui,"FeatureSettings$5",
null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){v(this.f$.typeCol,java.awt.Color)?(new jalview.appletgui.FeatureColourChooser(this.f$.me,this.f$.type),this.f$.check.updateColor(this.b$["jalview.appletgui.FeatureSettings"].fr.getFeatureStyle(this.f$.type))):new jalview.appletgui.UserDefinedColours(this.f$.me,this.f$.check.type,this.f$.typeCol)},"java.awt.event.ActionEvent");c$=z()}});p("jalview.api");M(jalview.api,"FeatureSettingsControllerI");p("jalview.appletgui");q(["awt2swing.Panel",
"java.awt.event.MouseListener","$.MouseMotionListener","java.lang.Thread","java.util.Vector"],"jalview.appletgui.IdPanel","jalview.appletgui.APopupMenu $.IdCanvas $.PaintRefresher $.Tooltip jalview.datamodel.SequenceGroup jalview.util.UrlLink java.awt.BorderLayout java.lang.Float $.StringBuffer".split(" "),function(){c$=s(function(){this.scrollThread=this.alignPanel=this.av=this.idCanvas=null;this.lastid=-1;this.mouseDragging=!1;this.tooltip=this.links=null;H("jalview.appletgui.IdPanel.ScrollThread")||
jalview.appletgui.IdPanel.$IdPanel$ScrollThread$();r(this,arguments)},jalview.appletgui,"IdPanel",awt2swing.Panel,[java.awt.event.MouseListener,java.awt.event.MouseMotionListener]);J(c$,function(){this.links=new java.util.Vector});m(c$,function(a,b){t(this,jalview.appletgui.IdPanel,[]);this.setName("idPanel");this.av=a;this.alignPanel=b;this.idCanvas=new jalview.appletgui.IdCanvas(a);this.setLayout(new java.awt.BorderLayout);this.add(this.idCanvas,"Center");this.idCanvas.addMouseListener(this);this.idCanvas.addMouseMotionListener(this);
null!=a.applet&&a.applet.getLinkParams(this.links);var c=this.links.indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");-1<c&&this.links.setElementAt("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",c);1>this.links.size()&&(this.links=new java.util.Vector,this.links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"))},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
e(c$,"mouseMoved",function(a){a=this.alignPanel.seqPanel.findSeq(a);a=this.av.getAlignment().getSequenceAt(a);var b=new StringBuffer;if(null!=a){null!=a.getDescription()&&(b.append(a.getDescription()),b.append("\n"));for(var c=a.getSequenceFeatures(),d=0;null!=c&&d<c.length;d++)if(c[d].begin==c[d].end&&0==c[d].begin){var e=!1;null!=c[d].getFeatureGroup()&&(b.append(c[d].getFeatureGroup()),e=!0);null!=c[d].getType()&&(b.append(" "),b.append(c[d].getType()),e=!0);null!=c[d].getDescription()&&(b.append(" "),
b.append(c[d].getDescription()),e=!0);!Float.isNaN(c[d].getScore())&&0!=c[d].getScore()&&(b.append(" Score = "),b.append(c[d].getScore()),e=!0);null!=c[d].getStatus()&&0<c[d].getStatus().length&&(b.append(" ("),b.append(c[d].getStatus()),b.append(")"),e=!0);e&&b.append("\n")}}0==b.length()?(null!=this.tooltip&&this.tooltip.setVisible(!1),this.tooltip=null):null==this.tooltip?this.tooltip=new jalview.appletgui.Tooltip(a.getDisplayId(!0)+"\n"+b.toString(),this.idCanvas):this.tooltip.setTip(a.getDisplayId(!0)+
"\n"+b.toString())},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){this.mouseDragging=!0;a=Math.max(0,this.alignPanel.seqPanel.findSeq(a));a<this.lastid?this.selectSeqs(this.lastid-1,a):a>this.lastid&&this.selectSeqs(this.lastid+1,a);this.lastid=a;this.alignPanel.paintAlignment(!1)},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(a){if(!(2>a.getClickCount())&&(a=this.alignPanel.seqPanel.findSeq(a),a=this.av.getAlignment().getSequenceAt(a),null!=a)){a=a.getName();for(var b=
null,c=null,d=0;null==c&&d<this.links.size();){var c=this.links.elementAt(d++).toString(),e=null;try{e=new jalview.util.UrlLink(c),b=e.getTarget()}catch(k){if(y(k,Exception)){System.err.println("Exception for URLLink '"+c+"'");k.printStackTrace();c=null;continue}else throw k;}e.isValid()?(c=e.makeUrls(a,!0),c=null==c||null==c[0]||1>c[0].length?null:c[1]):(System.err.println(e.getInvalidMessage()),c=null)}try{this.alignPanel.alignFrame.showURL(c,b)}catch(g){if(y(g,Exception))g.printStackTrace();else throw g;
}}},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){null!=this.scrollThread&&(this.scrollThread.running=!1)},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(a){this.av.getWrapAlignment()||(this.mouseDragging&&(0>a.getY()&&0<this.av.getStartSeq())&&(this.scrollThread=C(jalview.appletgui.IdPanel.ScrollThread,this,null,!0)),this.mouseDragging&&(a.getY()>=this.getSize().height&&this.av.getAlignment().getHeight()>this.av.getEndSeq())&&(this.scrollThread=C(jalview.appletgui.IdPanel.ScrollThread,
this,null,!1)))},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){if(!(1<a.getClickCount())){a.getY();this.av.getWrapAlignment()&&this.av.getCharHeight();var b=this.alignPanel.seqPanel.findSeq(a);if(4==(a.getModifiers()&4)){for(var b=this.av.getAlignment().getSequenceAt(b),c=new java.util.Vector,d=0,e=this.links.size();d<e;d++)c.addElement(this.links.elementAt(d));for(var k=null==b?null:b.getSequenceFeatures(),g=0;null!=k&&g<k.length;g++)if(k[g].begin==k[g].end&&0==k[g].begin&&null!=k[g].links&&
0<k[g].links.size()){d=0;for(e=k[g].links.size();d<e;d++)c.addElement(k[g].links.elementAt(d))}b=new jalview.appletgui.APopupMenu(this.alignPanel,b,c);this.add(b);b.show(this,a.getX(),a.getY())}else{if(null==this.av.getSelectionGroup()||!a.isControlDown()&&!a.isShiftDown()&&null!=this.av.getSelectionGroup())this.av.setSelectionGroup(new jalview.datamodel.SequenceGroup),this.av.getSelectionGroup().setStartRes(0),this.av.getSelectionGroup().setEndRes(this.av.getAlignment().getWidth()-1);a.isShiftDown()&&
-1!=this.lastid?this.selectSeqs(this.lastid,b):this.selectSeq(b);this.alignPanel.paintAlignment(!1)}}},"java.awt.event.MouseEvent");d(c$,"selectSeq",function(a){this.lastid=a;a=this.av.getAlignment().getSequenceAt(a);this.av.getSelectionGroup().addOrRemove(a,!0)},"~N");d(c$,"selectSeqs",function(a,b){this.lastid=a;b>=this.av.getAlignment().getHeight()&&(b=this.av.getAlignment().getHeight()-1);if(b<a){var c=a;a=b;this.lastid=b=c}null==this.av.getSelectionGroup()&&this.av.setSelectionGroup(new jalview.datamodel.SequenceGroup);
for(c=a;c<=b;c++)this.av.getSelectionGroup().addSequence(this.av.getAlignment().getSequenceAt(c),c==b)},"~N,~N");e(c$,"mouseReleased",function(){null!=this.scrollThread&&(this.scrollThread.running=!1);null!=this.av.getSelectionGroup()&&this.av.getSelectionGroup().recalcConservation();this.mouseDragging=!1;jalview.appletgui.PaintRefresher.Refresh(this,this.av.getSequenceSetId());this.av.sendSelection()},"java.awt.event.MouseEvent");d(c$,"highlightSearchResults",function(a){this.idCanvas.setHighlighted(a);
null!=a&&(a=this.av.getAlignment().findIndex(a.get(0)),(this.av.getStartSeq()>a||this.av.getEndSeq()<a)&&this.alignPanel.setScrollValues(this.av.getStartRes(),a))},"java.util.List");c$.$IdPanel$ScrollThread$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.running=!1;this.up=!0;r(this,arguments)},jalview.appletgui.IdPanel,"ScrollThread",Thread);m(c$,function(a){t(this,jalview.appletgui.IdPanel.ScrollThread,[]);this.up=a;this.start()},"~B");d(c$,"stopScrolling",function(){this.running=
!1});e(c$,"run",function(){for(this.running=!0;this.running;){if(this.b$["jalview.appletgui.IdPanel"].alignPanel.scrollUp(this.up)){var a=this.b$["jalview.appletgui.IdPanel"].av.getStartSeq();this.up||(a=this.b$["jalview.appletgui.IdPanel"].av.getEndSeq());a<this.b$["jalview.appletgui.IdPanel"].lastid?this.b$["jalview.appletgui.IdPanel"].selectSeqs(this.b$["jalview.appletgui.IdPanel"].lastid-1,a):a>this.b$["jalview.appletgui.IdPanel"].lastid&&a<this.b$["jalview.appletgui.IdPanel"].av.getAlignment().getHeight()&&
this.b$["jalview.appletgui.IdPanel"].selectSeqs(this.b$["jalview.appletgui.IdPanel"].lastid+1,a);this.b$["jalview.appletgui.IdPanel"].lastid=a}else this.running=!1;this.b$["jalview.appletgui.IdPanel"].alignPanel.paintAlignment(!0);try{Thread.sleep(100)}catch(b){if(!y(b,Exception))throw b;}}});c$=z()}});p("jalview.appletgui");q("awt2swing.PopupMenu java.awt.event.ActionListener $.ItemListener awt2swing.CheckboxMenuItem $.Menu $.MenuItem jalview.util.MessageManager".split(" "),"jalview.appletgui.APopupMenu",
"awt2swing.Frame jalview.analysis.AAFrequency $.AlignmentAnnotationUtils $.AlignmentUtils $.Conservation jalview.appletgui.AppletJmol $.CutAndPasteTransfer $.EditNameDialog $.SliderPanel $.UserDefinedColours jalview.bin.JalviewLite jalview.commands.ChangeCaseCommand $.EditCommand jalview.datamodel.SequenceFeature jalview.io.AppletFormatAdapter $.SequenceAnnotationReport jalview.schemes.Blosum62ColourScheme $.BuriedColourScheme $.ClustalxColourScheme $.HelixColourScheme $.HydrophobicColourScheme $.NucleotideColourScheme $.PIDColourScheme $.ResidueProperties $.StrandColourScheme $.TaylorColourScheme $.TurnColourScheme $.ZappoColourScheme jalview.util.DBRefUtils $.UrlLink java.lang.StringBuffer $.StringBuilder java.util.Arrays $.Collections $.LinkedHashMap $.TreeMap".split(" "),
function(){c$=s(function(){this.revealSeq=this.revealAll=this.seq=this.makeReferenceSeq=this.selSeqDetails=this.sequenceDetails=this.editSequence=this.sequenceFeature=this.sequenceName=this.repGroup=this.hideSeqs=this.pdb=this.seqMenu=this.outputmenu=this.toggleCase=this.toLower=this.toUpper=this.cut=this.copy=this.editMenu=this.groupAddReferenceAnnotations=this.groupHideAnnotationsMenu=this.groupShowAnnotationsMenu=this.seqAddReferenceAnnotations=this.seqHideAnnotationsMenu=this.seqShowAnnotationsMenu=
this.displayNonconserved=this.showColourText=this.showText=this.showBoxes=this.colourMenu=this.nucleotideMenuItem=this.createGroupMenuItem=this.unGroupMenuItem=this.ap=this.conservationMenuItem=this.noColourmenuItem=this.BLOSUM62Colour=this.PIDColour=this.userDefinedColour=this.abovePIDColour=this.buriedColour=this.turnColour=this.strandColour=this.helixColour=this.hydrophobicityColour=this.taylorColour=this.zappoColour=this.clustalColour=this.editGroupName=this.groupMenu=null;this.revealSeq_index=
-1;this.menu1=null;r(this,arguments)},jalview.appletgui,"APopupMenu",awt2swing.PopupMenu,[java.awt.event.ActionListener,java.awt.event.ItemListener]);J(c$,function(){this.groupMenu=new awt2swing.Menu;this.editGroupName=new awt2swing.MenuItem;this.clustalColour=new awt2swing.MenuItem;this.zappoColour=new awt2swing.MenuItem;this.taylorColour=new awt2swing.MenuItem;this.hydrophobicityColour=new awt2swing.MenuItem;this.helixColour=new awt2swing.MenuItem;this.strandColour=new awt2swing.MenuItem;this.turnColour=
new awt2swing.MenuItem;this.buriedColour=new awt2swing.MenuItem;this.abovePIDColour=new awt2swing.CheckboxMenuItem;this.userDefinedColour=new awt2swing.MenuItem;this.PIDColour=new awt2swing.MenuItem;this.BLOSUM62Colour=new awt2swing.MenuItem;this.noColourmenuItem=new awt2swing.MenuItem;this.conservationMenuItem=new awt2swing.CheckboxMenuItem;this.unGroupMenuItem=new awt2swing.MenuItem;this.createGroupMenuItem=new awt2swing.MenuItem;this.nucleotideMenuItem=new awt2swing.MenuItem;this.colourMenu=new awt2swing.Menu;
this.showBoxes=new awt2swing.CheckboxMenuItem;this.showText=new awt2swing.CheckboxMenuItem;this.showColourText=new awt2swing.CheckboxMenuItem;this.displayNonconserved=new awt2swing.CheckboxMenuItem;this.seqShowAnnotationsMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("label.show_annotations"));this.seqHideAnnotationsMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("label.hide_annotations"));this.seqAddReferenceAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.add_reference_annotations"));
this.groupShowAnnotationsMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("label.show_annotations"));this.groupHideAnnotationsMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("label.hide_annotations"));this.groupAddReferenceAnnotations=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.add_reference_annotations"));this.editMenu=new awt2swing.Menu(jalview.util.MessageManager.getString("action.edit"));this.copy=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.copy"));
this.cut=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.cut"));this.toUpper=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.to_upper_case"));this.toLower=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.to_lower_case"));this.toggleCase=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.toggle_case"));this.outputmenu=new awt2swing.Menu;this.seqMenu=new awt2swing.Menu;this.pdb=new awt2swing.MenuItem;this.hideSeqs=new awt2swing.MenuItem;
this.repGroup=new awt2swing.MenuItem;this.sequenceName=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.edit_name_description"));this.sequenceFeature=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.create_sequence_feature"));this.editSequence=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.edit_sequence"));this.sequenceDetails=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.sequence_details")+"...");this.selSeqDetails=
new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.sequence_details")+"...");this.makeReferenceSeq=new awt2swing.MenuItem;this.revealAll=new awt2swing.MenuItem;this.revealSeq=new awt2swing.MenuItem;this.menu1=new awt2swing.Menu});m(c$,function(a,b,c){t(this,jalview.appletgui.APopupMenu,[]);this.ap=a;this.seq=b;try{this.jbInit()}catch(d){if(y(d,Exception))d.printStackTrace();else throw d;}for(a=0;a<jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;a++){var e=new awt2swing.MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[a]);
e.addActionListener(this);this.outputmenu.add(e)}this.buildAnnotationSubmenus();a=this.ap.av.getSelectionGroup();null!=a&&0<a.getSize()?(this.editGroupName.setLabel(jalview.util.MessageManager.formatMessage("label.name_param",E(-1,[a.getName()]))),this.showText.setState(a.getDisplayText()),this.showColourText.setState(a.getColourText()),this.showBoxes.setState(a.getDisplayBoxes()),this.displayNonconserved.setState(a.getShowNonconserved()),this.ap.av.getAlignment().getGroups().contains(a)?(this.menu1.setLabel(jalview.util.MessageManager.getString("action.edit_group")),
this.groupMenu.remove(this.createGroupMenuItem)):(this.menu1.setLabel(jalview.util.MessageManager.getString("action.edit_new_group")),this.groupMenu.remove(this.unGroupMenuItem))):(this.remove(this.hideSeqs),this.remove(this.groupMenu));if(null!=c&&0<c.size()){e=new awt2swing.Menu(jalview.util.MessageManager.getString("action.link"));for(a=0;a<c.size();a++){var k=c.elementAt(a),k=new jalview.util.UrlLink(k);if(k.isValid()){var g=k.getTarget(),h=k.getLabel();if(null!=b&&k.isDynamic()){var g=jalview.util.DBRefUtils.selectRefs(b.getDBRef(),
E(-1,[g])),j=b.getName(),n=b.getDescription();null!=n&&1>n.length&&(n=null);if(null!=g)for(var m=0;m<g.length;m++){null!=j&&g[m].getAccessionId().equals(j)&&(j=null);var p=k.makeUrls(g[m].getAccessionId(),!0);if(null!=p)for(var q=0;q<p.length;q+=2)this.addshowLink(e,h+"|"+p[q],p[q+1])}if(null!=j&&(p=k.makeUrls(j,!0),null!=p))for(q=0;q<p.length;q+=2)this.addshowLink(e,h,p[q+1]);if(null!=n&&null!=k.getRegexReplace()&&(p=k.makeUrls(n,!0),null!=p))for(q=0;q<p.length;q+=2)this.addshowLink(e,h,p[q+1])}else this.addshowLink(e,
g,k.getUrl_prefix())}else System.err.println(k.getInvalidMessage())}0<e.getItemCount()&&(null!=b?this.seqMenu.add(e):this.add(e))}null!=b?(this.seqMenu.setLabel(b.getName()),b===this.ap.av.getAlignment().getSeqrep()?this.makeReferenceSeq.setLabel(jalview.util.MessageManager.getString("action.unmark_as_reference")):this.makeReferenceSeq.setLabel(jalview.util.MessageManager.getString("action.set_as_reference")),this.repGroup.setLabel(jalview.util.MessageManager.formatMessage("label.represent_group_with",
E(-1,[b.getName()])))):this.remove(this.seqMenu);this.ap.av.hasHiddenRows()?(b=this.ap.av.getAlignment().findIndex(b),1<this.ap.av.adjustForHiddenSeqs(b)-this.ap.av.adjustForHiddenSeqs(b-1)?this.revealSeq_index=b:this.remove(this.revealSeq)):(this.remove(this.revealAll),this.remove(this.revealSeq))},"jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceI,java.util.Vector");d(c$,"buildAnnotationSubmenus",function(){var a=null==this.seq?java.util.Collections.emptyList():java.util.Arrays.asList([this.seq]);
this.buildAnnotationTypesMenus(this.seqShowAnnotationsMenu,this.seqHideAnnotationsMenu,a);this.configureReferenceAnnotationsMenu(this.seqAddReferenceAnnotations,a);a=null==this.ap.av.getSelectionGroup()?java.util.Collections.emptyList():this.ap.av.getSelectionGroup().getSequences();this.buildAnnotationTypesMenus(this.groupShowAnnotationsMenu,this.groupHideAnnotationsMenu,a);this.configureReferenceAnnotationsMenu(this.groupAddReferenceAnnotations,a)});d(c$,"configureReferenceAnnotationsMenu",function(a,
b){a.setEnabled(!1);var c=new java.util.TreeMap,d=new java.util.LinkedHashMap,e=this.ap.av.getAlignment();jalview.analysis.AlignmentUtils.findAddableReferenceAnnotations(b,c,d,e);d.isEmpty()||((new StringBuilder(64)).append(jalview.util.MessageManager.getString("label.add_annotations_for")),a.setEnabled(!0),a.addActionListener((H("jalview.appletgui.APopupMenu$1")?0:jalview.appletgui.APopupMenu.$APopupMenu$1$(),C(jalview.appletgui.APopupMenu$1,this,T("candidates",d)))))},"awt2swing.MenuItem,java.util.List");
d(c$,"addReferenceAnnotations_actionPerformed",function(a){var b=this.ap.av.getSelectionGroup(),c=this.ap.getAlignment();jalview.analysis.AlignmentUtils.addReferenceAnnotations(a,c,b);this.refresh()},"java.util.Map");d(c$,"addshowLink",function(a,b,c){this.addshowLink(a,b,b,c)},"awt2swing.Menu,~S,~S");d(c$,"addshowLink",function(a,b,c,d){c=new awt2swing.MenuItem(c);c.addActionListener((H("jalview.appletgui.APopupMenu$2")?0:jalview.appletgui.APopupMenu.$APopupMenu$2$(),C(jalview.appletgui.APopupMenu$2,
this,T("url",d,"target",b))));a.add(c)},"awt2swing.Menu,~S,~S,~S");e(c$,"itemStateChanged",function(a){a.getSource()===this.abovePIDColour?this.abovePIDColour_itemStateChanged():a.getSource()===this.showColourText?this.showColourText_itemStateChanged():a.getSource()===this.showText?this.showText_itemStateChanged():a.getSource()===this.showBoxes?this.showBoxes_itemStateChanged():a.getSource()===this.displayNonconserved&&this.showNonconserved_itemStateChanged()},"java.awt.event.ItemEvent");e(c$,"actionPerformed",
function(a){var b=a.getSource();if(b===this.clustalColour)this.clustalColour_actionPerformed();else if(b===this.zappoColour)this.zappoColour_actionPerformed();else if(b===this.taylorColour)this.taylorColour_actionPerformed();else if(b===this.hydrophobicityColour)this.hydrophobicityColour_actionPerformed();else if(b===this.helixColour)this.helixColour_actionPerformed();else if(b===this.strandColour)this.strandColour_actionPerformed();else if(b===this.turnColour)this.turnColour_actionPerformed();else if(b===
this.buriedColour)this.buriedColour_actionPerformed();else if(b===this.nucleotideMenuItem)this.nucleotideMenuItem_actionPerformed();else if(b===this.userDefinedColour)this.userDefinedColour_actionPerformed();else if(b===this.PIDColour)this.PIDColour_actionPerformed();else if(b===this.BLOSUM62Colour)this.BLOSUM62Colour_actionPerformed();else if(b===this.noColourmenuItem)this.noColourmenuItem_actionPerformed();else if(b===this.conservationMenuItem)this.conservationMenuItem_itemStateChanged();else if(b===
this.unGroupMenuItem)this.unGroupMenuItem_actionPerformed();else if(b===this.createGroupMenuItem)this.createGroupMenuItem_actionPerformed();else if(b===this.sequenceName)this.editName();else if(b===this.makeReferenceSeq)this.makeReferenceSeq_actionPerformed();else if(b===this.sequenceDetails)this.showSequenceDetails();else if(b===this.selSeqDetails)this.showSequenceSelectionDetails();else if(b===this.pdb)this.addPDB();else if(b===this.hideSeqs)this.hideSequences(!1);else if(b===this.repGroup)this.hideSequences(!0);
else if(b===this.revealSeq)this.ap.av.showSequence(this.revealSeq_index);else if(b===this.revealAll)this.ap.av.showAllHiddenSeqs();else if(b===this.editGroupName){var c=new jalview.appletgui.EditNameDialog(this.getGroup().getName(),this.getGroup().getDescription(),"       Group Name","Group Description",this.ap.alignFrame,"Edit Group Name / Description",500,100,!0);c.accept&&(this.getGroup().setName(c.getName().$replace(" ","_")),this.getGroup().setDescription(c.getDescription()))}else if(b===this.copy)this.ap.alignFrame.copy_actionPerformed();
else if(b===this.cut)this.ap.alignFrame.cut_actionPerformed();else if(b===this.editSequence)a=this.ap.av.getSelectionGroup(),null!=a&&(null==this.seq&&(this.seq=a.getSequenceAt(0)),c=new jalview.appletgui.EditNameDialog(this.seq.getSequenceAsString(a.getStartRes(),a.getEndRes()+1),null,"Edit Sequence ",null,this.ap.alignFrame,"Edit Sequence",500,100,!0),c.accept&&(a=new jalview.commands.EditCommand(jalview.util.MessageManager.getString("label.edit_sequences"),jalview.commands.EditCommand.Action.REPLACE,
c.getName().$replace(" ",this.ap.av.getGapCharacter()),a.getSequencesAsArray(this.ap.av.getHiddenRepSequences()),a.getStartRes(),a.getEndRes()+1,this.ap.av.getAlignment()),this.ap.alignFrame.addHistoryItem(a),this.ap.av.firePropertyChange("alignment",null,this.ap.av.getAlignment().getSequences())));else if(b===this.toUpper||b===this.toLower||b===this.toggleCase){if(a=this.ap.av.getSelectionGroup(),null!=a){var c=this.ap.av.getVisibleRegionBoundaries(a.getStartRes(),a.getEndRes()+1),d;b===this.toggleCase?
(b="Toggle Case",d=jalview.commands.ChangeCaseCommand.TOGGLE_CASE):b===this.toUpper?(b="To Upper Case",d=jalview.commands.ChangeCaseCommand.TO_UPPER):(b="To Lower Case",d=jalview.commands.ChangeCaseCommand.TO_LOWER);a=new jalview.commands.ChangeCaseCommand(b,a.getSequencesAsArray(this.ap.av.getHiddenRepSequences()),c,d);this.ap.alignFrame.addHistoryItem(a);this.ap.av.firePropertyChange("alignment",null,this.ap.av.getAlignment().getSequences())}}else if(b===this.sequenceFeature){if(a=this.ap.av.getSelectionGroup(),
null!=a){var c=0,e=a.getSize(),b=Array(e);d=Array(e);for(var k=0;k<e;k++){var g=a.getSequenceAt(k).findPosition(a.getStartRes()),h=a.findEndRes(a.getSequenceAt(k));g<=h&&(b[c]=a.getSequenceAt(k),d[c]=new jalview.datamodel.SequenceFeature(null,null,null,g,h,"Jalview"),c++)}a=Array(c);e=Array(c);System.arraycopy(b,0,a,0,c);System.arraycopy(d,0,e,0,c);this.ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(a,e,!0,this.ap)&&(this.ap.alignFrame.sequenceFeatures.setState(!0),this.ap.av.setShowSequenceFeatures(!0),
this.ap.highlightSearchResults(null))}}else this.outputText(a)},"java.awt.event.ActionEvent");d(c$,"outputText",function(a){var b=new jalview.appletgui.CutAndPasteTransfer(!0,this.ap.alignFrame),c=new awt2swing.Frame;c.add(b);jalview.bin.JalviewLite.addFrame(c,jalview.util.MessageManager.formatMessage("label.selection_output_command",E(-1,[a.getActionCommand()])),600,500);b.setText((new jalview.io.AppletFormatAdapter).formatSequences(a.getActionCommand(),this.ap.av.getShowJVSuffix(),this.ap,!0))},
"java.awt.event.ActionEvent");d(c$,"showSequenceSelectionDetails",function(){this.createSequenceDetailsReport(this.ap.av.getSequenceSelection())});d(c$,"showSequenceDetails",function(){this.createSequenceDetailsReport(E(-1,[this.seq]))});d(c$,"createSequenceDetailsReport",function(a){for(var b=new jalview.appletgui.CutAndPasteTransfer(!1,this.ap.alignFrame),c=new StringBuffer,d,e=0;e<a.length&&((d=a[e])||1);e++)c.append(jalview.util.MessageManager.formatMessage("label.annotation_for_displayid",E(-1,
[d.getDisplayId(!0)]))),(new jalview.io.SequenceAnnotationReport(null)).createSequenceAnnotationReport(c,d,!0,!0,!1,null!=this.ap.seqPanel.seqCanvas.fr?this.ap.seqPanel.seqCanvas.fr.getMinMax():null),c.append("</p>");d=new awt2swing.Frame;d.add(b);jalview.bin.JalviewLite.addFrame(d,"Sequence Details for "+(1==a.length?a[0].getDisplayId(!0):"Selection"),600,500);b.setText(jalview.util.MessageManager.formatMessage("label.html_content",E(-1,[c.toString()])))},"~A");d(c$,"editName",function(){var a=new jalview.appletgui.EditNameDialog(this.seq.getName(),
this.seq.getDescription(),"       Sequence Name","Sequence Description",this.ap.alignFrame,"Edit Sequence Name / Description",500,100,!0);a.accept&&(this.seq.setName(a.getName()),this.seq.setDescription(a.getDescription()),this.ap.paintAlignment(!1))});d(c$,"addPDB",function(){if(null!=this.seq.getPDBId()){var a=this.seq.getPDBId().firstElement();this.ap.av.applet.jmolAvailable&&new jalview.appletgui.AppletJmol(a,E(-1,[this.seq]),null,this.ap,jalview.io.AppletFormatAdapter.URL)}else{a=new jalview.appletgui.CutAndPasteTransfer(!0,
this.ap.alignFrame);a.setText(jalview.util.MessageManager.getString("label.paste_pdb_file"));a.setPDBImport(this.seq);var b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.formatMessage("label.paste_pdb_file_for_sequence",E(-1,[this.seq.getName()])),400,300)}});d(c$,"jbInit",function(){this.groupMenu.setLabel(jalview.util.MessageManager.getString("label.selection"));this.sequenceFeature.addActionListener(this);this.editGroupName.addActionListener(this);
this.unGroupMenuItem.setLabel(jalview.util.MessageManager.getString("action.remove_group"));this.unGroupMenuItem.addActionListener(this);this.createGroupMenuItem.setLabel(jalview.util.MessageManager.getString("action.create_group"));this.createGroupMenuItem.addActionListener(this);this.nucleotideMenuItem.setLabel(jalview.util.MessageManager.getString("label.nucleotide"));this.nucleotideMenuItem.addActionListener(this);this.conservationMenuItem.addItemListener(this);this.abovePIDColour.addItemListener(this);
this.colourMenu.setLabel(jalview.util.MessageManager.getString("label.group_colour"));this.showBoxes.setLabel(jalview.util.MessageManager.getString("action.boxes"));this.showBoxes.setState(!0);this.showBoxes.addItemListener(this);this.sequenceName.addActionListener(this);this.sequenceDetails.addActionListener(this);this.selSeqDetails.addActionListener(this);this.displayNonconserved.setLabel(jalview.util.MessageManager.getString("label.show_non_conversed"));this.displayNonconserved.setState(!1);this.displayNonconserved.addItemListener(this);
this.showText.setLabel(jalview.util.MessageManager.getString("action.text"));this.showText.addItemListener(this);this.showColourText.setLabel(jalview.util.MessageManager.getString("label.colour_text"));this.showColourText.addItemListener(this);this.outputmenu.setLabel(jalview.util.MessageManager.getString("label.out_to_textbox"));this.seqMenu.setLabel(jalview.util.MessageManager.getString("label.sequence"));this.pdb.setLabel(jalview.util.MessageManager.getString("label.view_pdb_structure"));this.hideSeqs.setLabel(jalview.util.MessageManager.getString("action.hide_sequences"));
this.repGroup.setLabel(jalview.util.MessageManager.formatMessage("label.represent_group_with",E(-1,[""])));this.revealAll.setLabel(jalview.util.MessageManager.getString("action.reveal_all"));this.revealSeq.setLabel(jalview.util.MessageManager.getString("action.reveal_sequences"));this.menu1.setLabel(jalview.util.MessageManager.getString("label.group")+":");this.add(this.groupMenu);this.add(this.seqMenu);this.add(this.hideSeqs);this.add(this.revealSeq);this.add(this.revealAll);this.groupMenu.add(this.groupShowAnnotationsMenu);
this.groupMenu.add(this.groupHideAnnotationsMenu);this.groupMenu.add(this.groupAddReferenceAnnotations);this.groupMenu.add(this.editMenu);this.groupMenu.add(this.outputmenu);this.groupMenu.add(this.sequenceFeature);this.groupMenu.add(this.createGroupMenuItem);this.groupMenu.add(this.unGroupMenuItem);this.groupMenu.add(this.menu1);this.colourMenu.add(this.noColourmenuItem);this.colourMenu.add(this.clustalColour);this.colourMenu.add(this.BLOSUM62Colour);this.colourMenu.add(this.PIDColour);this.colourMenu.add(this.zappoColour);
this.colourMenu.add(this.taylorColour);this.colourMenu.add(this.hydrophobicityColour);this.colourMenu.add(this.helixColour);this.colourMenu.add(this.strandColour);this.colourMenu.add(this.turnColour);this.colourMenu.add(this.buriedColour);this.colourMenu.add(this.nucleotideMenuItem);this.colourMenu.add(this.userDefinedColour);this.colourMenu.addSeparator();this.colourMenu.add(this.abovePIDColour);this.colourMenu.add(this.conservationMenuItem);this.noColourmenuItem.setLabel(jalview.util.MessageManager.getString("label.none"));
this.noColourmenuItem.addActionListener(this);this.clustalColour.setLabel(jalview.util.MessageManager.getString("label.clustalx_colours"));this.clustalColour.addActionListener(this);this.zappoColour.setLabel(jalview.util.MessageManager.getString("label.zappo"));this.zappoColour.addActionListener(this);this.taylorColour.setLabel(jalview.util.MessageManager.getString("label.taylor"));this.taylorColour.addActionListener(this);this.hydrophobicityColour.setLabel(jalview.util.MessageManager.getString("label.hydrophobicity"));
this.hydrophobicityColour.addActionListener(this);this.helixColour.setLabel(jalview.util.MessageManager.getString("label.helix_propensity"));this.helixColour.addActionListener(this);this.strandColour.setLabel(jalview.util.MessageManager.getString("label.strand_propensity"));this.strandColour.addActionListener(this);this.turnColour.setLabel(jalview.util.MessageManager.getString("label.turn_propensity"));this.turnColour.addActionListener(this);this.buriedColour.setLabel(jalview.util.MessageManager.getString("label.buried_index"));
this.buriedColour.addActionListener(this);this.abovePIDColour.setLabel(jalview.util.MessageManager.getString("label.above_identity_percentage"));this.userDefinedColour.setLabel(jalview.util.MessageManager.getString("action.user_defined"));this.userDefinedColour.addActionListener(this);this.PIDColour.setLabel(jalview.util.MessageManager.getString("action.percentage_identity"));this.PIDColour.addActionListener(this);this.BLOSUM62Colour.setLabel("BLOSUM62");this.BLOSUM62Colour.addActionListener(this);
this.conservationMenuItem.setLabel(jalview.util.MessageManager.getString("label.conservation"));this.editMenu.add(this.copy);this.copy.addActionListener(this);this.editMenu.add(this.cut);this.cut.addActionListener(this);this.editMenu.add(this.editSequence);this.editSequence.addActionListener(this);this.editMenu.add(this.toUpper);this.toUpper.addActionListener(this);this.editMenu.add(this.toLower);this.toLower.addActionListener(this);this.editMenu.add(this.toggleCase);this.seqMenu.add(this.seqShowAnnotationsMenu);
this.seqMenu.add(this.seqHideAnnotationsMenu);this.seqMenu.add(this.seqAddReferenceAnnotations);this.seqMenu.add(this.sequenceName);this.seqMenu.add(this.makeReferenceSeq);this.ap.av.applet.useXtrnalSviewer||this.seqMenu.add(this.pdb);this.seqMenu.add(this.repGroup);this.menu1.add(this.editGroupName);this.menu1.add(this.colourMenu);this.menu1.add(this.showBoxes);this.menu1.add(this.showText);this.menu1.add(this.showColourText);this.menu1.add(this.displayNonconserved);this.toggleCase.addActionListener(this);
this.pdb.addActionListener(this);this.hideSeqs.addActionListener(this);this.repGroup.addActionListener(this);this.revealAll.addActionListener(this);this.revealSeq.addActionListener(this);this.makeReferenceSeq.addActionListener(this)});d(c$,"refresh",function(){this.ap.paintAlignment(!0)});d(c$,"clustalColour_actionPerformed",function(){var a=this.getGroup();a.cs=new jalview.schemes.ClustalxColourScheme(a,this.ap.av.getHiddenRepSequences());this.refresh()});d(c$,"zappoColour_actionPerformed",function(){this.getGroup().cs=
new jalview.schemes.ZappoColourScheme;this.refresh()});d(c$,"taylorColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.TaylorColourScheme;this.refresh()});d(c$,"hydrophobicityColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.HydrophobicColourScheme;this.refresh()});d(c$,"helixColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.HelixColourScheme;this.refresh()});d(c$,"strandColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.StrandColourScheme;
this.refresh()});d(c$,"turnColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.TurnColourScheme;this.refresh()});d(c$,"buriedColour_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.BuriedColourScheme;this.refresh()});d(c$,"nucleotideMenuItem_actionPerformed",function(){this.getGroup().cs=new jalview.schemes.NucleotideColourScheme;this.refresh()});d(c$,"abovePIDColour_itemStateChanged",function(){var a=this.getGroup();if(null!=a.cs){if(this.abovePIDColour.getState()){a.cs.setConsensus(jalview.analysis.AAFrequency.calculate(a.getSequences(this.ap.av.getHiddenRepSequences()),
0,this.ap.av.getAlignment().getWidth()));var b=jalview.appletgui.SliderPanel.setPIDSliderSource(this.ap,a.cs,this.getGroup().getName());a.cs.setThreshold(b,this.ap.av.isIgnoreGapsConsensus());jalview.appletgui.SliderPanel.showPIDSlider()}else a.cs.setThreshold(0,this.ap.av.isIgnoreGapsConsensus());this.refresh()}});d(c$,"userDefinedColour_actionPerformed",function(){new jalview.appletgui.UserDefinedColours(this.ap,this.getGroup())});d(c$,"PIDColour_actionPerformed",function(){var a=this.getGroup();
a.cs=new jalview.schemes.PIDColourScheme;a.cs.setConsensus(jalview.analysis.AAFrequency.calculate(a.getSequences(this.ap.av.getHiddenRepSequences()),0,this.ap.av.getAlignment().getWidth()));this.refresh()});d(c$,"BLOSUM62Colour_actionPerformed",function(){var a=this.getGroup();a.cs=new jalview.schemes.Blosum62ColourScheme;a.cs.setConsensus(jalview.analysis.AAFrequency.calculate(a.getSequences(this.ap.av.getHiddenRepSequences()),0,this.ap.av.getAlignment().getWidth()));this.refresh()});d(c$,"noColourmenuItem_actionPerformed",
function(){this.getGroup().cs=null;this.refresh()});d(c$,"conservationMenuItem_itemStateChanged",function(){var a=this.getGroup();null!=a.cs&&(this.conservationMenuItem.getState()?(a.cs.setConservation(jalview.analysis.Conservation.calculateConservation("Group",jalview.schemes.ResidueProperties.propHash,3,a.getSequences(this.ap.av.getHiddenRepSequences()),0,this.ap.av.getAlignment().getWidth(),!1,this.ap.av.getConsPercGaps(),!1)),jalview.appletgui.SliderPanel.setConservationSlider(this.ap,a.cs,a.getName()),
jalview.appletgui.SliderPanel.showConservationSlider()):a.cs.setConservation(null),this.refresh())});d(c$,"getGroup",function(){var a=this.ap.av.getSelectionGroup();null!=a&&this.ap.av.getAlignment().addGroup(a);return a});d(c$,"unGroupMenuItem_actionPerformed",function(){var a=this.ap.av.getSelectionGroup();this.ap.av.getAlignment().deleteGroup(a);this.ap.av.setSelectionGroup(null);this.ap.paintAlignment(!0)});d(c$,"createGroupMenuItem_actionPerformed",function(){this.getGroup();this.refresh()});
d(c$,"showColourText_itemStateChanged",function(){this.getGroup().setColourText(this.showColourText.getState());this.refresh()});d(c$,"showText_itemStateChanged",function(){this.getGroup().setDisplayText(this.showText.getState());this.refresh()});d(c$,"makeReferenceSeq_actionPerformed",function(){this.ap.av.getAlignment().hasSeqrep()?this.ap.av.getAlignment().getSeqrep()===this.seq?this.ap.av.getAlignment().setSeqrep(null):this.ap.av.getAlignment().setSeqrep(this.seq):(this.ap.av.setDisplayReferenceSeq(!0),
this.ap.av.setColourByReferenceSeq(!0),this.ap.av.getAlignment().setSeqrep(this.seq));this.refresh()});d(c$,"showNonconserved_itemStateChanged",function(){this.getGroup().setShowNonconserved(this.displayNonconserved.getState());this.refresh()});d(c$,"showBoxes_itemStateChanged",function(){this.getGroup().setDisplayBoxes(this.showBoxes.getState());this.refresh()});d(c$,"hideSequences",function(a){var b=this.ap.av.getSelectionGroup();if(null==b||1>b.getSize())this.ap.av.hideSequence(E(-1,[this.seq]));
else if(this.ap.av.setSelectionGroup(null),a)this.ap.av.hideRepSequences(this.seq,b);else{a=b.getSize();var c;c=Array(a);for(var d=0,e=0;e<a;e++)c[d++]=b.getSequenceAt(e);this.ap.av.hideSequence(c);this.ap.av.sendSelection()}},"~B");d(c$,"buildAnnotationTypesMenus",function(a,b,c){a.removeAll();b.removeAll();var d=java.util.Arrays.asList(["All"]);this.addAnnotationTypeToShowHide(a,c,"",d,!0,!0);this.addAnnotationTypeToShowHide(b,c,"",d,!0,!1);a.addSeparator();b.addSeparator();var e=this.ap.getAlignment().getAlignmentAnnotation(),
d=new java.util.LinkedHashMap,k=new java.util.LinkedHashMap;jalview.analysis.AlignmentAnnotationUtils.getShownHiddenTypes(d,k,jalview.analysis.AlignmentAnnotationUtils.asList(e),c);for(var g,e=k.keySet().iterator();e.hasNext()&&((g=e.next())||1);)for(var h,j=k.get(g).iterator();j.hasNext()&&((h=j.next())||1);)this.addAnnotationTypeToShowHide(a,c,g,h,!1,!0);a.setEnabled(!k.isEmpty());for(e=d.keySet().iterator();e.hasNext()&&((g=e.next())||1);)for(j=d.get(g).iterator();j.hasNext()&&((h=j.next())||1);)this.addAnnotationTypeToShowHide(b,
c,g,h,!1,!1);b.setEnabled(!d.isEmpty())},"awt2swing.Menu,awt2swing.Menu,java.util.List");d(c$,"addAnnotationTypeToShowHide",function(a,b,c,d,e,k){c=d.toString();c=c.substring(1,c.length-1);c=new awt2swing.MenuItem(c);c.addActionListener((H("jalview.appletgui.APopupMenu$3")?0:jalview.appletgui.APopupMenu.$APopupMenu$3$(),C(jalview.appletgui.APopupMenu$3,this,T("types",d,"forSequences",b,"allTypes",e,"actionIsShow",k))));a.add(c)},"awt2swing.Menu,java.util.List,~S,java.util.List,~B,~B");c$.$APopupMenu$1$=
function(){A(self.c$);c$=L(jalview.appletgui,"APopupMenu$1",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.APopupMenu"].addReferenceAnnotations_actionPerformed(this.f$.candidates)},"java.awt.event.ActionEvent");c$=z()};c$.$APopupMenu$2$=function(){A(self.c$);c$=L(jalview.appletgui,"APopupMenu$2",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.APopupMenu"].ap.alignFrame.showURL(this.f$.url,this.f$.target)},
"java.awt.event.ActionEvent");c$=z()};c$.$APopupMenu$3$=function(){A(self.c$);c$=L(jalview.appletgui,"APopupMenu$3",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations(this.b$["jalview.appletgui.APopupMenu"].ap.getAlignment(),this.f$.types,this.f$.forSequences,this.f$.allTypes,this.f$.actionIsShow);this.b$["jalview.appletgui.APopupMenu"].refresh()},"java.awt.event.ActionEvent");c$=z()};G(c$,"ALL_ANNOTATIONS","All")});
p("jalview.analysis");q(null,"jalview.analysis.AlignmentAnnotationUtils",["java.util.ArrayList","$.Arrays","$.BitSet","$.Collections","$.HashMap"],function(){c$=B(jalview.analysis,"AlignmentAnnotationUtils");c$.getShownHiddenTypes=d(c$,"getShownHiddenTypes",function(a,b,c,d){var e=jalview.analysis.AlignmentAnnotationUtils.getVisibleLineGraphGroups(c),k=new java.util.HashMap,g=new java.util.ArrayList,h=new java.util.ArrayList,j;for(c=c.iterator();c.hasNext()&&((j=c.next())||1);)if(null!=j.annotations&&
null!=d&&null!=j.sequenceRef&&d.contains(j.sequenceRef)){var n=j.getCalcId(),m=new java.util.ArrayList,p=j.label;m.add(p);if(2==j.graph&&-1<j.graphGroup){k.containsKey(n)||k.put(n,new java.util.HashMap);var q=k.get(n);q.containsKey(new Integer(j.graphGroup))?q.get(new Integer(j.graphGroup)).contains(p)||q.get(new Integer(j.graphGroup)).add(p):q.put(new Integer(j.graphGroup),m)}else p=n+"!"+p,j.visible&&!g.contains(p)?(a.containsKey(n)||a.put(n,new java.util.ArrayList),a.get(n).add(m),g.add(p)):!j.visible&&
!h.contains(p)&&(b.containsKey(n)||b.put(n,new java.util.ArrayList),b.get(n).add(m),h.add(p))}for(d=k.keySet().iterator();d.hasNext()&&((n=d.next())||1);)for(var r,g=k.get(n).keySet().iterator();g.hasNext()&&((r=g.next())||1);)h=k.get(n).get(new Integer(r)),java.util.Collections.sort(h),e.get(r)?(a.containsKey(n)||a.put(n,new java.util.ArrayList),a.get(n).contains(h)||a.get(n).add(h)):(b.containsKey(n)||b.put(n,new java.util.ArrayList),b.get(n).contains(h)||b.get(n).add(h))},"java.util.Map,java.util.Map,java.util.List,java.util.List");
c$.getVisibleLineGraphGroups=d(c$,"getVisibleLineGraphGroups",function(a){var b=new java.util.BitSet,c;for(a=a.iterator();a.hasNext()&&((c=a.next())||1);)if(2==c.graph&&c.visible){var d=c.graphGroup;-1<d&&b.set(d)}return b},"java.util.List");c$.asList=d(c$,"asList",function(a){return null==a?java.util.Collections.emptyList():java.util.Arrays.asList(a)},"~A")});p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ActionListener $.AdjustmentListener $.MouseListener awt2swing.Button $.Checkbox $.Label $.Scrollbar $.TextField java.awt.BorderLayout $.FlowLayout".split(" "),
"jalview.appletgui.SliderPanel","awt2swing.Frame jalview.bin.JalviewLite jalview.util.MessageManager java.awt.Color $.Font java.awt.event.WindowAdapter".split(" "),function(){c$=s(function(){this.ap=null;this.forConservation=!0;this.flowLayout2=this.borderLayout2=this.borderLayout1=this.allGroupsCheck=this.flowLayout1=this.undoButton=this.applyButton=this.jPanel2=this.jPanel1=this.label=this.valueField=this.slider=this.cs=null;r(this,arguments)},jalview.appletgui,"SliderPanel",awt2swing.Panel,[java.awt.event.ActionListener,
java.awt.event.AdjustmentListener,java.awt.event.MouseListener]);J(c$,function(){this.slider=new awt2swing.Scrollbar;this.valueField=new awt2swing.TextField;this.label=new awt2swing.Label;this.jPanel1=new awt2swing.Panel;this.jPanel2=new awt2swing.Panel;this.applyButton=new awt2swing.Button;this.undoButton=new awt2swing.Button;this.flowLayout1=new java.awt.FlowLayout;this.allGroupsCheck=new awt2swing.Checkbox;this.borderLayout1=new java.awt.BorderLayout;this.borderLayout2=new java.awt.BorderLayout;
this.flowLayout2=new java.awt.FlowLayout});c$.setConservationSlider=d(c$,"setConservationSlider",function(a,b,c){var d=null;null==jalview.appletgui.SliderPanel.conservationSlider?(d=new jalview.appletgui.SliderPanel(a,b.getConservationInc(),!0,b),jalview.appletgui.SliderPanel.conservationSlider=new awt2swing.Frame,jalview.appletgui.SliderPanel.conservationSlider.add(d)):(d=jalview.appletgui.SliderPanel.conservationSlider.getComponent(0),d.cs=b);jalview.appletgui.SliderPanel.conservationSlider.setTitle(jalview.util.MessageManager.formatMessage("label.conservation_colour_increment",
E(-1,[c])));null!=a.av.getAlignment().getGroups()?d.setAllGroupsCheckEnabled(!0):d.setAllGroupsCheckEnabled(!1);return d.getValue()},"jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S");c$.showConservationSlider=d(c$,"showConservationSlider",function(){try{jalview.appletgui.SliderPanel.PIDSlider.setVisible(!1),jalview.appletgui.SliderPanel.PIDSlider=null}catch(a){if(!y(a,Exception))throw a;}jalview.appletgui.SliderPanel.conservationSlider.isVisible()||(jalview.bin.JalviewLite.addFrame(jalview.appletgui.SliderPanel.conservationSlider,
jalview.appletgui.SliderPanel.conservationSlider.getTitle(),420,100),jalview.appletgui.SliderPanel.conservationSlider.addWindowListener((H("jalview.appletgui.SliderPanel$1")?0:jalview.appletgui.SliderPanel.$SliderPanel$1$(),C(jalview.appletgui.SliderPanel$1,this,null))))});c$.setPIDSliderSource=d(c$,"setPIDSliderSource",function(a,b,c){var d=null;null==jalview.appletgui.SliderPanel.PIDSlider?(d=new jalview.appletgui.SliderPanel(a,50,!1,b),jalview.appletgui.SliderPanel.PIDSlider=new awt2swing.Frame,
jalview.appletgui.SliderPanel.PIDSlider.add(d)):(d=jalview.appletgui.SliderPanel.PIDSlider.getComponent(0),d.cs=b);jalview.appletgui.SliderPanel.PIDSlider.setTitle(jalview.util.MessageManager.formatMessage("label.percentage_identity_thereshold",E(-1,[c])));null!=a.av.getAlignment().getGroups()?d.setAllGroupsCheckEnabled(!0):d.setAllGroupsCheckEnabled(!1);return d.getValue()},"jalview.appletgui.AlignmentPanel,jalview.schemes.ColourSchemeI,~S");c$.showPIDSlider=d(c$,"showPIDSlider",function(){try{jalview.appletgui.SliderPanel.conservationSlider.setVisible(!1),
jalview.appletgui.SliderPanel.conservationSlider=null}catch(a){if(!y(a,Exception))throw a;}jalview.appletgui.SliderPanel.PIDSlider.isVisible()||(jalview.bin.JalviewLite.addFrame(jalview.appletgui.SliderPanel.PIDSlider,jalview.appletgui.SliderPanel.PIDSlider.getTitle(),420,100),jalview.appletgui.SliderPanel.PIDSlider.addWindowListener((H("jalview.appletgui.SliderPanel$2")?0:jalview.appletgui.SliderPanel.$SliderPanel$2$(),C(jalview.appletgui.SliderPanel$2,this,null))))});m(c$,function(a,b,c,d){t(this,
jalview.appletgui.SliderPanel,[]);try{this.jbInit()}catch(e){if(y(e,Exception))e.printStackTrace();else throw e;}this.ap=a;this.cs=d;this.forConservation=c;this.undoButton.setVisible(!1);this.applyButton.setVisible(!1);this.forConservation?(this.label.setText(jalview.util.MessageManager.getString("label.modify_conservation_visibility")),this.slider.setMinimum(0),this.slider.setMaximum(50+this.slider.getVisibleAmount()),this.slider.setUnitIncrement(1)):(this.label.setText(jalview.util.MessageManager.getString("label.colour_residues_above_occurence")),
this.slider.setMinimum(0),this.slider.setMaximum(100+this.slider.getVisibleAmount()),this.slider.setBlockIncrement(1));this.slider.addAdjustmentListener(this);this.slider.addMouseListener(this);this.slider.setValue(b);this.valueField.setText(b+"")},"jalview.appletgui.AlignmentPanel,~N,~B,jalview.schemes.ColourSchemeI");d(c$,"valueChanged",function(a){if(null!=this.cs){var b=this.cs,c=null;for(this.allGroupsCheck.getState()&&(c=this.ap.av.getAlignment().getGroups().listIterator());null!=b;)if(this.forConservation?
b.setConservationInc(a):b.setThreshold(a,this.ap.av.isIgnoreGapsConsensus()),null!=c&&c.hasNext())for(;null==(b=c.next().cs)&&c.hasNext(););else b=null;this.ap.seqPanel.seqCanvas.repaint()}},"~N");d(c$,"setAllGroupsCheckEnabled",function(a){this.allGroupsCheck.setEnabled(a)},"~B");e(c$,"actionPerformed",function(a){a.getSource()===this.applyButton?this.applyButton_actionPerformed():a.getSource()===this.undoButton?this.undoButton_actionPerformed():a.getSource()===this.valueField&&this.valueField_actionPerformed()},
"java.awt.event.ActionEvent");e(c$,"adjustmentValueChanged",function(){this.valueField.setText(this.slider.getValue()+"");this.valueChanged(this.slider.getValue())},"java.awt.event.AdjustmentEvent");d(c$,"valueField_actionPerformed",function(){try{var a=Integer.parseInt(this.valueField.getText());this.slider.setValue(a)}catch(b){if(y(b,Exception))this.valueField.setText(this.slider.getValue()+"");else throw b;}});d(c$,"setValue",function(a){this.slider.setValue(a)},"~N");d(c$,"getValue",function(){return Integer.parseInt(this.valueField.getText())});
d(c$,"jbInit",function(){this.setLayout(this.borderLayout2);this.slider.setBackground(java.awt.Color.white);this.slider.setFont(new java.awt.Font("Verdana",0,11));this.slider.setOrientation(0);this.valueField.setFont(new java.awt.Font("Verdana",0,11));this.valueField.setText("   ");this.valueField.addActionListener(this);this.valueField.setColumns(3);this.label.setFont(new java.awt.Font("Verdana",0,11));this.label.setText(jalview.util.MessageManager.getString("label.set_this_label_text"));this.jPanel1.setLayout(this.borderLayout1);
this.jPanel2.setLayout(this.flowLayout1);this.applyButton.setFont(new java.awt.Font("Verdana",0,11));this.applyButton.setLabel(jalview.util.MessageManager.getString("action.apply"));this.applyButton.addActionListener(this);this.undoButton.setEnabled(!1);this.undoButton.setFont(new java.awt.Font("Verdana",0,11));this.undoButton.setLabel(jalview.util.MessageManager.getString("action.undo"));this.undoButton.addActionListener(this);this.allGroupsCheck.setEnabled(!1);this.allGroupsCheck.setFont(new java.awt.Font("Verdana",
0,11));this.allGroupsCheck.setLabel(jalview.util.MessageManager.getString("action.apply_threshold_all_groups"));this.allGroupsCheck.setName(jalview.util.MessageManager.getString("action.apply_all_groups"));this.setBackground(java.awt.Color.white);this.setForeground(java.awt.Color.black);this.jPanel2.add(this.label,null);this.jPanel2.add(this.applyButton,null);this.jPanel2.add(this.undoButton,null);this.jPanel2.add(this.allGroupsCheck);this.jPanel1.add(this.valueField,"East");this.jPanel1.add(this.slider,
"Center");this.add(this.jPanel1,"South");this.add(this.jPanel2,"Center")});d(c$,"applyButton_actionPerformed",function(){});d(c$,"undoButton_actionPerformed",function(){});e(c$,"mousePressed",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){this.ap.paintAlignment(!0)},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");
c$.$SliderPanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"SliderPanel$1",java.awt.event.WindowAdapter);e(c$,"windowClosing",function(){jalview.appletgui.SliderPanel.conservationSlider=null},"java.awt.event.WindowEvent");c$=z()};c$.$SliderPanel$2$=function(){A(self.c$);c$=L(jalview.appletgui,"SliderPanel$2",java.awt.event.WindowAdapter);e(c$,"windowClosing",function(){jalview.appletgui.SliderPanel.PIDSlider=null},"java.awt.event.WindowEvent");c$=z()};G(c$,"conservationSlider",null,"PIDSlider",
null)});p("jalview.commands");q(["jalview.commands.CommandI"],"jalview.commands.ChangeCaseCommand",["java.lang.StringBuffer"],function(){c$=s(function(){this.description=null;this.caseChange=-1;this.regions=this.seqs=null;r(this,arguments)},jalview.commands,"ChangeCaseCommand",null,jalview.commands.CommandI);m(c$,function(a,b,c,d){this.description=a;this.seqs=b;this.regions=c;this.caseChange=d;this.doCommand(null)},"~S,~A,java.util.List,~N");e(c$,"getDescription",function(){return this.description});
e(c$,"getSize",function(){return 1});e(c$,"doCommand",function(){this.changeCase(!0)},"~A");e(c$,"undoCommand",function(){this.changeCase(!1)},"~A");d(c$,"changeCase",function(a){for(var b,c,d,e,k,g=this.regions.iterator();g.hasNext()&&((k=g.next())||1);){c=k[0];for(var h=0;h<this.seqs.length;h++){b=this.seqs[h].getSequenceAsString();var j=new StringBuffer;d=k[1]>b.length?b.length:k[1];0<c&&j.append(b.substring(0,c));if(this.caseChange==jalview.commands.ChangeCaseCommand.TO_UPPER&&a||this.caseChange==
jalview.commands.ChangeCaseCommand.TO_LOWER&&!a)j.append(b.substring(c,d).toUpperCase());else if(this.caseChange==jalview.commands.ChangeCaseCommand.TO_LOWER&&a||this.caseChange==jalview.commands.ChangeCaseCommand.TO_UPPER&&!a)j.append(b.substring(c,d).toLowerCase());else for(var n=c;n<d;n++)e=b.charAt(n),"a"<=e&&"z">=e?e=String.fromCharCode(e.charCodeAt(0)-32):"A"<=e&&"Z">=e&&(e=String.fromCharCode(e.charCodeAt(0)+32)),j.append(e);d<b.length&&j.append(b.substring(d));this.seqs[h].setSequence(j.toString())}}},
"~B");G(c$,"TO_LOWER",0,"TO_UPPER",1,"TOGGLE_CASE",2)});p("jalview.io");q(null,"jalview.io.SequenceAnnotationReport",["jalview.util.DBRefUtils","$.UrlLink","java.lang.Float","java.util.ArrayList"],function(){c$=s(function(){this.linkImageURL=null;r(this,arguments)},jalview.io,"SequenceAnnotationReport");m(c$,function(a){this.linkImageURL=a},"~S");d(c$,"appendFeatures",function(a,b,c){this.appendFeatures(a,b,c,null)},"StringBuffer,~N,java.util.List");d(c$,"appendFeatures",function(a,b,c,d){var e;if(null!=
c){var k;for(c=c.iterator();c.hasNext()&&((k=c.next())||1);){if(k.getType().equals("disulfide bond")){if(k.getBegin()==b||k.getEnd()==b)6<a.length()&&a.append("<br>"),a.append("disulfide bond "+k.getBegin()+":"+k.getEnd())}else if(6<a.length()&&a.append("<br>"),null==k.getValue("linkonly")){a.append(k.getType()+" ");0!=b&&a.append(""+k.begin);k.begin!=k.end&&a.append(" "+k.end);if(null!=k.getDescription()&&!k.description.equals(k.getType())){e=k.getDescription();var g=e.toUpperCase(),h=g.indexOf("<HTML>");
-1<h&&(e=e.substring(h+6),g=g.substring(h+6));var j=g.indexOf("</BODY>");-1<j&&(e=e.substring(0,j),g=g.substring(0,j));j=g.indexOf("</HTML>");-1<j&&(e=e.substring(0,j));-1<h?a.append("; "+e):-1<e.indexOf("<")||-1<e.indexOf(">")?(e=e.replaceAll("<","&lt;"),e=e.replaceAll(">","&gt;"),a.append("; "),a.append(e)):a.append("; "+e)}Float.isNaN(k.getScore())||(e=null==d?null:d.get(k.getType()),null!=e&&(null!=e[0]&&e[0][0]!=e[0][1])&&a.append(" Score="+k.getScore()));null!=k.getValue("status")&&0<k.getValue("status").toString().length&&
a.append("; ("+k.getValue("status")+")")}if(null!=k.links)if(null!=this.linkImageURL)a.append(' <img src="'+this.linkImageURL+'">');else{var n;for(e=k.links.iterator();e.hasNext()&&((n=e.next())||1);)try{for(var m,g=0,p=this.createLinksFrom(null,n);g<p.length&&((m=p[g])||1);g++)a.append('<br/> <a href="'+m[3]+'" target="'+m[0]+'">'+(m[0].toLowerCase().equals(m[1].toLowerCase())?m[0]:m[0]+":"+m[1])+"</a></br>")}catch(q){if(y(q,Exception))System.err.println("problem when creating links from "+n),q.printStackTrace();
else throw q;}}}}},"StringBuffer,~N,java.util.List,java.util.Hashtable");d(c$,"createLinksFrom",function(a,b){var c=new java.util.ArrayList,d=new java.util.ArrayList,e=new jalview.util.UrlLink(b);if(!e.isValid())return System.err.println(e.getInvalidMessage()),null;var k=e.getTarget(),g=e.getLabel();if(null!=a&&e.isDynamic()){var h=jalview.util.DBRefUtils.selectRefs(a.getDBRef(),E(-1,[k])),j=a.getName(),n=a.getDescription();null!=n&&1>n.length&&(n=null);if(null!=h)for(var m=0;m<h.length;m++){null!=
j&&h[m].getAccessionId().equals(j)&&(j=null);var p=e.makeUrls(h[m].getAccessionId(),!0);if(null!=p)for(var q=0;q<p.length;q+=2){var r=p[q]+"|"+p[q+1];d.contains(r)||(c.add(E(-1,[k,g,p[q],p[q+1]])),d.add(r))}}if(null!=j&&(p=e.makeUrls(j,!0),null!=p))for(q=0;q<p.length;q+=2)r=p[q]+"|"+p[q+1],d.contains(r)||(c.add(E(-1,[k,g,p[q],p[q+1]])),d.add(r));if(null!=n&&null!=e.getRegexReplace()&&(p=e.makeUrls(n,!0),null!=p))for(q=0;q<p.length;q+=2)r=p[q]+"|"+p[q+1],d.contains(r)||(c.add(E(-1,[k,g,p[q],p[q+1]])),
d.add(r))}else r=g+"|"+e.getUrl_prefix(),d.contains(r)||(d.add(r),c.add(E(-1,[k,g,null,e.getUrl_prefix()])));return c.toArray(E(-1,[]))},"jalview.datamodel.SequenceI,~S");d(c$,"createSequenceAnnotationReport",function(a,b,c,d,e){this.createSequenceAnnotationReport(a,b,c,d,!0,e)},"StringBuffer,jalview.datamodel.SequenceI,~B,~B,java.util.Hashtable");d(c$,"createSequenceAnnotationReport",function(a,b,c,d,e,k){var g;a.append("<i>");var h=0;null!=b.getDescription()&&(g=b.getDescription(),a.append("<br>"+
g),h=Math.max(h,g.length));for(g=b;null!=g.getDatasetSequence();)g=g.getDatasetSequence();var j=g.getDBRef();if(c&&null!=j)for(c=0;c<j.length;c++)a.append("<br>"),g=j[c].getSource()+" "+j[c].getAccessionId(),a.append(g),h=Math.max(h,g.length);b=b.getSequenceFeatures();if(d&&null!=b)for(c=0;c<b.length;c++)0==b[c].begin&&0==b[c].end&&(d=-a.length(),g=new java.util.ArrayList,g.add(b[c]),this.appendFeatures(a,0,g,k),d+=a.length(),h=Math.max(h,d));e&&60<h&&(a.insert(0,"<table width=350 border=0><tr><td><i>"),
a.append("</i></td></tr></table>"))},"StringBuffer,jalview.datamodel.SequenceI,~B,~B,~B,java.util.Hashtable")});p("jalview.util");q(null,"jalview.util.UrlLink",["jalview.jsdev.RegExp","java.util.Vector"],function(){c$=s(function(){this.regexReplace=this.label=this.target=this.url_prefix=this.url_suffix=null;this.dynamic=!1;this.invalidMessage=null;r(this,arguments)},jalview.util,"UrlLink");m(c$,function(a){var b=a.indexOf("|"),c=a.indexOf("$SEQUENCE_ID");if(-1<c){this.dynamic=!0;var d=b;do b=d,d=
a.indexOf("|",b+1);while(d>b&&d<c);this.label=a.substring(0,b);this.target=-1<this.label.indexOf("|")?this.label.substring(0,this.label.indexOf("|")):2<this.label.indexOf(" ")?this.label.substring(0,this.label.indexOf(" ")):this.label;this.url_prefix=a.substring(b+1,c);if(a.indexOf("$SEQUENCE_ID=/")==c&&(d=a.indexOf("/=$",c+14))>c+14){this.url_suffix=a.substring(d+3);this.regexReplace=a.substring(c+14,d);try{null==jalview.jsdev.RegExp.perlCode("/"+this.regexReplace+"/")&&(this.invalidMessage="Invalid Regular Expression : '"+
this.regexReplace+"'\n")}catch(e){if(y(e,Exception))this.invalidMessage="Invalid Regular Expression : '"+this.regexReplace+"'\n";else throw e;}}else this.regexReplace=null,a.indexOf("$SEQUENCE_ID$")==c?(this.url_suffix=a.substring(c+13),this.regexReplace=null):this.invalidMessage="Warning: invalid regex structure for URL link : "+a}else this.target=a.substring(0,b),this.label=a.substring(0,b=a.lastIndexOf("|")),this.url_prefix=a.substring(b+1),this.url_suffix=this.regexReplace=null},"~S");d(c$,"getUrl_suffix",
function(){return this.url_suffix});d(c$,"getUrl_prefix",function(){return this.url_prefix});d(c$,"getTarget",function(){return this.target});d(c$,"getLabel",function(){return this.label});d(c$,"getRegexReplace",function(){return this.regexReplace});d(c$,"getInvalidMessage",function(){return this.invalidMessage});d(c$,"isValid",function(){return null==this.invalidMessage});d(c$,"makeUrls",function(a,b){if(this.dynamic){if(null!=this.regexReplace){var c=jalview.jsdev.RegExp.perlCode("/"+this.regexReplace+
"/");if(c.search(a)){var d=c.numSubs();if(0==d)return E(-1,[c.stringMatchedI(d),this.url_prefix+c.stringMatched()+this.url_suffix]);for(var e=0;e<=c.numSubs();e++)System.err.println("Sub "+e+" : "+c.matchedFromI(e)+" : "+c.matchedToI(e)+" : '"+c.stringMatchedI(e)+"'");for(var k=new java.util.Vector,e=0;e<=d;)if(e+1<=d&&-1<c.matchedToI(e)&&-1<c.matchedToI(e+1)&&c.matchedToI(e+1)<c.matchedToI(e)){for(var g=e+1,h="";g<=d&&c.matchedToI(g)<=c.matchedToI(e);)-1<c.matchedFromI(g)&&(h+=c.stringMatchedI(g)),
g++;0<h.length&&(k.addElement(h),k.addElement(this.url_prefix+h+this.url_suffix));e=g}else-1<c.matchedFromI(e)&&(k.addElement(c.stringMatchedI(e)),k.addElement(this.url_prefix+c.stringMatchedI(e)+this.url_suffix)),e++;c=Array(k.size());g=0;for(d=k.size();g<d;g++)c[g]=k.elementAt(g);k.removeAllElements();return c}if(b)return null}-1<a.indexOf("|")&&(a=a.substring(a.lastIndexOf("|")+1));return E(-1,[a,this.url_prefix+a+this.url_suffix])}return E(-1,["",this.url_prefix])},"~S,~B");e(c$,"toString",function(){return this.label+
"|"+this.url_prefix+(this.dynamic?"$SEQUENCE_ID"+(null!=this.regexReplace?"="+this.regexReplace+"=$":"$"):"")+(null==this.url_suffix?"":this.url_suffix)});d(c$,"isDynamic",function(){return this.dynamic});d(c$,"setLabel",function(a){this.label=a},"~S")});p("jalview.appletgui");q(["awt2swing.Panel"],"jalview.appletgui.IdCanvas","awt2swing.Util jalview.appletgui.AnnotationLabels $.AnnotationPanel $.PaintRefresher java.awt.Color $.Font".split(" "),function(){c$=s(function(){this.av=null;this.showScores=
!0;this.maxIdLength=-1;this.gg=this.image=this.maxIdStr=null;this.imgHeight=0;this.$fastPaint=!1;this.searchResults=null;this.avcharHeight=0;r(this,arguments)},jalview.appletgui,"IdCanvas",awt2swing.Panel);m(c$,function(a){t(this,jalview.appletgui.IdCanvas,[]);this.setLayout(null);this.av=a;jalview.appletgui.PaintRefresher.Register(this,a.getSequenceSetId())},"jalview.appletgui.AlignViewport");d(c$,"drawIdString",function(a,b,c,d,e,k){var g=this.av.getCharHeight();null!=this.searchResults&&this.searchResults.contains(c)?
(a.setColor(java.awt.Color.black),a.fillRect(0,(d-e)*g+k,this.getSize().width,g),a.setColor(java.awt.Color.white)):null!=this.av.getSelectionGroup()&&this.av.getSelectionGroup().getSequences(null).contains(c)?(a.setColor(java.awt.Color.lightGray),a.fillRect(0,(d-e)*g+k,this.getSize().width,g),a.setColor(java.awt.Color.white)):(a.setColor(this.av.getSequenceColour(c)),a.fillRect(0,(d-e)*g+k,this.getSize().width,g),a.setColor(java.awt.Color.black));awt2swing.Util.drawString(a,c.getDisplayId(this.av.getShowJVSuffix()),
0,(d-e)*g+k+g-F(g/5));b&&this.drawMarker(d,e,k)},"java.awt.Graphics,~B,jalview.datamodel.SequenceI,~N,~N,~N");d(c$,"fastPaint",function(a){if(null!=this.gg){this.gg.copyArea(0,0,this.getSize().width,this.imgHeight,0,-a*this.av.getCharHeight());var b=this.av.startSeq,c=this.av.endSeq,d=0;0<a?(b=c-a,b<this.av.startSeq?b=this.av.startSeq:d=this.imgHeight-a*this.av.getCharHeight()):0>a&&(c=b-a,c>this.av.endSeq&&(c=this.av.endSeq));this.gg.translate(0,d);this.drawIds(b,c);this.gg.translate(0,-d);this.$fastPaint=
!0}this.repaint()},"~N");e(c$,"paintComponent",function(a){if(!(0>this.getSize().height||0>this.getSize().width))if(this.$fastPaint)this.$fastPaint=!1,a.drawImage(this.image,0,0,this);else if(this.imgHeight=this.getSize().height,this.imgHeight-=this.imgHeight%this.av.getCharHeight(),!(1>this.imgHeight)){if(null==this.image||this.imgHeight!=this.image.getHeight(this))this.image=this.createImage(this.getSize().width,this.imgHeight),this.gg=this.image.getGraphics(),this.gg.setFont(this.av.getFont());
this.gg.setColor(java.awt.Color.white);var b=new java.awt.Font(this.av.getFont().getName(),2,this.av.getFont().getSize());this.gg.setFont(b);this.gg.fillRect(0,0,this.getSize().width,this.getSize().height);this.drawIds(this.av.startSeq,this.av.endSeq);a.drawImage(this.image,0,0,this)}},"java.awt.Graphics");d(c$,"drawIds",function(a,b){var c=new java.awt.Font(this.av.getFont().getName(),2,this.av.getFont().getSize());this.avcharHeight=this.av.getCharHeight();this.gg.setFont(c);var d=java.awt.Color.white,
e=java.awt.Color.black,k=this.av.isDisplayReferenceSeq()||this.av.hasHiddenRows(),g=this.av.hasHiddenRows()&&this.av.getShowHiddenMarkers();if(this.av.getWrapAlignment()){d=this.av.getAlignment().getWidth();e=this.av.getAlignment().getHeight();this.av.hasHiddenColumns()&&(d=this.av.getColumnSelection().findColumnPosition(d)-1);var h=0,j=null;this.av.isShowAnnotation()&&(h=(new jalview.appletgui.AnnotationPanel(this.av)).adjustPanelHeight(),j=new jalview.appletgui.AnnotationLabels(this.av));var n=
this.avcharHeight;this.av.getScaleAboveWrapped()&&(n+=this.avcharHeight);for(var h=e*this.avcharHeight+n+h,m=this.av.getEndRes()-this.av.getStartRes(),p=n,q=this.av.startRes;p<=this.getSize().height&&q<d;p+=h,q+=m){for(n=a;n<e;n++){var r=this.av.getAlignment().getSequenceAt(n);this.gg.setFont(c);k&&this.setHiddenFont(r);this.drawIdString(this.gg,g,r,n,0,p)}null!=j&&(this.gg.translate(0,p+e*this.avcharHeight),j.drawComponent(this.gg,this.getSize().width),this.gg.translate(0,-p-e*this.avcharHeight))}}else for(n=
a;n<b;n++)j=this.av.getAlignment().getSequenceAt(n),null!=j&&(this.gg.setFont(c),k&&this.setHiddenFont(j),null!=this.searchResults&&this.searchResults.contains(j)?(d=java.awt.Color.black,e=java.awt.Color.white):(d=null!=this.av.getSelectionGroup()&&this.av.getSelectionGroup().getSequences(null).contains(j)?java.awt.Color.lightGray:this.av.getSequenceColour(j),e=java.awt.Color.black),this.gg.setColor(d),this.gg.fillRect(0,(n-a)*this.avcharHeight,this.getSize().width,this.avcharHeight),this.gg.setColor(e),
awt2swing.Util.drawString(this.gg,j.getDisplayId(this.av.getShowJVSuffix()),0,(n-a)*this.avcharHeight+this.avcharHeight-F(this.avcharHeight/5)),g&&this.drawMarker(n,a,0))},"~N,~N");d(c$,"setHighlighted",function(a){this.searchResults=a;this.repaint()},"java.util.List");d(c$,"drawMarker",function(a,b,c){for(var d=this.av.getAlignment().getHiddenSequences().hiddenSequences,e=d.length,k=a,g=a-1,h=a+1,j=0;j<e;j++)null!=d[j]&&(j-1<k&&k++,j-1<g&&g++,j-1<h&&h++);d=k>g+1;k=h>k+1;this.gg.setColor(java.awt.Color.blue);
d&&this.gg.fillPolygon(w(-1,[this.getSize().width-this.avcharHeight,this.getSize().width-this.avcharHeight,this.getSize().width]),w(-1,[(a-b)*this.avcharHeight+c,(a-b)*this.avcharHeight+c+F(this.avcharHeight/4),(a-b)*this.avcharHeight+c]),3);k&&this.gg.fillPolygon(w(-1,[this.getSize().width-this.avcharHeight,this.getSize().width-this.avcharHeight,this.getSize().width]),w(-1,[(a-b+1)*this.avcharHeight+c,(a-b+1)*this.avcharHeight+c-F(this.avcharHeight/4),(a-b+1)*this.avcharHeight+c]),3)},"~N,~N,~N");
d(c$,"setHiddenFont",function(a){var b=new java.awt.Font(this.av.getFont().getName(),1,this.av.getFont().getSize());return this.av.isHiddenRepSequence(a)?(this.gg.setFont(b),!0):!1},"jalview.datamodel.SequenceI")});p("jalview.appletgui");q(["awt2swing.Panel","java.awt.event.MouseListener","$.MouseMotionListener"],"jalview.appletgui.IdwidthAdjuster",["java.awt.Color","$.Toolkit"],function(){c$=s(function(){this.active=!1;this.oldX=0;this.ap=this.image=null;r(this,arguments)},jalview.appletgui,"IdwidthAdjuster",
awt2swing.Panel,[java.awt.event.MouseListener,java.awt.event.MouseMotionListener]);m(c$,function(a){t(this,jalview.appletgui.IdwidthAdjuster,[]);this.setName("IdwidthAdjuster");this.setLayout(null);this.ap=a;a=this.getClass().getResource("/images/idwidth.gif");null!=a&&(this.image=java.awt.Toolkit.getDefaultToolkit().getImage(a));this.addMouseListener(this);this.addMouseMotionListener(this)},"jalview.appletgui.AlignmentPanel");e(c$,"mousePressed",function(a){this.oldX=a.getX()},"java.awt.event.MouseEvent");
e(c$,"mouseReleased",function(){this.active=!1;this.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){this.active=!0;this.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){this.active=!1;this.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){this.active=!0;var b=this.ap.idPanel.idCanvas.getSize(),c=a.getX()-this.oldX,d=b.width+c;if(20<d||0<c)this.ap.setIdWidth(d,b.height),this.setSize(d,this.getSize().height),this.oldX=a.getX()},"java.awt.event.MouseEvent");
e(c$,"mouseMoved",function(){},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");d(c$,"PaintComponent",function(a){a.setColor(java.awt.Color.white);a.fillRect(0,0,this.getSize().width,this.getSize().height);this.active&&null!=this.image&&a.drawImage(this.image,this.getSize().width-20,2,this)},"java.awt.Graphics")});p("jalview.appletgui");q(["awt2swing.Panel","java.awt.event.MouseListener","$.MouseMotionListener"],"jalview.appletgui.ScalePanel","awt2swing.MenuItem $.PopupMenu $.Util jalview.datamodel.SequenceGroup jalview.util.MessageManager java.awt.Color java.awt.event.ActionListener".split(" "),
function(){c$=s(function(){this.offy=4;this.$width=0;this.ap=this.av=null;this.stretchingGroup=!1;this.max=this.min=0;this.mouseDragging=!1;this.reveal=null;r(this,arguments)},jalview.appletgui,"ScalePanel",awt2swing.Panel,[java.awt.event.MouseMotionListener,java.awt.event.MouseListener]);m(c$,function(a,b){t(this,jalview.appletgui.ScalePanel,[]);this.setName("scalePanel");this.setLayout(null);this.av=a;this.ap=b;this.addMouseListener(this);this.addMouseMotionListener(this)},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");
e(c$,"mousePressed",function(a){var b=F(a.getX()/this.av.getCharWidth())+this.av.getStartRes();this.max=this.min=b=this.av.hasHiddenColumns()?this.av.getColumnSelection().adjustForHiddenColumns(b):b;if(4==(a.getModifiers()&4)){var c=new awt2swing.PopupMenu;if(null!=this.reveal){var d=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.reveal"));d.addActionListener((H("jalview.appletgui.ScalePanel$1")?0:jalview.appletgui.ScalePanel.$ScalePanel$1$(),C(jalview.appletgui.ScalePanel$1,
this,null)));c.add(d);this.av.getColumnSelection().hasManyHiddenColumns()&&(d=new awt2swing.MenuItem(jalview.util.MessageManager.getString("action.reveal_all")),d.addActionListener((H("jalview.appletgui.ScalePanel$2")?0:jalview.appletgui.ScalePanel.$ScalePanel$2$(),C(jalview.appletgui.ScalePanel$2,this,null))),c.add(d));this.add(c);c.show(this,a.getX(),a.getY())}else this.av.getColumnSelection().contains(b)&&(d=new awt2swing.MenuItem(jalview.util.MessageManager.getString("label.hide_columns")),d.addActionListener((H("jalview.appletgui.ScalePanel$3")?
0:jalview.appletgui.ScalePanel.$ScalePanel$3$(),C(jalview.appletgui.ScalePanel$3,this,T("res",b)))),c.add(d),this.add(c),c.show(this,a.getX(),a.getY()))}else{!a.isControlDown()&&!a.isShiftDown()&&this.av.getColumnSelection().clear();this.av.getColumnSelection().addElement(b);c=new jalview.datamodel.SequenceGroup;for(d=0;d<this.av.getAlignment().getSequences().size();d++)c.addSequence(this.av.getAlignment().getSequenceAt(d),!1);c.setStartRes(b);c.setEndRes(b);this.av.setSelectionGroup(c);if(a.isShiftDown()){a=
Math.min(this.av.getColumnSelection().getMin(),b);b=Math.max(this.av.getColumnSelection().getMax(),b);for(d=a;d<b;d++)this.av.getColumnSelection().addElement(d);c.setStartRes(a);c.setEndRes(b)}}this.ap.paintAlignment(!0);this.av.sendSelection()},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){this.mouseDragging=!1;a=F(a.getX()/this.av.getCharWidth())+this.av.getStartRes();a>this.av.getAlignment().getWidth()&&(a=this.av.getAlignment().getWidth()-1);this.av.hasHiddenColumns()&&(a=this.av.getColumnSelection().adjustForHiddenColumns(a));
if(this.stretchingGroup){var b=this.av.getSelectionGroup();a>b.getStartRes()?b.setEndRes(a):a<b.getStartRes()&&b.setStartRes(a);this.stretchingGroup=!1;this.ap.paintAlignment(!1);this.av.sendSelection()}else this.ap.paintAlignment(!1)},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){this.mouseDragging=!0;var b=F(a.getX()/this.av.getCharWidth())+this.av.getStartRes();0>b&&(b=0);this.av.hasHiddenColumns()&&(b=this.av.getColumnSelection().adjustForHiddenColumns(b));b>this.av.getAlignment().getWidth()&&
(b=this.av.getAlignment().getWidth()-1);b<this.min&&(this.min=b);b>this.max&&(this.max=b);a=this.av.getSelectionGroup();if(null!=a){this.stretchingGroup=!0;this.av.getColumnSelection().contains(b)||this.av.getColumnSelection().addElement(b);b>a.getStartRes()&&a.setEndRes(b);b<a.getStartRes()&&a.setStartRes(b);for(var c=this.min;c<=this.max;c++)b=this.av.getColumnSelection().adjustForHiddenColumns(c),b<a.getStartRes()||b>a.getEndRes()?this.av.getColumnSelection().removeElement(b):this.av.getColumnSelection().addElement(b);
this.ap.paintAlignment(!1)}},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){this.mouseDragging&&this.ap.seqPanel.scrollCanvas(null)},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(a){this.mouseDragging&&this.ap.seqPanel.scrollCanvas(a)},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(a){if(this.av.hasHiddenColumns()){a=F(a.getX()/this.av.getCharWidth())+this.av.getStartRes();a=this.av.getColumnSelection().adjustForHiddenColumns(a);
this.reveal=null;for(var b,c=this.av.getColumnSelection().getHiddenColumns().iterator();c.hasNext()&&((b=c.next())||1);)if(a+1==b[0]||a-1==b[1]){this.reveal=b;break}this.repaint()}},"java.awt.event.MouseEvent");e(c$,"paintComponent",function(a){this.av.getWrapAlignment()||this.drawScale(a,this.av.getStartRes(),this.av.getEndRes(),this.getSize().width,this.getSize().height)},"java.awt.Graphics");d(c$,"drawScale",function(a,b,c,d,e){a.setFont(this.av.getFont());a.setColor(java.awt.Color.white);a.fillRect(0,
0,d,e);a.setColor(java.awt.Color.black);var k=this.av.getColumnSelection();a.setColor(new java.awt.Color(220,0,0));d=this.av.getCharWidth();e=this.av.getCharHeight();for(var g=0;g<k.size();g++){var h=k.columnAt(g);this.av.hasHiddenColumns()&&(h=this.av.getColumnSelection().findColumnPosition(h));h>=b&&h<=c&&a.fillRect((h-b)*d,0,d,this.getSize().height)}a.setColor(java.awt.Color.black);var k=10*F(b/10),j=a.getFontMetrics(this.av.getFont()),h=e-j.getDescent();0==k%10&&(k+=5);for(var n,m=0,g=k;g<c;g+=
5)0==g%10?(n=String.valueOf(this.av.getColumnSelection().adjustForHiddenColumns(g)),(g-b-1)*d>m&&(awt2swing.Util.drawString(a,n,(g-b-1)*d,h),m=(g-b+1)*d+j.stringWidth(n)),a.drawLine((g-b-1)*d+F(d/2),h+2,(g-b-1)*d+F(d/2),h+2*j.getDescent())):a.drawLine((g-b-1)*d+F(d/2),h+j.getDescent(),(g-b-1)*d+F(d/2),h+2*j.getDescent());if(this.av.hasHiddenColumns()){a.setColor(java.awt.Color.blue);if(this.av.getShowHiddenMarkers())for(g=0;g<this.av.getColumnSelection().getHiddenColumns().size();g++)j=this.av.getColumnSelection().findHiddenRegionPosition(g)-
b,0>j||j>c-k||a.fillPolygon(w(-1,[j*d-F(e/4),j*d+F(e/4),j*d]),w(-1,[h-F(e/2),h-F(e/2),h+8]),3);null!=this.reveal&&(this.reveal[0]>b&&this.reveal[0]<c)&&awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.reveal_columns"),this.reveal[0]*d,0)}},"java.awt.Graphics,~N,~N,~N,~N");c$.$ScalePanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"ScalePanel$1",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.ScalePanel"].av.showColumn(this.b$["jalview.appletgui.ScalePanel"].reveal[0]);
this.b$["jalview.appletgui.ScalePanel"].reveal=null;this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment(!0);null!=this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel&&this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage()},"java.awt.event.ActionEvent");c$=z()};c$.$ScalePanel$2$=function(){A(self.c$);c$=L(jalview.appletgui,"ScalePanel$2",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.ScalePanel"].av.showAllHiddenColumns();
this.b$["jalview.appletgui.ScalePanel"].reveal=null;this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment(!0);null!=this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel&&this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage()},"java.awt.event.ActionEvent");c$=z()};c$.$ScalePanel$3$=function(){A(self.c$);c$=L(jalview.appletgui,"ScalePanel$3",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.ScalePanel"].av.hideColumns(this.f$.res,
this.f$.res);null!=this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup()&&this.b$["jalview.appletgui.ScalePanel"].av.getSelectionGroup().getSize()==this.b$["jalview.appletgui.ScalePanel"].av.getAlignment().getHeight()&&this.b$["jalview.appletgui.ScalePanel"].av.setSelectionGroup(null);this.b$["jalview.appletgui.ScalePanel"].ap.paintAlignment(!0);null!=this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel&&this.b$["jalview.appletgui.ScalePanel"].ap.overviewPanel.updateOverviewImage()},
"java.awt.event.ActionEvent");c$=z()}});p("jalview.appletgui");q("awt2swing.Panel jalview.structure.SelectionListener $.SequenceListener java.awt.event.MouseListener $.MouseMotionListener java.lang.Thread".split(" "),"jalview.appletgui.SeqPanel","jalview.api.AlignViewportI jalview.appletgui.APopupMenu $.AlignViewport $.PaintRefresher $.SeqCanvas $.SliderPanel $.Tooltip jalview.commands.EditCommand jalview.datamodel.ColumnSelection $.SearchResults $.SequenceGroup jalview.schemes.ResidueProperties jalview.structure.StructureSelectionManager jalview.util.Comparison $.MappingUtils $.MessageManager java.awt.BorderLayout $.Font java.lang.StringBuffer $.StringBuilder java.util.Vector".split(" "),
function(){c$=s(function(){this.ap=this.seqCanvas=null;this.startseq=this.lastres=0;this.av=null;this.seqEditOccurred=!1;this.scrollThread=null;this.groupEditing=this.editingSeqs=this.mouseDragging=!1;this.oldSeq=-1;this.changeStartRes=this.changeEndRes=this.changeStartSeq=this.changeEndSeq=!1;this.keyboardNo2=this.keyboardNo1=this.stretchGroup=null;this.mouseWheelPressed=!1;this.ssm=this.editCommand=this.lastMousePress=null;this.wrappedBlock=this.startWrapBlock=-1;this.tooltip=this.lastMessage=null;
H("jalview.appletgui.SeqPanel.ScrollThread")||jalview.appletgui.SeqPanel.$SeqPanel$ScrollThread$();r(this,arguments)},jalview.appletgui,"SeqPanel",awt2swing.Panel,[java.awt.event.MouseMotionListener,java.awt.event.MouseListener,jalview.structure.SequenceListener,jalview.structure.SelectionListener]);m(c$,function(a,b){t(this,jalview.appletgui.SeqPanel,[]);this.av=a;this.setName("seqPanel");this.seqCanvas=new jalview.appletgui.SeqCanvas(a);this.setLayout(new java.awt.BorderLayout);this.add(this.seqCanvas);
this.ap=b;this.seqCanvas.addMouseMotionListener(this);this.seqCanvas.addMouseListener(this);this.ssm=jalview.structure.StructureSelectionManager.getStructureSelectionManager(this.av.applet);this.ssm.addStructureViewerListener(this);this.ssm.addSelectionListener(this);this.seqCanvas.repaint()},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");d(c$,"endEditing",function(){null!=this.editCommand&&0<this.editCommand.getSize()&&(this.ap.alignFrame.addHistoryItem(this.editCommand),this.av.firePropertyChange("alignment",
null,this.av.getAlignment().getSequences()));this.lastres=this.startseq=-1;this.groupEditing=this.editingSeqs=!1;this.editCommand=this.keyboardNo2=this.keyboardNo1=null});d(c$,"setCursorRow",function(){this.seqCanvas.cursorY=this.getKeyboardNo1()-1;this.scrollToVisible()});d(c$,"setCursorColumn",function(){this.seqCanvas.cursorX=this.getKeyboardNo1()-1;this.scrollToVisible()});d(c$,"setCursorRowAndColumn",function(){null==this.keyboardNo2?this.keyboardNo2=new StringBuffer:(this.seqCanvas.cursorX=
this.getKeyboardNo1()-1,this.seqCanvas.cursorY=this.getKeyboardNo2()-1,this.scrollToVisible())});d(c$,"setCursorPosition",function(){var a=this.av.getAlignment().getSequenceAt(this.seqCanvas.cursorY);this.seqCanvas.cursorX=a.findIndex(this.getKeyboardNo1())-1;this.scrollToVisible()});d(c$,"moveCursor",function(a,b){this.seqCanvas.cursorX+=a;this.seqCanvas.cursorY+=b;if(this.av.hasHiddenColumns()&&!this.av.getColumnSelection().isVisible(this.seqCanvas.cursorX)){for(var c=this.seqCanvas.cursorX-a,d=
this.av.getAlignment().getWidth();!this.av.getColumnSelection().isVisible(this.seqCanvas.cursorX)&&this.seqCanvas.cursorX<d&&0<this.seqCanvas.cursorX;)this.seqCanvas.cursorX+=a;if(this.seqCanvas.cursorX>=d||!this.av.getColumnSelection().isVisible(this.seqCanvas.cursorX))this.seqCanvas.cursorX=c}this.scrollToVisible()},"~N,~N");d(c$,"scrollToVisible",function(){0>this.seqCanvas.cursorX?this.seqCanvas.cursorX=0:this.seqCanvas.cursorX>this.av.getAlignment().getWidth()-1&&(this.seqCanvas.cursorX=this.av.getAlignment().getWidth()-
1);0>this.seqCanvas.cursorY?this.seqCanvas.cursorY=0:this.seqCanvas.cursorY>this.av.getAlignment().getHeight()-1&&(this.seqCanvas.cursorY=this.av.getAlignment().getHeight()-1);this.endEditing();if(this.av.getWrapAlignment())this.ap.scrollToWrappedVisible(this.seqCanvas.cursorX);else{for(;this.seqCanvas.cursorY<this.av.startSeq;)this.ap.scrollUp(!0);for(;this.seqCanvas.cursorY+1>this.av.endSeq;)this.ap.scrollUp(!1);for(;this.seqCanvas.cursorX<this.av.getColumnSelection().adjustForHiddenColumns(this.av.startRes)&&
this.ap.scrollRight(!1););for(;this.seqCanvas.cursorX>this.av.getColumnSelection().adjustForHiddenColumns(this.av.endRes)&&this.ap.scrollRight(!0););}this.setStatusMessage(this.av.getAlignment().getSequenceAt(this.seqCanvas.cursorY),this.seqCanvas.cursorX,this.seqCanvas.cursorY);this.seqCanvas.repaint()});d(c$,"setSelectionAreaAtCursor",function(a){var b=this.av.getAlignment().getSequenceAt(this.seqCanvas.cursorY);if(null!=this.av.getSelectionGroup()){for(var c=this.av.getSelectionGroup(),d=this.av.getAlignment().getHeight(),
e=0,k=0;k<c.getSize();k++){var g=this.av.getAlignment().findIndex(c.getSequenceAt(k));g>e&&(e=g);g<d&&(d=g)}e++;a?(c.setStartRes(this.seqCanvas.cursorX),c.getEndRes()<this.seqCanvas.cursorX&&c.setEndRes(this.seqCanvas.cursorX),d=this.seqCanvas.cursorY):(c.setEndRes(this.seqCanvas.cursorX),c.getStartRes()>this.seqCanvas.cursorX&&c.setStartRes(this.seqCanvas.cursorX),e=this.seqCanvas.cursorY+1);if(d>e)this.av.setSelectionGroup(null);else{c.clear();for(k=d;k<e;k++)c.addSequence(this.av.getAlignment().getSequenceAt(k),
!1)}}null==this.av.getSelectionGroup()&&(c=new jalview.datamodel.SequenceGroup,c.setStartRes(this.seqCanvas.cursorX),c.setEndRes(this.seqCanvas.cursorX),c.addSequence(b,!1),this.av.setSelectionGroup(c));this.ap.paintAlignment(!1);this.av.sendSelection()},"~B");d(c$,"insertGapAtCursor",function(a){this.groupEditing=a;this.startseq=this.seqCanvas.cursorY;this.lastres=this.seqCanvas.cursorX;this.editSequence(!0,this.seqCanvas.cursorX+this.getKeyboardNo1());this.endEditing()},"~B");d(c$,"deleteGapAtCursor",
function(a){this.groupEditing=a;this.startseq=this.seqCanvas.cursorY;this.lastres=this.seqCanvas.cursorX+this.getKeyboardNo1();this.editSequence(!1,this.seqCanvas.cursorX);this.endEditing()},"~B");d(c$,"numberPressed",function(a){null==this.keyboardNo1&&(this.keyboardNo1=new StringBuffer);null!=this.keyboardNo2?this.keyboardNo2.append(a):this.keyboardNo1.append(a)},"~S");d(c$,"getKeyboardNo1",function(){try{if(null!=this.keyboardNo1){var a=Integer.parseInt(this.keyboardNo1.toString());this.keyboardNo1=
null;return a}}catch(b){if(!y(b,Exception))throw b;}this.keyboardNo1=null;return 1});d(c$,"getKeyboardNo2",function(){try{if(null!=this.keyboardNo2){var a=Integer.parseInt(this.keyboardNo2.toString());this.keyboardNo2=null;return a}}catch(b){if(!y(b,Exception))throw b;}this.keyboardNo2=null;return 1});d(c$,"setStatusMessage",function(a,b,c){var d=new StringBuilder(32);d.append("Sequence"+(-1==c?"":" "+(c+1))+" ID: "+a.getName());c=null;c=String.valueOf(a.getCharAt(b));this.av.getAlignment().isNucleotide()?
(c=jalview.schemes.ResidueProperties.nucleotideName.get(c),null!=c&&d.append(" Nucleotide: ").append(c)):(c="X".equalsIgnoreCase(c)?"X":jalview.schemes.ResidueProperties.aa2Triplet.get(c),null!=c&&d.append(" Residue: ").append(c));var e=-1;null!=c&&(e=a.findPosition(b),d.append(" (").append(Integer.toString(e)).append(")"));this.ap.alignFrame.setStatus(d.toString())},"jalview.datamodel.SequenceI,~N,~N");d(c$,"setStatusMessage",function(a){a=a.getResults();if(!a.isEmpty()){var b=a.get(0);a=b.getSequence();
var c=this.av.getAlignment().findIndex(a),b=b.getStart()-1;this.setStatusMessage(a,b,c)}},"jalview.datamodel.SearchResults");e(c$,"mousePressed",function(a){this.lastMousePress=a.getPoint();if(8==(a.getModifiers()&8)&&!this.av.MAC)this.mouseWheelPressed=!0;else if(a.isShiftDown()||a.isControlDown()||a.isAltDown()){if(a.isControlDown()||a.isAltDown())this.groupEditing=!0;this.editingSeqs=!0;var b=this.findSeq(a);a=this.findRes(a);0>b||0>a||(b<this.av.getAlignment().getHeight()&&a<this.av.getAlignment().getSequenceAt(b).getLength()?
(this.startseq=b,this.lastres=a):this.lastres=this.startseq=-1)}else this.doMousePressedDefineMode(a)},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(a){var b=this.av.getAlignment().getSequenceAt(this.findSeq(a));if(1<a.getClickCount()){null!=this.av.getSelectionGroup()&&(1==this.av.getSelectionGroup().getSize()&&2>this.av.getSelectionGroup().getEndRes()-this.av.getSelectionGroup().getStartRes())&&this.av.setSelectionGroup(null);a=this.findFeaturesAtRes(b,b.findPosition(this.findRes(a)));
if(null!=a&&0<a.length){var c=new jalview.datamodel.SearchResults;c.addResult(b,a[0].getBegin(),a[0].getEnd());this.seqCanvas.highlightSearchResults(c)}null!=a&&0<a.length&&(this.seqCanvas.getFeatureRenderer().amendFeatures(E(-1,[b]),a,!1,this.ap),this.seqCanvas.highlightSearchResults(null))}},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){this.mouseWheelPressed=this.mouseDragging=!1;this.ap.paintAlignment(!0);this.editingSeqs?this.endEditing():this.doMouseReleasedDefineMode(a)},"java.awt.event.MouseEvent");
d(c$,"findRes",function(a){var b=0,b=a.getX();if(this.av.getWrapAlignment()){var c=this.av.getCharHeight();this.av.getScaleAboveWrapped()&&(c+=this.av.getCharHeight());var d=this.av.getAlignment().getHeight()*this.av.getCharHeight()+c+this.seqCanvas.getAnnotationHeight();a=a.getY();a-=c;b-=this.seqCanvas.LABEL_WEST;c=this.seqCanvas.getWrappedCanvasWidth(this.getSize().width);if(1>c)return 0;this.wrappedBlock=F(a/d);this.wrappedBlock+=F(this.av.getStartRes()/c);b=this.wrappedBlock*c+F(b/this.av.getCharWidth())}else b=
F(b/this.av.getCharWidth())+this.av.getStartRes();this.av.hasHiddenColumns()&&(b=this.av.getColumnSelection().adjustForHiddenColumns(b));return b},"java.awt.event.MouseEvent");d(c$,"findSeq",function(a){a=this.findAlRow(a);return 0>a?0:a},"java.awt.event.MouseEvent");d(c$,"findAlRow",function(a){var b=0;a=a.getY();if(this.av.getWrapAlignment()){b=this.av.getCharHeight();this.av.getScaleAboveWrapped()&&(b+=this.av.getCharHeight());var c=this.av.getAlignment().getHeight()*this.av.getCharHeight()+b+
this.seqCanvas.getAnnotationHeight(),b=Math.min(F((a-b)%c/this.av.getCharHeight()),this.av.getAlignment().getHeight()-1)}else b=Math.min(F(a/this.av.getCharHeight())+this.av.getStartSeq(),this.av.getAlignment().getHeight()-1);0>b&&(b=-1);return b},"java.awt.event.MouseEvent");d(c$,"doMousePressed",function(a){var b=this.findSeq(a);a=this.findRes(a);b<this.av.getAlignment().getHeight()&&a<this.av.getAlignment().getSequenceAt(b).getLength()?(this.startseq=b,this.lastres=a):this.lastres=this.startseq=
-1},"java.awt.event.MouseEvent");e(c$,"mouseOverSequence",function(a,b,c){var d=a.hashCode()+b+"";(null==this.lastMessage||!this.lastMessage.equals(d))&&this.ssm.mouseOverSequence(a,b,c,this.av);this.lastMessage=d},"jalview.datamodel.SequenceI,~N,~N");e(c$,"highlightSequence",function(a){this.av.isFollowHighlight()&&this.ap.scrollToPosition(a,!0)&&this.ap.alignFrame.repaint();this.setStatusMessage(a);this.seqCanvas.highlightSearchResults(a)},"jalview.datamodel.SearchResults");e(c$,"getVamsasSource",
function(){return null==this.ap?null:this.ap.av});e(c$,"updateColours",function(){System.out.println("update the seqPanel colours")},"jalview.datamodel.SequenceI,~N");e(c$,"mouseMoved",function(a){var b=this.findRes(a),c=this.findSeq(a);if(c>=this.av.getAlignment().getHeight()||0>c||0>b)null!=this.tooltip&&this.tooltip.setTip("");else if(a=this.av.getAlignment().getSequenceAt(c),b>a.getLength())null!=this.tooltip&&this.tooltip.setTip("");else{var d=a.findPosition(b);null!=this.ssm&&this.mouseOverSequence(a,
b,d);var e=new StringBuilder;e.append("Sequence ").append(Integer.toString(c+1)).append(" ID: ").append(a.getName());c=null;c=String.valueOf(a.getCharAt(b));this.av.getAlignment().isNucleotide()?(c=jalview.schemes.ResidueProperties.nucleotideName.get(c),null!=c&&e.append(" Nucleotide: ").append(c)):(c="X".equalsIgnoreCase(c)?"X":jalview.schemes.ResidueProperties.aa2Triplet.get(c),null!=c&&e.append(" Residue: ").append(c));null!=c&&e.append(" (").append(Integer.toString(d)).append(")");this.ap.alignFrame.setStatus(e.toString());
d=new StringBuilder;e=this.av.getAlignment().findAllGroups(a);if(null!=e)for(c=0;c<e.length;c++)e[c].getStartRes()<=b&&e[c].getEndRes()>=b&&(!e[c].getName().startsWith("JTreeGroup")&&!e[c].getName().startsWith("JGroup")&&d.append(e[c].getName()).append(" "),null!=e[c].getDescription()&&d.append(e[c].getDescription()),d.append("\n"));b=this.findFeaturesAtRes(a,a.findPosition(b));for(a=0;a<b.length;)e=b[a],d.append(e.getType()+" "+e.begin+":"+e.end),null!=e.getDescription()&&d.append(" "+e.getDescription()),
null!=e.getValue("status")&&0<e.getValue("status").toString().length&&d.append(" ("+e.getValue("status")+")"),d.append("\n"),a++;null==this.tooltip?this.tooltip=new jalview.appletgui.Tooltip(d.toString(),this.seqCanvas):this.tooltip.setTip(d.toString())}},"java.awt.event.MouseEvent");d(c$,"findFeaturesAtRes",function(a,b){var c=new java.util.Vector,d=a.getSequenceFeatures();if(null!=d)for(var e=0;e<d.length;e++)null!=this.av.getFeaturesDisplayed()&&this.av.getFeaturesDisplayed().isVisible(d[e].getType())&&
(null==d[e].featureGroup||this.seqCanvas.fr.checkGroupVisibility(d[e].featureGroup,!1))&&d[e].getBegin()<=b&&d[e].getEnd()>=b&&c.addElement(d[e]);d=Array(c.size());c.copyInto(d);return d},"jalview.datamodel.SequenceI,~N");e(c$,"mouseDragged",function(a){if(this.mouseWheelPressed){var b=this.av.getCharWidth();if(Math.abs(a.getY()-this.lastMousePress.y)>Math.abs(a.getX()-this.lastMousePress.x)){var c=this.av.font.getSize();a.getY()<this.lastMousePress.y&&1<this.av.getCharHeight()?c--:a.getY()>this.lastMousePress.y&&
c++;1>c&&(c=1);this.av.setFont(new java.awt.Font(this.av.font.getName(),this.av.font.getStyle(),c));this.av.setCharWidth(b)}else a.getX()<this.lastMousePress.x&&1<this.av.getCharWidth()?this.av.setCharWidth(this.av.getCharWidth()-1):a.getX()>this.lastMousePress.x&&this.av.setCharWidth(this.av.getCharWidth()+1),1>this.av.getCharWidth()&&this.av.setCharWidth(1);this.ap.fontChanged();b=this.getFontMetrics(this.av.getFont());this.av.validCharWidth=b.charWidth("M")<=this.av.getCharWidth();this.lastMousePress=
a.getPoint();this.ap.paintAlignment(!1);this.ap.annotationPanel.image=null}else this.editingSeqs?(b=this.findRes(a),0>b&&(b=0),-1==this.lastres||this.lastres==b||(b<this.av.getAlignment().getWidth()&&b<this.lastres?this.editSequence(!1,b):this.editSequence(!0,b),this.mouseDragging=!0,null!=this.scrollThread&&this.scrollThread.setEvent(a))):this.doMouseDraggedDefineMode(a)},"java.awt.event.MouseEvent");d(c$,"editSequence",function(a,b){var c=-1,d=-1,e=!1,k=this.av.getSelectionGroup(),g=this.av.getAlignment().getSequenceAt(this.startseq);
!this.groupEditing&&this.av.hasHiddenRows()&&this.av.isHiddenRepSequence(g)&&(k=this.av.getRepresentedSequences(g),this.groupEditing=!0);var h=new StringBuffer;if(this.groupEditing)h.append(jalview.util.MessageManager.getString("action.edit_group")).append(":"),null==this.editCommand&&(this.editCommand=new jalview.commands.EditCommand(jalview.util.MessageManager.getString("action.edit_group")));else{h.append(jalview.util.MessageManager.getString("label.edit_sequence")).append(" "+g.getName());var j=
g.getName();10<j.length&&(j=j.substring(0,10));null==this.editCommand&&(this.editCommand=new jalview.commands.EditCommand(jalview.util.MessageManager.formatMessage("label.edit_params",E(-1,[j]))))}a?h.append(" insert "):h.append(" delete ");h.append(Math.abs(b-this.lastres)+" gaps.");this.ap.alignFrame.setStatus(h.toString());if(this.groupEditing||null!=k&&k.getSequences(this.av.getHiddenRepSequences()).contains(g)){e=!0;if(null==k){if(!this.av.isHiddenRepSequence(g)){this.endEditing();return}k=this.av.getRepresentedSequences(g)}c=
k.getStartRes();d=k.getEndRes();if(b<c&&this.lastres>=c||b>=c&&this.lastres<c||b>d&&this.lastres<=d||b<=d&&this.lastres>d){this.endEditing();return}c>b?(d=c-1,c=0):d<b&&(c=d,d=-1)}if(this.av.hasHiddenColumns()){e=!0;h=this.av.getColumnSelection().getHiddenBoundaryLeft(b);j=this.av.getColumnSelection().getHiddenBoundaryRight(b);if(a&&b>h&&this.lastres<h||!a&&b<j&&this.lastres>j){this.endEditing();return}if(c<h&&(d>j||-1==d)&&!(b>=j))d=j-1}if(this.groupEditing){g=k.getSequences(this.av.getHiddenRepSequences()).toArray([]);
if(a){0==k.getStartRes()&&(k.getEndRes()==d&&k.getEndRes()==this.av.getAlignment().getWidth()-1)&&(k.setEndRes(this.av.getAlignment().getWidth()+b-this.lastres),d=k.getEndRes());for(h=!1;d>this.lastres;d--){for(var h=!0,n,j=0,m=g;j<m.length&&((n=m[j])||1);j++)for(c=0;c<b-this.lastres;c++)if(!jalview.util.Comparison.isGap(n.getCharAt(d-c))){h=!1;break}if(h)break}if(!h)if(k.getSize()==this.av.getAlignment().getHeight()){if(this.av.hasHiddenColumns()&&b<this.av.getColumnSelection().getHiddenBoundaryRight(b)){this.endEditing();
return}d=this.av.getAlignment().getWidth();this.av.hasHiddenRows()&&(n=this.av.getAlignment().getHiddenSequences().getWidth(),n>d&&(d=n));k.setEndRes(k.getEndRes()+b-this.lastres);d=d+b-this.lastres}else{this.endEditing();return}}else if(!a){j=0;for(m=g;j<m.length&&((n=m[j])||1);j++)for(c=b;c<this.lastres;c++)if(!(n.getLength()<=c)&&!jalview.util.Comparison.isGap(n.getCharAt(c))){this.endEditing();return}}if(a)if(e&&-1!=d)for(c=this.lastres;c<b;c++)this.insertChar(c,g,d);else this.editCommand.appendEdit(jalview.commands.EditCommand.Action.INSERT_GAP,
g,b,b-this.lastres,this.av.getAlignment(),!0);else if(e&&-1!=d)for(c=this.lastres;c>b;c--)this.deleteChar(b,g,d);else this.editCommand.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,g,b,this.lastres-b,this.av.getAlignment(),!0)}else if(a)if(e&&-1!=d)for(c=this.lastres;c<b;c++)this.insertChar(c,E(-1,[g]),d);else this.editCommand.appendEdit(jalview.commands.EditCommand.Action.INSERT_GAP,E(-1,[g]),this.lastres,b-this.lastres,this.av.getAlignment(),!0);else if(e&&-1!=d)for(c=this.lastres;c>
b;c--){if(!jalview.util.Comparison.isGap(g.getCharAt(b))){this.endEditing();break}this.deleteChar(b,E(-1,[g]),d)}else{e=0;for(k=b;k<this.lastres&&jalview.util.Comparison.isGap(g.getCharAt(k));k++)e++;0<e&&this.editCommand.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,E(-1,[g]),b,e,this.av.getAlignment(),!0)}this.lastres=b;this.seqCanvas.repaint()},"~B,~N");d(c$,"insertChar",function(a,b,c){for(var d=c,e=0;e<b.length;e++){for(d=c;d>a&&!jalview.util.Comparison.isGap(b[e].getCharAt(d));d--);
if(d<=a){this.endEditing();return}}this.editCommand.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,b,d,1,this.av.getAlignment(),!0);this.editCommand.appendEdit(jalview.commands.EditCommand.Action.INSERT_GAP,b,a,1,this.av.getAlignment(),!0)},"~N,~A,~N");d(c$,"deleteChar",function(a,b,c){this.editCommand.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,b,a,1,this.av.getAlignment(),!0);this.editCommand.appendEdit(jalview.commands.EditCommand.Action.INSERT_GAP,b,c,1,this.av.getAlignment(),
!0)},"~N,~A,~N");d(c$,"doMousePressedDefineMode",function(a){null!=this.scrollThread&&(this.scrollThread.running=!1,this.scrollThread=null);var b=this.findRes(a),c=this.findSeq(a);this.oldSeq=c;this.startWrapBlock=this.wrappedBlock;if(-1!=c){var d=this.av.getAlignment().getSequenceAt(c);if(!(null==d||b>d.getLength())){this.stretchGroup=this.av.getSelectionGroup();if(null==this.stretchGroup)this.stretchGroup=this.av.getAlignment().findGroup(d),null!=this.stretchGroup&&b>this.stretchGroup.getStartRes()&&
b<this.stretchGroup.getEndRes()?this.av.setSelectionGroup(this.stretchGroup):this.stretchGroup=null;else if(!this.stretchGroup.getSequences(null).contains(d)||this.stretchGroup.getStartRes()>b||this.stretchGroup.getEndRes()<b){this.stretchGroup=null;var e=this.av.getAlignment().findAllGroups(d);if(null!=e)for(c=0;c<e.length;c++)if(e[c].getStartRes()<=b&&e[c].getEndRes()>=b){this.stretchGroup=e[c];break}this.av.setSelectionGroup(this.stretchGroup)}if(4==(a.getModifiers()&4)){b=this.findFeaturesAtRes(d,
d.findPosition(b));d=null;if(null!=b)for(c=0;c<b.length;c++)if(null!=b[c].links){null==d&&(d=new java.util.Vector);for(e=0;e<b[c].links.size();e++)d.addElement(b[c].links.elementAt(e))}c=new jalview.appletgui.APopupMenu(this.ap,null,d);this.add(c);c.show(this,a.getX(),a.getY())}else this.av.cursorMode?(this.seqCanvas.cursorX=this.findRes(a),this.seqCanvas.cursorY=this.findSeq(a),this.seqCanvas.repaint()):null==this.stretchGroup&&(a=new jalview.datamodel.SequenceGroup,a.setStartRes(b),a.setEndRes(b),
a.addSequence(d,!1),this.av.setSelectionGroup(a),this.stretchGroup=a,this.av.getConservationSelected()&&jalview.appletgui.SliderPanel.setConservationSlider(this.ap,this.av.getGlobalColourScheme(),"Background"),this.av.getAbovePIDThreshold()&&jalview.appletgui.SliderPanel.setPIDSliderSource(this.ap,this.av.getGlobalColourScheme(),"Background"))}}},"java.awt.event.MouseEvent");d(c$,"doMouseReleasedDefineMode",function(){null!=this.stretchGroup&&(this.stretchGroup.recalcConservation(),null!=this.stretchGroup.cs&&
(this.stretchGroup.cs.alignmentChanged(this.stretchGroup,this.av.getHiddenRepSequences()),this.stretchGroup.cs.conservationApplied()?jalview.appletgui.SliderPanel.setConservationSlider(this.ap,this.stretchGroup.cs,this.stretchGroup.getName()):jalview.appletgui.SliderPanel.setPIDSliderSource(this.ap,this.stretchGroup.cs,this.stretchGroup.getName())),this.changeStartRes=this.changeEndRes=!1,this.stretchGroup=null,jalview.appletgui.PaintRefresher.Refresh(this.ap,this.av.getSequenceSetId()),this.ap.paintAlignment(!0),
this.av.sendSelection())},"java.awt.event.MouseEvent");d(c$,"doMouseDraggedDefineMode",function(a){var b=this.findRes(a),c=this.findSeq(a);if(this.wrappedBlock==this.startWrapBlock&&null!=this.stretchGroup){this.mouseDragging=!0;c>this.av.getAlignment().getHeight()&&(c=this.av.getAlignment().getHeight()-1);b>=this.av.getAlignment().getWidth()&&(b=this.av.getAlignment().getWidth()-1);this.stretchGroup.getEndRes()==b?this.changeEndRes=!0:this.stretchGroup.getStartRes()==b&&(this.changeStartRes=!0);
0>b&&(b=0);this.changeEndRes?b>this.stretchGroup.getStartRes()-1&&this.stretchGroup.setEndRes(b):this.changeStartRes&&b<this.stretchGroup.getEndRes()+1&&this.stretchGroup.setStartRes(b);var d=0;for(c>this.oldSeq?d=1:c<this.oldSeq&&(d=-1);c!=this.oldSeq&&-1<this.oldSeq&&c<this.av.getAlignment().getHeight();){var e=this.av.getAlignment().getSequenceAt(this.oldSeq);this.oldSeq+=d;if(0>this.oldSeq)break;var k=this.av.getAlignment().getSequenceAt(this.oldSeq);this.stretchGroup.getSequences(null).contains(k)?
this.stretchGroup.deleteSequence(e,!1):(null!=e&&this.stretchGroup.addSequence(e,!1),this.stretchGroup.addSequence(k,!1))}0>this.oldSeq&&(this.oldSeq=-1);(b>this.av.endRes||b<this.av.startRes||c<this.av.startSeq||c>this.av.endSeq)&&this.mouseExited(a);null!=this.scrollThread&&this.scrollThread.setEvent(a);this.seqCanvas.repaint()}},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){0>this.oldSeq&&(this.oldSeq=0);null!=this.scrollThread&&(this.scrollThread.running=!1,this.scrollThread=null)},
"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){!this.av.getWrapAlignment()&&(this.mouseDragging&&null==this.scrollThread)&&(this.scrollThread=C(jalview.appletgui.SeqPanel.ScrollThread,this,null))},"java.awt.event.MouseEvent");d(c$,"scrollCanvas",function(a){null==a?(null!=this.scrollThread&&(this.scrollThread.running=!1,this.scrollThread=null),this.mouseDragging=!1):(null==this.scrollThread&&(this.scrollThread=C(jalview.appletgui.SeqPanel.ScrollThread,this,null)),this.mouseDragging=!0,
this.scrollThread.setEvent(a))},"java.awt.event.MouseEvent");e(c$,"selection",function(a,b,c){if(!(null!=this.av&&(this.av===c||!this.av.followSelection||v(c,jalview.appletgui.AlignViewport)&&c.getSequenceSetId().equals(this.av.getSequenceSetId())))&&!this.selectionFromTranslation(a,b,c)){var d=!1;c=!0;if(null==this.av.getSelectionGroup()||!this.av.isSelectionGroupChanged(!0)){d=null;if(null!=a&&0<a.getSize()){if(null==this.av.getAlignment()){System.out.println("Selection message: alignviewport av SeqSetId="+
this.av.getSequenceSetId()+" ViewId="+this.av.getViewId()+" 's alignment is NULL! returning immediatly.");return}d=a.intersect(this.av.getAlignment(),this.av.hasHiddenRows()?this.av.getHiddenRepSequences():null);if((null==d||0==d.getSize())&&(null==b||0==b.size()))c=!1}null!=d&&0<d.getSize()?this.av.setSelectionGroup(d):this.av.setSelectionGroup(null);d=this.av.isSelectionGroupChanged(!0)}if(c&&(null==this.av.getColumnSelection()||!this.av.isColSelChanged(!0)))null==b||0==b.size()?null!=this.av.getColumnSelection()&&
this.av.getColumnSelection().clear():null==this.av.getColumnSelection()?this.av.setColumnSelection(new jalview.datamodel.ColumnSelection(b)):this.av.getColumnSelection().setElementsFrom(b),d=(new Boolean(d|this.av.isColSelChanged(!0))).valueOf();c&&(this.av.hasHiddenColumns()&&(null==this.av.getColumnSelection()||null==this.av.getColumnSelection().getHiddenColumns()))&&System.err.println("Bad things");d&&(this.ap.scalePanelHolder.repaint(),this.ap.repaint())}},"jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource");
d(c$,"scrollTo",function(a,b){a=0>a?this.ap.av.startSeq:a;b=0>b?this.ap.av.startRes:b;this.ap.scrollTo(b,b,a,!0,!0)},"~N,~N");d(c$,"scrollToRow",function(a){a=0>a?this.ap.av.startSeq:a;this.ap.scrollTo(this.ap.av.startRes,this.ap.av.startRes,a,!0,!0)},"~N");d(c$,"scrollToColumn",function(a){a=0>a?this.ap.av.startRes:a;this.ap.scrollTo(a,a,this.ap.av.startSeq,!0,!0)},"~N");d(c$,"selectionFromTranslation",function(a,b,c){if(!v(c,jalview.api.AlignViewportI)||c.getCodingComplement()!==this.av&&this.av.getCodingComplement()!==
c)return!1;a=jalview.util.MappingUtils.mapSequenceGroup(a,c,this.av);this.av.setSelectionGroup(a);this.av.isSelectionGroupChanged(!0);b=jalview.util.MappingUtils.mapColumnSelection(b,c,this.av);this.av.setColumnSelection(b);this.av.isColSelChanged(!0);this.ap.scalePanelHolder.repaint();this.ap.repaint();return!0},"jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection,jalview.structure.SelectionSource");c$.$SeqPanel$ScrollThread$=function(){A(self.c$);c$=s(function(){O(this,arguments);
this.evt=null;this.running=!1;r(this,arguments)},jalview.appletgui.SeqPanel,"ScrollThread",Thread);m(c$,function(){t(this,jalview.appletgui.SeqPanel.ScrollThread,[]);this.start()});d(c$,"setEvent",function(a){this.evt=a},"java.awt.event.MouseEvent");d(c$,"stopScrolling",function(){this.running=!1});e(c$,"run",function(){for(this.running=!0;this.running;){null!=this.evt&&(this.b$["jalview.appletgui.SeqPanel"].mouseDragging&&(0>this.evt.getY()&&0<this.b$["jalview.appletgui.SeqPanel"].av.getStartSeq())&&
(this.running=this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp(!0)),this.b$["jalview.appletgui.SeqPanel"].mouseDragging&&(this.evt.getY()>=this.b$["jalview.appletgui.SeqPanel"].getSize().height&&this.b$["jalview.appletgui.SeqPanel"].av.getAlignment().getHeight()>this.b$["jalview.appletgui.SeqPanel"].av.getEndSeq())&&(this.running=this.b$["jalview.appletgui.SeqPanel"].ap.scrollUp(!1)),this.b$["jalview.appletgui.SeqPanel"].mouseDragging&&0>this.evt.getX()?this.running=this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight(!1):
this.b$["jalview.appletgui.SeqPanel"].mouseDragging&&this.evt.getX()>=this.b$["jalview.appletgui.SeqPanel"].getSize().width&&(this.running=this.b$["jalview.appletgui.SeqPanel"].ap.scrollRight(!0)));try{Thread.sleep(75)}catch(a){if(!y(a,Exception))throw a;}}});c$=z()}});p("jalview.structure");M(jalview.structure,"SelectionListener");p("jalview.appletgui");q(["awt2swing.Panel"],"jalview.appletgui.SeqCanvas","awt2swing.Util jalview.appletgui.AnnotationPanel $.FeatureRenderer $.PaintRefresher $.SequenceRenderer jalview.util.Comparison java.awt.Color".split(" "),
function(){c$=s(function(){this.gg=this.img=this.sr=this.fr=null;this.imgHeight=this.imgWidth=0;this.searchResults=this.av=null;this.$fastPaint=!1;this.LABEL_EAST=this.LABEL_WEST=this.lastsr=this.avcharWidth=this.avcharHeight=this.cursorY=this.cursorX=0;this.annotations=null;r(this,arguments)},jalview.appletgui,"SeqCanvas",awt2swing.Panel);m(c$,function(a){t(this,jalview.appletgui.SeqCanvas,[]);this.av=a;this.fr=new jalview.appletgui.FeatureRenderer(a);this.sr=new jalview.appletgui.SequenceRenderer(a);
jalview.appletgui.PaintRefresher.Register(this,a.getSequenceSetId());this.updateViewport()},"jalview.appletgui.AlignViewport");d(c$,"updateViewport",function(){this.avcharHeight=this.av.getCharHeight();this.avcharWidth=this.av.getCharWidth()});d(c$,"getViewport",function(){return this.av});d(c$,"getFeatureRenderer",function(){return this.fr});d(c$,"getSequenceRenderer",function(){return this.sr});d(c$,"drawNorthScale",function(a,b,c,d){var e=b-b%10+10;for(a.setColor(java.awt.Color.black);e<c;e+=10){var k=
e;this.av.hasHiddenColumns()&&(k=this.av.getColumnSelection().adjustForHiddenColumns(k));awt2swing.Util.drawString(a,String.valueOf(k),(e-b-1)*this.avcharWidth,d-F(this.avcharHeight/2));a.drawLine((e-b-1)*this.avcharWidth+F(this.avcharWidth/2),d+2-F(this.avcharHeight/2),(e-b-1)*this.avcharWidth+F(this.avcharWidth/2),d-2)}},"java.awt.Graphics,~N,~N,~N");d(c$,"drawWestScale",function(a,b,c,d){var e=this.getFontMetrics(this.av.getFont());d+=this.avcharHeight;this.av.hasHiddenColumns()&&(b=this.av.getColumnSelection().adjustForHiddenColumns(b),
c=this.av.getColumnSelection().adjustForHiddenColumns(c));var k=this.av.getAlignment().getWidth();this.av.hasHiddenColumns()&&this.av.getColumnSelection().findColumnPosition(k);for(k=0;k<this.av.getAlignment().getHeight();k++){for(var g=this.av.getAlignment().getSequenceAt(k),h=b,j=-1;h<c;)if(jalview.util.Comparison.isGap(g.getCharAt(h)))h++;else{j=this.av.getAlignment().getSequenceAt(k).findPosition(h);break}-1!=j&&(g=this.LABEL_WEST-e.stringWidth(String.valueOf(j))-F(this.avcharWidth/2),awt2swing.Util.drawString(a,
j+"",g,d+k*this.avcharHeight-F(this.avcharHeight/5)))}},"java.awt.Graphics,~N,~N,~N");d(c$,"drawEastScale",function(a,b,c,d){d+=this.avcharHeight;this.av.hasHiddenColumns()&&(c=this.av.getColumnSelection().adjustForHiddenColumns(c));for(var e,k=0;k<this.av.getAlignment().getHeight();k++){e=this.av.getAlignment().getSequenceAt(k);for(var g=c,h=-1;g>b;)if(jalview.util.Comparison.isGap(e.getCharAt(g)))g--;else{h=e.findPosition(g);break}-1!=h&&awt2swing.Util.drawString(a,String.valueOf(h),0,d+k*this.avcharHeight-
F(this.avcharHeight/5))}},"java.awt.Graphics,~N,~N,~N");d(c$,"fastPaint",function(a,b){if(!(this.$fastPaint||null==this.gg)){this.updateViewport();this.lastsr+a!=this.av.startRes&&(a=this.av.startRes-this.lastsr);this.lastsr=this.av.startRes;this.$fastPaint=!0;this.gg.copyArea(a*this.avcharWidth,b*this.avcharHeight,this.imgWidth-a*this.avcharWidth,this.imgHeight-b*this.avcharHeight,-a*this.avcharWidth,-b*this.avcharHeight);var c=this.av.startRes,d=this.av.endRes,e=this.av.startSeq,k=this.av.endSeq,
g=0,h=0;0<a?(g=(d-c-a)*this.avcharWidth,c=d-a):0>a?d=c-a:0<b?(e=k-b,e<this.av.startSeq?e=this.av.startSeq:h=this.imgHeight-b*this.avcharHeight):0>b&&(k=e-b,k>this.av.endSeq&&(k=this.av.endSeq));this.gg.translate(g,h);this.drawPanel(this.gg,c,d,e,k,0);this.gg.translate(-g,-h);this.repaint()}},"~N,~N");e(c$,"paintComponent",function(a){if(null!=this.img&&(this.$fastPaint||this.getSize().width!=a.getClipBounds().width||this.getSize().height!=a.getClipBounds().height))a.drawImage(this.img,0,0,this),this.$fastPaint=
!1;else if(this.$fastPaint)a.drawImage(this.img,0,0,this),this.$fastPaint=!1;else if(this.updateViewport(),this.imgWidth=this.getSize().width,this.imgHeight=this.getSize().height,this.imgWidth-=this.imgWidth%this.avcharWidth,this.imgHeight-=this.imgHeight%this.avcharHeight,!(1>this.imgWidth||1>this.imgHeight)){if(null==this.img||this.imgWidth!=this.img.getWidth(this)||this.imgHeight!=this.img.getHeight(this))this.img=this.createImage(this.imgWidth,this.imgHeight),this.gg=this.img.getGraphics(),this.gg.setFont(this.av.getFont());
this.gg.setColor(java.awt.Color.white);this.gg.fillRect(0,0,this.imgWidth,this.imgHeight);this.av.getWrapAlignment()?this.drawWrappedPanel(this.gg,this.imgWidth,this.imgHeight,this.av.startRes):this.drawPanel(this.gg,this.av.startRes,this.av.endRes,this.av.startSeq,this.av.endSeq,0);a.drawImage(this.img,0,0,this)}},"java.awt.Graphics");d(c$,"getWrappedCanvasWidth",function(a){a-=a%this.av.getCharWidth();var b=this.getFontMetrics(this.av.getFont());this.LABEL_WEST=this.LABEL_EAST=0;this.av.getScaleRightWrapped()&&
(this.LABEL_EAST=b.stringWidth(this.getMask()));this.av.getScaleLeftWrapped()&&(this.LABEL_WEST=b.stringWidth(this.getMask()));return F((a-this.LABEL_EAST-this.LABEL_WEST)/this.av.getCharWidth())},"~N");d(c$,"getMask",function(){for(var a="0",b=0,c,d=this.av.getAlignment(),e=0;e<d.getHeight();e++)c=d.getSequenceAt(e).getEnd(),c>b&&(b=c);for(e=b;0<e;e/=10)a+="0";return a});d(c$,"drawWrappedPanel",function(a,b,c,d){var e=this.av.getAlignment(),k=this.getFontMetrics(this.av.getFont());this.av.getScaleRightWrapped()&&
(this.LABEL_EAST=k.stringWidth(this.getMask()));this.av.getScaleLeftWrapped()&&(this.LABEL_WEST=k.stringWidth(this.getMask()));k=this.avcharHeight;this.av.getScaleAboveWrapped()&&(k+=this.avcharHeight);var g=F((b-this.LABEL_EAST-this.LABEL_WEST)/this.avcharWidth),h=this.av.getAlignment().getHeight()*this.avcharHeight;this.av.setWrappedWidth(g);this.av.endRes=this.av.startRes+g;var j,n=k,m=this.av.getAlignment().getWidth()-1;for(this.av.hasHiddenColumns()&&(m=this.av.getColumnSelection().findColumnPosition(m)-
1);n<=c&&d<m;){j=d+g-1;j>m&&(j=m);a.setColor(java.awt.Color.black);this.av.getScaleLeftWrapped()&&this.drawWestScale(a,d,j,n);this.av.getScaleRightWrapped()&&(a.translate(b-this.LABEL_EAST,0),this.drawEastScale(a,d,j,n),a.translate(-(b-this.LABEL_EAST),0));a.translate(this.LABEL_WEST,0);this.av.getScaleAboveWrapped()&&this.drawNorthScale(a,d,j,n);if(this.av.hasHiddenColumns()&&this.av.getShowHiddenMarkers()){a.setColor(java.awt.Color.blue);for(var p,q=0;q<this.av.getColumnSelection().getHiddenColumns().size();q++)p=
this.av.getColumnSelection().findHiddenRegionPosition(q)-d,0>p||p>j-d||this.gg.fillPolygon(w(-1,[p*this.avcharWidth-F(this.avcharHeight/4),p*this.avcharWidth+F(this.avcharHeight/4),p*this.avcharWidth]),w(-1,[n-F(this.avcharHeight/2),n-F(this.avcharHeight/2),n-F(this.avcharHeight/2)+8]),3)}null==a.getClip()&&a.setClip(0,0,g*this.avcharWidth,c);this.drawPanel(a,d,j,0,e.getHeight(),n);a.setClip(null);this.av.isShowAnnotation()&&(a.translate(0,h+n+4),null==this.annotations&&(this.annotations=new jalview.appletgui.AnnotationPanel(this.av)),
this.annotations.drawComponent(a,d,j+1),a.translate(0,-h-n-4));a.translate(-this.LABEL_WEST,0);n+=h+this.getAnnotationHeight()+k;d+=g}},"java.awt.Graphics,~N,~N,~N");d(c$,"getAnnotationHeight",function(){if(!this.av.isShowAnnotation())return 0;null==this.annotations&&(this.annotations=new jalview.appletgui.AnnotationPanel(this.av));return this.annotations.adjustPanelHeight()});d(c$,"drawPanel",function(a,b,c,d,e,k){if(this.av.hasHiddenColumns()){var g=0,h=b,j=c;if(this.av.hasHiddenColumns())for(var n,
m=this.av.getColumnSelection().getHiddenColumns().iterator();m.hasNext()&&((n=m.next())||1);){var j=n[0],p=n[1];j<=h?h+=p-j+1:(j-=1,a.translate(g*this.avcharWidth,0),this.draw(a,h,j,d,e,k),this.av.getShowHiddenMarkers()&&(a.setColor(java.awt.Color.blue),a.drawLine((j-h+1)*this.avcharWidth-1,0+k,(j-h+1)*this.avcharWidth-1,(e-d)*this.avcharHeight+k)),a.translate(-g*this.avcharWidth,0),g+=j-h+1,h=p+1)}g<=c-b&&(j=h+(c-b)-g,a.translate(g*this.avcharWidth,0),this.draw(a,h,j,d,e,k),a.translate(-g*this.avcharWidth,
0))}else this.draw(a,b,c,d,e,k)},"java.awt.Graphics,~N,~N,~N,~N,~N");d(c$,"draw",function(a,b,c,d,e,k){a.setFont(this.av.getFont());this.sr.prepare(a,this.av.isRenderGaps());this.updateViewport();for(var g,h=d;h<e;h++)if(g=this.av.getAlignment().getSequenceAt(h),null!=g){this.sr.drawSequence(g,this.av.getAlignment().findAllGroups(g),b,c,k+(h-d)*this.avcharHeight);this.av.isShowSequenceFeatures()&&this.fr.drawSequence(a,g,b,c,k+(h-d)*this.avcharHeight);if(null!=this.searchResults){var j=this.searchResults.getResults(g,
b,c);if(null!=j)for(var n=0;n<j.length;n+=2)this.sr.drawHighlightedText(g,j[n],j[n+1],(j[n]-b)*this.avcharWidth,k+(h-d)*this.avcharHeight)}this.av.cursorMode&&(this.cursorY==h&&this.cursorX>=b&&this.cursorX<=c)&&this.sr.drawCursor(g,this.cursorX,(this.cursorX-b)*this.avcharWidth,k+(h-d)*this.avcharHeight)}(null!=this.av.getSelectionGroup()||0<this.av.getAlignment().getGroups().size())&&this.drawGroupsBoundaries(a,b,c,d,e,k)},"java.awt.Graphics,~N,~N,~N,~N,~N");d(c$,"drawGroupsBoundaries",function(a,
b,c,d,e,k){var g=this.av.getSelectionGroup(),h=-1,j=-1,n=-1,m=-1;null==g&&0<this.av.getAlignment().getGroups().size()&&(g=this.av.getAlignment().getGroups().get(0),m=0);if(null!=g){do{for(var p=-1,q=0,r=!1,s=-1,t=-1,v=this.av.getAlignment().getHeight()-1,q=d;q<e;q++)if(h=(g.getStartRes()-b)*this.avcharWidth,j=k+(q-d)*this.avcharHeight,n=(g.getEndRes()+1-g.getStartRes())*this.avcharWidth-1,!(0>h+n||h>this.imgWidth))if(h<=(c-b)*this.avcharWidth&&g.getSequences(null).contains(this.av.getAlignment().getSequenceAt(q))){if(-1==
t&&(q>=v||!g.getSequences(null).contains(this.av.getAlignment().getSequenceAt(q+1))))t=j+this.avcharHeight;if(!r){if(-1==s&&0==q||!g.getSequences(null).contains(this.av.getAlignment().getSequenceAt(q-1)))s=j;p=j;r=!0;g===this.av.getSelectionGroup()?a.setColor(java.awt.Color.red):a.setColor(g.getOutlineColour())}}else r&&(0<=h&&h<this.imgWidth&&a.drawLine(h,p,h,j),h+n<this.imgWidth&&a.drawLine(h+n,p,h+n,j),0>h&&(n+=h,h=0),h+n>this.imgWidth?n=this.imgWidth:h+n>=(c-b+1)*this.avcharWidth&&(n=(c-b+1)*
this.avcharWidth),-1!=s&&(a.drawLine(h,s,h+n,s),s=-1),-1!=t&&(a.drawLine(h,t,h+n,t),t=-1),r=!1);r&&(j=k+(q-d)*this.avcharHeight,0<=h&&h<this.imgWidth&&a.drawLine(h,p,h,j),h+n<this.imgWidth&&a.drawLine(h+n,p,h+n,j),0>h&&(n+=h,h=0),h+n>this.imgWidth?n=this.imgWidth:h+n>=(c-b+1)*this.avcharWidth&&(n=(c-b+1)*this.avcharWidth),-1!=s&&a.drawLine(h,s,h+n,s),-1!=t&&a.drawLine(h,t-1,h+n,t-1));m++;if(m>=this.av.getAlignment().getGroups().size())break;g=this.av.getAlignment().getGroups().get(m)}while(m<this.av.getAlignment().getGroups().size())
}},"java.awt.Graphics,~N,~N,~N,~N,~N");d(c$,"highlightSearchResults",function(a){this.searchResults=a;this.repaint()},"jalview.datamodel.SearchResults")});p("jalview.appletgui");q(["jalview.api.SequenceRenderer"],"jalview.appletgui.SequenceRenderer",["awt2swing.Util","jalview.util.Comparison","java.awt.Color","$.Font"],function(){c$=s(function(){this.fm=this.av=null;this.renderGaps=!0;this.graphics=this.resBoxColour=this.allGroups=this.currentSequenceGroup=null;this.forOverview=!1;r(this,arguments)},
jalview.appletgui,"SequenceRenderer",null,jalview.api.SequenceRenderer);m(c$,function(a){this.av=a},"jalview.appletgui.AlignViewport");d(c$,"prepare",function(a,b){this.graphics=a;this.fm=a.getFontMetrics();this.renderGaps=b},"java.awt.Graphics,~B");e(c$,"getResidueBoxColour",function(a,b){this.allGroups=this.av.getAlignment().findAllGroups(a);this.inCurrentSequenceGroup(b)?this.currentSequenceGroup.getDisplayBoxes()&&this.getBoxColour(this.currentSequenceGroup.cs,a,b):this.av.getShowBoxes()&&this.getBoxColour(this.av.getGlobalColourScheme(),
a,b);return this.resBoxColour},"jalview.datamodel.SequenceI,~N");e(c$,"getResidueColour",function(a,b,c){var d=this.getResidueBoxColour(a,b);null!=c&&(d=c.findFeatureColour(d,a,b));return d},"jalview.datamodel.SequenceI,~N,jalview.api.FeatureRenderer");d(c$,"getBoxColour",function(a,b,c){this.resBoxColour=null!=a?a.findColourSeq(b.getCharAt(c),c,b):this.forOverview&&!jalview.util.Comparison.isGap(b.getCharAt(c))?java.awt.Color.lightGray:java.awt.Color.white},"jalview.schemes.ColourSchemeI,jalview.datamodel.SequenceI,~N");
d(c$,"findSequenceColour",function(a,b){this.allGroups=this.av.getAlignment().findAllGroups(a);this.drawBoxes(a,b,b,0);return this.resBoxColour},"jalview.datamodel.SequenceI,~N");d(c$,"drawSequence",function(a,b,c,d,e){null!=a&&(this.allGroups=b,this.drawBoxes(a,c,d,e),this.av.validCharWidth&&this.drawText(a,c,d,e))},"jalview.datamodel.SequenceI,~A,~N,~N,~N");d(c$,"drawBoxes",function(a,b,c,d){for(var e=b,k=a.getLength(),g=-1,h=this.av.getCharWidth(),j=this.av.getCharWidth(),n=this.av.getCharHeight(),
m=null;e<=c;)this.resBoxColour=java.awt.Color.white,e<k&&(this.inCurrentSequenceGroup(e)?this.currentSequenceGroup.getDisplayBoxes()&&this.getBoxColour(this.currentSequenceGroup.cs,a,e):this.av.getShowBoxes()&&this.getBoxColour(this.av.getGlobalColourScheme(),a,e)),this.resBoxColour!==m?(null!=m&&this.graphics.fillRect(j*(g-b),d,h,n),this.graphics.setColor(this.resBoxColour),g=e,h=j,m=this.resBoxColour):h+=j,e++;this.graphics.fillRect(j*(g-b),d,h,n)},"jalview.datamodel.SequenceI,~N,~N,~N");d(c$,"drawText",
function(a,b,c,d){var e=this.av.getCharWidth(),k=this.av.getCharHeight(),g=null,h=!1;this.av.isUpperCasebold()&&(g=new java.awt.Font(this.av.getFont().getName(),1,k),this.graphics.setFont(this.av.getFont()));d+=k-F(k/5);k=0;c+1>=a.getLength()&&(c=a.getLength()-1);for(var j=" ",n=this.av.isDisplayReferenceSeq(),m=b;m<=c;m++)if(this.graphics.setColor(java.awt.Color.black),j=a.getCharAt(m),this.renderGaps||!jalview.util.Comparison.isGap(j)){if(this.inCurrentSequenceGroup(m)){if(!this.currentSequenceGroup.getDisplayText())continue;
this.currentSequenceGroup.getColourText()&&(this.getBoxColour(this.currentSequenceGroup.cs,a,m),this.graphics.setColor(this.resBoxColour.darker()));this.currentSequenceGroup.getShowNonconserved()&&(j=this.getDisplayChar(n,m,j,"."))}else{if(!this.av.getShowText())continue;this.av.getColourText()&&(this.getBoxColour(this.av.getGlobalColourScheme(),a,m),this.av.getShowBoxes()?this.graphics.setColor(this.resBoxColour.darker()):this.graphics.setColor(this.resBoxColour));this.av.getShowUnconserved()&&(j=
this.getDisplayChar(n,m,j,"."))}this.av.isUpperCasebold()&&(this.fm=this.graphics.getFontMetrics(),"A"<=j&&"Z">=j?(h||this.graphics.setFont(g),h=!0):h&&(this.graphics.setFont(this.av.font),h=!1));k=F((e-this.fm.charWidth(j))/2);awt2swing.Util.drawString(this.graphics,String.valueOf(j),k+e*(m-b),d)}},"jalview.datamodel.SequenceI,~N,~N,~N");d(c$,"getDisplayChar",function(a,b,c,d){a=a?this.av.getAlignment().getSeqrep().getCharAt(b):this.av.getAlignmentConsensusAnnotation().annotations[b].displayCharacter.charAt(0);
"-"!=a&&c==a&&(c=d);return c},"~B,~N,~S,~S");d(c$,"inCurrentSequenceGroup",function(a){if(null==this.allGroups)return!1;for(var b=0;b<this.allGroups.length;b++)if(this.allGroups[b].getStartRes()<=a&&this.allGroups[b].getEndRes()>=a)return this.currentSequenceGroup=this.allGroups[b],!0;return!1},"~N");d(c$,"drawHighlightedText",function(a,b,c,d,e){var k=this.av.getCharWidth(),g=this.av.getCharHeight(),h=F(g/5),j=0;this.graphics.setColor(java.awt.Color.black);this.graphics.fillRect(d,e,k*(c-b+1),g);
this.graphics.setColor(java.awt.Color.white);var n="~";if(this.av.validCharWidth)for(var m=b;m<=c;m++)m<a.getLength()&&(n=a.getCharAt(m)),j=F((k-this.fm.charWidth(n))/2),awt2swing.Util.drawString(this.graphics,String.valueOf(n),j+d+k*(m-b),e+g-h)},"jalview.datamodel.SequenceI,~N,~N,~N,~N");d(c$,"drawCursor",function(a,b,c,d){var e=F(this.av.getCharHeight()/5),k=0;this.graphics.setColor(java.awt.Color.black);this.graphics.fillRect(c,d,this.av.getCharWidth(),this.av.getCharHeight());this.graphics.setColor(java.awt.Color.white);
this.graphics.setColor(java.awt.Color.white);a=a.getCharAt(b);this.av.validCharWidth&&(k=F((this.av.getCharWidth()-this.fm.charWidth(a))/2),awt2swing.Util.drawString(this.graphics,String.valueOf(a),k+c,d+this.av.getCharHeight()-e))},"jalview.datamodel.SequenceI,~N,~N,~N")});p("jalview.api");M(jalview.api,"SequenceRenderer");p("jalview.appletgui");q("awt2swing.Panel jalview.appletgui.AnnotationRowFilter $.TitledPanel java.awt.event.ActionListener $.AdjustmentListener $.ItemListener $.MouseListener awt2swing.Checkbox $.Choice $.TextField java.awt.BorderLayout $.CardLayout".split(" "),
"jalview.appletgui.AnnotationColumnChooser","awt2swing.Frame jalview.bin.JalviewLite jalview.datamodel.ColumnSelection $.GraphLine jalview.util.MessageManager jalview.viewmodel.annotationfilter.AnnotationFilterParameter java.awt.Color $.Dimension java.awt.event.MouseAdapter $.TextListener java.lang.Float java.util.Vector javax.swing.JPanel".split(" "),function(){c$=s(function(){this.ngFurtherActionPanel=this.gFurtherActionPanel=this.currentFurtherActionPanel=this.ngSearchPanel=this.gSearchPanel=this.currentSearchPanel=
this.currentStructureFilterPanel=this.ngStructureFilterPanel=this.gStructureFilterPanel=this.threshold=this.ngBorderLayout=this.gBorderLayout=this.borderLayout1=this.annotationComboBoxPanel=this.graphFilterView=this.noGraphFilterView=this.switchableViewsLayout=this.switchableViewsPanel=this.thresholdPanel=this.actionPanel=this.annotations=null;this.actionOption=1;this.oldColumnSelection=null;H("jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel")||jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$FurtherActionPanel$();
H("jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel")||jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$StructureFilterPanel$();H("jalview.appletgui.AnnotationColumnChooser.SearchPanel")||jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$SearchPanel$();r(this,arguments)},jalview.appletgui,"AnnotationColumnChooser",jalview.appletgui.AnnotationRowFilter,[java.awt.event.ActionListener,java.awt.event.AdjustmentListener,java.awt.event.ItemListener,java.awt.event.MouseListener]);
J(c$,function(){this.annotations=new awt2swing.Choice;this.actionPanel=new awt2swing.Panel;this.thresholdPanel=new jalview.appletgui.TitledPanel;this.switchableViewsPanel=new awt2swing.Panel(new java.awt.CardLayout);this.switchableViewsLayout=this.switchableViewsPanel.getLayout();this.noGraphFilterView=new awt2swing.Panel;this.graphFilterView=new awt2swing.Panel;this.annotationComboBoxPanel=new awt2swing.Panel;this.borderLayout1=new java.awt.BorderLayout;this.gBorderLayout=new java.awt.BorderLayout;
this.ngBorderLayout=new java.awt.BorderLayout;this.threshold=new awt2swing.Choice});m(c$,function(){t(this,jalview.appletgui.AnnotationColumnChooser,[]);try{this.jbInit()}catch(a){if(y(a,Exception))a.printStackTrace();else throw a;}});m(c$,function(a,b){t(this,jalview.appletgui.AnnotationColumnChooser,[a,b]);this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("label.select_by_annotation"),520,215);this.slider.addAdjustmentListener(this);
this.slider.addMouseListener(this);if(null!=a.getAlignment().getAlignmentAnnotation()){this.setOldColumnSelection(a.getColumnSelection());this.adjusting=!0;for(var c=new java.util.Vector,d=1,e=0;e<a.getAlignment().getAlignmentAnnotation().length;e++){var k=a.getAlignment().getAlignmentAnnotation()[e].label;c.contains(k)?c.addElement(k+"_"+d++):c.addElement(k)}for(e=0;e<c.size();e++)this.annotations.addItem(c.elementAt(e).toString());this.populateThresholdComboBox(this.threshold);null!=a.getAnnotationColumnSelectionState()&&
(this.currentSearchPanel=a.getAnnotationColumnSelectionState().getCurrentSearchPanel(),this.currentStructureFilterPanel=a.getAnnotationColumnSelectionState().getCurrentStructureFilterPanel(),this.annotations.select(new Integer(a.getAnnotationColumnSelectionState().getAnnotations().getSelectedIndex())),this.threshold.select(new Integer(a.getAnnotationColumnSelectionState().getThreshold().getSelectedIndex())),this.actionOption=a.getAnnotationColumnSelectionState().getActionOption());try{this.jbInit()}catch(g){if(!y(g,
Exception))throw g;}this.adjusting=!1;this.updateView();this.frame.invalidate();this.frame.pack()}},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");d(c$,"jbInit",function(){this.ok.setLabel(jalview.util.MessageManager.getString("action.ok"));this.cancel.setLabel(jalview.util.MessageManager.getString("action.cancel"));this.thresholdValue.setEnabled(!1);this.thresholdValue.setColumns(7);this.ok.addActionListener(this);this.cancel.addActionListener(this);this.annotations.addItemListener(this);
this.thresholdValue.addActionListener(this);this.threshold.addItemListener(this);this.slider.setBackground(java.awt.Color.white);this.slider.setEnabled(!1);this.slider.setPreferredSize(new java.awt.Dimension(100,32));this.thresholdPanel.setBackground(java.awt.Color.white);this.actionPanel.setBackground(java.awt.Color.white);this.graphFilterView.setLayout(this.gBorderLayout);this.graphFilterView.setBackground(java.awt.Color.white);this.noGraphFilterView.setLayout(this.ngBorderLayout);this.noGraphFilterView.setBackground(java.awt.Color.white);
this.annotationComboBoxPanel.setBackground(java.awt.Color.white);this.gSearchPanel=C(jalview.appletgui.AnnotationColumnChooser.SearchPanel,this,null,this);this.ngSearchPanel=C(jalview.appletgui.AnnotationColumnChooser.SearchPanel,this,null,this);this.gFurtherActionPanel=C(jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel,this,null,this);this.ngFurtherActionPanel=C(jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel,this,null,this);this.gStructureFilterPanel=C(jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel,
this,null,this);this.ngStructureFilterPanel=C(jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel,this,null,this);this.thresholdPanel.setTitle("Threshold Filter");this.thresholdPanel.add(this.getThreshold());this.thresholdPanel.add(this.slider);this.thresholdPanel.add(this.thresholdValue);this.actionPanel.add(this.ok);this.actionPanel.add(this.cancel);var a=new javax.swing.JPanel;a.setLayout(new java.awt.BorderLayout);a.setBackground(java.awt.Color.white);a.add(this.gSearchPanel,"North");
a.add(this.gStructureFilterPanel,"South");this.graphFilterView.add(a,"North");this.graphFilterView.add(this.thresholdPanel,"Center");this.graphFilterView.add(this.gFurtherActionPanel,"South");this.noGraphFilterView.add(this.ngSearchPanel,"First");this.noGraphFilterView.add(this.ngStructureFilterPanel,"Center");this.noGraphFilterView.add(this.ngFurtherActionPanel,"Center");this.annotationComboBoxPanel.add(this.getAnnotations());this.switchableViewsPanel.add(this.noGraphFilterView,jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW);
this.switchableViewsPanel.add(this.graphFilterView,jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW);this.setLayout(this.borderLayout1);this.add(this.annotationComboBoxPanel,"First");this.add(this.switchableViewsPanel,"Center");this.add(this.actionPanel,"South");this.selectedAnnotationChanged();this.validate()});e(c$,"reset",function(){if(null!=this.getOldColumnSelection()){this.av.getColumnSelection().clear();if(null!=this.av.getAnnotationColumnSelectionState()){var a=this.av.getAnnotationColumnSelectionState().getOldColumnSelection();
if(null!=a&&null!=a.getHiddenColumns()&&!a.getHiddenColumns().isEmpty())for(var b=a.getHiddenColumns().iterator();b.hasNext();){var c=b.next();this.av.hideColumns(c[0],c[1])}this.av.setColumnSelection(a)}this.ap.paintAlignment(!0)}});e(c$,"adjustmentValueChanged",function(){this.adjusting||(this.thresholdValue.setText(this.slider.getValue()/1E3+""),this.valueChanged(!this.sliderDragging))},"java.awt.event.AdjustmentEvent");d(c$,"addSliderMouseListeners",function(){this.slider.addMouseListener((H("jalview.appletgui.AnnotationColumnChooser$1")?
0:jalview.appletgui.AnnotationColumnChooser.$AnnotationColumnChooser$1$(),C(jalview.appletgui.AnnotationColumnChooser$1,this,null)))});e(c$,"valueChanged",function(){this.slider.isEnabled()&&(this.getCurrentAnnotation().threshold.value=this.slider.getValue()/1E3,this.updateView(),this.ap.paintAlignment(!1))},"~B");d(c$,"getThreshold",function(){return this.threshold});d(c$,"setThreshold",function(a){this.threshold=a},"awt2swing.Choice");d(c$,"getAnnotations",function(){return this.annotations});d(c$,
"setAnnotations",function(a){this.annotations=a},"awt2swing.Choice");e(c$,"updateView",function(){if(!this.adjusting){var a=new jalview.viewmodel.annotationfilter.AnnotationFilterParameter;this.setCurrentAnnotation(this.av.getAlignment().getAlignmentAnnotation()[this.getAnnotations().getSelectedIndex()]);var b=this.getSelectedThresholdItem(this.getThreshold().getSelectedIndex());this.slider.setEnabled(!0);this.thresholdValue.setEnabled(!0);-1==b?(this.slider.setEnabled(!1),this.thresholdValue.setEnabled(!1),
this.thresholdValue.setText("")):-1!=b&&(null==this.getCurrentAnnotation().threshold&&this.getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine((this.getCurrentAnnotation().graphMax-this.getCurrentAnnotation().graphMin)/2,"Threshold",java.awt.Color.black)),this.adjusting=!0,this.getCurrentAnnotation(),this.getCurrentAnnotation(),this.slider.setMinimum(I(1E3*this.getCurrentAnnotation().graphMin)),this.slider.setMaximum(I(1E3*this.getCurrentAnnotation().graphMax)),this.slider.setValue(I(1E3*
this.getCurrentAnnotation().threshold.value)),this.thresholdValue.setText(this.getCurrentAnnotation().threshold.value+""),this.slider.setEnabled(!0),this.thresholdValue.setEnabled(!0),this.adjusting=!1,a.setThresholdType(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.NO_THRESHOLD),0!=this.getCurrentAnnotation().graph&&(a.setThresholdValue(this.getCurrentAnnotation().threshold.value),1==b?a.setThresholdType(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD):
0==b&&a.setThresholdType(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD)));null!=this.currentStructureFilterPanel&&(this.currentStructureFilterPanel.alphaHelix.getState()&&a.setFilterAlphaHelix(!0),this.currentStructureFilterPanel.betaStrand.getState()&&a.setFilterBetaSheet(!0),this.currentStructureFilterPanel.turn.getState()&&a.setFilterTurn(!0));null!=this.currentSearchPanel&&(this.currentSearchPanel.searchBox.getText().isEmpty()?(this.currentSearchPanel.description.setEnabled(!1),
this.currentSearchPanel.displayName.setEnabled(!1)):(this.currentSearchPanel.description.setEnabled(!0),this.currentSearchPanel.displayName.setEnabled(!0),a.setRegexString(this.currentSearchPanel.searchBox.getText()),this.currentSearchPanel.displayName.getState()&&a.addRegexSearchField(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING),this.currentSearchPanel.description.getState()&&a.addRegexSearchField(jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION)));
this.av.getColumnSelection().filterAnnotations(this.getCurrentAnnotation().annotations,a);this.av.showAllHiddenColumns();this.getActionOption()==jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE&&this.av.hideSelectedColumns();this.av.setAnnotationColumnSelectionState(this);this.ap.paintAlignment(!0)}});d(c$,"getOldColumnSelection",function(){return this.oldColumnSelection});d(c$,"setOldColumnSelection",function(a){null!=a&&(this.oldColumnSelection=new jalview.datamodel.ColumnSelection(a))},
"jalview.datamodel.ColumnSelection");d(c$,"getCurrentFutherActionPanel",function(){return this.currentFurtherActionPanel});d(c$,"setCurrentFutherActionPanel",function(a){this.currentFurtherActionPanel=a},"jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel");d(c$,"getCurrentSearchPanel",function(){return this.currentSearchPanel});d(c$,"setCurrentSearchPanel",function(a){this.currentSearchPanel=a},"jalview.appletgui.AnnotationColumnChooser.SearchPanel");d(c$,"getActionOption",function(){return this.actionOption});
d(c$,"setActionOption",function(a){this.actionOption=a},"~N");d(c$,"getCurrentStructureFilterPanel",function(){return this.currentStructureFilterPanel});d(c$,"setCurrentStructureFilterPanel",function(a){this.currentStructureFilterPanel=a},"jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel");e(c$,"itemStateChanged",function(a){a.getSource()===this.annotations?this.selectedAnnotationChanged():a.getSource()===this.threshold&&this.threshold_actionPerformed(null)},"java.awt.event.ItemEvent");
d(c$,"selectedAnnotationChanged",function(){var a=jalview.appletgui.AnnotationColumnChooser.NO_GRAPH_VIEW;0!=this.av.getAlignment().getAlignmentAnnotation()[this.getAnnotations().getSelectedIndex()].graph&&(a=jalview.appletgui.AnnotationColumnChooser.GRAPH_VIEW);this.gSearchPanel.syncState();this.gFurtherActionPanel.syncState();this.gStructureFilterPanel.syncState();this.ngSearchPanel.syncState();this.ngFurtherActionPanel.syncState();this.ngStructureFilterPanel.syncState();this.switchableViewsLayout.show(this.switchableViewsPanel,
a);this.updateView()});e(c$,"actionPerformed",function(a){if(a.getSource()===this.thresholdValue)try{var b=(new Float(this.thresholdValue.getText())).floatValue();this.slider.setValue(I(1E3*b));this.adjustmentValueChanged(null)}catch(c){if(!y(c,NumberFormatException))throw c;}else a.getSource()===this.ok?this.ok_actionPerformed(null):a.getSource()===this.cancel?this.cancel_actionPerformed(null):a.getSource()===this.thresholdValue?this.thresholdValue_actionPerformed(null):this.updateView()},"java.awt.event.ActionEvent");
e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){a.getSource()===this.slider&&this.updateView()},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){a.getSource()===this.slider&&this.updateView()},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(a){a.getSource()===this.slider&&this.updateView()},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(a){a.getSource()===this.slider&&this.updateView()},"java.awt.event.MouseEvent");c$.$AnnotationColumnChooser$FurtherActionPanel$=
function(){A(self.c$);c$=s(function(){O(this,arguments);this.furtherAction=this.aColChooser=null;r(this,arguments)},jalview.appletgui.AnnotationColumnChooser,"FurtherActionPanel",awt2swing.Panel,java.awt.event.ItemListener);J(c$,function(){this.furtherAction=new awt2swing.Choice});m(c$,function(a){t(this,jalview.appletgui.AnnotationColumnChooser.FurtherActionPanel,[]);this.aColChooser=a;this.furtherAction.addItem("Select");this.furtherAction.addItem("Hide");this.furtherAction.addItemListener(this);
this.syncState();this.add(this.furtherAction)},"jalview.appletgui.AnnotationColumnChooser");d(c$,"syncState",function(){this.aColChooser.getActionOption()==jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE?this.furtherAction.select("Hide"):this.furtherAction.select("Select")});e(c$,"itemStateChanged",function(){this.aColChooser.setCurrentFutherActionPanel(this);this.furtherAction.getSelectedItem().toString().equalsIgnoreCase("Select")?this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption(1):
this.b$["jalview.appletgui.AnnotationColumnChooser"].setActionOption(jalview.appletgui.AnnotationColumnChooser.ACTION_OPTION_HIDE);this.b$["jalview.appletgui.AnnotationColumnChooser"].updateView()},"java.awt.event.ItemEvent");c$=z()};c$.$AnnotationColumnChooser$StructureFilterPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.all=this.turn=this.betaStrand=this.alphaHelix=this.aColChooser=null;r(this,arguments)},jalview.appletgui.AnnotationColumnChooser,"StructureFilterPanel",jalview.appletgui.TitledPanel,
java.awt.event.ItemListener);J(c$,function(){this.alphaHelix=new awt2swing.Checkbox;this.betaStrand=new awt2swing.Checkbox;this.turn=new awt2swing.Checkbox;this.all=new awt2swing.Checkbox});m(c$,function(a){t(this,jalview.appletgui.AnnotationColumnChooser.StructureFilterPanel,[]);this.aColChooser=a;this.alphaHelix.setLabel(jalview.util.MessageManager.getString("label.alpha_helix"));this.alphaHelix.setBackground(java.awt.Color.white);this.alphaHelix.addItemListener(this);this.betaStrand.setLabel(jalview.util.MessageManager.getString("label.beta_strand"));
this.betaStrand.setBackground(java.awt.Color.white);this.betaStrand.addItemListener(this);this.turn.setLabel(jalview.util.MessageManager.getString("label.turn"));this.turn.setBackground(java.awt.Color.white);this.turn.addItemListener(this);this.all.setLabel(jalview.util.MessageManager.getString("label.select_all"));this.all.setBackground(java.awt.Color.white);this.all.addItemListener(this);this.setBackground(java.awt.Color.white);this.setTitle("Structure Filter");this.add(this.all);this.add(this.alphaHelix);
this.add(this.betaStrand);this.add(this.turn)},"jalview.appletgui.AnnotationColumnChooser");d(c$,"alphaHelix_actionPerformed",function(){this.updateSelectAllState();this.aColChooser.setCurrentStructureFilterPanel(this);this.aColChooser.updateView()});d(c$,"betaStrand_actionPerformed",function(){this.updateSelectAllState();this.aColChooser.setCurrentStructureFilterPanel(this);this.aColChooser.updateView()});d(c$,"turn_actionPerformed",function(){this.updateSelectAllState();this.aColChooser.setCurrentStructureFilterPanel(this);
this.aColChooser.updateView()});d(c$,"all_actionPerformed",function(){this.all.getState()?(this.alphaHelix.setState(!0),this.betaStrand.setState(!0),this.turn.setState(!0)):(this.alphaHelix.setState(!1),this.betaStrand.setState(!1),this.turn.setState(!1));this.aColChooser.setCurrentStructureFilterPanel(this);this.aColChooser.updateView()});d(c$,"updateSelectAllState",function(){this.alphaHelix.getState()&&this.betaStrand.getState()&&this.turn.getState()?this.all.setState(!0):this.all.setState(!1)});
d(c$,"syncState",function(){var a=this.aColChooser.getCurrentStructureFilterPanel();null!=a&&(this.alphaHelix.setState(a.alphaHelix.getState()),this.betaStrand.setState(a.betaStrand.getState()),this.turn.setState(a.turn.getState()),a.all.getState()&&(this.all.setState(!0),this.alphaHelix.setState(!0),this.betaStrand.setState(!0),this.turn.setState(!0)))});e(c$,"itemStateChanged",function(a){a.getSource()===this.alphaHelix?this.alphaHelix_actionPerformed():a.getSource()===this.betaStrand?this.betaStrand_actionPerformed():
a.getSource()===this.turn?this.turn_actionPerformed():a.getSource()===this.all&&this.all_actionPerformed()},"java.awt.event.ItemEvent");c$=z()};c$.$AnnotationColumnChooser$SearchPanel$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.searchBox=this.description=this.displayName=this.aColChooser=null;r(this,arguments)},jalview.appletgui.AnnotationColumnChooser,"SearchPanel",jalview.appletgui.TitledPanel,java.awt.event.ItemListener);J(c$,function(){this.displayName=new awt2swing.Checkbox;
this.description=new awt2swing.Checkbox;this.searchBox=new awt2swing.TextField(10)});m(c$,function(a){t(this,jalview.appletgui.AnnotationColumnChooser.SearchPanel,[]);this.aColChooser=a;this.searchBox.addTextListener((H("jalview.appletgui.AnnotationColumnChooser$SearchPanel$1")?0:jalview.appletgui.AnnotationColumnChooser.SearchPanel.$AnnotationColumnChooser$SearchPanel$1$(),C(jalview.appletgui.AnnotationColumnChooser$SearchPanel$1,this,null)));this.displayName.setLabel(jalview.util.MessageManager.getString("label.display_name"));
this.displayName.setEnabled(!1);this.displayName.addItemListener(this);this.description.setLabel(jalview.util.MessageManager.getString("label.description"));this.description.setEnabled(!1);this.description.addItemListener(this);this.setTitle("Search Filter");this.syncState();this.add(this.searchBox);this.add(this.displayName);this.add(this.description)},"jalview.appletgui.AnnotationColumnChooser");d(c$,"displayNameCheckboxAction",function(){this.aColChooser.setCurrentSearchPanel(this);this.aColChooser.updateView()});
d(c$,"discriptionCheckboxAction",function(){this.aColChooser.setCurrentSearchPanel(this);this.aColChooser.updateView()});d(c$,"searchStringAction",function(){this.aColChooser.setCurrentSearchPanel(this);this.aColChooser.updateView()});d(c$,"syncState",function(){var a=this.aColChooser.getCurrentSearchPanel();null!=a&&(this.description.setEnabled(a.description.isEnabled()),this.description.setState(a.description.getState()),this.displayName.setEnabled(a.displayName.isEnabled()),this.displayName.setState(a.displayName.getState()),
this.searchBox.setText(a.searchBox.getText()))});e(c$,"itemStateChanged",function(a){a.getSource()===this.displayName?this.displayNameCheckboxAction():a.getSource()===this.description&&this.discriptionCheckboxAction()},"java.awt.event.ItemEvent");c$.$AnnotationColumnChooser$SearchPanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"AnnotationColumnChooser$SearchPanel$1",null,java.awt.event.TextListener);e(c$,"textValueChanged",function(){this.b$["jalview.appletgui.AnnotationColumnChooser.SearchPanel"].searchStringAction()},
"java.awt.event.TextEvent");c$=z()};c$=z()};c$.$AnnotationColumnChooser$1$=function(){A(self.c$);c$=L(jalview.appletgui,"AnnotationColumnChooser$1",java.awt.event.MouseAdapter);d(c$,"mousePressed",function(a){this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging=!0;K(this,jalview.appletgui.AnnotationColumnChooser$1,"mousePressed",[a])},"java.awt.event.MouseEvent");d(c$,"mouseDragged",function(a){this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging=!0;K(this,jalview.appletgui.AnnotationColumnChooser$1,
"mouseDragged",[a])},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging&&(this.b$["jalview.appletgui.AnnotationColumnChooser"].sliderDragging=!1,this.b$["jalview.appletgui.AnnotationColumnChooser"].valueChanged(!0));this.b$["jalview.appletgui.AnnotationColumnChooser"].ap.paintAlignment(!0)},"java.awt.event.MouseEvent");c$=z()};G(c$,"ACTION_OPTION_SELECT",1,"ACTION_OPTION_HIDE",2,"NO_GRAPH_VIEW","0","GRAPH_VIEW","1")});p("jalview.appletgui");
q(["awt2swing.Panel","$.Button","$.Checkbox","$.Scrollbar","$.TextField"],"jalview.appletgui.AnnotationRowFilter",["jalview.util.MessageManager","java.lang.Float","java.util.Vector"],function(){c$=s(function(){this.annmap=this.ap=this.av=null;this.enableSeqAss=!1;this.currentAnnotation=null;this.adjusting=!1;this.cancel=this.ok=this.frame=this.thresholdValue=this.slider=this.thresholdIsMin=this.seqAssociated=this.maxColour=this.minColour=this.currentColours=null;this.sliderDragging=!1;r(this,arguments)},
jalview.appletgui,"AnnotationRowFilter",awt2swing.Panel);J(c$,function(){this.currentColours=new awt2swing.Checkbox;this.minColour=new awt2swing.Panel;this.maxColour=new awt2swing.Panel;this.seqAssociated=new awt2swing.Checkbox;this.thresholdIsMin=new awt2swing.Checkbox;this.slider=new awt2swing.Scrollbar(0);this.thresholdValue=new awt2swing.TextField(20);this.ok=new awt2swing.Button;this.cancel=new awt2swing.Button});m(c$,function(a,b){t(this,jalview.appletgui.AnnotationRowFilter,[]);this.av=a;this.ap=
b},"jalview.appletgui.AlignViewport,jalview.appletgui.AlignmentPanel");m(c$,function(){t(this,jalview.appletgui.AnnotationRowFilter,[])});d(c$,"getAnnotationItems",function(a){for(var b=new java.util.Vector,c=1,d=w(this.av.getAlignment().getAlignmentAnnotation().length,0),e=0;e<this.av.getAlignment().getAlignmentAnnotation().length;e++){if(null==this.av.getAlignment().getAlignmentAnnotation()[e].sequenceRef){if(a)continue}else this.enableSeqAss=!0;var k=this.av.getAlignment().getAlignmentAnnotation()[e].label;
b.contains(k)?a||(d[b.size()]=e,b.add(k+"_"+c++)):(d[b.size()]=e,b.add(k))}this.annmap=w(b.size(),0);System.arraycopy(d,0,this.annmap,0,this.annmap.length);return b},"~B");d(c$,"getSelectedThresholdItem",function(a){var b=-1;1==a?b=1:2==a&&(b=0);return b},"~N");d(c$,"modelChanged",function(){this.seqAssociated.setEnabled(this.enableSeqAss)});d(c$,"ok_actionPerformed",function(){this.updateView();this.frame.setVisible(!1)},"java.awt.event.ActionEvent");d(c$,"cancel_actionPerformed",function(){this.reset();
this.ap.paintAlignment(!0);this.frame.setVisible(!1)},"java.awt.event.ActionEvent");d(c$,"thresholdCheck_actionPerformed",function(){this.updateView()},"java.awt.event.ActionEvent");d(c$,"annotations_actionPerformed",function(){this.updateView()},"java.awt.event.ActionEvent");d(c$,"threshold_actionPerformed",function(){this.updateView()},"java.awt.event.ActionEvent");d(c$,"thresholdValue_actionPerformed",function(){try{var a=Float.parseFloat(this.thresholdValue.getText());this.slider.setValue(I(1E3*
a));this.updateView()}catch(b){if(!y(b,NumberFormatException))throw b;}},"java.awt.event.ActionEvent");d(c$,"populateThresholdComboBox",function(a){a.addItem(jalview.util.MessageManager.getString("label.threshold_feature_no_thereshold"));a.addItem(jalview.util.MessageManager.getString("label.threshold_feature_above_thereshold"));a.addItem(jalview.util.MessageManager.getString("label.threshold_feature_below_thereshold"))},"awt2swing.Choice");d(c$,"getCurrentAnnotation",function(){return this.currentAnnotation});
d(c$,"setCurrentAnnotation",function(a){this.currentAnnotation=a},"jalview.datamodel.AlignmentAnnotation")});p("jalview.appletgui");q(["awt2swing.Panel","java.awt.Insets"],"jalview.appletgui.TitledPanel",["awt2swing.Util"],function(){c$=s(function(){this.$insets=this.title=null;r(this,arguments)},jalview.appletgui,"TitledPanel",awt2swing.Panel);J(c$,function(){this.$insets=new java.awt.Insets(10,10,10,10)});m(c$,function(){this.construct("")});m(c$,function(a){t(this,jalview.appletgui.TitledPanel,
[]);this.setTitle(a)},"~S");d(c$,"getInsets",function(){return this.$insets});d(c$,"paintComponent",function(a){K(this,jalview.appletgui.TitledPanel,"paintComponent",[a]);a.setColor(this.getForeground());a.drawRect(5,5,this.getWidth()-10,this.getHeight()-10);var b=a.getFontMetrics().stringWidth(this.getTitle());a.setColor(this.getBackground());a.fillRect(10,0,b,10);a.setColor(this.getForeground());awt2swing.Util.drawString(a,this.getTitle(),10,10)},"java.awt.Graphics");d(c$,"getTitle",function(){return this.title});
d(c$,"setTitle",function(a){this.title=a},"~S")});p("java.awt");q(["java.awt.LayoutManager2","java.io.ObjectStreamField","java.util.Hashtable","$.Vector"],"java.awt.CardLayout",["java.lang.IllegalArgumentException","java.awt.Dimension"],function(){c$=s(function(){this.vector=null;H("java.awt.CardLayout.Card")||java.awt.CardLayout.$CardLayout$Card$();this.vgap=this.hgap=this.currentCard=0;r(this,arguments)},java.awt,"CardLayout",null,[java.awt.LayoutManager2,java.io.Serializable]);J(c$,function(){this.vector=
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d(c$,"addLayoutComponent",function(a,b){this.vector.isEmpty()||b.setVisible(!1);for(var c=0;c<this.vector.size();c++)if(this.vector.get(c).name.equals(a)){this.vector.get(c).comp=b;return}this.vector.add(C(java.awt.CardLayout.Card,this,null,a,b))},"~S,java.awt.Component");e(c$,"removeLayoutComponent",function(a){for(var b=0;b<this.vector.size();b++)if(this.vector.get(b).comp===a){a.isVisible()&&null!=a.getParent()&&this.next(a.getParent());this.vector.remove(b);this.currentCard>b&&this.currentCard--;
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g.width);g.height>e&&(e=g.height)}return new java.awt.Dimension(b.left+b.right+d+2*this.hgap,b.top+b.bottom+e+2*this.vgap)},"java.awt.Container");e(c$,"maximumLayoutSize",function(){return new java.awt.Dimension(2147483647,2147483647)},"java.awt.Container");e(c$,"getLayoutAlignmentX",function(){return 0.5},"java.awt.Container");e(c$,"getLayoutAlignmentY",function(){return 0.5},"java.awt.Container");e(c$,"invalidateLayout",function(){},"java.awt.Container");e(c$,"layoutContainer",function(a){for(var b=
a.getInsets(),c=a.getComponentCount(),d=null,e=!1,k=0;k<c;k++)d=a.getComponent(k),d.setBounds(this.hgap+b.left,this.vgap+b.top,a.width-(2*this.hgap+b.left+b.right),a.height-(2*this.vgap+b.top+b.bottom)),d.isVisible()&&(e=!0);!e&&0<c&&a.getComponent(0).setVisible(!0)},"java.awt.Container");d(c$,"checkLayout",function(a){if(a.getLayout()!==this)throw new IllegalArgumentException("wrong parent for CardLayout");},"java.awt.Container");d(c$,"first",function(a){this.checkLayout(a);for(var b=a.getComponentCount(),
c=0;c<b;c++){var d=a.getComponent(c);if(d.isVisible()){d.setVisible(!1);break}}0<b&&(this.currentCard=0,a.getComponent(0).setVisible(!0),a.validate())},"java.awt.Container");d(c$,"next",function(a){this.checkLayout(a);for(var b=a.getComponentCount(),c=0;c<b;c++){var d=a.getComponent(c);if(d.isVisible()){d.setVisible(!1);this.currentCard=(c+1)%b;d=a.getComponent(this.currentCard);d.setVisible(!0);a.validate();return}}this.showDefaultComponent(a)},"java.awt.Container");d(c$,"previous",function(a){this.checkLayout(a);
for(var b=a.getComponentCount(),c=0;c<b;c++){var d=a.getComponent(c);if(d.isVisible()){d.setVisible(!1);this.currentCard=0<c?c-1:b-1;d=a.getComponent(this.currentCard);d.setVisible(!0);a.validate();return}}this.showDefaultComponent(a)},"java.awt.Container");d(c$,"showDefaultComponent",function(a){0<a.getComponentCount()&&(this.currentCard=0,a.getComponent(0).setVisible(!0),a.validate())},"java.awt.Container");d(c$,"last",function(a){this.checkLayout(a);for(var b=a.getComponentCount(),c=0;c<b;c++){var d=
a.getComponent(c);if(d.isVisible()){d.setVisible(!1);break}}0<b&&(this.currentCard=b-1,a.getComponent(this.currentCard).setVisible(!0),a.validate())},"java.awt.Container");d(c$,"show",function(a,b){this.checkLayout(a);for(var c=null,d=this.vector.size(),e=0;e<d;e++){var k=this.vector.get(e);if(k.name.equals(b)){c=k.comp;this.currentCard=e;break}}if(null!=c&&!c.isVisible()){d=a.getComponentCount();for(e=0;e<d;e++)if(k=a.getComponent(e),k.isVisible()){k.setVisible(!1);break}c.setVisible(!0);a.validate()}},
"java.awt.Container,~S");e(c$,"toString",function(){return this.getClass().getName()+"[hgap="+this.hgap+",vgap="+this.vgap+"]"});c$.$CardLayout$Card$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.comp=this.name=null;r(this,arguments)},java.awt.CardLayout,"Card",null,java.io.Serializable);m(c$,function(a,b){this.name=a;this.comp=b},"~S,java.awt.Component");c$=z()};c$.serialPersistentFields=c$.prototype.serialPersistentFields=E(-1,[new java.io.ObjectStreamField("tab",java.util.Hashtable),
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function(){c$=s(function(){this.searchResults=this.frame=this.ap=this.av=null;this.seqIndex=0;this.resIndex=-1;this.searchDescription=this.caseSensitive=this.createNewGroup=this.gridLayout1=this.actionsPanel=this.findNext=this.findAll=this.textfield=this.jLabel1=null;r(this,arguments)},jalview.appletgui,"Finder",awt2swing.Panel,java.awt.event.ActionListener);J(c$,function(){this.jLabel1=new awt2swing.Label;this.textfield=new awt2swing.TextField;this.findAll=new awt2swing.Button;this.findNext=new awt2swing.Button;
this.actionsPanel=new awt2swing.Panel;this.gridLayout1=new java.awt.GridLayout;this.createNewGroup=new awt2swing.Button;this.caseSensitive=new awt2swing.Checkbox;this.searchDescription=new awt2swing.Checkbox});m(c$,function(a){t(this,jalview.appletgui.Finder,[]);try{this.jbInit()}catch(b){if(y(b,Exception))b.printStackTrace();else throw b;}this.av=a.av;this.ap=a;this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("action.find"),
340,120);this.frame.repaint();this.frame.addWindowListener((H("jalview.appletgui.Finder$1")?0:jalview.appletgui.Finder.$Finder$1$(),C(jalview.appletgui.Finder$1,this,T("ap",a))));this.textfield.requestFocus()},"jalview.appletgui.AlignmentPanel");e(c$,"actionPerformed",function(a){a.getSource()===this.textfield?this.doSearch(!1):a.getSource()===this.findNext?this.doSearch(!1):a.getSource()===this.findAll?(this.resIndex=-1,this.seqIndex=0,this.doSearch(!0)):a.getSource()===this.createNewGroup&&this.createNewGroup_actionPerformed()},
"java.awt.event.ActionEvent");d(c$,"createNewGroup_actionPerformed",function(){for(var a=Array(this.searchResults.getSize()),b=Array(this.searchResults.getSize()),c=0;c<this.searchResults.getSize();c++)a[c]=this.searchResults.getResultSequence(c),b[c]=new jalview.datamodel.SequenceFeature(this.textfield.getText().trim(),"Search Results",null,this.searchResults.getResultStart(c),this.searchResults.getResultEnd(c),"Search Results");this.ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(a,b,!0,
this.ap)&&(this.ap.alignFrame.sequenceFeatures.setState(!0),this.av.setShowSequenceFeatures(!0),this.ap.highlightSearchResults(null))});d(c$,"doSearch",function(a){null!=this.ap.av.applet.currentAlignFrame&&(this.ap=this.ap.av.applet.currentAlignFrame.alignPanel,this.av=this.ap.av);this.createNewGroup.setEnabled(!1);var b=new jalview.analysis.Finder(this.av.getAlignment(),this.av.getSelectionGroup(),this.seqIndex,this.resIndex);b.setCaseSensitive(this.caseSensitive.getState());b.setIncludeDescription(this.searchDescription.getState());
b.setFindAll(a);var c=this.textfield.getText();b.find(c);this.seqIndex=b.getSeqIndex();this.resIndex=b.getResIndex();this.searchResults=b.getSearchResults();var b=b.getIdMatch(),d=!1;0<b.size()?(d=!0,this.ap.idPanel.highlightSearchResults(b)):this.ap.idPanel.highlightSearchResults(null);0<this.searchResults.getSize()?(d=!0,this.createNewGroup.setEnabled(!0)):this.searchResults=null;this.ap.highlightSearchResults(this.searchResults);d?a?(a=0<b.size()?""+b.size()+" IDs":"",0<b.size()&&(null!=this.searchResults&&
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0,12));this.jLabel1.setText(jalview.util.MessageManager.getString("action.find"));this.jLabel1.setBounds(new java.awt.Rectangle(3,30,34,15));this.setLayout(null);this.textfield.setFont(new java.awt.Font("Verdana",0,10));this.textfield.setText("");this.textfield.setBounds(new java.awt.Rectangle(40,17,133,21));this.textfield.addKeyListener((H("jalview.appletgui.Finder$2")?0:jalview.appletgui.Finder.$Finder$2$(),C(jalview.appletgui.Finder$2,this,null)));this.textfield.addActionListener(this);this.findAll.setFont(new java.awt.Font("Verdana",
0,10));this.findAll.setLabel(jalview.util.MessageManager.getString("action.find_all"));this.findAll.addActionListener(this);this.findNext.setEnabled(!1);this.findNext.setFont(new java.awt.Font("Verdana",0,10));this.findNext.setLabel(jalview.util.MessageManager.getString("action.find_next"));this.findNext.addActionListener(this);this.actionsPanel.setBounds(new java.awt.Rectangle(195,5,141,64));this.actionsPanel.setLayout(this.gridLayout1);this.gridLayout1.setHgap(0);this.gridLayout1.setRows(3);this.gridLayout1.setVgap(2);
this.createNewGroup.setEnabled(!1);this.createNewGroup.setFont(new java.awt.Font("Verdana",0,10));this.createNewGroup.setLabel(jalview.util.MessageManager.getString("label.new_feature"));this.createNewGroup.addActionListener(this);this.caseSensitive.setLabel(jalview.util.MessageManager.getString("label.match_case"));this.caseSensitive.setBounds(new java.awt.Rectangle(30,39,126,23));this.searchDescription.setLabel(jalview.util.MessageManager.getString("label.include_description"));this.searchDescription.setBounds(new java.awt.Rectangle(30,
59,170,23));this.actionsPanel.add(this.findNext,null);this.actionsPanel.add(this.findAll,null);this.actionsPanel.add(this.createNewGroup,null);this.add(this.caseSensitive);this.add(this.textfield,null);this.add(this.jLabel1,null);this.add(this.actionsPanel,null);this.add(this.searchDescription)});d(c$,"textfield_keyTyped",function(){this.findNext.setEnabled(!0)},"java.awt.event.KeyEvent");c$.$Finder$1$=function(){A(self.c$);c$=L(jalview.appletgui,"Finder$1",java.awt.event.WindowAdapter);e(c$,"windowClosing",
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s(function(){this.idMatch=this.selection=this.alignment=this.searchResults=null;this.findAll=this.includeDescription=this.caseSensitive=!1;this.regex=null;this.seqIndex=0;this.resIndex=-1;r(this,arguments)},jalview.analysis,"Finder");m(c$,function(a,b){this.alignment=a;this.selection=b},"jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup");m(c$,function(a,b,c,d){this.construct(a,b);this.seqIndex=c;this.resIndex=d},"jalview.datamodel.AlignmentI,jalview.datamodel.SequenceGroup,~N,~N");d(c$,
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(this.idMatch.addElement(c),b=!0,!this.findAll))break}d=c.getSequenceAsString();null!=this.selection&&this.selection.getEndRes()<this.alignment.getWidth()-1&&(d=d.substring(0,this.selection.getEndRes()+1));for(var j=new StringBuffer,n=0,m=new java.util.Vector,p=0;p<d.length;p++)jalview.util.Comparison.isGap(d.charAt(p))?n++:(j.append(d.charAt(p)),m.addElement(new Integer(n)));d=j.toString();for(j=this.resIndex;j<d.length;j++)if(this.regex.searchFrom(d,j)){if(this.resIndex=this.regex.matchedFrom(),
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"~S");d(c$,"getAlignment",function(){return this.alignment});d(c$,"setAlignment",function(a){this.alignment=a},"jalview.datamodel.AlignmentI");d(c$,"isCaseSensitive",function(){return this.caseSensitive});d(c$,"setCaseSensitive",function(a){this.caseSensitive=a},"~B");d(c$,"isFindAll",function(){return this.findAll});d(c$,"setFindAll",function(a){this.findAll=a},"~B");d(c$,"getSelection",function(){return this.selection});d(c$,"setSelection",function(a){this.selection=a},"jalview.datamodel.SequenceGroup");
d(c$,"getIdMatch",function(){return this.idMatch});d(c$,"getRegex",function(){return this.regex});d(c$,"getSearchResults",function(){return this.searchResults});d(c$,"getResIndex",function(){return this.resIndex});d(c$,"setResIndex",function(a){this.resIndex=a},"~N");d(c$,"getSeqIndex",function(){return this.seqIndex});d(c$,"setSeqIndex",function(a){this.seqIndex=a},"~N");d(c$,"isIncludeDescription",function(){return this.includeDescription});d(c$,"setIncludeDescription",function(a){this.includeDescription=
a},"~B")});p("java.awt.event");q(["java.awt.event.KeyListener"],"java.awt.event.KeyAdapter",null,function(){c$=B(java.awt.event,"KeyAdapter",null,java.awt.event.KeyListener);e(c$,"keyTyped",function(){},"java.awt.event.KeyEvent");e(c$,"keyPressed",function(){},"java.awt.event.KeyEvent");e(c$,"keyReleased",function(){},"java.awt.event.KeyEvent")});p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ItemListener awt2swing.Button $.Checkbox $.Choice java.awt.Font".split(" "),"jalview.appletgui.FontChooser",
"awt2swing.Frame $.Label jalview.appletgui.JVDialog jalview.bin.JalviewLite jalview.util.MessageManager java.awt.BorderLayout $.Color $.FlowLayout $.Toolkit java.awt.event.ActionListener".split(" "),function(){c$=s(function(){this.oldFont=this.tp=this.ap=this.cancel=this.ok=this.scaleAsCdna=this.fontName=this.fontStyle=this.fontSize=null;this.oldCharWidth=0;this.oldScaleProtein=!1;this.lastSelected=null;this.lastSelSize=this.lastSelStyle=0;this.$init=!0;this.frame=null;r(this,arguments)},jalview.appletgui,
"FontChooser",awt2swing.Panel,java.awt.event.ItemListener);J(c$,function(){this.fontSize=new awt2swing.Choice;this.fontStyle=new awt2swing.Choice;this.fontName=new awt2swing.Choice;this.scaleAsCdna=new awt2swing.Checkbox;this.ok=new awt2swing.Button;this.cancel=new awt2swing.Button});m(c$,function(a){t(this,jalview.appletgui.FontChooser,[]);try{this.jbInit()}catch(b){if(y(b,Exception))b.printStackTrace();else throw b;}this.tp=a;this.oldFont=a.getTreeFont();this.init()},"jalview.appletgui.TreePanel");
m(c$,function(a){t(this,jalview.appletgui.FontChooser,[]);this.ap=a;this.oldFont=a.av.getFont();this.oldCharWidth=a.av.getViewStyle().getCharWidth();this.oldScaleProtein=a.av.getViewStyle().isScaleProteinAsCdna();try{this.jbInit()}catch(b){if(y(b,Exception))b.printStackTrace();else throw b;}this.init()},"jalview.appletgui.AlignmentPanel");d(c$,"init",function(){for(var a=java.awt.Toolkit.getDefaultToolkit().getFontList(),b=0;b<a.length;b++)this.fontName.addItem(a[b]);for(b=1;31>b;b++)this.fontSize.addItem(b+
"");this.fontStyle.addItem("plain");this.fontStyle.addItem("bold");this.fontStyle.addItem("italic");this.fontName.select(this.oldFont.getName());this.fontSize.select(this.oldFont.getSize()+"");this.fontStyle.select(new Integer(this.oldFont.getStyle()));this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("action.change_font"),440,115);this.$init=!1});e(c$,"itemStateChanged",function(a){a=a.getSource();a===this.fontName?
this.fontName_actionPerformed():a===this.fontSize?this.fontSize_actionPerformed():a===this.fontStyle?this.fontStyle_actionPerformed():a===this.scaleAsCdna&&this.scaleAsCdna_actionPerformed()},"java.awt.event.ItemEvent");d(c$,"ok_actionPerformed",function(){this.frame.setVisible(!1);null!=this.ap&&null!=this.ap.getOverviewPanel()&&this.ap.getOverviewPanel().updateOverviewImage()});d(c$,"cancel_actionPerformed",function(){if(null!=this.ap){this.ap.av.setScaleProteinAsCdna(this.oldScaleProtein);null!=
this.ap.av.getCodingComplement()&&(this.ap.av.getCodingComplement().setScaleProteinAsCdna(this.oldScaleProtein),this.ap.alignFrame.getSplitFrame().repaint());this.ap.av.setFont(this.oldFont);var a=this.ap.av.getViewStyle();a.getCharWidth()!=this.oldCharWidth&&(a.setCharWidth(this.oldCharWidth),this.ap.av.setViewStyle(a));this.ap.paintAlignment(!0)}else null!=this.tp&&(this.tp.setTreeFont(this.oldFont),this.tp.treeCanvas.repaint());this.fontName.select(this.oldFont.getName());this.fontSize.select(this.oldFont.getSize()+
"");this.fontStyle.select(new Integer(this.oldFont.getStyle()));this.frame.setVisible(!1)});d(c$,"changeFont",function(){null==this.lastSelected&&(this.lastSelected=this.oldFont,this.lastSelSize=this.oldFont.getSize(),this.lastSelStyle=this.oldFont.getStyle());var a=new java.awt.Font(this.fontName.getSelectedItem().toString(),this.fontStyle.getSelectedIndex(),Integer.parseInt(this.fontSize.getSelectedItem().toString())),b=this.getGraphics().getFontMetrics(a),c=b.getStringBounds("M",this.getGraphics()).getWidth(),
b=b.getStringBounds("I",this.getGraphics()).getWidth();1>c||1>b?(this.fontName.select(this.lastSelected.getName()),this.fontStyle.select(new Integer(this.lastSelStyle)),this.fontSize.select(""+this.lastSelSize),a=new jalview.appletgui.JVDialog(this.frame,jalview.util.MessageManager.getString("label.invalid_font"),!0,350,200),c=new awt2swing.Panel,a.cancel.setVisible(!1),c.setLayout(new java.awt.FlowLayout),c.add(new awt2swing.Label("Font doesn't have letters defined\nso cannot be used\nwith alignment data.")),
a.setMainPanel(c),a.setVisible(!0)):(null!=this.tp?this.tp.setTreeFont(a):null!=this.ap&&(this.ap.av.setFont(a),this.ap.fontChanged()),this.lastSelected=a)});d(c$,"fontName_actionPerformed",function(){this.$init||this.changeFont()});d(c$,"fontSize_actionPerformed",function(){this.$init||this.changeFont()});d(c$,"fontStyle_actionPerformed",function(){this.$init||this.changeFont()});d(c$,"jbInit",function(){this.setLayout(new java.awt.BorderLayout);this.setBackground(java.awt.Color.white);var a=new awt2swing.Label(jalview.util.MessageManager.getString("label.font"));
a.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);a.setAlignment(4);this.fontSize.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.fontSize.addItemListener(this);this.fontStyle.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.fontStyle.addItemListener(this);var b=new awt2swing.Label(jalview.util.MessageManager.getString("label.size"));b.setAlignment(4);b.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);var c=new awt2swing.Label(jalview.util.MessageManager.getString("label.style"));
c.setAlignment(4);c.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.fontName.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.fontName.addItemListener(this);this.scaleAsCdna.setLabel(jalview.util.MessageManager.getString("label.scale_as_cdna"));this.scaleAsCdna.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.scaleAsCdna.addItemListener(this);this.scaleAsCdna.setState(this.ap.av.isScaleProteinAsCdna());this.ok.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.ok.setLabel(jalview.util.MessageManager.getString("action.ok"));
this.ok.addActionListener((H("jalview.appletgui.FontChooser$1")?0:jalview.appletgui.FontChooser.$FontChooser$1$(),C(jalview.appletgui.FontChooser$1,this,null)));this.cancel.setFont(jalview.appletgui.FontChooser.VERDANA_11PT);this.cancel.setLabel(jalview.util.MessageManager.getString("action.cancel"));this.cancel.addActionListener((H("jalview.appletgui.FontChooser$2")?0:jalview.appletgui.FontChooser.$FontChooser$2$(),C(jalview.appletgui.FontChooser$2,this,null)));var d=new awt2swing.Panel;d.setLayout(new java.awt.BorderLayout);
var e=new awt2swing.Panel;e.setLayout(new java.awt.BorderLayout);var k=new awt2swing.Panel;k.setLayout(new java.awt.BorderLayout);var g=new awt2swing.Panel;g.setLayout(new java.awt.BorderLayout);var h=new awt2swing.Panel,j=new awt2swing.Panel;d.setBackground(java.awt.Color.white);e.setBackground(java.awt.Color.white);k.setBackground(java.awt.Color.white);h.setBackground(java.awt.Color.white);j.setBackground(java.awt.Color.white);d.add(a,"West");d.add(this.fontName,"Center");e.add(c,"West");e.add(this.fontStyle,
"Center");k.add(b,"West");k.add(this.fontSize,"Center");g.add(this.scaleAsCdna,"Center");h.add(this.ok,null);h.add(this.cancel,null);j.add(d,null);j.add(k,null);j.add(e,null);this.add(j,"North");null!=this.ap.alignFrame.getSplitFrame()&&this.add(g,"Center");this.add(h,"South")});d(c$,"scaleAsCdna_actionPerformed",function(){this.ap.av.setScaleProteinAsCdna(this.scaleAsCdna.getState());this.ap.av.getCodingComplement().setScaleProteinAsCdna(this.scaleAsCdna.getState());this.ap.alignFrame.getSplitFrame().adjustLayout();
this.ap.paintAlignment(!0);this.ap.alignFrame.getSplitFrame().repaint()});c$.$FontChooser$1$=function(){A(self.c$);c$=L(jalview.appletgui,"FontChooser$1",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.FontChooser"].ok_actionPerformed()},"java.awt.event.ActionEvent");c$=z()};c$.$FontChooser$2$=function(){A(self.c$);c$=L(jalview.appletgui,"FontChooser$2",null,java.awt.event.ActionListener);e(c$,"actionPerformed",function(){this.b$["jalview.appletgui.FontChooser"].cancel_actionPerformed()},
"java.awt.event.ActionEvent");c$=z()};c$.VERDANA_11PT=c$.prototype.VERDANA_11PT=new java.awt.Font("Verdana",0,11)});p("jalview.appletgui");q(["awt2swing.Panel","java.awt.event.MouseListener","$.MouseMotionListener"],"jalview.appletgui.OverviewPanel","awt2swing.Frame jalview.appletgui.FeatureRenderer $.SequenceRenderer java.awt.Color $.Dimension java.awt.event.ComponentAdapter java.lang.Thread".split(" "),function(){c$=s(function(){this.ap=this.av=this.offscreen=this.miniMe=null;this.scaleh=this.scalew=
1;this.sequencesHeight=this.$width=0;this.graphHeight=20;this.boxHeight=this.boxWidth=this.boxY=this.boxX=-1;this.resizing=!1;this.nullFrame=this.fr=this.sr=null;this.resizeAgain=!1;r(this,arguments)},jalview.appletgui,"OverviewPanel",awt2swing.Panel,[Runnable,java.awt.event.MouseMotionListener,java.awt.event.MouseListener]);m(c$,function(a){t(this,jalview.appletgui.OverviewPanel,[]);this.av=a.av;this.ap=a;this.setLayout(null);this.nullFrame=new awt2swing.Frame;this.nullFrame.addNotify();this.sr=
new jalview.appletgui.SequenceRenderer(this.av);this.sr.graphics=this.nullFrame.getGraphics();this.sr.renderGaps=!1;this.sr.forOverview=!0;this.fr=new jalview.appletgui.FeatureRenderer(this.av);a=this.av.getAlignment().getWidth()/this.av.getAlignment().getHeight();null==this.av.getSequenceConsensusHash()&&(this.graphHeight=0);this.av.getAlignment().getWidth()>this.av.getAlignment().getHeight()?(this.$width=400,this.sequencesHeight=I(400/a),40>this.sequencesHeight&&(this.sequencesHeight=40)):(this.$width=
I(400*a),this.sequencesHeight=300,120>this.$width&&(this.$width=120));this.setSize(new java.awt.Dimension(this.$width,this.sequencesHeight+this.graphHeight));this.addComponentListener((H("jalview.appletgui.OverviewPanel$1")?0:jalview.appletgui.OverviewPanel.$OverviewPanel$1$(),C(jalview.appletgui.OverviewPanel$1,this,null)));this.addMouseMotionListener(this);this.addMouseListener(this);this.updateOverviewImage()},"jalview.appletgui.AlignmentPanel");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");
e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){this.boxX=a.getX();this.boxY=a.getY();this.checkValid()},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(a){this.boxX=a.getX();this.boxY=a.getY();this.checkValid()},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){this.boxX=a.getX();this.boxY=a.getY();this.checkValid()},
"java.awt.event.MouseEvent");d(c$,"checkValid",function(){0>this.boxY&&(this.boxY=0);this.boxY>this.sequencesHeight-this.boxHeight&&(this.boxY=this.sequencesHeight-this.boxHeight+1);0>this.boxX&&(this.boxX=0);this.boxX>this.$width-this.boxWidth&&(this.av.hasHiddenColumns()&&(this.boxWidth=I((this.av.endRes-this.av.startRes+1)*this.av.getCharWidth()*this.scalew)),this.boxX=this.$width-this.boxWidth);var a=I(this.boxX/this.scalew/this.av.getCharWidth()),b=I(this.boxY/this.scaleh/this.av.getCharHeight());
if(this.av.hasHiddenColumns()){if(!this.av.getColumnSelection().isVisible(a))return;a=this.av.getColumnSelection().findColumnPosition(a)}this.av.hasHiddenRows()&&(b=this.av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(b));this.ap.setScrollValues(a,b);this.ap.paintAlignment(!1)});d(c$,"updateOverviewImage",function(){this.resizing?this.resizeAgain=!0:(this.av.isShowSequenceFeatures()&&this.fr.transferSettings(this.ap.seqPanel.seqCanvas.fr),this.resizing=!0,0<this.getSize().width&&
0<this.getSize().height&&(this.$width=this.getSize().width,this.sequencesHeight=this.getSize().height-this.graphHeight),this.setSize(new java.awt.Dimension(this.$width,this.sequencesHeight+this.graphHeight)),(new Thread(this)).start(),this.repaint())});e(c$,"run",function(){this.miniMe=null;var a=this.av.getAlignment().getWidth(),b=this.av.getAlignment().getHeight();this.av.isShowSequenceFeatures()&&this.fr.transferSettings(this.ap.seqPanel.seqCanvas.getFeatureRenderer());0<this.getSize().width&&
0<this.getSize().height&&(this.$width=this.getSize().width,this.sequencesHeight=this.getSize().height-this.graphHeight);this.setSize(new java.awt.Dimension(this.$width,this.sequencesHeight+this.graphHeight));var c=a*this.av.getCharWidth(),d=b*this.av.getCharHeight();this.scalew=this.$width/c;this.scaleh=this.sequencesHeight/d;this.miniMe=this.nullFrame.createImage(this.$width,this.sequencesHeight+this.graphHeight);this.offscreen=this.nullFrame.createImage(this.$width,this.sequencesHeight+this.graphHeight);
var c=this.miniMe.getGraphics(),a=a/this.$width,b=b/this.sequencesHeight,e=d=0,k=0,g=0,h=java.awt.Color.yellow,j,n,m=0,p=0,q,r=this.av.hasHiddenRows(),s=this.av.hasHiddenColumns(),t=!1,v=this.av.getAlignment();for(j=0;j<=this.sequencesHeight;j++)if(I(j*b)==e)m++;else{t=!1;r?(q=v.getHiddenSequences().getHiddenSequence(e),null==q?(h=v.getHiddenSequences().findIndexWithoutHiddenSeqs(e),q=v.getSequenceAt(h)):t=!0):q=v.getSequenceAt(e);for(n=0;n<this.$width;n++)if(I(n*a)==d&&I(j*b)==e)p++;else{d=I(n*a);
q.getLength()>d?(h=this.sr.getResidueBoxColour(q,d),this.av.isShowSequenceFeatures()&&(h=this.fr.findFeatureColour(h,q,d))):h=java.awt.Color.white;if(t||s&&!this.av.getColumnSelection().isVisible(d))h=h.darker().darker();c.setColor(h);1==p&&1==m?c.drawLine(k,g,k,g):c.fillRect(k,g,p,m);k=n;p=1}e=I(j*b);g=j;m=1}if(null!=this.av.getAlignmentConservationAnnotation())for(n=0;n<this.$width;n++)I(n*a),c.translate(n,this.sequencesHeight),this.ap.annotationPanel.renderer.drawGraph(c,this.av.getAlignmentConservationAnnotation(),
this.av.getAlignmentConservationAnnotation().annotations,I(a)+1,this.graphHeight,I(n*a),I(n*a)+1),c.translate(-n,-this.sequencesHeight);System.gc();this.resizing=!1;this.setBoxPosition();this.resizeAgain&&(this.resizeAgain=!1,this.updateOverviewImage())});d(c$,"setBoxPosition",function(){var a=this.av.getAlignment().getWidth()*this.av.getCharWidth(),b=(this.av.getAlignment().getHeight()+this.av.getAlignment().getHiddenSequences().getSize())*this.av.getCharHeight(),c=this.av.getStartRes(),d=this.av.getEndRes();
this.av.hasHiddenColumns()&&(c=this.av.getColumnSelection().adjustForHiddenColumns(c),d=this.av.getColumnSelection().adjustForHiddenColumns(d));var e=this.av.startSeq,k=this.av.endSeq;this.av.hasHiddenRows()&&(e=this.av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(e),k=this.av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(k));this.scalew=this.$width/a;this.scaleh=this.sequencesHeight/b;this.boxX=I(c*this.av.getCharWidth()*this.scalew);this.boxY=I(e*this.av.getCharHeight()*this.scaleh);
this.av.hasHiddenColumns();this.boxWidth=I((d-c+1)*this.av.getCharWidth()*this.scalew);this.boxHeight=I((k-e)*this.av.getCharHeight()*this.scaleh);this.repaint()});e(c$,"update",function(a){this.paint(a)},"java.awt.Graphics");e(c$,"paintComponent",function(a){var b=this.offscreen.getGraphics();null!=this.miniMe&&(b.drawImage(this.miniMe,0,0,this),b.setColor(java.awt.Color.red),b.drawRect(this.boxX,this.boxY,this.boxWidth,this.boxHeight),b.drawRect(this.boxX+1,this.boxY+1,this.boxWidth-2,this.boxHeight-
2),a.drawImage(this.offscreen,0,0,this))},"java.awt.Graphics");c$.$OverviewPanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"OverviewPanel$1",java.awt.event.ComponentAdapter);e(c$,"componentResized",function(){(this.b$["jalview.appletgui.OverviewPanel"].getSize().width!=this.b$["jalview.appletgui.OverviewPanel"].$width||this.b$["jalview.appletgui.OverviewPanel"].getSize().height!=this.b$["jalview.appletgui.OverviewPanel"].sequencesHeight+this.b$["jalview.appletgui.OverviewPanel"].graphHeight)&&
this.b$["jalview.appletgui.OverviewPanel"].updateOverviewImage()},"java.awt.event.ComponentEvent");c$=z()}});p("jalview.appletgui");q("jalview.appletgui.EmbmenuFrame java.awt.event.ActionListener $.ItemListener awt2swing.Button $.CheckboxMenuItem $.Choice $.Label $.Menu $.MenuBar $.MenuItem $.Panel java.awt.BorderLayout $.FlowLayout".split(" "),"jalview.appletgui.PCAPanel","awt2swing.Frame jalview.appletgui.AlignFrame $.CutAndPasteTransfer $.RotatableCanvas jalview.bin.JalviewLite jalview.datamodel.Alignment jalview.util.MessageManager jalview.viewmodel.PCAModel java.awt.Color $.Font java.lang.Thread".split(" "),
function(){c$=s(function(){this.pcaModel=this.av=this.rc=null;this.top=0;this.inputData=this.values=this.nuclSetting=this.protSetting=this.labels=this.calcSettings=this.menu2=this.menu1=this.menuBar1=this.borderLayout1=this.flowLayout1=this.resetButton=this.zCombobox=this.yCombobox=this.xCombobox=this.jLabel3=this.jLabel2=this.jLabel1=this.jPanel2=null;r(this,arguments)},jalview.appletgui,"PCAPanel",jalview.appletgui.EmbmenuFrame,[Runnable,java.awt.event.ActionListener,java.awt.event.ItemListener]);
J(c$,function(){this.jPanel2=new awt2swing.Panel;this.jLabel1=new awt2swing.Label;this.jLabel2=new awt2swing.Label;this.jLabel3=new awt2swing.Label;this.xCombobox=new awt2swing.Choice;this.yCombobox=new awt2swing.Choice;this.zCombobox=new awt2swing.Choice;this.resetButton=new awt2swing.Button;this.flowLayout1=new java.awt.FlowLayout;this.borderLayout1=new java.awt.BorderLayout;this.menuBar1=new awt2swing.MenuBar;this.menu1=new awt2swing.Menu;this.menu2=new awt2swing.Menu;this.calcSettings=new awt2swing.Menu;
this.labels=new awt2swing.CheckboxMenuItem;this.protSetting=new awt2swing.CheckboxMenuItem;this.nuclSetting=new awt2swing.CheckboxMenuItem;this.values=new awt2swing.MenuItem;this.inputData=new awt2swing.MenuItem});m(c$,function(a){t(this,jalview.appletgui.PCAPanel,[]);try{this.jbInit()}catch(b){if(y(b,Exception))b.printStackTrace();else throw b;}for(var c=1;8>c;c++)this.xCombobox.addItem("dim "+c),this.yCombobox.addItem("dim "+c),this.zCombobox.addItem("dim "+c);this.av=a;var c=null!=a.getSelectionGroup()&&
0<a.getSelectionGroup().getSize(),d=a.getAlignmentView(c),e=a.getAlignment().isNucleotide(),k;k=c?a.getSelectionGroup().getSequencesInOrder(a.getAlignment()):a.getAlignment().getSequencesArray();for(var g=d.getSequences(),h=g[0].getWidth(),c=0;c<k.length;c++)if(g[c].getWidth()!=h){System.out.println("Sequences must be equal length for PCA analysis");return}this.pcaModel=new jalview.viewmodel.PCAModel(d,k,e);this.rc=new jalview.appletgui.RotatableCanvas(a);this.embedMenuIfNeeded(this.rc);this.add(this.rc,
"Center");jalview.bin.JalviewLite.addFrame(this,jalview.util.MessageManager.getString("label.principal_component_analysis"),475,400);(new Thread(this)).start()},"jalview.appletgui.AlignViewport");e(c$,"run",function(){this.calcSettings.setEnabled(!1);this.rc.setEnabled(!1);try{this.nuclSetting.setState(this.pcaModel.isNucleotide()),this.protSetting.setState(!this.pcaModel.isNucleotide()),this.pcaModel.run(),this.xCombobox.select(new Integer(0)),this.yCombobox.select(new Integer(1)),this.zCombobox.select(new Integer(2)),
this.pcaModel.updateRc(this.rc),this.top=this.pcaModel.getTop()}catch(a){if(y(a,OutOfMemoryError)){System.err.println("Out of memory when calculating PCA.");return}throw a;}this.calcSettings.setEnabled(!0);this.rc.setEnabled(!0);this.rc.repaint();this.repaint()});d(c$,"doDimensionChange",function(){if(0!=this.top){var a=this.top-this.xCombobox.getSelectedIndex(),b=this.top-this.yCombobox.getSelectedIndex(),c=this.top-this.zCombobox.getSelectedIndex();this.pcaModel.updateRcView(a,b,c);this.rc.img=
null;this.rc.rotmat.setIdentity();this.rc.initAxes();this.rc.paint(this.rc.getGraphics())}});e(c$,"actionPerformed",function(a){a.getSource()===this.inputData&&this.showOriginalData();a.getSource()===this.resetButton&&(this.xCombobox.select(new Integer(0)),this.yCombobox.select(new Integer(1)),this.zCombobox.select(new Integer(2)),this.doDimensionChange());a.getSource()===this.values&&this.values_actionPerformed()},"java.awt.event.ActionEvent");e(c$,"itemStateChanged",function(a){a.getSource()===
this.xCombobox?this.xCombobox_actionPerformed():a.getSource()===this.yCombobox?this.yCombobox_actionPerformed():a.getSource()===this.zCombobox?this.zCombobox_actionPerformed():a.getSource()===this.labels?this.labels_itemStateChanged(a):a.getSource()===this.nuclSetting?this.pcaModel.isNucleotide()||(this.pcaModel.setNucleotide(!0),(new Thread(this)).start()):a.getSource()===this.protSetting&&this.pcaModel.isNucleotide()&&(this.pcaModel.setNucleotide(!1),(new Thread(this)).start())},"java.awt.event.ItemEvent");
d(c$,"xCombobox_actionPerformed",function(){this.doDimensionChange()});d(c$,"yCombobox_actionPerformed",function(){this.doDimensionChange()});d(c$,"zCombobox_actionPerformed",function(){this.doDimensionChange()});d(c$,"values_actionPerformed",function(){var a=new jalview.appletgui.CutAndPasteTransfer(!1,null),b=new awt2swing.Frame;b.add(a);jalview.bin.JalviewLite.addFrame(b,jalview.util.MessageManager.getString("label.pca_details"),500,500);a.setText(this.pcaModel.getDetails())});d(c$,"showOriginalData",
function(){var a="-";try{a=this.av.getGapCharacter()}catch(b){if(!y(b,Exception))throw b;}a=this.pcaModel.getSeqtrings().getAlignmentAndColumnSelection(a);if(null!=a&&null!=a[0]){var c=new jalview.datamodel.Alignment(a[0]);(new jalview.appletgui.AlignFrame(c,this.av.applet,"Original Data for PCA",!1)).viewport.setHiddenColumns(a[1])}});d(c$,"labels_itemStateChanged",function(){this.rc.showLabels(this.labels.getState())},"java.awt.event.ItemEvent");d(c$,"jbInit",function(){this.setLayout(this.borderLayout1);
this.jPanel2.setLayout(this.flowLayout1);this.jLabel1.setFont(new java.awt.Font("Verdana",0,12));this.jLabel1.setText("x=");this.jLabel2.setFont(new java.awt.Font("Verdana",0,12));this.jLabel2.setText("y=");this.jLabel3.setFont(new java.awt.Font("Verdana",0,12));this.jLabel3.setText("z=");this.jPanel2.setBackground(java.awt.Color.white);this.zCombobox.setFont(new java.awt.Font("Verdana",0,12));this.zCombobox.addItemListener(this);this.yCombobox.setFont(new java.awt.Font("Verdana",0,12));this.yCombobox.addItemListener(this);
this.xCombobox.setFont(new java.awt.Font("Verdana",0,12));this.xCombobox.addItemListener(this);this.resetButton.setFont(new java.awt.Font("Verdana",0,12));this.resetButton.setLabel(jalview.util.MessageManager.getString("action.reset"));this.resetButton.addActionListener(this);this.setMenuBar(this.menuBar1);this.menu1.setLabel(jalview.util.MessageManager.getString("action.file"));this.menu2.setLabel(jalview.util.MessageManager.getString("action.view"));this.calcSettings.setLabel(jalview.util.MessageManager.getString("action.change_params"));
this.labels.setLabel(jalview.util.MessageManager.getString("label.labels"));this.labels.addItemListener(this);this.values.setLabel(jalview.util.MessageManager.getString("label.output_values"));this.values.addActionListener(this);this.inputData.setLabel(jalview.util.MessageManager.getString("label.input_data"));this.nuclSetting.setLabel(jalview.util.MessageManager.getString("label.nucleotide_matrix"));this.nuclSetting.addItemListener(this);this.protSetting.setLabel(jalview.util.MessageManager.getString("label.protein_matrix"));
this.protSetting.addItemListener(this);this.add(this.jPanel2,"South");this.jPanel2.add(this.jLabel1,null);this.jPanel2.add(this.xCombobox,null);this.jPanel2.add(this.jLabel2,null);this.jPanel2.add(this.yCombobox,null);this.jPanel2.add(this.jLabel3,null);this.jPanel2.add(this.zCombobox,null);this.jPanel2.add(this.resetButton,null);this.menuBar1.add(this.menu1);this.menuBar1.add(this.menu2);this.menuBar1.add(this.calcSettings);this.menu2.add(this.labels);this.menu1.add(this.values);this.menu1.add(this.inputData);
this.calcSettings.add(this.nuclSetting);this.calcSettings.add(this.protSetting);this.inputData.addActionListener(this)})});p("jalview.appletgui");q("awt2swing.Panel jalview.api.RotatableCanvasI java.awt.event.KeyListener $.MouseListener $.MouseMotionListener jalview.math.RotatableMatrix".split(" "),"jalview.appletgui.RotatableCanvas","awt2swing.Util jalview.appletgui.PaintRefresher jalview.datamodel.SequenceGroup jalview.util.Format $.MessageManager java.awt.Color $.Dimension $.Font".split(" "),function(){c$=
s(function(){this.tooltip=this.rotmat=this.objmat=this.idmat=null;this.tooly=this.toolx=0;this.$drawAxes=!0;this.my=this.omy=this.mx=this.omx=0;this.min=this.max=this.$width=this.centre=this.prefsize=this.ig=this.img=null;this.npoint=this.scale=this.maxwidth=0;this.axes=this.orig=this.points=null;this.recty2=this.rectx2=this.recty1=this.rectx1=this.lasty=this.lastx=this.starty=this.startx=0;this.scalefactor=1;this.av=null;this.$showLabels=!1;r(this,arguments)},jalview.appletgui,"RotatableCanvas",
awt2swing.Panel,[java.awt.event.MouseListener,java.awt.event.MouseMotionListener,java.awt.event.KeyListener,jalview.api.RotatableCanvasI]);J(c$,function(){this.idmat=new jalview.math.RotatableMatrix(3,3);this.objmat=new jalview.math.RotatableMatrix(3,3);this.rotmat=new jalview.math.RotatableMatrix(3,3);this.centre=Q(3,0);this.$width=Q(3,0);this.max=Q(3,0);this.min=Q(3,0)});m(c$,function(a){t(this,jalview.appletgui.RotatableCanvas,[]);this.av=a},"jalview.viewmodel.AlignmentViewport");d(c$,"showLabels",
function(a){this.$showLabels=a;this.repaint()},"~B");e(c$,"setPoints",function(a,b){this.points=a;this.npoint=b;jalview.appletgui.PaintRefresher.Register(this,this.av.getSequenceSetId());this.prefsize=this.getPreferredSize();this.orig=Q(b,3,0);for(var c=0;c<b;c++)for(var d=a.elementAt(c),e=0;3>e;e++)this.orig[c][e]=d.coord[e];for(c=0;3>c;c++)for(e=0;3>e;e++)this.idmat.addElement(c,e,0),this.objmat.addElement(c,e,0),this.rotmat.addElement(c,e,0);this.axes=Q(3,3,0);this.initAxes();this.findCentre();
this.findWidth();this.scale=this.findScale();this.addMouseListener(this);this.addKeyListener(this);this.addMouseMotionListener(this)},"java.util.Vector,~N");d(c$,"initAxes",function(){for(var a=0;3>a;a++)for(var b=0;3>b;b++)this.axes[a][b]=a!=b?0:1});d(c$,"findWidth",function(){this.max=Q(3,0);this.min=Q(3,0);this.max[0]=-1E30;this.max[1]=-1E30;this.max[2]=-1E30;this.min[0]=1E30;this.min[1]=1E30;this.min[2]=1E30;for(var a=0;3>a;a++)for(var b=0;b<this.npoint;b++){var c=this.points.elementAt(b);c.coord[a]>=
this.max[a]&&(this.max[a]=c.coord[a]);c.coord[a]<=this.min[a]&&(this.min[a]=c.coord[a])}this.$width[0]=Math.abs(this.max[0]-this.min[0]);this.$width[1]=Math.abs(this.max[1]-this.min[1]);this.$width[2]=Math.abs(this.max[2]-this.min[2]);this.maxwidth=this.$width[0];this.$width[1]>this.$width[0]&&(this.maxwidth=this.$width[1]);this.$width[2]>this.$width[1]&&(this.maxwidth=this.$width[2])});d(c$,"findScale",function(){var a,b;0!=this.getSize().width?(a=this.getSize().width,b=this.getSize().height):(a=
this.prefsize.width,b=this.prefsize.height);return(a<b?a:b)*this.scalefactor/(2*this.maxwidth)});d(c$,"findCentre",function(){this.findWidth();this.centre[0]=(this.max[0]+this.min[0])/2;this.centre[1]=(this.max[1]+this.min[1])/2;this.centre[2]=(this.max[2]+this.min[2])/2});e(c$,"getPreferredSize",function(){return null!=this.prefsize?this.prefsize:new java.awt.Dimension(400,400)});e(c$,"getMinimumSize",function(){return this.getPreferredSize()});e(c$,"update",function(a){this.paint(a)},"java.awt.Graphics");
d(c$,"PaintComponent",function(a){if(null==this.points)a.setFont(new java.awt.Font("Verdana",0,18)),awt2swing.Util.drawString(a,jalview.util.MessageManager.getString("label.calculating_pca")+"....",20,F(this.getSize().height/2));else{if(null==this.img||this.prefsize.width!=this.getSize().width||this.prefsize.height!=this.getSize().height)this.prefsize.width=this.getSize().width,this.prefsize.height=this.getSize().height,this.scale=this.findScale(),this.img=this.createImage(this.getSize().width,this.getSize().height),
this.ig=this.img.getGraphics();this.drawBackground(this.ig,java.awt.Color.black);this.drawScene(this.ig);!0==this.$drawAxes&&this.drawAxes(this.ig);null!=this.tooltip&&(this.ig.setColor(java.awt.Color.red),awt2swing.Util.drawString(this.ig,this.tooltip,this.toolx,this.tooly));a.drawImage(this.img,0,0,this)}},"java.awt.Graphics");d(c$,"drawAxes",function(a){a.setColor(java.awt.Color.yellow);for(var b=0;3>b;b++)a.drawLine(F(this.getSize().width/2),F(this.getSize().height/2),I(this.axes[b][0]*this.scale*
this.max[0]+F(this.getSize().width/2)),I(this.axes[b][1]*this.scale*this.max[1]+F(this.getSize().height/2)))},"java.awt.Graphics");d(c$,"drawBackground",function(a,b){a.setColor(b);a.fillRect(0,0,this.prefsize.width,this.prefsize.height)},"java.awt.Graphics,java.awt.Color");d(c$,"drawScene",function(a){for(var b=F(this.getSize().width/2),c=F(this.getSize().height/2),d=0;d<this.npoint;d++){var e=this.points.elementAt(d),k=I((e.coord[0]-this.centre[0])*this.scale)+b,g=I((e.coord[1]-this.centre[1])*
this.scale)+c,h=e.coord[1]-this.centre[2];this.av.getSequenceColour(e.sequence)===java.awt.Color.black?a.setColor(java.awt.Color.white):a.setColor(this.av.getSequenceColour(e.sequence));null!=this.av.getSelectionGroup()&&this.av.getSelectionGroup().getSequences(null).contains(this.points.elementAt(d).sequence)&&a.setColor(java.awt.Color.gray);0>h&&a.setColor(a.getColor().darker());a.fillRect(k-3,g-3,6,6);this.$showLabels&&(a.setColor(java.awt.Color.red),awt2swing.Util.drawString(a,this.points.elementAt(d).sequence.getName(),
k-3,g-4))}},"java.awt.Graphics");d(c$,"minimumsize",function(){return this.prefsize});d(c$,"preferredsize",function(){return this.prefsize});e(c$,"keyTyped",function(){},"java.awt.event.KeyEvent");e(c$,"keyReleased",function(){},"java.awt.event.KeyEvent");e(c$,"keyPressed",function(a){38==a.getKeyCode()?(this.scalefactor*=1.1,this.scale=this.findScale()):40==a.getKeyCode()?(this.scalefactor*=0.9,this.scale=this.findScale()):"s"==a.getKeyChar()&&(System.err.println("DEBUG: Rectangle selection"),-1!=
this.rectx2&&-1!=this.recty2&&this.rectSelect(this.rectx1,this.recty1,this.rectx2,this.recty2));this.repaint()},"java.awt.event.KeyEvent");d(c$,"printPoints",function(){for(var a=0;a<this.npoint;a++){var b=this.points.elementAt(a);jalview.util.Format.printLong(System.out,"%5d ",a);for(var c=0;3>c;c++)jalview.util.Format.printDouble(System.out,"%13.3f  ",b.coord[c]);System.out.println()}});e(c$,"mouseClicked",function(){},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");
e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");e(c$,"mouseReleased",function(){},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){var b=a.getX();a=a.getY();this.mx=b;this.my=a;this.omx=this.mx;this.omy=this.my;this.startx=b;this.starty=a;this.rectx1=b;this.recty1=a;this.recty2=this.rectx2=-1;b=this.findPoint(b,a);null!=b&&(null==this.av.getSelectionGroup()&&this.av.setSelectionGroup(new jalview.datamodel.SequenceGroup),this.av.getSelectionGroup().addOrRemove(b,!0),this.av.getSelectionGroup().setEndRes(this.av.getAlignment().getWidth()-
1),jalview.appletgui.PaintRefresher.Refresh(this,this.av.getSequenceSetId()),this.av.sendSelection());this.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(a){var b=this.findPoint(a.getX(),a.getY());null==b?this.tooltip=null:(this.tooltip=b.getName(),this.toolx=a.getX(),this.tooly=a.getY());this.repaint()},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(a){this.mx=a.getX();this.my=a.getY();this.rotmat.setIdentity();this.rotmat.rotate(this.my-this.omy,"x");this.rotmat.rotate(this.mx-
this.omx,"y");for(a=0;a<this.npoint;a++){var b=this.points.elementAt(a);b.coord[0]-=this.centre[0];b.coord[1]-=this.centre[1];b.coord[2]-=this.centre[2];b.coord=this.rotmat.vectorMultiply(b.coord);b.coord[0]+=this.centre[0];b.coord[1]+=this.centre[1];b.coord[2]+=this.centre[2]}for(a=0;3>a;a++)this.axes[a]=this.rotmat.vectorMultiply(this.axes[a]);this.omx=this.mx;this.omy=this.my;this.paint(this.getGraphics())},"java.awt.event.MouseEvent");d(c$,"rectSelect",function(a,b,c,d){for(var e=0;e<this.npoint;e++){var k=
this.points.elementAt(e),g=F((k.coord[0]-this.centre[0])*this.scale+this.getSize().width/2),h=F((k.coord[1]-this.centre[1])*this.scale+this.getSize().height/2);g>a&&g<c&&h>b&&h<d&&null!=this.av&&(this.av.getSelectionGroup().getSequences(null).contains(k.sequence)||this.av.getSelectionGroup().addSequence(k.sequence,!0))}},"~N,~N,~N,~N");d(c$,"findPoint",function(a,b){for(var c=F(this.getSize().width/2),d=F(this.getSize().height/2),e=-1,k=0;k<this.npoint;k++){var g=this.points.elementAt(k),h=I((g.coord[0]-
this.centre[0])*this.scale)+c,g=I((g.coord[1]-this.centre[1])*this.scale)+d;3>Math.abs(h-a)&&3>Math.abs(g-b)&&(e=k)}return-1!=e?this.points.elementAt(e).sequence:null},"~N,~N")});p("jalview.api");M(jalview.api,"RotatableCanvasI");p("jalview.math");c$=s(function(){this.rot=this.temp=this.matrix=null;r(this,arguments)},jalview.math,"RotatableMatrix");m(c$,function(a,b){this.matrix=Q(a,b,0);this.temp=Q(3,0);this.rot=Q(3,3,0)},"~N,~N");d(c$,"addElement",function(a,b,c){this.matrix[a][b]=c},"~N,~N,~N");
d(c$,"print",function(){System.out.println(this.matrix[0][0]+" "+this.matrix[0][1]+" "+this.matrix[0][2]);System.out.println(this.matrix[1][0]+" "+this.matrix[1][1]+" "+this.matrix[1][2]);System.out.println(this.matrix[2][0]+" "+this.matrix[2][1]+" "+this.matrix[2][2])});d(c$,"rotate",function(a,b){var c=Math.cos(3.141592653589793*a/180),d=Math.sin(3.141592653589793*a/180);"z"==b&&(this.rot[0][0]=c,this.rot[0][1]=-d,this.rot[0][2]=0,this.rot[1][0]=d,this.rot[1][1]=c,this.rot[1][2]=0,this.rot[2][0]=
0,this.rot[2][1]=0,this.rot[2][2]=1,this.preMultiply(this.rot));"x"==b&&(this.rot[0][0]=1,this.rot[0][1]=0,this.rot[0][2]=0,this.rot[1][0]=0,this.rot[1][1]=c,this.rot[1][2]=d,this.rot[2][0]=0,this.rot[2][1]=-d,this.rot[2][2]=c,this.preMultiply(this.rot));"y"==b&&(this.rot[0][0]=c,this.rot[0][1]=0,this.rot[0][2]=-d,this.rot[1][0]=0,this.rot[1][1]=1,this.rot[1][2]=0,this.rot[2][0]=d,this.rot[2][1]=0,this.rot[2][2]=c,this.preMultiply(this.rot))},"~N,~S");d(c$,"vectorMultiply",function(a){this.temp[0]=
a[0];this.temp[1]=a[1];this.temp[2]=a[2];for(var b=0;3>b;b++)this.temp[b]=this.matrix[b][0]*a[0]+this.matrix[b][1]*a[1]+this.matrix[b][2]*a[2];a[0]=this.temp[0];a[1]=this.temp[1];a[2]=this.temp[2];return a},"~A");d(c$,"preMultiply",function(a){for(var b=Q(3,3,0),c=0;3>c;c++)for(var d=0;3>d;d++)b[c][d]=a[c][0]*this.matrix[0][d]+a[c][1]*this.matrix[1][d]+a[c][2]*this.matrix[2][d];for(c=0;3>c;c++)for(d=0;3>d;d++)this.matrix[c][d]=b[c][d]},"~A");d(c$,"postMultiply",function(a){for(var b=Q(3,3,0),c=0;3>
c;c++)for(var d=0;3>d;d++)b[c][d]=this.matrix[c][0]*a[0][d]+this.matrix[c][1]*a[1][d]+this.matrix[c][2]*a[2][d];for(c=0;3>c;c++)for(d=0;3>d;d++)this.matrix[c][d]=b[c][d]},"~A");d(c$,"setIdentity",function(){this.matrix[0][0]=1;this.matrix[1][1]=1;this.matrix[2][2]=1;this.matrix[0][1]=0;this.matrix[0][2]=0;this.matrix[1][0]=0;this.matrix[1][2]=0;this.matrix[2][0]=0;this.matrix[2][1]=0});p("jalview.viewmodel");q(null,"jalview.viewmodel.PCAModel",["jalview.analysis.PCA","jalview.datamodel.SequencePoint",
"java.lang.StringBuffer","java.util.Vector"],function(){c$=s(function(){this.pca=null;this.top=0;this.score_matrix=this.seqs=this.seqstrings=null;this.nucleotide=!1;this.points=null;this.jvCalcMode=!0;r(this,arguments)},jalview.viewmodel,"PCAModel");m(c$,function(a,b,c){this.seqstrings=a;this.seqs=b;this.score_matrix=(this.nucleotide=c)?"PID":"BLOSUM62"},"jalview.datamodel.AlignmentView,~A,~B");d(c$,"isJvCalcMode",function(){return this.jvCalcMode});d(c$,"run",function(){this.pca=new jalview.analysis.PCA(this.seqstrings.getSequenceStrings(" "),
this.nucleotide,this.score_matrix);this.pca.setJvCalcMode(this.jvCalcMode);this.pca.run();for(var a=0;a<this.seqs.length&&null!=this.seqs[a];)a++;for(var b=U(a,a,0),c=0;c<a;c++)1E-4<this.pca.getEigenvalue(c)&&(b[c]=this.pca.component(c));this.top=this.pca.getM().rows-1;this.points=new java.util.Vector;a=this.pca.getComponents(this.top-1,this.top-2,this.top-3,100);for(c=0;c<this.pca.getM().rows;c++)b=new jalview.datamodel.SequencePoint(this.seqs[c],a[c]),this.points.addElement(b)});d(c$,"updateRc",
function(a){a.setPoints(this.points,this.pca.getM().rows)},"jalview.api.RotatableCanvasI");d(c$,"isNucleotide",function(){return this.nucleotide});d(c$,"setNucleotide",function(a){this.nucleotide=a},"~B");d(c$,"getTop",function(){return this.top});d(c$,"updateRcView",function(a,b,c){a=this.pca.getComponents(a-1,b-1,c-1,100);for(b=0;b<this.pca.getM().rows;b++)this.points.elementAt(b).coord=a[b]},"~N,~N,~N");d(c$,"getDetails",function(){return this.pca.getDetails()});d(c$,"getSeqtrings",function(){return this.seqstrings});
d(c$,"getPointsasCsv",function(a,b,c,d){var e=new StringBuffer;e.append('"Sequence"');if(a)e.append(","),e.append(""+b),e.append(","),e.append(""+c),e.append(","),e.append(""+d);else{b=1;for(c=this.pca.component(1).length;b<=c;b++)e.append(","+b)}e.append("\n");for(c=0;c<this.seqs.length;c++){e.append('"'+this.seqs[c].getName()+'"');if(a){d=this.getPointPosition(c);for(b=0;b<d.length;b++)e.append(","),e.append(d[b])}else{d=this.pca.component(c);for(b=d.length-1;0<=b;b--)e.append(","),e.append(d[b])}e.append("\n")}return e.toString()},
"~B,~N,~N,~N");d(c$,"getPointPosition",function(a){var b=U(3,0);a=this.points.elementAt(a).coord;b[0]=a[0];b[1]=a[1];b[2]=a[2];return b},"~N");d(c$,"setJvCalcMode",function(a){this.jvCalcMode=a},"~B");d(c$,"getScore_matrix",function(){return this.score_matrix});d(c$,"setScore_matrix",function(a){this.score_matrix=a},"~S")});p("jalview.analysis");q(["java.lang.StringBuffer"],"jalview.analysis.PCA",["jalview.datamodel.BinarySequence","jalview.math.Matrix","jalview.schemes.ResidueProperties"],function(){c$=
s(function(){this.details=this.eigenvector=this.eigenvalue=this.m2=this.symm=this.m=null;this.jvCalcMode=!0;r(this,arguments)},jalview.analysis,"PCA",null,Runnable);J(c$,function(){this.details=new StringBuffer});m(c$,function(a){this.construct(a,!1)},"~A");m(c$,function(a,b){this.construct(a,b,null)},"~A,~B");m(c$,function(a,b,c){for(var d=Array(a.length),e=0;e<a.length&&null!=a[e];)d[e]=new jalview.datamodel.BinarySequence(a[e],b),d[e].encode(),e++;var k=Array(a.length),e=0,g=null;null!=c&&(g=jalview.schemes.ResidueProperties.getScoreMatrix(c));
null==g&&(g=jalview.schemes.ResidueProperties.getScoreMatrix(c=b?"DNA":"BLOSUM62"));for(this.details.append("PCA calculation using "+c+" sequence similarity matrix\n========\n\n");e<a.length&&null!=a[e];){k[e]=new jalview.datamodel.BinarySequence(a[e],b);if(null!=g)try{k[e].matrixEncode(g)}catch(h){if(y(h,jalview.datamodel.BinarySequence.InvalidSequenceTypeException))this.details.append("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n");else throw h;}e++}for(a=
0;a<d.length&&null!=d[a];)a++;b=U(a,d[0].getDBinary().length,0);e=U(a,k[0].getDBinary().length,0);for(g=0;g<a;)b[g]=d[g].getDBinary(),e[g]=k[g].getDBinary(),g++;this.m=new jalview.math.Matrix(b,a,d[0].getDBinary().length);this.m2=new jalview.math.Matrix(e,a,k[0].getDBinary().length)},"~A,~B,~S");d(c$,"getM",function(){return this.m});d(c$,"getEigenvalue",function(a){return this.eigenvector.d[a]},"~N");d(c$,"getComponents",function(a,b,c,d){for(var e=Q(this.m.rows,3,0),k=0;k<this.m.rows;k++)e[k][0]=
this.component(k,a)*d,e[k][1]=this.component(k,b)*d,e[k][2]=this.component(k,c)*d;return e},"~N,~N,~N,~N");d(c$,"component",function(a){for(var b=U(this.m.rows,0),c=0;c<this.m.rows;c++)b[c]=this.component(c,a);return b},"~N");d(c$,"component",function(a,b){for(var c=0,d=0;d<this.symm.cols;d++)c+=this.symm.value[a][d]*this.eigenvector.value[d][b];return c/this.eigenvector.d[b]},"~N,~N");d(c$,"getDetails",function(){return this.details.toString()});e(c$,"run",function(){var a=(H("jalview.analysis.PCA$1")?
0:jalview.analysis.PCA.$PCA$1$(),C(jalview.analysis.PCA$1,this,null,System.out));try{this.details.append("PCA Calculation Mode is "+(this.jvCalcMode?"Jalview variant":"Original SeqSpace")+"\n");var b=this.m.transpose();this.details.append(" --- OrigT * Orig ---- \n");this.eigenvector=this.jvCalcMode?b.preMultiply(this.m2):b.preMultiply(this.m);this.eigenvector.print(a);this.symm=this.eigenvector.copy();this.eigenvector.tred();this.details.append(" ---Tridiag transform matrix ---\n");this.details.append(" --- D vector ---\n");
this.eigenvector.printD(a);a.println();this.details.append("--- E vector ---\n");this.eigenvector.printE(a);a.println();this.eigenvector.tqli()}catch(c){if(y(c,Exception))c.printStackTrace(),this.details.append("\n*** Unexpected exception when performing PCA ***\n"+c.getLocalizedMessage()),this.details.append("*** Matrices below may not be fully diagonalised. ***\n");else throw c;}this.details.append(" --- New diagonalization matrix ---\n");this.eigenvector.print(a);this.details.append(" --- Eigenvalues ---\n");
this.eigenvector.printD(a);a.println()});d(c$,"setJvCalcMode",function(a){this.jvCalcMode=a},"~B");c$.$PCA$1$=function(){A(self.c$);c$=L(jalview.analysis,"PCA$1",java.io.PrintStream);d(c$,"print",function(a){this.b$["jalview.analysis.PCA"].details.append(a)},"~S");d(c$,"println",function(){this.b$["jalview.analysis.PCA"].details.append("\n")});c$=z()}});p("jalview.datamodel");q(["jalview.datamodel.Sequence","java.lang.Exception"],"jalview.datamodel.BinarySequence",["jalview.schemes.ResidueProperties"],
function(){c$=s(function(){H("jalview.datamodel.BinarySequence.InvalidSequenceTypeException")||jalview.datamodel.BinarySequence.$BinarySequence$InvalidSequenceTypeException$();this.dbinary=this.binary=null;this.isNa=!1;r(this,arguments)},jalview.datamodel,"BinarySequence",jalview.datamodel.Sequence);m(c$,function(a,b){t(this,jalview.datamodel.BinarySequence,["",a,0,a.length]);this.isNa=b},"~S,~B");d(c$,"initMatrixGetNoRes",function(){var a=this.isNa?10:23;this.dbinary=U(this.getSequence().length*
a,0);for(var b=0;b<this.dbinary.length;b++)this.dbinary[b]=0;return a});d(c$,"getSymbolmatrix",function(){return this.isNa?jalview.schemes.ResidueProperties.nucleotideIndex:jalview.schemes.ResidueProperties.aaIndex});d(c$,"encode",function(){for(var a=this.initMatrixGetNoRes(),b=this.getSymbolmatrix(),c=0;c<this.getSequence().length;c++){var d=a-1;try{d=b[this.getCharAt(c).charCodeAt(0)]}catch(e){if(y(e,NullPointerException))d=a-1;else throw e;}d>=a&&(d=a-1);this.dbinary[c*a+d]=1}});d(c$,"matrixEncode",
function(a){if(this.isNa!=a.isDNA())throw C(jalview.datamodel.BinarySequence.InvalidSequenceTypeException,this,null,"matrix "+a.getClass().getCanonicalName()+" is not a valid matrix for "+(this.isNa?"nucleotide":"protein")+"sequences");this.matrixEncode(a.isDNA()?jalview.schemes.ResidueProperties.nucleotideIndex:jalview.schemes.ResidueProperties.aaIndex,a.getMatrix())},"jalview.schemes.ScoreMatrix");d(c$,"matrixEncode",function(a,b){for(var c=this.initMatrixGetNoRes(),d=0,e=this.getSequence().length;d<
e;d++){var k=c-1;try{k=a[this.getCharAt(d).charCodeAt(0)]}catch(g){if(y(g,NullPointerException))k=c-1;else throw g;}k>=c&&(k=c-1);for(var h=0;h<c;h++)this.dbinary[d*c+h]=b[k][h]}},"~A,~A");d(c$,"toBinaryString",function(){for(var a="",b=0;b<this.binary.length;b++)a+=(new Integer(this.binary[b])).toString(),b<this.binary.length-1&&(a+=" ");return a});d(c$,"getDBinary",function(){return this.dbinary});c$.$BinarySequence$InvalidSequenceTypeException$=function(){A(self.c$);c$=s(function(){O(this,arguments);
r(this,arguments)},jalview.datamodel.BinarySequence,"InvalidSequenceTypeException",Exception);c$=z()}});p("jalview.math");q(null,"jalview.math.Matrix",["jalview.util.Format","$.MessageManager","java.lang.Exception"],function(){c$=s(function(){this.value=null;this.cols=this.rows=0;this.e=this.d=null;this.maxIter=45;r(this,arguments)},jalview.math,"Matrix");m(c$,function(a,b,c){this.rows=b;this.cols=c;this.value=a},"~A,~N,~N");d(c$,"transpose",function(){for(var a=U(this.cols,this.rows,0),b=0;b<this.cols;b++)for(var c=
0;c<this.rows;c++)a[b][c]=this.value[c][b];return new jalview.math.Matrix(a,this.cols,this.rows)});d(c$,"print",function(a){for(var b=0;b<this.rows;b++){for(var c=0;c<this.cols;c++)jalview.util.Format.printDouble(a,"%8.2f",this.value[b][c]);a.println()}},"java.io.PrintStream");d(c$,"preMultiply",function(a){for(var b=U(a.rows,this.cols,0),c=0;c<a.rows;c++)for(var d=0;d<this.cols;d++)for(var e=b[c][d]=0;e<a.cols;e++)b[c][d]+=a.value[c][e]*this.value[e][d];return new jalview.math.Matrix(b,a.rows,this.cols)},
"jalview.math.Matrix");d(c$,"vectorPostMultiply",function(a){for(var b=U(a.length,0),c=0;c<a.length;c++)for(var d=b[c]=0;d<a.length;d++)b[c]+=this.value[c][d]*a[d];return b},"~A");d(c$,"postMultiply",function(a){for(var b=U(this.rows,a.cols,0),c=0;c<this.rows;c++)for(var d=0;d<a.cols;d++)for(var e=b[c][d]=0;e<this.rows;e++)b[c][d]+=this.value[c][e]*a.value[e][d];return new jalview.math.Matrix(b,this.cols,a.rows)},"jalview.math.Matrix");d(c$,"copy",function(){for(var a=U(this.rows,this.cols,0),b=0;b<
this.rows;b++)for(var c=0;c<this.cols;c++)a[b][c]=this.value[b][c];return new jalview.math.Matrix(a,this.rows,this.cols)});d(c$,"tred",function(){var a=this.rows,b,c,d,e,k,g,h,j;this.d=U(this.rows,0);this.e=U(this.rows,0);for(e=a;2<=e;e--){b=e-1;d=g=0;if(1<b){for(c=1;c<=b;c++)d+=Math.abs(this.value[e-1][c-1]);if(0==d)this.e[e-1]=this.value[e-1][b-1];else{for(c=1;c<=b;c++)this.value[e-1][c-1]/=d,g+=this.value[e-1][c-1]*this.value[e-1][c-1];j=this.value[e-1][b-1];h=0<j?-1*Math.sqrt(g):Math.sqrt(g);
this.e[e-1]=d*h;g-=j*h;this.value[e-1][b-1]=j-h;j=0;for(d=1;d<=b;d++){this.value[d-1][e-1]=this.value[e-1][d-1]/g;h=0;for(c=1;c<=d;c++)h+=this.value[d-1][c-1]*this.value[e-1][c-1];for(c=d+1;c<=b;c++)h+=this.value[c-1][d-1]*this.value[e-1][c-1];this.e[d-1]=h/g;j+=this.e[d-1]*this.value[e-1][d-1]}k=j/(g+g);for(d=1;d<=b;d++){j=this.value[e-1][d-1];h=this.e[d-1]-k*j;this.e[d-1]=h;for(c=1;c<=d;c++)this.value[d-1][c-1]-=j*this.e[c-1]+h*this.value[e-1][c-1]}}}else this.e[e-1]=this.value[e-1][b-1];this.d[e-
1]=g}this.d[0]=0;this.e[0]=0;for(e=1;e<=a;e++){b=e-1;if(0!=this.d[e-1])for(d=1;d<=b;d++){h=0;for(c=1;c<=b;c++)h+=this.value[e-1][c-1]*this.value[c-1][d-1];for(c=1;c<=b;c++)this.value[c-1][d-1]-=h*this.value[c-1][e-1]}this.d[e-1]=this.value[e-1][e-1];for(d=this.value[e-1][e-1]=1;d<=b;d++)this.value[d-1][e-1]=0,this.value[e-1][d-1]=0}});d(c$,"tqli",function(){var a=this.rows,b,c,d,e,k,g,h,j,n,m,p;for(e=2;e<=a;e++)this.e[e-2]=this.e[e-1];this.e[a-1]=0;for(c=1;c<=a;c++){d=0;do{for(b=c;b<=a-1&&!(e=Math.abs(this.d[b-
1])+Math.abs(this.d[b]),Math.abs(this.e[b-1])+e==e);b++);if(b!=c){d++;if(d==this.maxIter)throw new Exception(jalview.util.MessageManager.formatMessage("exception.matrix_too_many_iteration",E(-1,["tqli",Integer.$valueOf(this.maxIter).toString()])));j=(this.d[c]-this.d[c-1])/(2*this.e[c-1]);k=Math.sqrt(j*j+1);j=this.d[b-1]-this.d[c-1]+this.e[c-1]/(j+this.sign(k,j));g=m=1;h=0;for(e=b-1;e>=c;e--){n=g*this.e[e-1];p=m*this.e[e-1];Math.abs(n)>=Math.abs(j)?(m=j/n,k=Math.sqrt(m*m+1),this.e[e]=n*k,g=1/k,m*=
g):(g=n/j,k=Math.sqrt(g*g+1),this.e[e]=j*k,m=1/k,g*=m);j=this.d[e]-h;k=(this.d[e-1]-j)*g+2*m*p;h=g*k;this.d[e]=j+h;j=m*k-p;for(k=1;k<=a;k++)n=this.value[k-1][e],this.value[k-1][e]=g*this.value[k-1][e-1]+m*n,this.value[k-1][e-1]=m*this.value[k-1][e-1]-g*n}this.d[c-1]-=h;this.e[c-1]=j;this.e[b-1]=0}}while(b!=c)}});d(c$,"tred2",function(){var a=this.rows,b,c,d,e,k,g,h,j;this.d=U(this.rows,0);this.e=U(this.rows,0);for(e=a-1;1<=e;e--){b=e-1;d=g=0;if(0<b){for(c=0;c<b;c++)d+=Math.abs(this.value[e][c]);if(0==
d)this.e[e]=this.value[e][b];else{for(c=0;c<b;c++)this.value[e][c]/=d,g+=this.value[e][c]*this.value[e][c];j=this.value[e][b];h=0<j?-1*Math.sqrt(g):Math.sqrt(g);this.e[e]=d*h;g-=j*h;this.value[e][b]=j-h;for(d=j=0;d<b;d++){this.value[d][e]=this.value[e][d]/g;for(c=h=0;c<d;c++)h+=this.value[d][c]*this.value[e][c];for(c=d;c<b;c++)h+=this.value[c][d]*this.value[e][c];this.e[d]=h/g;j+=this.e[d]*this.value[e][d]}k=j/(g+g);for(d=0;d<b;d++){j=this.value[e][d];h=this.e[d]-k*j;this.e[d]=h;for(c=0;c<d;c++)this.value[d][c]-=
j*this.e[c]+h*this.value[e][c]}}}else this.e[e]=this.value[e][b];this.d[e]=g}this.d[0]=0;for(e=this.e[0]=0;e<a;e++){b=e-1;if(0!=this.d[e])for(d=0;d<b;d++){for(c=h=0;c<b;c++)h+=this.value[e][c]*this.value[c][d];for(c=0;c<b;c++)this.value[c][d]-=h*this.value[c][e]}this.d[e]=this.value[e][e];this.value[e][e]=1;for(d=0;d<b;d++)this.value[d][e]=0,this.value[e][d]=0}});d(c$,"tqli2",function(){var a=this.rows,b,c,d,e,k,g,h,j,n,m,p;for(e=2;e<=a;e++)this.e[e-2]=this.e[e-1];this.e[a-1]=0;for(c=1;c<=a;c++){d=
0;do{for(b=c;b<=a-1&&!(e=Math.abs(this.d[b-1])+Math.abs(this.d[b]),Math.abs(this.e[b-1])+e==e);b++);if(b!=c){d++;if(d==this.maxIter)throw new Exception(jalview.util.MessageManager.formatMessage("exception.matrix_too_many_iteration",E(-1,["tqli2",Integer.$valueOf(this.maxIter).toString()])));j=(this.d[c]-this.d[c-1])/(2*this.e[c-1]);k=Math.sqrt(j*j+1);j=this.d[b-1]-this.d[c-1]+this.e[c-1]/(j+this.sign(k,j));g=m=1;h=0;for(e=b-1;e>=c;e--){n=g*this.e[e-1];p=m*this.e[e-1];Math.abs(n)>=Math.abs(j)?(m=j/
n,k=Math.sqrt(m*m+1),this.e[e]=n*k,g=1/k,m*=g):(g=n/j,k=Math.sqrt(g*g+1),this.e[e]=j*k,m=1/k,g*=m);j=this.d[e]-h;k=(this.d[e-1]-j)*g+2*m*p;h=g*k;this.d[e]=j+h;j=m*k-p;for(k=1;k<=a;k++)n=this.value[k-1][e],this.value[k-1][e]=g*this.value[k-1][e-1]+m*n,this.value[k-1][e-1]=m*this.value[k-1][e-1]-g*n}this.d[c-1]-=h;this.e[c-1]=j;this.e[b-1]=0}}while(b!=c)}});d(c$,"sign",function(a,b){return 0>b?-Math.abs(a):Math.abs(a)},"~N,~N");d(c$,"getColumn",function(a){for(var b=U(this.rows,0),c=0;c<this.rows;c++)b[c]=
this.value[c][a];return b},"~N");d(c$,"printD",function(a){for(var b=0;b<this.rows;b++)jalview.util.Format.printDouble(a,"%15.4e",this.d[b])},"java.io.PrintStream");d(c$,"printE",function(a){for(var b=0;b<this.rows;b++)jalview.util.Format.printDouble(a,"%15.4e",this.e[b])},"java.io.PrintStream")});p("jalview.datamodel");c$=s(function(){this.isPlaceholder=!1;this.coord=this.sequence=null;r(this,arguments)},jalview.datamodel,"SequencePoint");m(c$,function(a,b){this.sequence=a;this.coord=b},"jalview.datamodel.SequenceI,~A");
p("jalview.appletgui");q("awt2swing.Panel java.awt.event.ActionListener awt2swing.Button $.ScrollPane $.TextArea java.awt.BorderLayout java.util.Vector".split(" "),"jalview.appletgui.PairwiseAlignPanel","jalview.analysis.AlignSeq jalview.appletgui.AlignFrame jalview.datamodel.Alignment jalview.util.Format $.MessageManager java.awt.Font".split(" "),function(){c$=s(function(){this.borderLayout1=this.jPanel1=this.viewInEditorButton=this.textarea=this.scrollPane=this.ap=this.sequences=null;r(this,arguments)},
jalview.appletgui,"PairwiseAlignPanel",awt2swing.Panel,java.awt.event.ActionListener);J(c$,function(){this.sequences=new java.util.Vector;this.scrollPane=new awt2swing.ScrollPane;this.textarea=new awt2swing.TextArea;this.viewInEditorButton=new awt2swing.Button;this.jPanel1=new awt2swing.Panel;this.borderLayout1=new java.awt.BorderLayout});m(c$,function(a){t(this,jalview.appletgui.PairwiseAlignPanel,[]);try{this.jbInit()}catch(b){if(y(b,Exception))b.printStackTrace();else throw b;}this.ap=a;this.sequences=
new java.util.Vector;var c,d=a.av.getViewAsString(!0);c=null==a.av.getSelectionGroup()?a.av.getAlignment().getSequencesArray():a.av.getSelectionGroup().getSequencesInOrder(a.av.getAlignment());var e=Q(c.length,c.length,0),k=0,g=a.av.getSelectionGroup().getSize();a=a.av.getAlignment().isNucleotide()?"dna":"pep";for(var h=1;h<g;h++)for(var j=0;j<h;j++){var n=new jalview.analysis.AlignSeq(c[h],d[h],c[j],d[j],a);0==n.s1str.length||0==n.s2str.length||(n.calcScoreMatrix(),n.traceAlignment(),n.printAlignment(System.out),
e[h][j]=n.getMaxScore()/n.getASeq1().length,k+=e[h][j],this.textarea.append(n.getOutput()),this.sequences.add(n.getAlignedSeq1()),this.sequences.add(n.getAlignedSeq1()))}if(2<g){System.out.println("Pairwise alignment scaled similarity score matrix\n");for(h=0;h<g;h++)jalview.util.Format.print(System.out,"%s \n",""+h+" "+c[h].getName());System.out.println("\n");for(h=0;h<g;h++)for(j=0;j<h;j++)jalview.util.Format.printDouble(System.out,"%7.3f",e[h][j]/k);System.out.println("\n")}},"jalview.appletgui.AlignmentPanel");
e(c$,"actionPerformed",function(a){a.getSource()===this.viewInEditorButton&&this.viewInEditorButton_actionPerformed()},"java.awt.event.ActionEvent");d(c$,"viewInEditorButton_actionPerformed",function(){for(var a=Array(this.sequences.size()),b=0;b<this.sequences.size();b++)a[b]=this.sequences.elementAt(b);new jalview.appletgui.AlignFrame(new jalview.datamodel.Alignment(a),this.ap.av.applet,"Pairwise Aligned Sequences",!1)});d(c$,"jbInit",function(){this.setLayout(this.borderLayout1);this.textarea.setFont(new java.awt.Font("Monospaced",
0,12));this.textarea.setText("");this.viewInEditorButton.setFont(new java.awt.Font("Verdana",0,12));this.viewInEditorButton.setLabel(jalview.util.MessageManager.getString("label.view_alignment_editor"));this.viewInEditorButton.addActionListener(this);this.add(this.scrollPane,"Center");this.scrollPane.add(this.textarea);this.add(this.jPanel1,"South");this.jPanel1.add(this.viewInEditorButton,null)})});p("jalview.appletgui");q(["jalview.appletgui.SliderPanel","java.awt.event.WindowListener","java.util.Stack"],
"jalview.appletgui.RedundancyPanel","awt2swing.Frame jalview.analysis.AlignSeq jalview.appletgui.PaintRefresher jalview.bin.JalviewLite jalview.commands.EditCommand jalview.util.MessageManager java.awt.event.AdjustmentListener java.lang.Thread java.util.ArrayList $.Vector".split(" "),function(){c$=s(function(){this.redundantSeqs=this.frame=this.originalSequences=this.redundancy=this.historyList=null;r(this,arguments)},jalview.appletgui,"RedundancyPanel",jalview.appletgui.SliderPanel,[Runnable,java.awt.event.WindowListener]);
J(c$,function(){this.historyList=new java.util.Stack});m(c$,function(a){t(this,jalview.appletgui.RedundancyPanel,[a,0,!1,null]);this.redundantSeqs=new java.util.Vector;this.ap=a;this.undoButton.setVisible(!0);this.applyButton.setVisible(!0);this.allGroupsCheck.setVisible(!1);this.label.setText(jalview.util.MessageManager.getString("label.enter_redundancy_threshold"));this.valueField.setText("100");this.slider.setVisibleAmount(1);this.slider.setMinimum(0);this.slider.setMaximum(100+this.slider.getVisibleAmount());
this.slider.setValue(100);this.slider.addAdjustmentListener((H("jalview.appletgui.RedundancyPanel$1")?0:jalview.appletgui.RedundancyPanel.$RedundancyPanel$1$(),C(jalview.appletgui.RedundancyPanel$1,this,null)));this.frame=new awt2swing.Frame;this.frame.add(this);jalview.bin.JalviewLite.addFrame(this.frame,jalview.util.MessageManager.getString("label.redundancy_threshold_selection"),400,100);this.frame.addWindowListener(this);(new Thread(this)).start()},"jalview.appletgui.AlignmentPanel");e(c$,"run",
function(){this.label.setText(jalview.util.MessageManager.getString("label.calculating"));this.slider.setVisible(!1);this.applyButton.setEnabled(!1);this.valueField.setVisible(!1);this.validate();var a=this.ap.av.getSelectionGroup(),b;null!=a&&1<=a.getSize()?(this.originalSequences=a.getSequencesInOrder(this.ap.av.getAlignment()),b=a.getStartRes(),a=a.getEndRes()):(this.originalSequences=this.ap.av.getAlignment().getSequencesArray(),b=0,a=this.ap.av.getAlignment().getWidth());this.redundancy=jalview.analysis.AlignSeq.computeRedundancyMatrix(this.originalSequences,
null,b,a,!1);this.label.setText(jalview.util.MessageManager.getString("label.enter_redundancy_threshold"));this.slider.setVisible(!0);this.applyButton.setEnabled(!0);this.valueField.setVisible(!0);this.validate();this.sliderValueChanged()});d(c$,"sliderValueChanged",function(){if(null!=this.redundancy){for(var a=this.slider.getValue(),b=new java.util.ArrayList,c=0;c<this.redundancy.length;c++)a<=this.redundancy[c]&&b.add(this.originalSequences[c]);this.ap.idPanel.idCanvas.setHighlighted(b);jalview.appletgui.PaintRefresher.Refresh(this,
this.ap.av.getSequenceSetId(),!0,!0)}});e(c$,"applyButton_actionPerformed",function(){var a=new java.util.Vector;this.undoButton.setEnabled(!0);for(var b=this.slider.getValue(),c=this.ap.av.getSelectionGroup(),d=0;d<this.redundancy.length;d++)b<=this.redundancy[d]&&a.addElement(this.originalSequences[d]);if(0<a.size()){for(var b=Array(a.size()),e=0,d=0;d<a.size();d++)b[d]=a.elementAt(d),b[d].getLength()>e&&(e=b[d].getLength());for(var e=new jalview.commands.EditCommand(jalview.util.MessageManager.getString("action.remove_redundancy"),
jalview.commands.EditCommand.Action.CUT,b,0,e,this.ap.av.getAlignment()),k=this.ap.av.getAlignment(),d=0;d<a.size();d++)k.deleteSequence(b[d]),null!=c&&c.deleteSequence(b[d],!1);this.historyList.push(e);this.ap.alignFrame.addHistoryItem(e);jalview.appletgui.PaintRefresher.Refresh(this,this.ap.av.getSequenceSetId(),!0,!0);this.ap.av.firePropertyChange("alignment",null,this.ap.av.getAlignment().getSequences())}});e(c$,"undoButton_actionPerformed",function(){var a=this.historyList.pop();a.undoCommand(null);
this.ap.av.getHistoryList().contains(a)&&(this.ap.av.getHistoryList().remove(a),this.ap.alignFrame.updateEditMenuBar(),this.ap.av.firePropertyChange("alignment",null,this.ap.av.getAlignment().getSequences()));this.ap.paintAlignment(!0);0==this.historyList.size()&&this.undoButton.setEnabled(!1)});d(c$,"valueField_actionPerformed",function(){try{var a=Integer.parseInt(this.valueField.getText());this.slider.setValue(a)}catch(b){if(y(b,Exception))this.valueField.setText(this.slider.getValue()+"");else throw b;
}},"java.awt.event.ActionEvent");e(c$,"windowOpened",function(){},"java.awt.event.WindowEvent");e(c$,"windowClosing",function(){this.ap.idPanel.idCanvas.setHighlighted(null)},"java.awt.event.WindowEvent");e(c$,"windowClosed",function(){},"java.awt.event.WindowEvent");e(c$,"windowActivated",function(){},"java.awt.event.WindowEvent");e(c$,"windowDeactivated",function(){},"java.awt.event.WindowEvent");e(c$,"windowIconified",function(){},"java.awt.event.WindowEvent");e(c$,"windowDeiconified",function(){},
"java.awt.event.WindowEvent");c$.$RedundancyPanel$1$=function(){A(self.c$);c$=L(jalview.appletgui,"RedundancyPanel$1",null,java.awt.event.AdjustmentListener);e(c$,"adjustmentValueChanged",function(){this.b$["jalview.appletgui.RedundancyPanel"].valueField.setText(this.b$["jalview.appletgui.RedundancyPanel"].slider.getValue()+"");this.b$["jalview.appletgui.RedundancyPanel"].sliderValueChanged()},"java.awt.event.AdjustmentEvent");c$=z()}});p("jalview.appletgui");q("jalview.appletgui.EmbmenuFrame java.awt.event.ActionListener $.ItemListener java.lang.Thread awt2swing.CheckboxMenuItem $.Menu $.MenuBar $.MenuItem $.ScrollPane java.awt.BorderLayout".split(" "),
"jalview.appletgui.TreePanel","awt2swing.Frame jalview.analysis.NJTree jalview.api.analysis.ViewBasedAnalysisI jalview.appletgui.AlignFrame $.CutAndPasteTransfer $.FontChooser $.TreeCanvas jalview.bin.JalviewLite jalview.datamodel.Alignment jalview.io.NewickFile jalview.schemes.ResidueProperties jalview.util.MessageManager java.awt.Color $.Font".split(" "),function(){c$=s(function(){this.pwtype=this.$type=this.seq=null;this.end=this.start=0;this.av=this.ap=this.tree=this.treeCanvas=null;H("jalview.appletgui.TreePanel.TreeLoader")||
jalview.appletgui.TreePanel.$TreePanel$TreeLoader$();this.inputData=this.newickOutput=this.fileMenu=this.fitToWindow=this.placeholdersMenu=this.distanceMenu=this.bootstrapMenu=this.fontSize=this.jMenu2=this.jMenuBar1=this.scrollPane=this.borderLayout1=null;r(this,arguments)},jalview.appletgui,"TreePanel",jalview.appletgui.EmbmenuFrame,[java.awt.event.ActionListener,java.awt.event.ItemListener]);J(c$,function(){this.borderLayout1=new java.awt.BorderLayout;this.scrollPane=new awt2swing.ScrollPane;this.jMenuBar1=
new awt2swing.MenuBar;this.jMenu2=new awt2swing.Menu;this.fontSize=new awt2swing.MenuItem;this.bootstrapMenu=new awt2swing.CheckboxMenuItem;this.distanceMenu=new awt2swing.CheckboxMenuItem;this.placeholdersMenu=new awt2swing.CheckboxMenuItem;this.fitToWindow=new awt2swing.CheckboxMenuItem;this.fileMenu=new awt2swing.Menu;this.newickOutput=new awt2swing.MenuItem;this.inputData=new awt2swing.MenuItem});d(c$,"getTree",function(){return this.tree});d(c$,"finalize",function(){this.av=this.ap=null;K(this,
jalview.appletgui.TreePanel,"finalize",[])});m(c$,function(a,b,c){t(this,jalview.appletgui.TreePanel,[]);try{this.jbInit(),this.setMenuBar(this.jMenuBar1)}catch(d){if(y(d,Exception))d.printStackTrace();else throw d;}this.initTreePanel(a,b,c,null)},"jalview.appletgui.AlignmentPanel,~S,~S");m(c$,function(a,b,c,d){t(this,jalview.appletgui.TreePanel,[]);try{this.jbInit(),this.setMenuBar(this.jMenuBar1)}catch(e){if(y(e,Exception))e.printStackTrace();else throw e;}this.initTreePanel(a,b,c,d)},"jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");
d(c$,"initTreePanel",function(a,b,c,d){this.ap=a;this.av=a.av;this.$type=b;this.pwtype=c;this.treeCanvas=new jalview.appletgui.TreeCanvas(a,this.scrollPane);C(jalview.appletgui.TreePanel.TreeLoader,this,null,d).start();this.embedMenuIfNeeded(this.treeCanvas);this.scrollPane.add(this.treeCanvas,"Center")},"jalview.appletgui.AlignmentPanel,~S,~S,jalview.io.NewickFile");d(c$,"showOriginalData",function(){if(null!=this.tree.seqData){var a="-";try{a=this.av.getGapCharacter()}catch(b){if(!y(b,Exception))throw b;
}a=this.tree.seqData.getAlignmentAndColumnSelection(a);if(null!=a&&null!=a[0]){var c=new jalview.datamodel.Alignment(a[0]);(new jalview.appletgui.AlignFrame(c,this.av.applet,"Original Data for Tree",!1)).viewport.setHiddenColumns(a[1])}}else System.out.println("Original Tree Data not available")});e(c$,"actionPerformed",function(a){a.getSource()===this.newickOutput?this.newickOutput_actionPerformed():a.getSource()===this.fontSize?this.fontSize_actionPerformed():a.getSource()===this.inputData&&this.showOriginalData()},
"java.awt.event.ActionEvent");e(c$,"itemStateChanged",function(a){a.getSource()===this.fitToWindow?this.treeCanvas.fitToWindow=this.fitToWindow.getState():a.getSource()===this.distanceMenu?this.treeCanvas.setShowDistances(this.distanceMenu.getState()):a.getSource()===this.bootstrapMenu?this.treeCanvas.setShowBootstrap(this.bootstrapMenu.getState()):a.getSource()===this.placeholdersMenu&&this.treeCanvas.setMarkPlaceholders(this.placeholdersMenu.getState());this.treeCanvas.repaint()},"java.awt.event.ItemEvent");
d(c$,"newickOutput_actionPerformed",function(){var a=(new jalview.io.NewickFile(this.tree.getTopNode())).print(!1,!0),b=new jalview.appletgui.CutAndPasteTransfer(!1,null);b.setText(a);a=new awt2swing.Frame;a.add(b);jalview.bin.JalviewLite.addFrame(a,this.$type+" "+this.pwtype,500,100)});d(c$,"getTreeFont",function(){return this.treeCanvas.$font});d(c$,"setTreeFont",function(a){this.treeCanvas.$font=a;this.treeCanvas.repaint()},"java.awt.Font");d(c$,"fontSize_actionPerformed",function(){null!=this.treeCanvas&&
new jalview.appletgui.FontChooser(this)});d(c$,"jbInit",function(){this.setLayout(this.borderLayout1);this.setBackground(java.awt.Color.white);this.setFont(new java.awt.Font("Verdana",0,12));this.jMenu2.setLabel(jalview.util.MessageManager.getString("action.view"));this.fontSize.setLabel(jalview.util.MessageManager.getString("action.font"));this.fontSize.addActionListener(this);this.bootstrapMenu.setLabel(jalview.util.MessageManager.getString("label.show_bootstrap_values"));this.bootstrapMenu.addItemListener(this);
this.distanceMenu.setLabel(jalview.util.MessageManager.getString("label.show_distances"));this.distanceMenu.addItemListener(this);this.placeholdersMenu.setLabel(jalview.util.MessageManager.getString("label.mark_unassociated_leaves"));this.placeholdersMenu.addItemListener(this);this.fitToWindow.setState(!0);this.fitToWindow.setLabel(jalview.util.MessageManager.getString("label.fit_to_window"));this.fitToWindow.addItemListener(this);this.fileMenu.setLabel(jalview.util.MessageManager.getString("action.file"));
this.newickOutput.setLabel(jalview.util.MessageManager.getString("label.newick_format"));this.newickOutput.addActionListener(this);this.inputData.setLabel(jalview.util.MessageManager.getString("label.input_data"));this.add(this.scrollPane,"Center");this.jMenuBar1.add(this.fileMenu);this.jMenuBar1.add(this.jMenu2);this.jMenu2.add(this.fitToWindow);this.jMenu2.add(this.fontSize);this.jMenu2.add(this.distanceMenu);this.jMenu2.add(this.bootstrapMenu);this.jMenu2.add(this.placeholdersMenu);this.fileMenu.add(this.newickOutput);
this.fileMenu.add(this.inputData);this.inputData.addActionListener(this)});c$.$TreePanel$TreeLoader$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.odata=this.newtree=null;r(this,arguments)},jalview.appletgui.TreePanel,"TreeLoader",Thread);m(c$,function(a){t(this,jalview.appletgui.TreePanel.TreeLoader,[]);this.newtree=a},"jalview.io.NewickFile");e(c$,"run",function(){if(null!=this.newtree)this.b$["jalview.appletgui.TreePanel"].tree=null==this.odata?new jalview.analysis.NJTree(this.b$["jalview.appletgui.TreePanel"].av.getAlignment().getSequencesArray(),
this.newtree):new jalview.analysis.NJTree(this.b$["jalview.appletgui.TreePanel"].av.getAlignment().getSequencesArray(),this.odata,this.newtree);else{var a,b,c;a=null!=this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup()&&1<this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup().getSize();var d=this.b$["jalview.appletgui.TreePanel"].av.getAlignmentView(a);a?(a=this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup().getStartRes(),b=this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup().getEndRes()+
1,c=this.b$["jalview.appletgui.TreePanel"].av.getSelectionGroup().getSequencesInOrder(this.b$["jalview.appletgui.TreePanel"].av.getAlignment())):(a=0,b=this.b$["jalview.appletgui.TreePanel"].av.getAlignment().getWidth(),c=this.b$["jalview.appletgui.TreePanel"].av.getAlignment().getSequencesArray());var e=jalview.schemes.ResidueProperties.getScoreModel(this.b$["jalview.appletgui.TreePanel"].pwtype);if(v(e,jalview.api.analysis.ViewBasedAnalysisI)){try{e=e.getClass().newInstance(),e.configureFromAlignmentView(this.b$["jalview.appletgui.TreePanel"].treeCanvas.ap)}catch(k){if(y(k,
Exception))System.err.println("Couldn't create a scoremodel instance for "+e.getName()),k.printStackTrace();else throw k;}this.b$["jalview.appletgui.TreePanel"].tree=new jalview.analysis.NJTree(c,d,this.b$["jalview.appletgui.TreePanel"].$type,this.b$["jalview.appletgui.TreePanel"].pwtype,e,a,b)}else this.b$["jalview.appletgui.TreePanel"].tree=new jalview.analysis.NJTree(c,d,this.b$["jalview.appletgui.TreePanel"].$type,this.b$["jalview.appletgui.TreePanel"].pwtype,null,a,b)}this.b$["jalview.appletgui.TreePanel"].tree.reCount(this.b$["jalview.appletgui.TreePanel"].tree.getTopNode());
this.b$["jalview.appletgui.TreePanel"].tree.findHeight(this.b$["jalview.appletgui.TreePanel"].tree.getTopNode());this.b$["jalview.appletgui.TreePanel"].treeCanvas.setTree(this.b$["jalview.appletgui.TreePanel"].tree);null!=this.newtree&&(a=this.newtree.HasDistances()&&this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter("showTreeDistances",this.newtree.HasDistances()),b=this.newtree.HasBootstrap()&&this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter("showTreeBootstraps",
this.newtree.HasBootstrap()),this.b$["jalview.appletgui.TreePanel"].distanceMenu.setState(a),this.b$["jalview.appletgui.TreePanel"].bootstrapMenu.setState(b),this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowBootstrap(b),this.b$["jalview.appletgui.TreePanel"].treeCanvas.setShowDistances(a),this.b$["jalview.appletgui.TreePanel"].treeCanvas.setMarkPlaceholders(this.b$["jalview.appletgui.TreePanel"].av.applet.getDefaultParameter("showUnlinkedTreeNodes",!1)));this.b$["jalview.appletgui.TreePanel"].treeCanvas.repaint();
this.b$["jalview.appletgui.TreePanel"].av.setCurrentTree(this.b$["jalview.appletgui.TreePanel"].tree)});c$=z()}});p("jalview.analysis");q(["java.util.Vector"],["jalview.analysis.Cluster","$.NJTree"],"jalview.analysis.SequenceIdMatcher jalview.datamodel.AlignmentView $.CigarArray $.NodeTransformI $.SeqCigar $.Sequence $.SequenceI $.SequenceNode jalview.io.NewickFile jalview.schemes.ResidueProperties jalview.util.Format java.lang.StringBuffer".split(" "),function(){c$=s(function(){this.done=this.seqData=
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"THISISAPLACEHLDER")),k.setPlaceholder(!0))}}},"java.util.List");d(c$,"renameAssociatedNodes",function(){this.applyToNodes((H("jalview.analysis.NJTree$1")?0:jalview.analysis.NJTree.$NJTree$1$(),C(jalview.analysis.NJTree$1,this,null)))});d(c$,"cluster",function(){for(;2<this.noClus;){this.type.equals("NJ")?this.findMinNJDistance():this.findMinDistance();var a=this.joinClusters(this.mini,this.minj);this.done[this.minj]=1;this.$cluster.setElementAt(null,this.minj);this.$cluster.setElementAt(a,this.mini);
this.noClus--}for(var a=!1,b=-1,c=-1,d=0;d<this.noseqs;d++)1!=this.done[d]&&(!1==a?(c=d,a=!0):b=d);this.joinClusters(b,c);this.top=this.node.elementAt(b);this.reCount(this.top);this.findHeight(this.top);this.findMaxDist(this.top)});d(c$,"joinClusters",function(a,b){for(var c=this.distance[a][b],d=this.$cluster.elementAt(a).value.length,e=this.$cluster.elementAt(b).value.length,k=w(d+e,0),g=0;g<d;g++)k[g]=this.$cluster.elementAt(a).value[g];for(g=d;g<d+e;g++)k[g]=this.$cluster.elementAt(b).value[g-
d];d=new jalview.analysis.Cluster(k);this.ri=this.findr(a,b);this.rj=this.findr(b,a);this.type.equals("NJ")?this.findClusterNJDistance(a,b):this.findClusterDistance(a,b);e=new jalview.datamodel.SequenceNode;e.setLeft(this.node.elementAt(a));e.setRight(this.node.elementAt(b));k=this.node.elementAt(a);g=this.node.elementAt(b);this.type.equals("NJ")?this.findNewNJDistances(k,g,c):this.findNewDistances(k,g,c);k.setParent(e);g.setParent(e);this.node.setElementAt(e,a);return d},"~N,~N");d(c$,"findNewNJDistances",
function(a,b,c){a.dist=(c+this.ri-this.rj)/2;b.dist=c-a.dist;0>a.dist&&(a.dist=0);0>b.dist&&(b.dist=0)},"jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");d(c$,"findNewDistances",function(a,b,c){for(var d=0,e=0,k=a,g=b;null!=k;)d+=k.dist,k=k.left();for(;null!=g;)e+=g.dist,g=g.left();a.dist=c/2-d;b.dist=c/2-e},"jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode,~N");d(c$,"findClusterDistance",function(a,b){for(var c=this.$cluster.elementAt(a).value.length,d=this.$cluster.elementAt(b).value.length,
e=Q(this.noseqs,0),k=0;k<this.noseqs;k++)e[k]=k!=a&&k!=b?(this.distance[a][k]*c+this.distance[b][k]*d)/(c+d):0;for(c=0;c<this.noseqs;c++)this.distance[a][c]=e[c],this.distance[c][a]=e[c]},"~N,~N");d(c$,"findClusterNJDistance",function(a,b){for(var c=Q(this.noseqs,0),d=0;d<this.noseqs;d++)c[d]=d!=a&&d!=b?(this.distance[a][d]+this.distance[b][d]-this.distance[a][b])/2:0;for(d=0;d<this.noseqs;d++)this.distance[a][d]=c[d],this.distance[d][a]=c[d]},"~N,~N");d(c$,"findr",function(a,b){for(var c=1,d=0;d<
this.noseqs;d++)d!=a&&(d!=b&&1!=this.done[d])&&(c+=this.distance[a][d]);2<this.noClus&&(c/=this.noClus-2);return c},"~N,~N");d(c$,"findMinNJDistance",function(){for(var a=1E5,b=0;b<this.noseqs-1;b++)for(var c=b+1;c<this.noseqs;c++)if(1!=this.done[b]&&1!=this.done[c]){var d=this.distance[b][c]-(this.findr(b,c)+this.findr(c,b));d<a&&(this.mini=b,this.minj=c,a=d)}return a});d(c$,"findMinDistance",function(){for(var a=1E5,b=0;b<this.noseqs-1;b++)for(var c=b+1;c<this.noseqs;c++)1!=this.done[b]&&1!=this.done[c]&&
this.distance[b][c]<a&&(this.mini=b,this.minj=c,a=this.distance[b][c]);return a});d(c$,"findDistances",function(a){var b=Q(this.noseqs,this.noseqs,0);null==a&&(a=jalview.schemes.ResidueProperties.getScoreModel(this.pwtype),null==a&&(a=jalview.schemes.ResidueProperties.getScoreMatrix("BLOSUM62")));return b=a.findDistances(this.seqData)},"jalview.api.analysis.ScoreModelI");d(c$,"makeLeaves",function(){this.$cluster=new java.util.Vector;for(var a=0;a<this.noseqs;a++){var b=new jalview.datamodel.SequenceNode;
b.setElement(this.sequence[a]);b.setName(this.sequence[a].getName());this.node.addElement(b);b=w(1,0);b[0]=a;b=new jalview.analysis.Cluster(b);this.$cluster.addElement(b)}});d(c$,"findLeaves",function(a,b){if(null==a)return b;null==a.left()&&null==a.right()?b.addElement(a):(this.findLeaves(a.left(),b),this.findLeaves(a.right(),b));return b},"jalview.datamodel.SequenceNode,java.util.Vector");d(c$,"findLeaf",function(a,b){return this.found=this._findLeaf(a,b)},"jalview.datamodel.SequenceNode,~N");d(c$,
"_findLeaf",function(a,b){if(null==a)return null;a.ycount==b?this.found=a.element():(this._findLeaf(a.left(),b),this._findLeaf(a.right(),b));return this.found},"jalview.datamodel.SequenceNode,~N");d(c$,"printNode",function(a){null!=a&&(null==a.left()&&null==a.right()?(System.out.println("Leaf = "+a.element().getName()),System.out.println("Dist "+a.dist),System.out.println("Boot "+a.getBootstrap())):(System.out.println("Dist "+a.dist),this.printNode(a.left()),this.printNode(a.right())))},"jalview.datamodel.SequenceNode");
d(c$,"findMaxDist",function(a){if(null!=a)if(null==a.left()&&null==a.right()){var b=a.dist;b>this.maxDistValue&&(this.maxdist=a,this.maxDistValue=b)}else this.findMaxDist(a.left()),this.findMaxDist(a.right())},"jalview.datamodel.SequenceNode");d(c$,"getGroups",function(){return this.groups});d(c$,"getMaxHeight",function(){return this.maxheight});d(c$,"groupNodes",function(a,b){null!=a&&(a.height/this.maxheight>b?this.groups.addElement(a):(this.groupNodes(a.left(),b),this.groupNodes(a.right(),b)))},
"jalview.datamodel.SequenceNode,~N");d(c$,"findHeight",function(a){if(null==a)return this.maxheight;if(null==a.left()&&null==a.right()){if(a.height=a.parent().height+a.dist,a.height>this.maxheight)return a.height}else null!=a.parent()?a.height=a.parent().height+a.dist:(this.maxheight=0,a.height=0),this.maxheight=this.findHeight(a.left()),this.maxheight=this.findHeight(a.right());return this.maxheight},"jalview.datamodel.SequenceNode");d(c$,"reRoot",function(){if(null!=this.maxdist){this.ycount=0;
var a=this.maxdist.dist,b=new jalview.datamodel.SequenceNode;b.setParent(null);var c=this.maxdist.parent();this.changeDirection(c,this.maxdist);System.out.println("Printing reversed tree");this.printN(c);c.dist=a/2;this.maxdist.dist=a/2;c.setParent(b);this.maxdist.setParent(b);b.setRight(c);b.setLeft(this.maxdist);this.top=b;this.ycount=0;this.reCount(this.top);this.findHeight(this.top)}return this.top});d(c$,"hasOriginalSequenceData",function(){return null!=this.seqData});d(c$,"printOriginalSequenceData",
function(a){if(null==this.seqData)return null;var b=new StringBuffer;a=this.seqData.getSequenceStrings(a);for(var c=0;c<a.length;c++)b.append((new jalview.util.Format("%-15s")).form(this.sequence[c].getName())),b.append(" "+a[c]+"\n");return b.toString()},"~S");d(c$,"printN",function(a){null!=a&&(null!=a.left()&&null!=a.right()?(this.printN(a.left()),this.printN(a.right())):System.out.println(" name = "+a.element().getName()),System.out.println(" dist = "+a.dist+" "+a.count+" "+a.height))},"jalview.datamodel.SequenceNode");
d(c$,"reCount",function(a){this._lycount=this.ycount=0;this._reCount(a)},"jalview.datamodel.SequenceNode");d(c$,"_reCount",function(a){if(null!=a){this._lycount++;if(null!=a.left()&&null!=a.right()){this._reCount(a.left());this._reCount(a.right());var b=a.left(),c=a.right();a.count=b.count+c.count;a.ycount=(b.ycount+c.ycount)/2}else a.count=1,a.ycount=this.ycount++;this._lycount--}},"jalview.datamodel.SequenceNode");d(c$,"swapNodes",function(a){if(null!=a){var b=a.left();a.setLeft(a.right());a.setRight(b)}},
"jalview.datamodel.SequenceNode");d(c$,"changeDirection",function(a,b){if(null!=a)if(a.parent()!==this.top){this.changeDirection(a.parent(),a);var c=a.parent();b===a.left()?(a.setParent(b),a.setLeft(c)):b===a.right()&&(a.setParent(b),a.setRight(c))}else b===a.left()?(a.setParent(a.left()),this.top.left()===a?a.setRight(this.top.right()):a.setRight(this.top.left())):(a.setParent(a.right()),this.top.left()===a?a.setLeft(this.top.right()):a.setLeft(this.top.left()))},"jalview.datamodel.SequenceNode,jalview.datamodel.SequenceNode");
d(c$,"getMaxDist",function(){return this.maxdist});d(c$,"getTopNode",function(){return this.top});d(c$,"isHasDistances",function(){return this.hasDistances});d(c$,"isHasBootstrap",function(){return this.hasBootstrap});d(c$,"isHasRootDistance",function(){return this.hasRootDistance});d(c$,"applyToNodes",function(a){for(var b=this.node.elements();b.hasMoreElements();a.transform(b.nextElement()));},"jalview.datamodel.NodeTransformI");c$.$NJTree$1$=function(){A(self.c$);c$=L(jalview.analysis,"NJTree$1",
null,jalview.datamodel.NodeTransformI);d(c$,"transform",function(a){var b=a.element();null!=b&&v(b,jalview.datamodel.SequenceI)&&a.setName(b.getName())},"jalview.datamodel.BinaryNode");c$=z()};c$=s(function(){this.value=null;r(this,arguments)},jalview.analysis,"Cluster");m(c$,function(a){this.value=a},"~A")});p("jalview.datamodel");M(jalview.datamodel,"NodeTransformI");p("jalview.appletgui");q(["awt2swing.Panel","java.awt.event.MouseListener","$.MouseMotionListener","java.util.Hashtable"],"jalview.appletgui.TreeCanvas",
"awt2swing.Util jalview.analysis.Conservation jalview.appletgui.PaintRefresher jalview.datamodel.SequenceGroup $.SequenceI $.SequenceNode jalview.schemes.ColourSchemeProperty $.ResidueProperties $.UserColourScheme jalview.util.Format $.MappingUtils java.awt.Color $.Dimension $.Point $.Rectangle java.util.Vector".split(" "),function(){c$=s(function(){this.$font=this.av=this.scrollPane=this.tree=null;this.fitToWindow=!0;this.markPlaceholders=this.showBootstrap=this.showDistances=!1;this.offx=20;this.threshold=
this.offy=0;this.longestName=null;this.labelLength=-1;this.ap=this.highlightNode=this.nodeHash=this.nameHash=null;r(this,arguments)},jalview.appletgui,"TreeCanvas",awt2swing.Panel,[java.awt.event.MouseListener,java.awt.event.MouseMotionListener]);J(c$,function(){this.nameHash=new java.util.Hashtable;this.nodeHash=new java.util.Hashtable});m(c$,function(a,b){t(this,jalview.appletgui.TreeCanvas,[]);this.ap=a;this.av=a.av;this.$font=this.av.getFont();this.scrollPane=b;this.addMouseListener(this);this.addMouseMotionListener(this);
this.setLayout(null);jalview.appletgui.PaintRefresher.Register(this,this.av.getSequenceSetId())},"jalview.appletgui.AlignmentPanel,awt2swing.ScrollPane");d(c$,"treeSelectionChanged",function(a){var b=this.av.getSelectionGroup();null==b&&(b=new jalview.datamodel.SequenceGroup,this.av.setSelectionGroup(b));b.setEndRes(this.av.getAlignment().getWidth()-1);b.addOrRemove(a,!0)},"jalview.datamodel.SequenceI");d(c$,"setTree",function(a){this.tree=a;a.findHeight(a.getTopNode());a=a.findLeaves(a.getTopNode(),
new java.util.Vector);var b=!1;this.longestName="";for(var c=0;c<a.size();c++){var d=a.elementAt(c);d.isPlaceholder()&&(b=!0);this.longestName.length<d.element().getName().length&&(this.longestName=" * "+d.element().getName())}this.setMarkPlaceholders(b)},"jalview.analysis.NJTree");d(c$,"drawNode",function(a,b,c,d,e,k,g){if(null!=b)if(null==b.left()&&null==b.right()){var h=b.height;e=b.dist;var j=I((h-e)*d)+k,n=I(h*d)+k;e=I(b.ycount*c)+g;v(b.element(),jalview.datamodel.SequenceI)?(d=b.element(),this.av.getSequenceColour(d)===
java.awt.Color.white?a.setColor(java.awt.Color.black):a.setColor(this.av.getSequenceColour(d).darker())):a.setColor(java.awt.Color.black);a.drawLine(j,e,n,e);d="";this.showDistances&&0<b.dist&&(d=(new jalview.util.Format("%-.2f")).formDouble(b.dist));this.showBootstrap&&(k=b.getBootstrap(),-1<k&&(this.showDistances&&(d+=" : "),d+=String.valueOf(b.getBootstrap())));d.equals("")||awt2swing.Util.drawString(a,d,j+2,e-2);j=this.markPlaceholders&&b.isPlaceholder()?" * "+b.getName():b.getName();k=a.getFontMetrics(this.$font);
d=k.stringWidth(j)+3;k=k.getHeight();h=new java.awt.Rectangle(n+10,e-k,d,k);this.nameHash.put(b.element(),h);h=this.av.getSelectionGroup();null!=h&&h.getSequences(null).contains(b.element())&&(a.setColor(java.awt.Color.gray),a.fillRect(n+10,e-k+3,d,k),a.setColor(java.awt.Color.white));awt2swing.Util.drawString(a,j,n+10,e);a.setColor(java.awt.Color.black)}else{this.drawNode(a,b.left(),c,d,e,k,g);this.drawNode(a,b.right(),c,d,e,k,g);h=b.height;e=b.dist;j=I((h-e)*d)+k;n=I(h*d)+k;e=I(b.ycount*c)+g;a.setColor(b.color.darker());
a.drawLine(j,e,n,e);b===this.highlightNode?a.fillRect(n-3,e-3,6,6):a.fillRect(n-2,e-2,4,4);var m=I(b.left().ycount*c)+g;c=I(b.right().ycount*c)+g;n=new java.awt.Rectangle(n-2,e-2,5,5);this.nodeHash.put(b,n);a.drawLine(I(h*d)+k,m,I(h*d)+k,c);d="";this.showDistances&&0<b.dist&&(d=(new jalview.util.Format("%-.2f")).formDouble(b.dist));this.showBootstrap&&(k=b.getBootstrap(),-1<k&&(this.showDistances&&(d+=" : "),d+=String.valueOf(b.getBootstrap())));d.equals("")||awt2swing.Util.drawString(a,d,j+2,e-2)}},
"java.awt.Graphics,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");d(c$,"findElement",function(a,b){for(var c=this.nameHash.keys();c.hasMoreElements();){var d=c.nextElement(),e=this.nameHash.get(d);if(a>=e.x&&a<=e.x+e.width&&b>=e.y&&b<=e.y+e.height)return d}for(c=this.nodeHash.keys();c.hasMoreElements();)if(d=c.nextElement(),e=this.nodeHash.get(d),a>=e.x&&a<=e.x+e.width&&b>=e.y&&b<=e.y+e.height)return d;return null},"~N,~N");d(c$,"pickNodes",function(a){var b=this.getSize().width,c=this.getSize().height,
d=this.tree.getTopNode(),e=(0.8*b-2*this.offx)/this.tree.getMaxHeight();0==d.count&&(d.count=d.left().count+d.right().count);this.pickNode(a,d,(c-this.offy)/d.count,e,b,this.offx,this.offy)},"java.awt.Rectangle");d(c$,"pickNode",function(a,b,c,d,e,k,g){null!=b&&(null==b.left()&&null==b.right()?(d=I(b.height*d)+k,c=I(b.ycount*c)+g,a.contains(new java.awt.Point(d,c))&&v(b.element(),jalview.datamodel.SequenceI)&&(a=b.element(),b=this.av.getSelectionGroup(),null!=b&&b.addOrRemove(a,!0))):(this.pickNode(a,
b.left(),c,d,e,k,g),this.pickNode(a,b.right(),c,d,e,k,g)))},"java.awt.Rectangle,jalview.datamodel.SequenceNode,~N,~N,~N,~N,~N");d(c$,"setColor",function(a,b){null!=a&&(null==a.left()&&null==a.right()?(a.color=b,v(a.element(),jalview.datamodel.SequenceI)&&this.av.setSequenceColour(a.element(),b)):(a.color=b,this.setColor(a.left(),b),this.setColor(a.right(),b)))},"jalview.datamodel.SequenceNode,java.awt.Color");e(c$,"update",function(a){this.paint(a)},"java.awt.Graphics");e(c$,"paintComponent",function(a){if(null!=
this.tree){0==this.nameHash.size()&&this.repaint();var b=this.scrollPane.getSize().width,c=this.scrollPane.getSize().height;this.fitToWindow||(c=a.getFontMetrics(this.$font).getHeight()*this.nameHash.size());this.getSize().width>b?(this.setSize(new java.awt.Dimension(b,c)),this.scrollPane.validate()):(this.setSize(new java.awt.Dimension(b,c)),a.setFont(this.$font),this.draw(a,b,c),this.validate())}},"java.awt.Graphics");d(c$,"draw",function(a,b,c){this.offy=this.$font.getSize()+10;a.setColor(java.awt.Color.white);
a.fillRect(0,0,b,c);this.labelLength=a.getFontMetrics(this.$font).stringWidth(this.longestName)+20;var d=(b-this.labelLength-2*this.offx)/this.tree.getMaxHeight(),e=this.tree.getTopNode();0==e.count&&(e.count=e.left().count+e.right().count);c=(c-this.offy)/e.count;this.drawNode(a,this.tree.getTopNode(),c,d,b,this.offx,this.offy);0!=this.threshold&&(this.av.getCurrentTree()===this.tree?a.setColor(java.awt.Color.red):a.setColor(java.awt.Color.gray),b=I(this.threshold*(this.getSize().width-this.labelLength-
2*this.offx)+this.offx),a.drawLine(b,0,b,this.getSize().height))},"java.awt.Graphics,~N,~N");e(c$,"mouseReleased",function(){},"java.awt.event.MouseEvent");e(c$,"mouseEntered",function(){},"java.awt.event.MouseEvent");e(c$,"mouseExited",function(){},"java.awt.event.MouseEvent");e(c$,"mouseClicked",function(a){if(null!=this.highlightNode){if(1<a.getClickCount())this.tree.swapNodes(this.highlightNode),this.tree.reCount(this.tree.getTopNode()),this.tree.findHeight(this.tree.getTopNode());else{a=new java.util.Vector;
this.tree.findLeaves(this.highlightNode,a);for(var b=0;b<a.size();b++){var c=a.elementAt(b).element();this.treeSelectionChanged(c)}}jalview.appletgui.PaintRefresher.Refresh(this,this.av.getSequenceSetId());this.repaint();this.av.sendSelection()}},"java.awt.event.MouseEvent");e(c$,"mouseDragged",function(){},"java.awt.event.MouseEvent");e(c$,"mouseMoved",function(a){this.av.setCurrentTree(this.tree);a=this.findElement(a.getX(),a.getY());v(a,jalview.datamodel.SequenceNode)?(this.highlightNode=a,this.repaint()):
null!=this.highlightNode&&(this.highlightNode=null,this.repaint())},"java.awt.event.MouseEvent");e(c$,"mousePressed",function(a){this.av.setCurrentTree(this.tree);var b=a.getX();a=a.getY();a=this.findElement(b,a);v(a,jalview.datamodel.SequenceI)?(this.treeSelectionChanged(a),jalview.appletgui.PaintRefresher.Refresh(this,this.av.getSequenceSetId()),this.repaint(),this.av.sendSelection()):(!v(a,jalview.datamodel.SequenceNode)&&0!=this.tree.getMaxHeight()&&(this.threshold=(b-this.offx)/(this.getSize().width-
this.labelLength-2*this.offx),this.tree.getGroups().removeAllElements(),this.tree.groupNodes(this.tree.getTopNode(),this.threshold),this.setColor(this.tree.getTopNode(),java.awt.Color.black),this.av.setSelectionGroup(null),this.av.getAlignment().deleteAllGroups(),this.av.clearSequenceColours(),b=this.av.getCodingComplement(),null!=b&&(b.setSelectionGroup(null),b.getAlignment().deleteAllGroups(),b.clearSequenceColours()),this.colourGroups()),jalview.appletgui.PaintRefresher.Refresh(this,this.av.getSequenceSetId()),
this.repaint())},"java.awt.event.MouseEvent");d(c$,"colourGroups",function(){for(var a=0;a<this.tree.getGroups().size();a++){var b=new java.awt.Color(F(255*Math.random()),F(255*Math.random()),F(255*Math.random()));this.setColor(this.tree.getGroups().elementAt(a),b.brighter());for(var c=this.tree.findLeaves(this.tree.getGroups().elementAt(a),new java.util.Vector),d=new java.util.Vector,e=0;e<c.size();e++){var k=c.elementAt(e).element();d.contains(k)||d.addElement(k)}c=null;d=new jalview.datamodel.SequenceGroup(d,
"",c,!0,!0,!1,0,this.av.getAlignment().getWidth()-1);null!=this.av.getGlobalColourScheme()&&(c=v(this.av.getGlobalColourScheme(),jalview.schemes.UserColourScheme)?new jalview.schemes.UserColourScheme(this.av.getGlobalColourScheme().getColours()):jalview.schemes.ColourSchemeProperty.getColour(d,jalview.schemes.ColourSchemeProperty.getColourName(this.av.getGlobalColourScheme())),null!=c&&c.setThreshold(this.av.getGlobalColourScheme().getThreshold(),this.av.isIgnoreGapsConsensus()));d.cs=c;d.setName("JTreeGroup:"+
d.hashCode());d.setIdColour(b);null!=this.av.getGlobalColourScheme()&&this.av.getGlobalColourScheme().conservationApplied()&&(e=new jalview.analysis.Conservation("Group",jalview.schemes.ResidueProperties.propHash,3,d.getSequences(null),d.getStartRes(),d.getEndRes()),e.calculate(),e.verdict(!1,this.av.getConsPercGaps()),c.setConservation(e),d.cs=c);this.av.getAlignment().addGroup(d);this.av.getAlignment().addGroup(d);c=this.av.getCodingComplement();if(null!=c&&(d=jalview.util.MappingUtils.mapSequenceGroup(d,
this.av,c),0<d.getSequences().size())){c.getAlignment().addGroup(d);for(var g,d=d.getSequences().iterator();d.hasNext()&&((g=d.next())||1);)c.setSequenceColour(g,b)}}this.ap.updateAnnotation();null!=this.av.getCodingComplement()&&this.av.getCodingComplement().firePropertyChange("alignment",null,this.ap.av.getAlignment().getSequences())});d(c$,"setShowDistances",function(a){this.showDistances=a;this.repaint()},"~B");d(c$,"setShowBootstrap",function(a){this.showBootstrap=a;this.repaint()},"~B");d(c$,
"setMarkPlaceholders",function(a){this.markPlaceholders=a;this.repaint()},"~B");G(c$,"PLACEHOLDER"," * ")});p("jalview.commands");q(["jalview.commands.EditCommand"],"jalview.commands.RemoveGapColCommand",["jalview.util.Comparison"],function(){c$=s(function(){this.columnsDeleted=0;r(this,arguments)},jalview.commands,"RemoveGapColCommand",jalview.commands.EditCommand);m(c$,function(a,b,c,d,e){t(this,jalview.commands.RemoveGapColCommand,[]);this.description=a;a=b.length;var k=-1,g=-1;this.columnsDeleted=
0;this.clearEdits();for(var h=!0,j=c;j<=d;j++){h=!0;for(c=0;c<a;c++)if(b[c].getLength()>j&&!jalview.util.Comparison.isGap(b[c].getCharAt(j))){h&&(g=j);h=!1;break}h&&-1==k&&(k=j);!h&&-1<k&&(this.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,b,k-this.columnsDeleted,g-k,e,!1,null),this.columnsDeleted+=g-k,g=k=-1)}h&&-1<k&&(this.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,b,k-this.columnsDeleted,d-k+1,e,!1,null),this.columnsDeleted+=d-k+1);this.performEdit(0,null)},"~S,~A,~N,~N,jalview.datamodel.AlignmentI");
e(c$,"getSize",function(){return this.columnsDeleted})});p("jalview.commands");q(["jalview.commands.EditCommand"],"jalview.commands.RemoveGapsCommand",["jalview.util.Comparison"],function(){c$=B(jalview.commands,"RemoveGapsCommand",jalview.commands.EditCommand);m(c$,function(a,b,c){t(this,jalview.commands.RemoveGapsCommand,[]);this.description=a;for(var d=a=0;d<b.length;d++)b[d].getLength()>a&&(a=b[d].getLength());this.findGaps(b,0,a,c)},"~S,~A,jalview.datamodel.AlignmentI");m(c$,function(a,b,c,d,
e){t(this,jalview.commands.RemoveGapsCommand,[]);this.description=a;this.findGaps(b,c,d,e)},"~S,~A,~N,~N,jalview.datamodel.AlignmentI");d(c$,"findGaps",function(a,b,c,d){var e=-1,k=-1,g=0,h,j;this.clearEdits();for(var n=!0,m,p=0;p<a.length;p++){g=0;k=e=-1;m=a[p].getSequence(b,c+1);j=m.length;for(h=0;h<j;h++)n=!0,jalview.util.Comparison.isGap(m[h])||(n&&(k=h),n=!1),n&&-1==e&&(e=h),!n&&-1<e&&(this.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,E(-1,[a[p]]),b+e-g,k-e,d,!1,null),g+=k-e,k=e=
-1);n&&-1<e&&this.appendEdit(jalview.commands.EditCommand.Action.DELETE_GAP,E(-1,[a[p]]),b+e-g,j-e,d,!1,null)}this.performEdit(0,null)},"~A,~N,~N,jalview.datamodel.AlignmentI")});p("jalview.commands");q(["jalview.commands.EditCommand"],"jalview.commands.SlideSequencesCommand",["jalview.util.Comparison"],function(){c$=s(function(){this.gapsInsertedBegin=!1;r(this,arguments)},jalview.commands,"SlideSequencesCommand",jalview.commands.EditCommand);m(c$,function(a,b,c,d,e){t(this,jalview.commands.SlideSequencesCommand,
[]);this.description=a;a=b.length;this.gapsInsertedBegin=!1;var k,g;for(k=0;k<a;k++)for(g=0;g<d;g++)if(!jalview.util.Comparison.isGap(b[k].getCharAt(g))){this.gapsInsertedBegin=!0;break}a=null;a=this.gapsInsertedBegin?C(jalview.commands.EditCommand.Edit,this,null,jalview.commands.EditCommand.Action.INSERT_GAP,c,0,d,e):C(jalview.commands.EditCommand.Edit,this,null,jalview.commands.EditCommand.Action.DELETE_GAP,b,0,d,e);this.setEdit(a);jalview.commands.EditCommand.performEdit(a,null)},"~S,~A,~A,~N,~S");
d(c$,"getGapsInsertedBegin",function(){return this.gapsInsertedBegin});d(c$,"appendSlideCommand",function(a){var b=!1;if(a.getEdit(0).seqs.length==this.getEdit(0).seqs.length)for(var b=!0,c=0;c<a.getEdit(0).seqs.length;c++)this.getEdit(0).seqs[c]!==a.getEdit(0).seqs[c]&&(b=!1);b&&a.addEdit(this.getEdit(0));return b},"jalview.commands.SlideSequencesCommand")});p("jalview.commands");q(["jalview.commands.EditCommand"],"jalview.commands.TrimRegionCommand",null,function(){c$=s(function(){this.deletedHiddenColumns=
this.selectionGroup=this.shiftList=this.start=this.colSel=null;this.columnsDeleted=0;r(this,arguments)},jalview.commands,"TrimRegionCommand",jalview.commands.EditCommand);m(c$,function(a,b,c,d,e,k,g){t(this,jalview.commands.TrimRegionCommand,[]);this.description=a;this.selectionGroup=g;this.colSel=k;if(b.equalsIgnoreCase(jalview.commands.TrimRegionCommand.TRIM_LEFT)){if(0==d)return;this.columnsDeleted=d;this.setEdit(C(jalview.commands.EditCommand.Edit,this,null,jalview.commands.EditCommand.Action.CUT,
c,0,d,e))}else if(b.equalsIgnoreCase(jalview.commands.TrimRegionCommand.TRIM_RIGHT)){a=e.getWidth()-d-1;if(2>a)return;this.columnsDeleted=a-1;this.setEdit(C(jalview.commands.EditCommand.Edit,this,null,jalview.commands.EditCommand.Action.CUT,c,d+1,a,e))}d=this.getEdit(0).seqs.length;this.start=w(d,0);for(c=0;c<d;c++)this.start[c]=this.getEdit(0).seqs[c].getStart();this.performEdit(0,null)},"~S,~S,~A,~N,jalview.datamodel.AlignmentI,jalview.datamodel.ColumnSelection,jalview.datamodel.SequenceGroup");
d(c$,"cut",function(a){var b,c,d=a.seqs.length;for(c=0;c<d;c++)0==a.position?(b=a.seqs[c].findPosition(a.number),a.seqs[c].setStart(b)):(b=a.seqs[c].findPosition(a.position)-1,a.seqs[c].setEnd(b));K(this,jalview.commands.TrimRegionCommand,"cut",[a,null]);0==a.position?(this.deletedHiddenColumns=this.colSel.compensateForEdit(0,a.number),null!=this.selectionGroup&&this.selectionGroup.adjustForRemoveLeft(a.number)):(this.deletedHiddenColumns=this.colSel.compensateForEdit(a.position,a.number),null!=this.selectionGroup&&
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b=e.nextSetBit(h))}else for(h=e.nextSetBit(g);h>=g;h=e.nextSetBit(h+1))c&&n.contains(h)?n.removeElement(h):n.addElement(h);this.viewport.setColumnSelection(n);this.alignPanel.paintAlignment(!0);this.avcg.setStatus(jalview.util.MessageManager.formatMessage("label.view_controller_toggled_marked",E(-1,[c?jalview.util.MessageManager.getString("label.toggled"):jalview.util.MessageManager.getString("label.marked"),a?Integer.$valueOf(k-g-e.cardinality()).toString():Integer.$valueOf(e.cardinality()).toString(),
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g=0;var p;for(n=d.keySet().iterator();n.hasNext()&&((p=n.next())||1);)c=new jalview.datamodel.SequenceGroup(d.get(p),"Subseq: "+p,null,!0,!0,!1,0,k-1),a[g++]=c;d.clear();e.clear();return a},"~A,jalview.datamodel.ColumnSelection,java.util.List");c$.divideByFeature=d(c$,"divideByFeature",function(){},"~A,~A,~N,~N,~A,java.util.Vector,~S")});p("jalview.io");q(null,"jalview.io.AlignmentProperties",["java.lang.StringBuffer"],function(){c$=s(function(){this.alignment=null;r(this,arguments)},jalview.io,"AlignmentProperties");
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k);a.append(c);a.append("Average Length: "+I(d));if(null!=this.alignment.alignmentProperties){a.append(c);a.append(c);b&&a.append('<table border="1">');d=this.alignment.alignmentProperties;for(e=d.keys();e.hasMoreElements();)if(k=e.nextElement().toString(),g=d.get(k).toString(),b){var h=new StringBuffer,j=0,n;do n=g.indexOf("\n",j),-1==n?h.append(g.substring(j)):(h.append(g.substring(j,n)),h.append("<br>")),j=n+1;while(-1!=n);a.append("<tr><td>"+k+"</td><td>"+h+"</td></tr>")}else a.append(c+k+"\t"+
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a.getAlignment().getAlignmentAnnotation()[e].label;c.contains(k)?c.addElement(k+"_"+d++):c.addElement(k)}this.adjusting=!1;this.changeColour()},"jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");d(c$,"changeColour",function(){if(!this.adjusting){var a=null,a=new jalview.schemes.RNAHelicesColour(this.av.getAlignment());this.av.setGlobalColourScheme(a);if(null!=this.av.getAlignment().getGroups())for(var b,a=this.ap.getAlignment().getGroups().iterator();a.hasNext()&&((b=a.next())||1);)null!=
b.cs&&(b.cs=new jalview.schemes.RNAHelicesColour(b));this.ap.paintAlignment(!1)}});d(c$,"reset",function(){this.av.setGlobalColourScheme(this.oldcs);if(null!=this.av.getAlignment().getGroups())for(var a,b=this.ap.getAlignment().getGroups().iterator();b.hasNext()&&((a=b.next())||1);)a.cs=this.oldgroupColours.get(a)});d(c$,"annotations_actionPerformed",function(){this.changeColour()},"java.awt.event.ActionEvent")});p("jalview.schemes");q(["jalview.schemes.ResidueColourScheme"],"jalview.schemes.RNAInteractionColourScheme",
["jalview.schemes.ResidueProperties","java.awt.Color"],function(){c$=B(jalview.schemes,"RNAInteractionColourScheme",jalview.schemes.ResidueColourScheme);e(c$,"findColour",function(a){return this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)]]},"~S");e(c$,"findColourSeq",function(a,b){var c;if(0==this.threshold||this.aboveThreshold(a,b))try{c=this.colors[jalview.schemes.ResidueProperties.nucleotideIndex[a.charCodeAt(0)]]}catch(d){if(y(d,Exception))return java.awt.Color.white;
throw d;}else return java.awt.Color.white;this.conservationColouring&&(c=this.applyConservation(c,b));return c},"~S,~N,jalview.datamodel.SequenceI")});p("java.net");c$=B(java.net,"URLEncoder");c$.encode=d(c$,"encode",function(a){return encodeURIComponent(a)},"~S");c$.encode=d(c$,"encode",function(a){return encodeURIComponent(a)},"~S,~S");G(c$,"digits","0123456789ABCDEF");p("jalview.io");q(null,"jalview.io.JnetAnnotationMaker",["jalview.datamodel.AlignmentAnnotation","$.Annotation","jalview.util.MessageManager",
"java.lang.Exception","$.Float"],function(){c$=B(jalview.io,"JnetAnnotationMaker");c$.add_annotation=d(c$,"add_annotation",function(a,b,c,d){jalview.io.JnetAnnotationMaker.add_annotation(a,b,c,d,ha("Array"))},"jalview.io.AlignFile,jalview.datamodel.AlignmentI,~N,~B");c$.add_annotation=d(c$,"add_annotation",function(a,b,c,d,e){var k=0;a=a.getSeqsAsArray();var g=b.getSequenceAt(c),h=a[0].getSequence().length,j=b.getSequenceAt(c).gapMap();if(null!=e&&e.length>h||null==e&&j.length!=h)throw new Exception(jalview.util.MessageManager.formatMessage("exception.number_of_residues_in_query_sequence_differ_from_prediction",
E(-1,[null==e?"":jalview.util.MessageManager.getString("label.mapped"),b.getSequenceAt(c).getName(),b.getSequenceAt(c).getSequenceAsString(),Integer.$valueOf(h).toString()])));var n;n=null;c=0;null!=b.getAlignmentAnnotation()&&(c=b.getAlignmentAnnotation().length);for(var m=Array(b.getWidth()),p=!0;k<a.length;){var q=a[k].getName().toUpperCase();if(q.startsWith("LUPAS")||q.startsWith("JNET")||q.startsWith("JPRED")){if(q.startsWith("JNETSOL")){n=q.endsWith("25")?3:q.endsWith("5")?6:9;for(q=0;q<h;q++){var r=
null==e?j[q]:j[e[q]];p&&(m[r]=new jalview.datamodel.Annotation(0));if("B"==a[k].getCharAt(q)&&(0==m[r].value||m[r].value<n))m[r].value=n}p=!1}else{n=Array(b.getWidth());if(q.equals("JNETPRED")||q.equals("JNETPSSM")||q.equals("JNETFREQ")||q.equals("JNETHMM")||q.equals("JNETALIGN")||q.equals("JPRED"))if(null==e)for(r=0;r<h;r++)n[j[r]]=new jalview.datamodel.Annotation("","",a[k].getCharAt(r),0);else for(r=0;r<h;r++)n[j[e[r]]]=new jalview.datamodel.Annotation("","",a[k].getCharAt(r),0);else if(q.equals("JNETCONF"))if(null==
e)for(r=0;r<h;r++){var s=(new Float(a[k].getCharAt(r)+"")).floatValue();n[j[r]]=new jalview.datamodel.Annotation(a[k].getCharAt(r)+"","",a[k].getCharAt(r),s)}else for(r=0;r<h;r++)s=(new Float(a[k].getCharAt(r)+"")).floatValue(),n[j[e[r]]]=new jalview.datamodel.Annotation(a[k].getCharAt(r)+"","",a[k].getCharAt(r),s);else if(null==e)for(r=0;r<h;r++)n[j[r]]=new jalview.datamodel.Annotation(a[k].getCharAt(r)+"",""," ",0);else for(r=0;r<h;r++)n[j[e[r]]]=new jalview.datamodel.Annotation(a[k].getCharAt(r)+
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a.iterator();c.hasNext()&&((b=c.next())||1);)b.jvlite=null;a.removeAllElements();a.notifyAll()}}this.executor=this.jvlite=null});d(c$,"run",function(){for(;null!=this.jsExecQueue;)if(0<this.jsExecQueue.size()){var a=this.jsExecQueue.elementAt(0);this.jsExecQueue.removeElementAt(0);try{a.run()}catch(b){if(y(b,Exception))a=b,a.printStackTrace();else if(y(b,Error))a=b,a.printStackTrace();else throw b;}}else try{this.jsExecQueue.wait(1E3)}catch(c){if(!y(c,Exception))throw c;}});d(c$,"executeJavascriptFunction",
function(a,b){this.executeJavascriptFunction(!1,a,b)},"~S,~A");d(c$,"executeJavascriptFunction",function(a,b,c){this.executeJavascriptFunction(a,b,c,null)},"~B,~S,~A");d(c$,"executeJavascriptFunction",function(a,b,c,d){var e=Array(null!=c?c.length:0);null!=c&&System.arraycopy(c,0,e,0,c.length);c=Array(1);b=(H("jalview.javascript.JSFunctionExec$1")?0:jalview.javascript.JSFunctionExec.$JSFunctionExec$1$(),C(jalview.javascript.JSFunctionExec$1,this,T("dbgMsg",d,"_listener",b,"objects",e,"jsex",c,"async",
a)));if(a)null==this.executor&&(this.executor=new Thread(new jalview.javascript.JSFunctionExec(this.jvlite)),this.executor.start()),this.jsExecQueue.addElement(b),this.jsExecQueue.notify();else if(b.run(),null!=c[0])throw c[0];},"~B,~S,~A,~S");c$.$JSFunctionExec$1$=function(){A(self.c$);c$=L(jalview.javascript,"JSFunctionExec$1",null,Runnable);d(c$,"run",function(){try{var a=null;try{a=netscape.javascript.JSObject.getWindow(this.b$["jalview.javascript.JSFunctionExec"].jvlite)}catch(b){if(!y(b,Exception))throw b;
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e(c$,"verifyButtonClick",function(){return!0},"~B");e(c$,"installJSUI",function(){this.installDefaults(this.c);this.installListeners(this.c);this.installKeyboardActions(this.c)});e(c$,"uninstallJSUI",function(){this.uninstallKeyboardActions(this.c);this.uninstallListeners(this.c)});e(c$,"installListeners",function(a){var b=new swingjs.plaf.JSButtonListener(a);null!=b&&(a.addMouseListener(b),a.addMouseMotionListener(b),a.addFocusListener(b),a.addPropertyChangeListener(b),a.addChangeListener(b))},"javax.swing.AbstractButton");
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"javax.swing.AbstractButton");e(c$,"getPropertyPrefix",function(){return"Button."});e(c$,"installDefaults",function(a){var b=this.getPropertyPrefix();this.$defaultTextShiftOffset=javax.swing.UIManager.getInt(b+"textShiftOffset");(null==a.getMargin()||v(a.getMargin(),javax.swing.plaf.UIResource))&&a.setMargin(javax.swing.UIManager.getInsets(b+"margin"));javax.swing.LookAndFeel.installColorsAndFont(a,b+"background",b+"foreground",b+"font");javax.swing.LookAndFeel.installProperty(a,"iconTextGap",new Integer(4))},
"javax.swing.AbstractButton")});p("swingjs.plaf");q(["swingjs.plaf.JSCheckBoxUI"],"swingjs.plaf.JSCheckBoxMenuItemUI",null,function(){c$=B(swingjs.plaf,"JSCheckBoxMenuItemUI",swingjs.plaf.JSCheckBoxUI);e(c$,"getDOMObject",function(){return this.getButtonObject("checkBox")});e(c$,"getPropertyPrefix",function(){return"CheckBoxMenuItem."})});p("swingjs.plaf");q(["swingjs.plaf.JSRadioButtonUI"],"swingjs.plaf.JSCheckBoxUI",null,function(){c$=B(swingjs.plaf,"JSCheckBoxUI",swingjs.plaf.JSRadioButtonUI);
e(c$,"getDOMObject",function(){return this.getButtonObject("checkBox")});e(c$,"getPropertyPrefix",function(){return"CheckBox."})});p("swingjs.plaf");q(["swingjs.plaf.JSComponentUI"],"swingjs.plaf.JSLabelUI",["swingjs.api.DOMNode"],function(){c$=B(swingjs.plaf,"JSLabelUI",swingjs.plaf.JSComponentUI);e(c$,"getDOMObject",function(){null==this.domNode&&(this.textNode=this.domNode=this.createDOMObject("label",this.id,[]));swingjs.plaf.JSComponentUI.vCenter(this.domNode,10);return this.setCssFont(swingjs.api.DOMNode.setAttr(this.domNode,
"innerHTML",this.c.getText()),this.c.getFont())});e(c$,"installJSUI",function(){});e(c$,"uninstallJSUI",function(){})});p("swingjs.plaf");q(["swingjs.plaf.JSMenuUI"],"swingjs.plaf.JSPopupMenuUI",["java.awt.Dimension","javax.swing.LookAndFeel"],function(){c$=B(swingjs.plaf,"JSPopupMenuUI",swingjs.plaf.JSMenuUI);m(c$,function(){t(this,swingjs.plaf.JSPopupMenuUI,[]);this.isContainer=!0;this.setDoc()});e(c$,"getDOMObject",function(){null==this.domNode&&(this.domNode=this.createDOMObject("select",this.id,
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function(){c$=B(swingjs.plaf,"JSPopupMenuSeparatorUI",swingjs.plaf.JSSeparatorUI);e(c$,"getDOMObject",function(){null==this.domNode&&(this.textNode=this.domNode=this.createDOMObject("label",this.id,[]));swingjs.plaf.JSComponentUI.vCenter(this.domNode,10);return this.setCssFont(swingjs.api.DOMNode.setAttr(this.domNode,"innerHTML",this.c.getText()),this.c.getFont())});e(c$,"installJSUI",function(){});e(c$,"uninstallJSUI",function(){})});p("swingjs.plaf");q(["swingjs.plaf.JSComponentUI"],"swingjs.plaf.JSScrollBarUI",
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0;this._imgNode=this.pix=null;this.height=this.width=0;r(this,arguments)},swingjs,"JSImage",java.awt.image.BufferedImage);m(c$,function(a,b,c){t(this,swingjs.JSImage,[b,c,2]);this.width=b;this.height=c;this.pix=a},"~A,~N,~N");d(c$,"toIntARGB",function(a){for(var b=F(a.length/4),c=w(b,0),d=0,e=0;d<b;e++)c[d++]=a[e++]<<16|a[e++]<<8|a[e++]|4278190080;return c},"~A");d(c$,"getDOMImage",function(a,b){var c="data:image/"+b+";base64,"+JU.Base64.getBase64(a).toString(),d=null,d=new Image(this.width,this.height);
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q(["jssun.awt.image.IntegerComponentRaster"],"jssun.awt.image.IntegerInterleavedRaster","java.lang.ArrayIndexOutOfBoundsException java.awt.Point $.Rectangle java.awt.image.DataBufferInt $.RasterFormatException $.SinglePixelPackedSampleModel".split(" "),function(){c$=s(function(){this.$maxY=this.$maxX=0;r(this,arguments)},jssun.awt.image,"IntegerInterleavedRaster",jssun.awt.image.IntegerComponentRaster);m(c$,function(a,b){t(this,jssun.awt.image.IntegerInterleavedRaster,[]);this.setIntInterRaster(a,
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m(c$,function(a,b,c,d,e){t(this,jssun.awt.image.IntegerInterleavedRaster,[]);this.setIntInterRaster(a,b,c,d,e)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,jssun.awt.image.IntegerInterleavedRaster");d(c$,"setIntInterRaster",function(a,b,c,d,e){this.setIntCompRaster(a,b,c,d,e);this.$maxX=this.minX+this.width;this.$maxY=this.minY+this.height;if(!v(b,java.awt.image.DataBufferInt))throw new java.awt.image.RasterFormatException("IntegerInterleavedRasters must haveinteger DataBuffers");
this.data=jssun.awt.image.SunWritableRaster.stealData(b,0);if(v(a,java.awt.image.SinglePixelPackedSampleModel))this.scanlineStride=a.getScanlineStride(),this.pixelStride=1,this.dataOffsets=w(1,0),this.dataOffsets[0]=b.getOffset(),this.bandOffset=this.dataOffsets[0],this.dataOffsets[0]+=c.x-d.x+(c.y-d.y)*this.scanlineStride,this.numDataElems=a.getNumDataElements();else throw new java.awt.image.RasterFormatException("IntegerInterleavedRasters must have SinglePixelPackedSampleModel");this.verify()},
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a>=this.$maxX||b>=this.$maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");c=null==c?w(1,0):c;c[0]=this.data[(b-this.minY)*this.scanlineStride+(a-this.minX)+this.dataOffsets[0]];return c},"~N,~N,~O");d(c$,"getDataElements",function(a,b,c,d,e){if(a<this.minX||b<this.minY||a+c>this.$maxX||b+d>this.$maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");e=v(e,Array)?e:w(c*d,0);a=(b-this.minY)*this.scanlineStride+(a-this.minX)+this.dataOffsets[0];for(var k=
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e,this.data,a,c),e+=k,a+=this.scanlineStride;this.markDirty()}else{h=null;for(j=0;j<d;j++)h=e.getDataElements(k,g+j,c,1,h),this.setDataElements(a,b+j,c,1,h)}}},"~N,~N,~N,~N,java.awt.image.Raster");d(c$,"setDataElements",function(a,b,c,d,e){if(a<this.minX||b<this.minY||a+c>this.$maxX||b+d>this.$maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");a=(b-this.minY)*this.scanlineStride+(a-this.minX)+this.dataOffsets[0];for(var k=b=0;k<d;k++)System.arraycopy(e,b,this.data,a,c),b+=
c,a+=this.scanlineStride;this.markDirty()},"~N,~N,~N,~N,~O");e(c$,"createWritableChild",function(a,b,c,d,e,k,g){if(a<this.minX)throw new java.awt.image.RasterFormatException("x lies outside raster");if(b<this.minY)throw new java.awt.image.RasterFormatException("y lies outside raster");if(a+c<a||a+c>this.minX+this.width)throw new java.awt.image.RasterFormatException("(x + width) is outside raster");if(b+d<b||b+d>this.minY+this.height)throw new java.awt.image.RasterFormatException("(y + height) is outside raster");
g=null!=g?this.sampleModel.createSubsetSampleModel(g):this.sampleModel;a=e-a;b=k-b;return new jssun.awt.image.IntegerInterleavedRaster(g,this.dataBuffer,new java.awt.Rectangle(e,k,c,d),new java.awt.Point(this.sampleModelTranslateX+a,this.sampleModelTranslateY+b),this)},"~N,~N,~N,~N,~N,~N,~A");e(c$,"createChild",function(a,b,c,d,e,k,g){return this.createWritableChild(a,b,c,d,e,k,g)},"~N,~N,~N,~N,~N,~N,~A");d(c$,"createCompatibleWritableRaster",function(a,b){if(0>=a||0>=b)throw new java.awt.image.RasterFormatException("negative "+
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" dataOffset[0] "+this.dataOffsets[0])})});p("jssun.awt.image");q(["jssun.awt.image.SunWritableRaster"],"jssun.awt.image.IntegerComponentRaster","java.lang.ArrayIndexOutOfBoundsException java.awt.Point $.Rectangle java.awt.image.DataBufferInt $.RasterFormatException $.SinglePixelPackedSampleModel".split(" "),function(){c$=s(function(){this.bandOffset=0;this.dataOffsets=null;this.pixelStride=this.scanlineStride=0;this.data=null;this.maxY=this.maxX=this.type=this.numDataElems=0;r(this,arguments)},jssun.awt.image,
"IntegerComponentRaster",jssun.awt.image.SunWritableRaster);m(c$,function(a,b){t(this,jssun.awt.image.IntegerComponentRaster,[]);this.setIntCompRaster(a,a.createDataBuffer(),new java.awt.Rectangle(b.x,b.y,a.getWidth(),a.getHeight()),b,null)},"java.awt.image.SampleModel,java.awt.Point");m(c$,function(a,b,c){t(this,jssun.awt.image.IntegerComponentRaster,[]);this.setIntCompRaster(a,b,new java.awt.Rectangle(c.x,c.y,a.getWidth(),a.getHeight()),c,null)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Point");
m(c$,function(){t(this,jssun.awt.image.IntegerComponentRaster,[])});m(c$,function(a,b,c,d,e){t(this,jssun.awt.image.IntegerComponentRaster,[]);this.setIntCompRaster(a,b,c,d,e)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");d(c$,"setIntCompRaster",function(a,b,c,d,e){this.setSunRaster(a,b,c,d,e);this.maxX=this.minX+this.width;this.maxY=this.minY+this.height;if(!v(b,java.awt.image.DataBufferInt))throw new java.awt.image.RasterFormatException("IntegerComponentRasters must haveinteger DataBuffers");
if(1!=b.getNumBanks())throw new java.awt.image.RasterFormatException("DataBuffer for IntegerComponentRasters must only have 1 bank.");this.data=jssun.awt.image.SunWritableRaster.stealData(b,0);if(v(a,java.awt.image.SinglePixelPackedSampleModel)){e=a.getBitOffsets();for(var k=!1,g=1;g<e.length;g++)0!=e[g]%8&&(k=!0);this.type=k?9:10;this.scanlineStride=a.getScanlineStride();this.pixelStride=1;this.dataOffsets=w(1,0);this.dataOffsets[0]=b.getOffset();this.bandOffset=this.dataOffsets[0];this.dataOffsets[0]+=
c.x-d.x+(c.y-d.y)*this.scanlineStride;this.numDataElems=a.getNumDataElements()}else throw new java.awt.image.RasterFormatException("IntegerComponentRasters must have SinglePixelPackedSampleModel");this.verify()},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");d(c$,"getDataOffsets",function(){return this.dataOffsets.clone()});d(c$,"getDataOffset",function(a){return this.dataOffsets[a]},"~N");d(c$,"getScanlineStride",function(){return this.scanlineStride});
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b<this.minY||a>=this.maxX||b>=this.maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");a=(b-this.minY)*this.scanlineStride+(a-this.minX)*this.pixelStride;for(b=0;b<this.numDataElements;b++)this.data[this.dataOffsets[b]+a]=c[b];this.markDirty()},"~N,~N,~O");e(c$,"setDataElementsRaster",function(a,b,c){a+=c.getMinX();b+=c.getMinY();var d=c.getWidth(),e=c.getHeight();if(a<this.minX||b<this.minY||a+d>this.maxX||b+e>this.maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");
this.setDataElementsRaster4(a,b,d,e,c)},"~N,~N,java.awt.image.Raster");d(c$,"setDataElementsRaster4",function(a,b,c,d,e){if(!(0>=c||0>=d)){var k=e.getMinX(),g=e.getMinY(),h=null;if(v(e,jssun.awt.image.IntegerComponentRaster)&&1==this.pixelStride&&1==this.numDataElements){if(1!=e.getNumDataElements())throw new ArrayIndexOutOfBoundsException("Number of bands does not match");var h=e.getDataStorage(),j=e.getScanlineStride(),m=e.getDataOffset(0),p=this.dataOffsets[0]+(b-this.minY)*this.scanlineStride+
(a-this.minX);if(e.getPixelStride()==this.pixelStride){c*=this.pixelStride;for(var q=0;q<d;q++)System.arraycopy(h,m,this.data,p,c),m+=j,p+=this.scanlineStride;this.markDirty();return}}h=null;for(q=0;q<d;q++)h=e.getDataElements(k,g+q,c,1,h),this.setDataElements(a,b+q,c,1,h)}},"~N,~N,~N,~N,java.awt.image.Raster");d(c$,"setDataElements",function(a,b,c,d,e){if(a<this.minX||b<this.minY||a+c>this.maxX||b+d>this.maxY)throw new ArrayIndexOutOfBoundsException("Coordinate out of bounds!");a=(b-this.minY)*this.scanlineStride+
(a-this.minX)*this.pixelStride;var k=0,g,h;for(h=0;h<d;h++,a+=this.scanlineStride){b=a;for(g=0;g<c;g++,b+=this.pixelStride)for(var j=0;j<this.numDataElements;j++)this.data[this.dataOffsets[j]+b]=e[k++]}this.markDirty()},"~N,~N,~N,~N,~O");e(c$,"createWritableChild",function(a,b,c,d,e,k,g){if(a<this.minX)throw new java.awt.image.RasterFormatException("x lies outside raster");if(b<this.minY)throw new java.awt.image.RasterFormatException("y lies outside raster");if(a+c<a||a+c>this.minX+this.width)throw new java.awt.image.RasterFormatException("(x + width) is outside raster");
if(b+d<b||b+d>this.minY+this.height)throw new java.awt.image.RasterFormatException("(y + height) is outside raster");g=null!=g?this.sampleModel.createSubsetSampleModel(g):this.sampleModel;a=e-a;b=k-b;return new jssun.awt.image.IntegerComponentRaster(g,this.dataBuffer,new java.awt.Rectangle(e,k,c,d),new java.awt.Point(this.sampleModelTranslateX+a,this.sampleModelTranslateY+b),this)},"~N,~N,~N,~N,~N,~N,~A");e(c$,"createChild",function(a,b,c,d,e,k,g){return this.createWritableChild(a,b,c,d,e,k,g)},"~N,~N,~N,~N,~N,~N,~A");
d(c$,"createCompatibleWritableRaster",function(a,b){if(0>=a||0>=b)throw new java.awt.image.RasterFormatException("negative "+(0>=a?"width":"height"));var c=this.sampleModel.createCompatibleSampleModel(a,b);return new jssun.awt.image.IntegerComponentRaster(c,new java.awt.Point(0,0))},"~N,~N");d(c$,"createCompatibleWritableRaster",function(){return this.createCompatibleWritableRaster(this.width,this.height)});d(c$,"verify",function(){if(0>=this.width||0>=this.height||this.height>F(2147483647/this.width))throw new java.awt.image.RasterFormatException("Invalid raster dimension");
if(0>this.dataOffsets[0])throw new java.awt.image.RasterFormatException("Data offset ("+this.dataOffsets[0]+") must be >= 0");if(0>this.minX-this.sampleModelTranslateX||0>this.minY-this.sampleModelTranslateY)throw new java.awt.image.RasterFormatException("Incorrect origin/translate: ("+this.minX+", "+this.minY+") / ("+this.sampleModelTranslateX+", "+this.sampleModelTranslateY+")");if(0>this.scanlineStride||this.scanlineStride>F(2147483647/this.height))throw new java.awt.image.RasterFormatException("Incorrect scanline stride: "+
this.scanlineStride);if((1<this.height||0<this.minY-this.sampleModelTranslateY)&&this.scanlineStride>this.data.length)throw new java.awt.image.RasterFormatException("Incorrect scanline stride: "+this.scanlineStride);var a=(this.height-1)*this.scanlineStride;if(0>this.pixelStride||this.pixelStride>F(2147483647/this.width)||this.pixelStride>this.data.length)throw new java.awt.image.RasterFormatException("Incorrect pixel stride: "+this.pixelStride);var b=(this.width-1)*this.pixelStride;if(b>2147483647-
a)throw new java.awt.image.RasterFormatException("Incorrect raster attributes");for(var b=b+a,c=0,d=0;d<this.numDataElements;d++){if(this.dataOffsets[d]>2147483647-b)throw new java.awt.image.RasterFormatException("Incorrect band offset: "+this.dataOffsets[d]);a=b+this.dataOffsets[d];a>c&&(c=a)}if(this.data.length<=c)throw new java.awt.image.RasterFormatException("Data array too small (should be > "+c+" )");});e(c$,"toString",function(){return String.instantialize("IntegerComponentRaster: width = "+
this.width+" height = "+this.height+" #Bands = "+this.numBands+" #DataElements "+this.numDataElements+" xOff = "+this.sampleModelTranslateX+" yOff = "+this.sampleModelTranslateY+" dataOffset[0] "+this.dataOffsets[0])});G(c$,"TYPE_CUSTOM",0,"TYPE_BYTE_SAMPLES",1,"TYPE_USHORT_SAMPLES",2,"TYPE_INT_SAMPLES",3,"TYPE_BYTE_BANDED_SAMPLES",4,"TYPE_USHORT_BANDED_SAMPLES",5,"TYPE_INT_BANDED_SAMPLES",6,"TYPE_BYTE_PACKED_SAMPLES",7,"TYPE_USHORT_PACKED_SAMPLES",8,"TYPE_INT_PACKED_SAMPLES",9,"TYPE_INT_8BIT_SAMPLES",
10,"TYPE_BYTE_BINARY_SAMPLES",11)});p("jssun.awt.image");q(["java.awt.image.WritableRaster","jssun.awt.image.DataStealer"],"jssun.awt.image.SunWritableRaster",["jssun.java2d.StateTrackable","$.StateTrackableDelegate"],function(){c$=s(function(){this.theTrackable=null;r(this,arguments)},jssun.awt.image,"SunWritableRaster",java.awt.image.WritableRaster);c$.getStealer=d(c$,"getStealer",function(){return null==jssun.awt.image.SunWritableRaster.stealer?jssun.awt.image.SunWritableRaster.stealer=(H("jssun.awt.image.SunWritableRaster$1")?
0:jssun.awt.image.SunWritableRaster.$SunWritableRaster$1$(),C(jssun.awt.image.SunWritableRaster$1,this,null)):jssun.awt.image.SunWritableRaster.stealer});c$.stealData=d(c$,"stealData",function(a,b){return jssun.awt.image.SunWritableRaster.getStealer().getData(a,b)},"java.awt.image.DataBufferByte,~N");c$.stealData=d(c$,"stealData",function(a,b){return jssun.awt.image.SunWritableRaster.getStealer().getData(a,b)},"java.awt.image.DataBufferInt,~N");c$.stealTrackable=d(c$,"stealTrackable",function(a){return jssun.awt.image.SunWritableRaster.getStealer().getTrackable(a)},
"java.awt.image.DataBuffer");c$.setTrackable=d(c$,"setTrackable",function(a,b){jssun.awt.image.SunWritableRaster.getStealer().setTrackable(a,b)},"java.awt.image.DataBuffer,jssun.java2d.StateTrackableDelegate");c$.makeTrackable=d(c$,"makeTrackable",function(a){jssun.awt.image.SunWritableRaster.getStealer().setTrackable(a,jssun.java2d.StateTrackableDelegate.createInstance(jssun.java2d.StateTrackable.State.STABLE))},"java.awt.image.DataBuffer");c$.markDirty=d(c$,"markDirty",function(a){jssun.awt.image.SunWritableRaster.getStealer().getTrackable(a).markDirty()},
"java.awt.image.DataBuffer");c$.markDirty=d(c$,"markDirty",function(a){v(a,jssun.awt.image.SunWritableRaster)?a.markDirty():jssun.awt.image.SunWritableRaster.markDirty(a.getDataBuffer())},"java.awt.image.WritableRaster");m(c$,function(a,b){t(this,jssun.awt.image.SunWritableRaster,[a,b]);this.theTrackable=jssun.awt.image.SunWritableRaster.stealTrackable(this.dataBuffer)},"java.awt.image.SampleModel,java.awt.Point");m(c$,function(a,b,c){t(this,jssun.awt.image.SunWritableRaster,[a,b,c]);this.theTrackable=
jssun.awt.image.SunWritableRaster.stealTrackable(b)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Point");m(c$,function(){t(this,jssun.awt.image.SunWritableRaster,[])});m(c$,function(a,b,c,d,e){t(this,jssun.awt.image.SunWritableRaster,[]);this.setSunRaster(a,b,c,d,e)},"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");d(c$,"setSunRaster",function(a,b,c,d,e){this.setRaster(a,b,c,d,e);this.theTrackable=jssun.awt.image.SunWritableRaster.stealTrackable(b)},
"java.awt.image.SampleModel,java.awt.image.DataBuffer,java.awt.Rectangle,java.awt.Point,java.awt.image.Raster");d(c$,"markDirty",function(){this.theTrackable.markDirty()});c$.$SunWritableRaster$1$=function(){A(self.c$);c$=L(jssun.awt.image,"SunWritableRaster$1",null,jssun.awt.image.DataStealer);d(c$,"getData",function(a,b){return a.bankdata[b]},"java.awt.image.DataBufferByte,~N");d(c$,"getData",function(a,b){return a.bankdata[b]},"java.awt.image.DataBufferInt,~N");d(c$,"getTrackable",function(a){return a.theTrackable},
"java.awt.image.DataBuffer");d(c$,"setTrackable",function(a,b){a.theTrackable=b},"java.awt.image.DataBuffer,jssun.java2d.StateTrackableDelegate");c$=z()};G(c$,"stealer",null)});p("jssun.awt.image");M(jssun.awt.image,"DataStealer")})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,
Clazz.exceptionOf,Clazz.newIntArray,Clazz.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,
Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.checkPrivateMethod,Clazz.cloneFinals);