X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fappletgui%2FAlignFrame.js;h=0d207b94a5aadfd04a3076704f0575e8f1e4961d;hp=9e0b710c9b9070ec77903e1c17eaa2dd401e19cf;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6 diff --git a/site/j2s/jalview/appletgui/AlignFrame.js b/site/j2s/jalview/appletgui/AlignFrame.js index 9e0b710..0d207b9 100644 --- a/site/j2s/jalview/appletgui/AlignFrame.js +++ b/site/j2s/jalview/appletgui/AlignFrame.js @@ -1,2390 +1,2390 @@ -Clazz.declarePackage ("jalview.appletgui"); -Clazz.load (["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"], "jalview.appletgui.AlignFrame", ["awt2swing.Frame", "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", "$.Vector"], function () { -c$ = Clazz.decorateAsClass (function () { -this.avc = null; -this.alignPanel = null; -this.viewport = null; -this.frameWidth = 700; -this.frameHeight = 500; -this.jalviewServletURL = null; -this.showAutoCalculatedAbove = false; -this.annotationSortOrder = null; -this.alignFrameMenuBar = null; -this.fileMenu = null; -this.loadApplication = null; -this.$loadTree = null; -this.$loadAnnotations = null; -this.$outputFeatures = null; -this.$outputAnnotations = null; -this.closeMenuItem = null; -this.selectAllSequenceMenuItem = null; -this.deselectAllSequenceMenuItem = null; -this.invertSequenceMenuItem = null; -this.remove2LeftMenuItem = null; -this.remove2RightMenuItem = null; -this.removeGappedColumnMenuItem = null; -this.removeAllGapsMenuItem = null; -this.viewBoxesMenuItem = null; -this.viewTextMenuItem = null; -this.sortPairwiseMenuItem = null; -this.sortIDMenuItem = null; -this.sortLengthMenuItem = null; -this.sortGroupMenuItem = null; -this.removeRedundancyMenuItem = null; -this.pairwiseAlignmentMenuItem = null; -this.PCAMenuItem = null; -this.averageDistanceTreeMenuItem = null; -this.neighbourTreeMenuItem = null; -this.borderLayout1 = null; -this.statusBar = null; -this.clustalColour = null; -this.zappoColour = null; -this.taylorColour = null; -this.hydrophobicityColour = null; -this.helixColour = null; -this.strandColour = null; -this.turnColour = null; -this.buriedColour = null; -this.purinePyrimidineColour = null; -this.RNAInteractionColour = null; -this.RNAHelixColour = null; -this.userDefinedColour = null; -this.PIDColour = null; -this.BLOSUM62Colour = null; -this.tcoffeeColour = null; -this.njTreeBlosumMenuItem = null; -this.avDistanceTreeBlosumMenuItem = null; -this.annotationPanelMenuItem = null; -this.colourTextMenuItem = null; -this.displayNonconservedMenuItem = null; -this.alProperties = null; -this.overviewMenuItem = null; -this.undoMenuItem = null; -this.redoMenuItem = null; -this.conservationMenuItem = null; -this.noColourmenuItem = null; -this.wrapMenuItem = null; -this.renderGapsMenuItem = null; -this.findMenuItem = null; -this.abovePIDThreshold = null; -this.nucleotideColour = null; -this.deleteGroups = null; -this.grpsFromSelection = null; -this.createGroup = null; -this.unGroup = null; -this.$delete = null; -this.copy = null; -this.cut = null; -this.pasteMenu = null; -this.pasteNew = null; -this.pasteThis = null; -this.applyToAllGroups = null; -this.$font = null; -this.scaleAbove = null; -this.scaleLeft = null; -this.scaleRight = null; -this.modifyPID = null; -this.modifyConservation = null; -this.autoCalculate = null; -this.$sortByTree = null; -this.sortByTreeMenu = null; -this.inputText = null; -this.documentation = null; -this.about = null; -this.seqLimits = null; -this.centreColumnLabelFlag = null; -this.followMouseOverFlag = null; -this.showSequenceLogo = null; -this.applyAutoAnnotationSettings = null; -this.showConsensusHistogram = null; -this.showGroupConsensus = null; -this.showGroupConservation = null; -this.normSequenceLogo = null; -this.featureSettings = null; -this.sequenceFeatures = null; -this.annotationColour = null; -this.annotationColumnSelection = null; -this.invertColSel = null; -this.showColumns = null; -this.showSeqs = null; -this.hideColumns = null; -this.hideSequences = null; -this.hideAllButSelection = null; -this.hideAllSelection = null; -this.showAllHidden = null; -this.$newView = null; -this.showAlignmentAnnotations = null; -this.showSequenceAnnotations = null; -this.sortAnnBySequence = null; -this.sortAnnByLabel = null; -this.showAutoFirst = null; -this.showAutoLast = null; -this.splitFrame = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignFrame", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.KeyListener, jalview.api.AlignViewControllerGuiI]); -Clazz.prepareFields (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", true); -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.$newView = new awt2swing.MenuItem (); -}); -Clazz.makeConstructor (c$, -function (al, applet, title, embedded) { -this.construct (al, applet, title, embedded, true); -}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B"); -Clazz.makeConstructor (c$, -function (al, applet, title, embedded, addToDisplay) { -this.construct (al, null, null, applet, title, embedded, addToDisplay); -}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B"); -Clazz.makeConstructor (c$, -function (al, hiddenSeqs, columnSelection, applet, title, embedded) { -this.construct (al, hiddenSeqs, columnSelection, applet, title, embedded, true); -}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B"); -Clazz.makeConstructor (c$, -function (al, hiddenSeqs, columnSelection, applet, title, embedded, addToDisplay) { -Clazz.superConstructor (this, jalview.appletgui.AlignFrame, []); -if (applet != null) { -this.jalviewServletURL = applet.jalviewServletURL; -}try { -this.jbInit (); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (applet != null) { -var param; -try { -param = applet.windowWidth; -if (param != null) { -var width = Integer.parseInt (param); -this.frameWidth = width; -}param = applet.windowHeight; -if (param != null) { -var height = Integer.parseInt (param); -this.frameHeight = height; -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}this.viewport = new jalview.appletgui.AlignViewport (al, applet); -if (hiddenSeqs != null && hiddenSeqs.length > 0) { -this.viewport.hideSequence (hiddenSeqs); -}if (columnSelection != null) { -this.viewport.setColumnSelection (columnSelection); -}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 ()); -if (applet != null) { -var param = applet.sortBy; -if (param != null) { -if (param.equalsIgnoreCase ("Id")) { -this.sortIDMenuItem_actionPerformed (); -} else if (param.equalsIgnoreCase ("Pairwise Identity")) { -this.sortPairwiseMenuItem_actionPerformed (); -} else if (param.equalsIgnoreCase ("Length")) { -this.sortLengthMenuItem_actionPerformed (); -}}param = applet.wrap; -if (param != null) { -if (param.equalsIgnoreCase ("true")) { -this.wrapMenuItem.setState (true); -this.wrapMenuItem_actionPerformed (); -}}param = applet.centrecolumnlabels; -if (param != null) { -this.centreColumnLabelFlag.setState (true); -this.centreColumnLabelFlag_stateChanged (); -}}if (this.viewport.getAlignment ().isNucleotide ()) { -this.viewport.updateStrucConsensus (this.alignPanel); -if (this.viewport.getAlignment ().hasRNAStructure ()) { -this.RNAHelixColour.setEnabled (true); -} else { -this.RNAHelixColour.setEnabled (false); -}} else { -this.RNAHelixColour.setEnabled (false); -this.purinePyrimidineColour.setEnabled (false); -}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); -if (addToDisplay) { -this.addToDisplay (embedded); -}}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B"); -Clazz.defineMethod (c$, "addToDisplay", -function (embedded) { -this.createAlignFrameWindow (embedded); -this.validate (); -this.alignPanel.adjustAnnotationHeight (); -this.alignPanel.paintAlignment (true); -}, "~B"); -Clazz.defineMethod (c$, "getAlignViewport", -function () { -return this.viewport; -}); -Clazz.defineMethod (c$, "getSeqcanvas", -function () { -return this.alignPanel.seqPanel.seqCanvas; -}); -Clazz.defineMethod (c$, "parseFeaturesFile", -function (file, type) { -return this.parseFeaturesFile (file, type, true); -}, "~S,~S"); -Clazz.defineMethod (c$, "parseFeaturesFile", -function (file, type, autoenabledisplay) { -var featureLinks = new java.util.Hashtable (); -var featuresFile = false; -try { -featuresFile = new jalview.io.FeaturesFile (file, type).parse (this.viewport.getAlignment (), this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().getFeatureColours (), featureLinks, true, this.viewport.applet.getDefaultParameter ("relaxedidmatch", false)); -} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -ex.printStackTrace (); -} else { -throw ex; -} -} -if (featuresFile) { -if (featureLinks.size () > 0) { -this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().featureLinks = featureLinks; -}if (autoenabledisplay) { -this.viewport.setShowSequenceFeatures (true); -this.sequenceFeatures.setState (true); -}if (this.alignPanel.seqPanel.seqCanvas.fr != null) { -this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures (true); -}if (this.viewport.featureSettings != null) { -this.viewport.featureSettings.refreshTable (); -}this.alignPanel.paintAlignment (true); -this.setStatus (jalview.util.MessageManager.getString ("label.successfully_added_features_alignment")); -}return featuresFile; -}, "~S,~S,~B"); -Clazz.overrideMethod (c$, "keyPressed", -function (evt) { -if (this.viewport.cursorMode && ((evt.getKeyCode () >= 48 && evt.getKeyCode () <= 57) || (evt.getKeyCode () >= 96 && evt.getKeyCode () <= 105)) && Character.isDigit (evt.getKeyChar ())) { -this.alignPanel.seqPanel.numberPressed (evt.getKeyChar ()); -}switch (evt.getKeyCode ()) { -case 27: -this.deselectAllSequenceMenuItem_actionPerformed (); -this.alignPanel.alabels.cancelDrag (); -break; -case 88: -if (evt.isControlDown () || evt.isMetaDown ()) { -this.cut_actionPerformed (); -}break; -case 67: -if (this.viewport.cursorMode && !evt.isControlDown ()) { -this.alignPanel.seqPanel.setCursorColumn (); -}if (evt.isControlDown () || evt.isMetaDown ()) { -this.copy_actionPerformed (); -}break; -case 86: -if (evt.isControlDown ()) { -this.paste (evt.isShiftDown ()); -}break; -case 65: -if (evt.isControlDown () || evt.isMetaDown ()) { -this.selectAllSequenceMenuItem_actionPerformed (); -}break; -case 40: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (0, 1); -} else { -this.moveSelectedSequences (false); -}break; -case 38: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (0, -1); -} else { -this.moveSelectedSequences (true); -}break; -case 37: -if (evt.isAltDown () || !this.viewport.cursorMode) { -this.slideSequences (false, this.alignPanel.seqPanel.getKeyboardNo1 ()); -} else { -this.alignPanel.seqPanel.moveCursor (-1, 0); -}break; -case 39: -if (evt.isAltDown () || !this.viewport.cursorMode) { -this.slideSequences (true, this.alignPanel.seqPanel.getKeyboardNo1 ()); -} else { -this.alignPanel.seqPanel.moveCursor (1, 0); -}break; -case 32: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.insertGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); -}break; -case 127: -case 8: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.deleteGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); -} else { -this.cut_actionPerformed (); -this.alignPanel.seqPanel.seqCanvas.repaint (); -}break; -case 83: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorRow (); -}break; -case 80: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorPosition (); -}break; -case 10: -case 44: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setCursorRowAndColumn (); -}break; -case 81: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setSelectionAreaAtCursor (true); -}break; -case 77: -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.setSelectionAreaAtCursor (false); -}break; -case 113: -this.viewport.cursorMode = !this.viewport.cursorMode; -this.setStatus (jalview.util.MessageManager.formatMessage ("label.keyboard_editing_mode", Clazz.newArray (-1, [(this.viewport.cursorMode ? "on" : "off")]))); -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.seqCanvas.cursorX = this.viewport.startRes; -this.alignPanel.seqPanel.seqCanvas.cursorY = this.viewport.startSeq; -}break; -case 70: -if (evt.isControlDown ()) { -this.findMenuItem_actionPerformed (); -}break; -case 72: -{ -var toggleSeqs = !evt.isControlDown (); -var toggleCols = !evt.isShiftDown (); -this.toggleHiddenRegions (toggleSeqs, toggleCols); -break; -}case 33: -if (this.viewport.getWrapAlignment ()) { -this.alignPanel.scrollUp (true); -} else { -this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq - this.viewport.endSeq + this.viewport.startSeq); -}break; -case 34: -if (this.viewport.getWrapAlignment ()) { -this.alignPanel.scrollUp (false); -} else { -this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq + this.viewport.endSeq - this.viewport.startSeq); -}break; -case 90: -if (evt.isControlDown ()) { -this.undoMenuItem_actionPerformed (); -}break; -case 89: -if (evt.isControlDown ()) { -this.redoMenuItem_actionPerformed (); -}break; -case 76: -if (evt.isControlDown ()) { -this.trimAlignment (true); -}break; -case 82: -if (evt.isControlDown ()) { -this.trimAlignment (false); -}break; -case 69: -if (evt.isControlDown ()) { -if (evt.isShiftDown ()) { -this.removeAllGapsMenuItem_actionPerformed (); -} else { -this.removeGappedColumnMenuItem_actionPerformed (); -}}break; -case 73: -if (evt.isControlDown ()) { -if (evt.isAltDown ()) { -this.invertColSel_actionPerformed (); -} else { -this.invertSequenceMenuItem_actionPerformed (); -}}break; -case 71: -if (evt.isControlDown ()) { -if (evt.isShiftDown ()) { -this.unGroup_actionPerformed (); -} else { -this.createGroup_actionPerformed (); -}}break; -case 85: -if (evt.isControlDown ()) { -this.deleteGroups_actionPerformed (); -}break; -case 84: -if (evt.isControlDown ()) { -this.newView (null); -}break; -} -this.alignPanel.paintAlignment (true); -}, "java.awt.event.KeyEvent"); -Clazz.defineMethod (c$, "toggleHiddenRegions", - function (toggleSeqs, toggleCols) { -var hide = false; -var sg = this.viewport.getSelectionGroup (); -if (!toggleSeqs && !toggleCols) { -if ((this.viewport.getColumnSelection () != null && this.viewport.getColumnSelection ().getSelected () != null && this.viewport.getColumnSelection ().getSelected ().size () > 0) || (sg != null && sg.getSize () > 0 && sg.getStartRes () <= sg.getEndRes ())) { -if (sg != null) { -this.invertSequenceMenuItem_actionPerformed (); -sg = this.viewport.getSelectionGroup (); -toggleSeqs = true; -}this.viewport.expandColSelection (sg, true); -this.invertColSel_actionPerformed (); -toggleCols = true; -}}if (toggleSeqs) { -if (sg != null && sg.getSize () != this.viewport.getAlignment ().getHeight ()) { -hide = true; -this.viewport.hideAllSelectedSeqs (); -} else if (!(toggleCols && this.viewport.getColumnSelection ().getSelected ().size () > 0)) { -this.viewport.showAllHiddenSeqs (); -}}if (toggleCols) { -if (this.viewport.getColumnSelection ().getSelected ().size () > 0) { -this.viewport.hideSelectedColumns (); -if (!toggleSeqs) { -this.viewport.setSelectionGroup (sg); -}} else if (!hide) { -this.viewport.showAllHiddenColumns (); -}}}, "~B,~B"); -Clazz.overrideMethod (c$, "keyReleased", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "keyTyped", -function (evt) { -}, "java.awt.event.KeyEvent"); -Clazz.overrideMethod (c$, "itemStateChanged", -function (evt) { -var source = evt.getSource (); -if (source === this.displayNonconservedMenuItem) { -this.displayNonconservedMenuItem_actionPerformed (); -} else if (source === this.colourTextMenuItem) { -this.colourTextMenuItem_actionPerformed (); -} else if (source === this.wrapMenuItem) { -this.wrapMenuItem_actionPerformed (); -} else if (source === this.scaleAbove) { -this.viewport.setScaleAboveWrapped (this.scaleAbove.getState ()); -} else if (source === this.scaleLeft) { -this.viewport.setScaleLeftWrapped (this.scaleLeft.getState ()); -} else if (source === this.scaleRight) { -this.viewport.setScaleRightWrapped (this.scaleRight.getState ()); -} else if (source === this.seqLimits) { -this.seqLimits_itemStateChanged (); -} else if (source === this.viewBoxesMenuItem) { -this.viewport.setShowBoxes (this.viewBoxesMenuItem.getState ()); -} else if (source === this.viewTextMenuItem) { -this.viewport.setShowText (this.viewTextMenuItem.getState ()); -} else if (source === this.renderGapsMenuItem) { -this.viewport.setRenderGaps (this.renderGapsMenuItem.getState ()); -} else if (source === this.annotationPanelMenuItem) { -this.viewport.setShowAnnotation (this.annotationPanelMenuItem.getState ()); -this.alignPanel.setAnnotationVisible (this.annotationPanelMenuItem.getState ()); -} else if (source === this.sequenceFeatures) { -this.viewport.setShowSequenceFeatures (this.sequenceFeatures.getState ()); -this.alignPanel.seqPanel.seqCanvas.repaint (); -} else if (source === this.showAlignmentAnnotations) { -this.setAnnotationsVisibility (); -} else if (source === this.showSequenceAnnotations) { -this.setAnnotationsVisibility (); -} else if (source === this.sortAnnBySequence) { -var newState = this.sortAnnBySequence.getState (); -this.sortAnnByLabel.setState (false); -this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); -this.setViewportAnnotationOrder (); -} else if (source === this.sortAnnByLabel) { -var newState = this.sortAnnByLabel.getState (); -this.sortAnnBySequence.setState (false); -this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); -this.setViewportAnnotationOrder (); -} else if (source === this.showAutoFirst) { -this.showAutoLast.setState (!this.showAutoFirst.getState ()); -this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); -this.setViewportAnnotationOrder (); -} else if (source === this.showAutoLast) { -this.showAutoFirst.setState (!this.showAutoLast.getState ()); -this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); -this.setViewportAnnotationOrder (); -} else if (source === this.conservationMenuItem) { -this.conservationMenuItem_actionPerformed (); -} else if (source === this.abovePIDThreshold) { -this.abovePIDThreshold_actionPerformed (); -} else if (source === this.applyToAllGroups) { -this.viewport.setColourAppliesToAllGroups (this.applyToAllGroups.getState ()); -} else if (source === this.autoCalculate) { -this.viewport.autoCalculateConsensus = this.autoCalculate.getState (); -} else if (source === this.$sortByTree) { -this.viewport.sortByTree = this.$sortByTree.getState (); -} else if (source === this.centreColumnLabelFlag) { -this.centreColumnLabelFlag_stateChanged (); -} else if (source === this.followMouseOverFlag) { -this.mouseOverFlag_stateChanged (); -} else if (source === this.showGroupConsensus) { -this.showGroupConsensus_actionPerformed (); -} else if (source === this.showGroupConservation) { -this.showGroupConservation_actionPerformed (); -} else if (source === this.showSequenceLogo) { -this.showSequenceLogo_actionPerformed (); -} else if (source === this.normSequenceLogo) { -this.normSequenceLogo_actionPerformed (); -} else if (source === this.showConsensusHistogram) { -this.showConsensusHistogram_actionPerformed (); -} else if (source === this.applyAutoAnnotationSettings) { -this.applyAutoAnnotationSettings_actionPerformed (); -}this.alignPanel.paintAlignment (true); -}, "java.awt.event.ItemEvent"); -Clazz.defineMethod (c$, "setAnnotationsVisibility", - function () { -var showForAlignment = this.showAlignmentAnnotations.getState (); -var showForSequences = this.showSequenceAnnotations.getState (); -for (var aa, $aa = 0, $$aa = this.alignPanel.getAlignment ().getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { -var visible = (aa.sequenceRef == null ? showForAlignment : showForSequences); -aa.visible = visible; -} -this.alignPanel.validateAnnotationDimensions (true); -this.validate (); -this.repaint (); -}); -Clazz.defineMethod (c$, "setAnnotationSortOrder", - function (order) { -this.annotationSortOrder = order; -}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); -Clazz.defineMethod (c$, "setViewportAnnotationOrder", - function () { -this.alignPanel.av.setSortAnnotationsBy (this.annotationSortOrder); -this.alignPanel.av.setShowAutocalculatedAbove (this.showAutoCalculatedAbove); -}); -Clazz.defineMethod (c$, "setShowAutoCalculatedAbove", - function (showAbove) { -this.showAutoCalculatedAbove = showAbove; -}, "~B"); -Clazz.defineMethod (c$, "mouseOverFlag_stateChanged", - function () { -this.viewport.setFollowHighlight (this.followMouseOverFlag.getState ()); -}); -Clazz.defineMethod (c$, "centreColumnLabelFlag_stateChanged", - function () { -this.viewport.centreColumnLabels = this.centreColumnLabelFlag.getState (); -this.alignPanel.annotationPanel.repaint (); -}); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -var source = evt.getSource (); -if (source === this.inputText) { -this.inputText_actionPerformed (); -} else if (source === this.$loadTree) { -this.loadTree_actionPerformed (); -} else if (source === this.loadApplication) { -this.launchFullApplication (); -} else if (source === this.$loadAnnotations) { -this.loadAnnotations (); -} else if (source === this.$outputAnnotations) { -this.outputAnnotations (true); -} else if (source === this.$outputFeatures) { -this.outputFeatures (true, "Jalview"); -} else if (source === this.closeMenuItem) { -this.closeMenuItem_actionPerformed (); -} else if (source === this.copy) { -this.copy_actionPerformed (); -} else if (source === this.undoMenuItem) { -this.undoMenuItem_actionPerformed (); -} else if (source === this.redoMenuItem) { -this.redoMenuItem_actionPerformed (); -} else if (source === this.inputText) { -this.inputText_actionPerformed (); -} else if (source === this.closeMenuItem) { -this.closeMenuItem_actionPerformed (); -} else if (source === this.undoMenuItem) { -this.undoMenuItem_actionPerformed (); -} else if (source === this.redoMenuItem) { -this.redoMenuItem_actionPerformed (); -} else if (source === this.copy) { -this.copy_actionPerformed (); -} else if (source === this.pasteNew) { -this.pasteNew_actionPerformed (); -} else if (source === this.pasteThis) { -this.pasteThis_actionPerformed (); -} else if (source === this.cut) { -this.cut_actionPerformed (); -} else if (source === this.$delete) { -this.delete_actionPerformed (); -} else if (source === this.grpsFromSelection) { -this.makeGrpsFromSelection_actionPerformed (); -} else if (source === this.deleteGroups) { -this.deleteGroups_actionPerformed (); -} else if (source === this.selectAllSequenceMenuItem) { -this.selectAllSequenceMenuItem_actionPerformed (); -} else if (source === this.deselectAllSequenceMenuItem) { -this.deselectAllSequenceMenuItem_actionPerformed (); -} else if (source === this.invertSequenceMenuItem) { -this.invertSequenceMenuItem_actionPerformed (); -} else if (source === this.invertColSel) { -this.viewport.invertColumnSelection (); -this.alignPanel.paintAlignment (true); -} else if (source === this.remove2LeftMenuItem) { -this.trimAlignment (true); -} else if (source === this.remove2RightMenuItem) { -this.trimAlignment (false); -} else if (source === this.removeGappedColumnMenuItem) { -this.removeGappedColumnMenuItem_actionPerformed (); -} else if (source === this.removeAllGapsMenuItem) { -this.removeAllGapsMenuItem_actionPerformed (); -} else if (source === this.findMenuItem) { -this.findMenuItem_actionPerformed (); -} else if (source === this.$font) { - new jalview.appletgui.FontChooser (this.alignPanel); -} else if (source === this.$newView) { -this.newView (null); -} else if (source === this.showColumns) { -this.viewport.showAllHiddenColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showSeqs) { -this.viewport.showAllHiddenSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideColumns) { -this.viewport.hideSelectedColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideSequences && this.viewport.getSelectionGroup () != null) { -this.viewport.hideAllSelectedSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideAllButSelection) { -this.toggleHiddenRegions (false, false); -this.alignPanel.paintAlignment (true); -} else if (source === this.hideAllSelection) { -var sg = this.viewport.getSelectionGroup (); -this.viewport.expandColSelection (sg, false); -this.viewport.hideAllSelectedSeqs (); -this.viewport.hideSelectedColumns (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showAllHidden) { -this.viewport.showAllHiddenColumns (); -this.viewport.showAllHiddenSeqs (); -this.alignPanel.paintAlignment (true); -} else if (source === this.showGroupConsensus) { -this.showGroupConsensus_actionPerformed (); -} else if (source === this.showGroupConservation) { -this.showGroupConservation_actionPerformed (); -} else if (source === this.showSequenceLogo) { -this.showSequenceLogo_actionPerformed (); -} else if (source === this.normSequenceLogo) { -this.normSequenceLogo_actionPerformed (); -} else if (source === this.showConsensusHistogram) { -this.showConsensusHistogram_actionPerformed (); -} else if (source === this.applyAutoAnnotationSettings) { -this.applyAutoAnnotationSettings_actionPerformed (); -} else if (source === this.featureSettings) { - new jalview.appletgui.FeatureSettings (this.alignPanel); -} else if (source === this.alProperties) { -var contents = new jalview.io.AlignmentProperties (this.viewport.getAlignment ()).formatAsString (); -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); -cap.setText (contents.toString ()); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_properties", Clazz.newArray (-1, [this.getTitle ()])), 400, 250); -} else if (source === this.overviewMenuItem) { -this.overviewMenuItem_actionPerformed (); -} else if (source === this.noColourmenuItem) { -this.changeColour (null); -} else if (source === this.clustalColour) { -this.abovePIDThreshold.setState (false); -this.changeColour ( new jalview.schemes.ClustalxColourScheme (this.viewport.getAlignment (), null)); -} else if (source === this.zappoColour) { -this.changeColour ( new jalview.schemes.ZappoColourScheme ()); -} else if (source === this.taylorColour) { -this.changeColour ( new jalview.schemes.TaylorColourScheme ()); -} else if (source === this.hydrophobicityColour) { -this.changeColour ( new jalview.schemes.HydrophobicColourScheme ()); -} else if (source === this.helixColour) { -this.changeColour ( new jalview.schemes.HelixColourScheme ()); -} else if (source === this.strandColour) { -this.changeColour ( new jalview.schemes.StrandColourScheme ()); -} else if (source === this.turnColour) { -this.changeColour ( new jalview.schemes.TurnColourScheme ()); -} else if (source === this.buriedColour) { -this.changeColour ( new jalview.schemes.BuriedColourScheme ()); -} else if (source === this.nucleotideColour) { -this.changeColour ( new jalview.schemes.NucleotideColourScheme ()); -} else if (source === this.purinePyrimidineColour) { -this.changeColour ( new jalview.schemes.PurinePyrimidineColourScheme ()); -} else if (source === this.RNAInteractionColour) { -this.changeColour ( new jalview.schemes.RNAInteractionColourScheme ()); -} else if (source === this.RNAHelixColour) { - new jalview.schemes.RNAHelicesColourChooser (this.viewport, this.alignPanel); -} else if (source === this.modifyPID) { -this.modifyPID_actionPerformed (); -} else if (source === this.modifyConservation) { -this.modifyConservation_actionPerformed (); -} else if (source === this.userDefinedColour) { - new jalview.appletgui.UserDefinedColours (this.alignPanel, null); -} else if (source === this.PIDColour) { -this.changeColour ( new jalview.schemes.PIDColourScheme ()); -} else if (source === this.BLOSUM62Colour) { -this.changeColour ( new jalview.schemes.Blosum62ColourScheme ()); -} else if (source === this.tcoffeeColour) { -this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); -} else if (source === this.annotationColour) { - new jalview.appletgui.AnnotationColourChooser (this.viewport, this.alignPanel); -} else if (source === this.annotationColumnSelection) { - new jalview.appletgui.AnnotationColumnChooser (this.viewport, this.alignPanel); -} else if (source === this.sortPairwiseMenuItem) { -this.sortPairwiseMenuItem_actionPerformed (); -} else if (source === this.sortIDMenuItem) { -this.sortIDMenuItem_actionPerformed (); -} else if (source === this.sortLengthMenuItem) { -this.sortLengthMenuItem_actionPerformed (); -} else if (source === this.sortGroupMenuItem) { -this.sortGroupMenuItem_actionPerformed (); -} else if (source === this.removeRedundancyMenuItem) { -this.removeRedundancyMenuItem_actionPerformed (); -} else if (source === this.pairwiseAlignmentMenuItem) { -this.pairwiseAlignmentMenuItem_actionPerformed (); -} else if (source === this.PCAMenuItem) { -this.PCAMenuItem_actionPerformed (); -} else if (source === this.averageDistanceTreeMenuItem) { -this.averageDistanceTreeMenuItem_actionPerformed (); -} else if (source === this.neighbourTreeMenuItem) { -this.neighbourTreeMenuItem_actionPerformed (); -} else if (source === this.njTreeBlosumMenuItem) { -this.njTreeBlosumMenuItem_actionPerformed (); -} else if (source === this.avDistanceTreeBlosumMenuItem) { -this.avTreeBlosumMenuItem_actionPerformed (); -} else if (source === this.documentation) { -this.documentation_actionPerformed (); -} else if (source === this.about) { -this.about_actionPerformed (); -}}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "inputText_actionPerformed", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.input_cut_paste"), 500, 500); -}); -Clazz.defineMethod (c$, "outputText_actionPerformed", -function (e) { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); -var fr = this.alignPanel.cloneFeatureRenderer (); -cap.setText ( new jalview.io.AppletFormatAdapter (this.alignPanel).formatSequences (e.getActionCommand (), this.viewport.getAlignment (), this.viewport.getShowJVSuffix ())); -}, "java.awt.event.ActionEvent"); -Clazz.defineMethod (c$, "loadAnnotations", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -cap.setText (jalview.util.MessageManager.getString ("label.paste_features_annotations_Tcoffee_here")); -cap.setAnnotationImport (); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.paste_annotations"), 400, 300); -}); -Clazz.defineMethod (c$, "outputAnnotations", -function (displayTextbox) { -var annotation = new jalview.io.AnnotationFile ().printAnnotationsForView (this.viewport); -if (displayTextbox) { -var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.annotations"), 600, 500); -cap.setText (annotation); -}return annotation; -}, "~B"); -Clazz.defineMethod (c$, "getDisplayedFeatureCols", - function () { -if (this.alignPanel.getFeatureRenderer () != null && this.viewport.getFeaturesDisplayed () != null) { -return this.alignPanel.getFeatureRenderer ().getDisplayedFeatureCols (); -}return null; -}); -Clazz.defineMethod (c$, "outputFeatures", -function (displayTextbox, format) { -var features; -if (format.equalsIgnoreCase ("Jalview")) { -features = new jalview.io.FeaturesFile ().printJalviewFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); -} else { -features = new jalview.io.FeaturesFile ().printGFFFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); -}if (displayTextbox) { -var frimport = false; -if (features == null || features.equals ("No Features Visible")) { -features = "# No features visible - paste some and import them here."; -frimport = true; -}var cap = new jalview.appletgui.CutAndPasteTransfer (frimport, this); -if (frimport) { -cap.setAnnotationImport (); -}var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.features"), 600, 500); -cap.setText (features); -} else { -if (features == null) { -features = ""; -}}return features; -}, "~B,~S"); -Clazz.defineMethod (c$, "launchFullApplication", -function () { -var url = new StringBuffer (this.jalviewServletURL); -var firstSep = url.lastIndexOf ("?") > url.lastIndexOf ("/") ? "&" : "?"; -url.append (firstSep); -var applet = this.viewport.applet; -var s = applet.startupFile; -url.append ("open=" + this.appendProtocol (s)); -if (this.viewport.applet.features != null) { -url.append ("&features="); -url.append (this.appendProtocol (applet.features)); -}if (applet.annotations != null) { -url.append ("&annotations="); -url.append (this.appendProtocol (applet.annotations)); -}if (applet.jnetFile != null) { -url.append ("&annotations="); -url.append (this.appendProtocol (applet.jnetFile)); -}if (applet.defaultColour != null) { -url.append ("&colour=" + this.removeWhiteSpace (applet.defaultColour)); -}if (applet.userDefinedColour != null) { -url.append ("&colour=" + this.removeWhiteSpace (applet.userDefinedColour)); -}if (applet.treeFile != null) { -url.append ("&tree=" + this.appendProtocol (applet.treeFile)); -}this.showURL (url.toString (), "FULL_APP"); -}); -Clazz.defineMethod (c$, "removeWhiteSpace", -function (colour) { -var sb = new StringBuffer (); -for (var i = 0; i < colour.length; i++) { -if (Character.isWhitespace (colour.charAt (i))) { -sb.append ("%20"); -} else { -sb.append (colour.charAt (i)); -}} -return sb.toString (); -}, "~S"); -Clazz.defineMethod (c$, "appendProtocol", -function (url) { -try { - new java.net.URL (url); -url = java.net.URLEncoder.encode (url); -} catch (ex) { -if (Clazz.exceptionOf (ex, java.net.MalformedURLException)) { -url = this.viewport.applet.getCodeBase () + url; -} else { -throw ex; -} -} -return url; -}, "~S"); -Clazz.defineMethod (c$, "closeMenuItem_actionPerformed", -function () { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel); -if (this.alignPanel.seqPanel != null && this.alignPanel.seqPanel.seqCanvas != null) { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.seqPanel.seqCanvas); -}if (this.alignPanel.idPanel != null && this.alignPanel.idPanel.idCanvas != null) { -jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.idPanel.idCanvas); -}if (jalview.appletgui.PaintRefresher.components.size () == 0 && this.viewport.applet == null) { -System.exit (0); -} else { -}this.viewport = null; -this.alignPanel = null; -this.dispose (); -}); -Clazz.defineMethod (c$, "updateEditMenuBar", -function () { -if (this.viewport.getHistoryList ().size () > 0) { -this.undoMenuItem.setEnabled (true); -var command = this.viewport.getHistoryList ().peek (); -this.undoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.undo_command", Clazz.newArray (-1, [command.getDescription ()]))); -} else { -this.undoMenuItem.setEnabled (false); -this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); -}if (this.viewport.getRedoList ().size () > 0) { -this.redoMenuItem.setEnabled (true); -var command = this.viewport.getRedoList ().peek (); -this.redoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.redo_command", Clazz.newArray (-1, [command.getDescription ()]))); -} else { -this.redoMenuItem.setEnabled (false); -this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); -}}); -Clazz.overrideMethod (c$, "addHistoryItem", -function (command) { -if (command.getSize () > 0) { -this.viewport.addToHistoryList (command); -this.viewport.clearRedoList (); -this.updateEditMenuBar (); -this.viewport.updateHiddenColumns (); -}}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "undoMenuItem_actionPerformed", -function () { -if (this.viewport.getHistoryList ().isEmpty ()) { -return; -}var command = this.viewport.getHistoryList ().pop (); -this.viewport.addToRedoList (command); -command.undoCommand (null); -var originalSource = this.getOriginatingSource (command); -if (originalSource !== this.viewport) { -System.err.println ("Warning: Viewport object mismatch whilst undoing"); -}originalSource.updateHiddenColumns (); -this.updateEditMenuBar (); -originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "redoMenuItem_actionPerformed", -function () { -if (this.viewport.getRedoList ().isEmpty ()) { -return; -}var command = this.viewport.getRedoList ().pop (); -this.viewport.addToHistoryList (command); -command.doCommand (null); -var originalSource = this.getOriginatingSource (command); -if (originalSource !== this.viewport) { -System.err.println ("Warning: Viewport object mismatch whilst re-doing"); -}originalSource.updateHiddenColumns (); -this.updateEditMenuBar (); -originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "getOriginatingSource", -function (command) { -var originalSource = null; -var al = null; -if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { -var editCommand = command; -al = editCommand.getAlignment (); -var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); -for (var i = 0; i < comps.size (); i++) { -if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { -if (al === (comps.elementAt (i)).av.getAlignment ()) { -originalSource = (comps.elementAt (i)).av; -break; -}}} -}if (originalSource == null) { -if (al != null) { -jalview.appletgui.PaintRefresher.validateSequences (al, this.viewport.getAlignment ()); -}originalSource = this.viewport; -}return originalSource; -}, "jalview.commands.CommandI"); -Clazz.defineMethod (c$, "moveSelectedSequences", -function (up) { -var sg = this.viewport.getSelectionGroup (); -if (sg == null) { -return; -}this.viewport.getAlignment ().moveSelectedSequencesByOne (sg, up ? null : this.viewport.getHiddenRepSequences (), up); -this.alignPanel.paintAlignment (true); -var complement = this.viewport.getCodingComplement (); -if (complement != null) { -var mappedSelection = jalview.util.MappingUtils.mapSequenceGroup (sg, this.viewport, complement); -complement.getAlignment ().moveSelectedSequencesByOne (mappedSelection, up ? null : complement.getHiddenRepSequences (), up); -}}, "~B"); -Clazz.defineMethod (c$, "slideSequences", -function (right, size) { -var sg = new java.util.Vector (); -if (this.viewport.cursorMode) { -sg.add (this.viewport.getAlignment ().getSequenceAt (this.alignPanel.seqPanel.seqCanvas.cursorY)); -} else if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () != this.viewport.getAlignment ().getHeight ()) { -sg = this.viewport.getSelectionGroup ().getSequences (this.viewport.getHiddenRepSequences ()); -}if (sg.size () < 1) { -return; -}var invertGroup = new java.util.Vector (); -for (var i = 0; i < this.viewport.getAlignment ().getHeight (); i++) { -if (!sg.contains (this.viewport.getAlignment ().getSequenceAt (i))) { -invertGroup.addElement (this.viewport.getAlignment ().getSequenceAt (i)); -}} -var seqs1 = sg.toArray ( new Array (sg.size ())); -var seqs2 = invertGroup.toArray ( new Array (invertGroup.size ())); -for (var i = 0; i < invertGroup.size (); i++) { -seqs2[i] = invertGroup.elementAt (i); -} -var ssc; -if (right) { -ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs2, seqs1, size, this.viewport.getGapCharacter ()); -} else { -ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs1, seqs2, size, this.viewport.getGapCharacter ()); -}var groupAdjustment = 0; -if (ssc.getGapsInsertedBegin () && right) { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (size, 0); -} else { -groupAdjustment = size; -}} else if (!ssc.getGapsInsertedBegin () && !right) { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.moveCursor (-size, 0); -} else { -groupAdjustment = -size; -}}if (groupAdjustment != 0) { -this.viewport.getSelectionGroup ().setStartRes (this.viewport.getSelectionGroup ().getStartRes () + groupAdjustment); -this.viewport.getSelectionGroup ().setEndRes (this.viewport.getSelectionGroup ().getEndRes () + groupAdjustment); -}var appendHistoryItem = false; -var historyList = this.viewport.getHistoryList (); -if (historyList != null && historyList.size () > 0 && Clazz.instanceOf (historyList.peek (), jalview.commands.SlideSequencesCommand)) { -appendHistoryItem = ssc.appendSlideCommand (historyList.peek ()); -}if (!appendHistoryItem) { -this.addHistoryItem (ssc); -}this.repaint (); -}, "~B,~N"); -Clazz.defineMethod (c$, "copy_actionPerformed", -function () { -if (this.viewport.getSelectionGroup () == null) { -return; -}var sg = this.viewport.getSelectionGroup (); -jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); -var orderedSeqs = new java.util.HashMap (); -for (var i = 0; i < sg.getSize (); i++) { -var seq = sg.getSequenceAt (i); -var index = this.viewport.getAlignment ().findIndex (seq); -orderedSeqs.put (new Integer (index), seq); -} -var index = 0; -var startRes; -var endRes; -var ch; -if (this.viewport.hasHiddenColumns () && this.viewport.getSelectionGroup () != null) { -jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); -var hiddenOffset = this.viewport.getSelectionGroup ().getStartRes (); -for (var region, $region = this.viewport.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { -jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0] - hiddenOffset, region[1] - hiddenOffset])); -} -} else { -jalview.appletgui.AlignFrame.copiedHiddenColumns = null; -}for (var i = 0; i < sg.getSize (); i++) { -var seq = null; -while (seq == null) { -if (orderedSeqs.containsKey (new Integer (index))) { -seq = orderedSeqs.get (new Integer (index)); -index++; -break; -} else { -index++; -}} -startRes = seq.findPosition (sg.getStartRes ()); -endRes = 0; -for (var j = 0; j < sg.getEndRes () + 1 && j < seq.getLength (); j++) { -ch = seq.getCharAt (j); -if (!jalview.util.Comparison.isGap ((ch))) { -endRes++; -}} -if (endRes > 0) { -endRes += seq.getStart () - 1; -}jalview.appletgui.AlignFrame.copiedSequences.append (seq.getName () + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1) + "\n"); -} -}); -Clazz.defineMethod (c$, "pasteNew_actionPerformed", -function () { -this.paste (true); -}); -Clazz.defineMethod (c$, "pasteThis_actionPerformed", -function () { -this.paste (false); -}); -Clazz.defineMethod (c$, "paste", -function (newAlignment) { -try { -if (jalview.appletgui.AlignFrame.copiedSequences == null) { -return; -}var st = new java.util.StringTokenizer (jalview.appletgui.AlignFrame.copiedSequences.toString ()); -var seqs = new java.util.Vector (); -while (st.hasMoreElements ()) { -var name = st.nextToken (); -var start = Integer.parseInt (st.nextToken ()); -var end = Integer.parseInt (st.nextToken ()); -seqs.addElement ( new jalview.datamodel.Sequence (name, st.nextToken (), start, end)); -} -var newSeqs = new Array (seqs.size ()); -for (var i = 0; i < seqs.size (); i++) { -newSeqs[i] = seqs.elementAt (i); -} -if (newAlignment) { -var newtitle = jalview.util.MessageManager.getString ("label.copied_sequences"); -if (this.getTitle ().startsWith (jalview.util.MessageManager.getString ("label.copied_sequences"))) { -newtitle = this.getTitle (); -} else { -newtitle = newtitle.concat (jalview.util.MessageManager.formatMessage ("label.from_msname", Clazz.newArray (-1, [this.getTitle ()]))); -}var af = new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (newSeqs), this.viewport.applet, newtitle, false); -if (jalview.appletgui.AlignFrame.copiedHiddenColumns != null) { -for (var i = 0; i < jalview.appletgui.AlignFrame.copiedHiddenColumns.size (); i++) { -var region = jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt (i); -af.viewport.hideColumns (region[0], region[1]); -} -}jalview.bin.JalviewLite.addFrame (af, newtitle, this.frameWidth, this.frameHeight); -} else { -this.addSequences (newSeqs); -}} catch (ex) { -if (Clazz.exceptionOf (ex, Exception)) { -} else { -throw ex; -} -} -}, "~B"); -Clazz.defineMethod (c$, "addSequences", -function (seqs) { -for (var i = 0; i < seqs.length; i++) { -this.viewport.getAlignment ().addSequence (seqs[i]); -} -this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.add_sequences"), jalview.commands.EditCommand.Action.PASTE, seqs, 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"); -Clazz.defineMethod (c$, "cut_actionPerformed", -function () { -this.copy_actionPerformed (); -this.delete_actionPerformed (); -}); -Clazz.defineMethod (c$, "delete_actionPerformed", -function () { -var sg = this.viewport.getSelectionGroup (); -if (sg == null) { -return; -}var seqs = new java.util.Vector (); -var seq; -for (var i = 0; i < sg.getSize (); i++) { -seq = sg.getSequenceAt (i); -seqs.addElement (seq); -} -if (sg.getSize () == this.viewport.getAlignment ().getHeight ()) { -this.viewport.getColumnSelection ().removeElements (sg.getStartRes (), sg.getEndRes () + 1); -}var cut = new Array (seqs.size ()); -for (var i = 0; i < seqs.size (); i++) { -cut[i] = seqs.elementAt (i); -} -this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.cut_sequences"), jalview.commands.EditCommand.Action.CUT, cut, sg.getStartRes (), sg.getEndRes () - sg.getStartRes () + 1, this.viewport.getAlignment ())); -this.viewport.setSelectionGroup (null); -this.viewport.getAlignment ().deleteGroup (sg); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -if (this.viewport.getAlignment ().getHeight () < 1) { -this.setVisible (false); -}this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "showGroupConsensus_actionPerformed", -function () { -this.viewport.setShowGroupConsensus (this.showGroupConsensus.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showGroupConservation_actionPerformed", -function () { -this.viewport.setShowGroupConservation (this.showGroupConservation.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showConsensusHistogram_actionPerformed", -function () { -this.viewport.setShowConsensusHistogram (this.showConsensusHistogram.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "showSequenceLogo_actionPerformed", -function () { -this.viewport.setShowSequenceLogo (this.showSequenceLogo.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "normSequenceLogo_actionPerformed", -function () { -this.showSequenceLogo.setState (true); -this.viewport.setShowSequenceLogo (true); -this.viewport.setNormaliseSequenceLogo (this.normSequenceLogo.getState ()); -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "applyAutoAnnotationSettings_actionPerformed", -function () { -this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); -}); -Clazz.defineMethod (c$, "makeGrpsFromSelection_actionPerformed", -function () { -if (this.avc.makeGroupsFromSelection ()) { -jalview.appletgui.PaintRefresher.Refresh (this, this.viewport.getSequenceSetId ()); -this.alignPanel.updateAnnotation (); -this.alignPanel.paintAlignment (true); -}}); -Clazz.defineMethod (c$, "createGroup_actionPerformed", -function () { -this.avc.createGroup (); -}); -Clazz.defineMethod (c$, "unGroup_actionPerformed", -function () { -if (this.avc.unGroup ()) { -this.alignPanel.alignmentChanged (); -}}); -Clazz.defineMethod (c$, "deleteGroups_actionPerformed", -function () { -if (this.avc.deleteGroups ()) { -this.alignPanel.alignmentChanged (); -}}); -Clazz.defineMethod (c$, "selectAllSequenceMenuItem_actionPerformed", -function () { -var sg = new jalview.datamodel.SequenceGroup (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -sg.addSequence (this.viewport.getAlignment ().getSequenceAt (i), false); -} -sg.setEndRes (this.viewport.getAlignment ().getWidth () - 1); -this.viewport.setSelectionGroup (sg); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "deselectAllSequenceMenuItem_actionPerformed", -function () { -if (this.viewport.cursorMode) { -this.alignPanel.seqPanel.keyboardNo1 = null; -this.alignPanel.seqPanel.keyboardNo2 = null; -}this.viewport.setSelectionGroup (null); -this.viewport.getColumnSelection ().clear (); -this.viewport.setSelectionGroup (null); -this.alignPanel.idPanel.idCanvas.searchResults = null; -this.alignPanel.seqPanel.seqCanvas.highlightSearchResults (null); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "invertSequenceMenuItem_actionPerformed", -function () { -var sg = this.viewport.getSelectionGroup (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -sg.addOrRemove (this.viewport.getAlignment ().getSequenceAt (i), false); -} -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "invertColSel_actionPerformed", -function () { -this.viewport.invertColumnSelection (); -this.alignPanel.paintAlignment (true); -jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); -this.viewport.sendSelection (); -}); -Clazz.defineMethod (c$, "trimAlignment", -function (trimLeft) { -var colSel = this.viewport.getColumnSelection (); -var column; -if (colSel.size () > 0) { -if (trimLeft) { -column = colSel.getMin (); -} else { -column = colSel.getMax (); -}var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var trimRegion; -if (trimLeft) { -trimRegion = new jalview.commands.TrimRegionCommand ("Remove Left", jalview.commands.TrimRegionCommand.TRIM_LEFT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); -this.viewport.setStartRes (0); -} else { -trimRegion = new jalview.commands.TrimRegionCommand ("Remove Right", jalview.commands.TrimRegionCommand.TRIM_RIGHT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); -}this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_columns", Clazz.newArray (-1, [Integer.$valueOf (trimRegion.getSize ()).toString ()]))); -this.addHistoryItem (trimRegion); -for (var sg, $sg = this.viewport.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { -if ((trimLeft && !sg.adjustForRemoveLeft (column)) || (!trimLeft && !sg.adjustForRemoveRight (column))) { -this.viewport.getAlignment ().deleteGroup (sg); -}} -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}}, "~B"); -Clazz.defineMethod (c$, "removeGappedColumnMenuItem_actionPerformed", -function () { -var start = 0; -var end = this.viewport.getAlignment ().getWidth () - 1; -var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -start = this.viewport.getSelectionGroup ().getStartRes (); -end = this.viewport.getSelectionGroup ().getEndRes (); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var removeGapCols = new jalview.commands.RemoveGapColCommand ("Remove Gapped Columns", seqs, start, end, this.viewport.getAlignment ()); -this.addHistoryItem (removeGapCols); -this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_empty_columns", Clazz.newArray (-1, [Integer.$valueOf (removeGapCols.getSize ()).toString ()]))); -var seq = this.viewport.getAlignment ().getSequenceAt (0); -var startRes = seq.findPosition (this.viewport.startRes); -this.viewport.setStartRes (seq.findIndex (startRes) - 1); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "removeAllGapsMenuItem_actionPerformed", -function () { -var start = 0; -var end = this.viewport.getAlignment ().getWidth () - 1; -var seqs; -if (this.viewport.getSelectionGroup () != null) { -seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); -start = this.viewport.getSelectionGroup ().getStartRes (); -end = this.viewport.getSelectionGroup ().getEndRes (); -} else { -seqs = this.viewport.getAlignment ().getSequencesArray (); -}var seq = this.viewport.getAlignment ().getSequenceAt (0); -var startRes = seq.findPosition (this.viewport.startRes); -this.addHistoryItem ( new jalview.commands.RemoveGapsCommand ("Remove Gaps", seqs, start, end, this.viewport.getAlignment ())); -this.viewport.setStartRes (seq.findIndex (startRes) - 1); -this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); -}); -Clazz.defineMethod (c$, "findMenuItem_actionPerformed", -function () { - new jalview.appletgui.Finder (this.alignPanel); -}); -Clazz.defineMethod (c$, "newView", -function (viewtitle) { -var newal; -if (this.viewport.hasHiddenRows ()) { -newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getHiddenSequences ().getFullAlignment ().getSequencesArray ()); -} else { -newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getSequencesArray ()); -}if (this.viewport.getAlignment ().getAlignmentAnnotation () != null) { -for (var i = 0; i < this.viewport.getAlignment ().getAlignmentAnnotation ().length; i++) { -if (!this.viewport.getAlignment ().getAlignmentAnnotation ()[i].autoCalculated) { -newal.addAnnotation (this.viewport.getAlignment ().getAlignmentAnnotation ()[i]); -}} -}var newaf = new jalview.appletgui.AlignFrame (newal, this.viewport.applet, "", false); -newaf.viewport.setSequenceSetId (this.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (this.alignPanel, this.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId ()); -jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId ()); -var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); -var viewSize = -1; -for (var i = 0; i < comps.size (); i++) { -if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { -viewSize++; -}} -var title = String.instantialize (this.getTitle ()); -if (viewtitle != null) { -title = viewtitle + " ( " + title + ")"; -} else { -if (title.indexOf ("(View") > -1) { -title = title.substring (0, title.indexOf ("(View")); -}title += "(View " + viewSize + ")"; -}newaf.setTitle (title.toString ()); -newaf.viewport.setHistoryList (this.viewport.getHistoryList ()); -newaf.viewport.setRedoList (this.viewport.getRedoList ()); -return newaf; -}, "~S"); -Clazz.defineMethod (c$, "getFeatureGroups", -function () { -var fr = null; -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -var gps = fr.getFeatureGroups (); -var _gps = gps.toArray ( new Array (gps.size ())); -return _gps; -}return null; -}); -Clazz.defineMethod (c$, "getFeatureGroupsOfState", -function (visible) { -var fr = null; -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -var gps = fr.getGroups (visible); -var _gps = gps.toArray ( new Array (gps.size ())); -return _gps; -}return null; -}, "~B"); -Clazz.defineMethod (c$, "setFeatureGroupState", -function (groups, state) { -var fr = null; -this.sequenceFeatures.setState (true); -this.viewport.setShowSequenceFeatures (true); -if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { -fr.setGroupVisibility (java.util.Arrays.asList (groups), state); -this.alignPanel.seqPanel.seqCanvas.repaint (); -if (this.alignPanel.overviewPanel != null) { -this.alignPanel.overviewPanel.updateOverviewImage (); -}}}, "~A,~B"); -Clazz.defineMethod (c$, "seqLimits_itemStateChanged", -function () { -this.viewport.setShowJVSuffix (this.seqLimits.getState ()); -this.alignPanel.fontChanged (); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "colourTextMenuItem_actionPerformed", -function () { -this.viewport.setColourText (this.colourTextMenuItem.getState ()); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "displayNonconservedMenuItem_actionPerformed", -function () { -this.viewport.setShowUnconserved (this.displayNonconservedMenuItem.getState ()); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (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 (true); -}); -Clazz.defineMethod (c$, "overviewMenuItem_actionPerformed", -function () { -if (this.alignPanel.overviewPanel != null) { -return; -}var frame = new awt2swing.Frame (); -var overview = new jalview.appletgui.OverviewPanel (this.alignPanel); -frame.add (overview); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.overview_params", Clazz.newArray (-1, [this.getTitle ()])), overview.getPreferredSize ().width, overview.getPreferredSize ().height + 50); -frame.pack (); -var ap = this.alignPanel; -frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1, this, Clazz.cloneFinals ("ap", ap)))); -this.alignPanel.setOverviewPanel (overview); -}); -Clazz.overrideMethod (c$, "changeColour", -function (cs) { -var threshold = 0; -if (cs != null) { -if (this.viewport.getAbovePIDThreshold ()) { -this.viewport.setThreshold (jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, cs, "Background")); -}if (this.viewport.getConservationSelected ()) { -cs.setConservationApplied (true); -this.viewport.setIncrement (jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, cs, "Background")); -} else { -cs.setConservationApplied (false); -}}this.viewport.setGlobalColourScheme (cs); -if (this.alignPanel.getOverviewPanel () != null) { -this.alignPanel.getOverviewPanel ().updateOverviewImage (); -}jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.viewport.applet).sequenceColoursChanged (this.alignPanel); -this.alignPanel.paintAlignment (true); -}, "jalview.schemes.ColourSchemeI"); -Clazz.defineMethod (c$, "modifyPID_actionPerformed", -function () { -if (this.viewport.getAbovePIDThreshold () && this.viewport.getGlobalColourScheme () != null) { -jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); -jalview.appletgui.SliderPanel.showPIDSlider (); -}}); -Clazz.defineMethod (c$, "modifyConservation_actionPerformed", -function () { -if (this.viewport.getConservationSelected () && this.viewport.getGlobalColourScheme () != null) { -jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); -jalview.appletgui.SliderPanel.showConservationSlider (); -}}); -Clazz.defineMethod (c$, "conservationMenuItem_actionPerformed", -function () { -this.viewport.setConservationSelected (this.conservationMenuItem.getState ()); -this.viewport.setAbovePIDThreshold (false); -this.abovePIDThreshold.setState (false); -this.changeColour (this.viewport.getGlobalColourScheme ()); -this.modifyConservation_actionPerformed (); -}); -Clazz.defineMethod (c$, "abovePIDThreshold_actionPerformed", -function () { -this.viewport.setAbovePIDThreshold (this.abovePIDThreshold.getState ()); -this.conservationMenuItem.setState (false); -this.viewport.setConservationSelected (false); -this.changeColour (this.viewport.getGlobalColourScheme ()); -this.modifyPID_actionPerformed (); -}); -Clazz.defineMethod (c$, "sortPairwiseMenuItem_actionPerformed", -function () { -var oldOrder = 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", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortIDMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByID (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("ID Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortLengthMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByLength (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("Length Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "sortGroupMenuItem_actionPerformed", -function () { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByGroup (this.viewport.getAlignment ()); -this.addHistoryItem ( new jalview.commands.OrderCommand ("Group Sort", oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}); -Clazz.defineMethod (c$, "removeRedundancyMenuItem_actionPerformed", -function () { - new jalview.appletgui.RedundancyPanel (this.alignPanel); -}); -Clazz.defineMethod (c$, "pairwiseAlignmentMenuItem_actionPerformed", -function () { -if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) { -var frame = new awt2swing.Frame (); -frame.add ( new jalview.appletgui.PairwiseAlignPanel (this.alignPanel)); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.pairwise_alignment"), 600, 500); -}}); -Clazz.defineMethod (c$, "PCAMenuItem_actionPerformed", -function () { -if (!this.viewport.getAlignment ().isAligned (false)) { -var current; -var Width = this.viewport.getAlignment ().getWidth (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -current = this.viewport.getAlignment ().getSequenceAt (i); -if (current.getLength () < Width) { -current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); -}} -this.alignPanel.paintAlignment (true); -}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () < 4 && this.viewport.getSelectionGroup ().getSize () > 0) || this.viewport.getAlignment ().getHeight () < 4) { -return; -}try { - new jalview.appletgui.PCAPanel (this.viewport); -} catch (ex) { -if (Clazz.exceptionOf (ex, OutOfMemoryError)) { -} else { -throw ex; -} -} -}); -Clazz.defineMethod (c$, "averageDistanceTreeMenuItem_actionPerformed", -function () { -this.NewTreePanel ("AV", "PID", "Average distance tree using PID"); -}); -Clazz.defineMethod (c$, "neighbourTreeMenuItem_actionPerformed", -function () { -this.NewTreePanel ("NJ", "PID", "Neighbour joining tree using PID"); -}); -Clazz.defineMethod (c$, "njTreeBlosumMenuItem_actionPerformed", -function () { -this.NewTreePanel ("NJ", "BL", "Neighbour joining tree using BLOSUM62"); -}); -Clazz.defineMethod (c$, "avTreeBlosumMenuItem_actionPerformed", -function () { -this.NewTreePanel ("AV", "BL", "Average distance tree using BLOSUM62"); -}); -Clazz.defineMethod (c$, "NewTreePanel", -function (type, pwType, title) { -if (!this.viewport.getAlignment ().isAligned (false)) { -var current; -var Width = this.viewport.getAlignment ().getWidth (); -for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { -current = this.viewport.getAlignment ().getSequenceAt (i); -if (current.getLength () < Width) { -current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); -}} -this.alignPanel.paintAlignment (true); -}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) || (this.viewport.getAlignment ().getHeight () > 1)) { -var tp = new jalview.appletgui.TreePanel (this.alignPanel, type, pwType); -this.addTreeMenuItem (tp, title); -jalview.bin.JalviewLite.addFrame (tp, title, 600, 500); -}}, "~S,~S,~S"); -Clazz.defineMethod (c$, "loadTree_actionPerformed", -function () { -var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); -cap.setText (jalview.util.MessageManager.getString ("label.paste_newick_tree_file")); -cap.setTreeImport (); -var frame = new awt2swing.Frame (); -frame.add (cap); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.paste_newick_file"), 400, 300); -}); -Clazz.defineMethod (c$, "loadTree", -function (tree, treeFile) { -var tp = new jalview.appletgui.TreePanel (this.alignPanel, treeFile, jalview.util.MessageManager.getString ("label.load_tree_from_file"), tree); -jalview.bin.JalviewLite.addFrame (tp, treeFile, 600, 500); -this.addTreeMenuItem (tp, treeFile); -}, "jalview.io.NewickFile,~S"); -Clazz.defineMethod (c$, "sortByTree", -function (treePanel, title) { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -jalview.analysis.AlignmentSorter.sortByTree (this.viewport.getAlignment (), treePanel.getTree ()); -this.addHistoryItem ( new jalview.commands.OrderCommand (jalview.util.MessageManager.formatMessage ("label.order_by_params", Clazz.newArray (-1, [title])), oldOrder, this.viewport.getAlignment ())); -this.alignPanel.paintAlignment (true); -}, "jalview.appletgui.TreePanel,~S"); -Clazz.defineMethod (c$, "addTreeMenuItem", -function (treePanel, title) { -var item = new awt2swing.MenuItem (title); -this.sortByTreeMenu.add (item); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$2") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$2, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title)))); -treePanel.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$3") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$3, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title, "item", item)))); -}, "jalview.appletgui.TreePanel,~S"); -Clazz.defineMethod (c$, "sortBy", -function (alorder, undoname) { -var oldOrder = this.viewport.getAlignment ().getSequencesArray (); -if ((this.viewport.applet, jalview.bin.JalviewLite).debug) { -System.err.println ("Sorting " + alorder.getOrder ().size () + " in alignment '" + this.getTitle () + "'"); -}jalview.analysis.AlignmentSorter.sortBy (this.viewport.getAlignment (), alorder); -if (undoname != null) { -this.addHistoryItem ( new jalview.commands.OrderCommand (undoname, oldOrder, this.viewport.getAlignment ())); -}this.alignPanel.paintAlignment (true); -return true; -}, "jalview.datamodel.AlignmentOrder,~S"); -Clazz.defineMethod (c$, "documentation_actionPerformed", -function () { -this.alignPanel.av.applet.openJalviewHelpUrl (); -}); -Clazz.defineMethod (c$, "about_actionPerformed", -function () { -if (!Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1AboutPanel")) { -jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$ (); -} -var frame = new awt2swing.Frame (); -frame.add (Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1AboutPanel, this, null, jalview.bin.JalviewLite.getVersion (), jalview.bin.JalviewLite.getBuildDate ())); -jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.jalview"), 580, 220); -}); -Clazz.defineMethod (c$, "showURL", -function (url, target) { -if (this.viewport.applet == null) { -System.out.println ("Not running as applet - no browser available."); -} else { -this.viewport.applet.showURL (url, target); -}}, "~S,~S"); -Clazz.defineMethod (c$, "jbInit", - function () { -this.setMenuBar (this.alignFrameMenuBar); -this.inputText.setLabel (jalview.util.MessageManager.getString ("label.input_from_textbox")); -this.inputText.addActionListener (this); -var outputTextboxMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.out_to_textbox")); -for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { -var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); -item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$4") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$4, this, null))); -outputTextboxMenu.add (item); -} -this.closeMenuItem.addActionListener (this); -this.loadApplication.addActionListener (this); -this.$loadTree.addActionListener (this); -this.$loadAnnotations.addActionListener (this); -this.$outputFeatures.addActionListener (this); -this.$outputAnnotations.addActionListener (this); -this.undoMenuItem.setEnabled (false); -this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); -this.undoMenuItem.addActionListener (this); -this.redoMenuItem.setEnabled (false); -this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); -this.redoMenuItem.addActionListener (this); -this.copy.setLabel (jalview.util.MessageManager.getString ("action.copy")); -this.copy.addActionListener (this); -this.cut.setLabel (jalview.util.MessageManager.getString ("action.cut")); -this.cut.addActionListener (this); -this.$delete.setLabel (jalview.util.MessageManager.getString ("action.delete")); -this.$delete.addActionListener (this); -this.pasteMenu.setLabel (jalview.util.MessageManager.getString ("action.paste")); -this.pasteNew.setLabel (jalview.util.MessageManager.getString ("label.to_new_alignment")); -this.pasteNew.addActionListener (this); -this.pasteThis.setLabel (jalview.util.MessageManager.getString ("label.to_this_alignment")); -this.pasteThis.addActionListener (this); -this.remove2LeftMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_left")); -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")); -this.invertSequenceMenuItem.addActionListener (this); -this.invertColSel.setLabel (jalview.util.MessageManager.getString ("action.invert_column_selection")); -this.invertColSel.addActionListener (this); -this.deleteGroups.setLabel (jalview.util.MessageManager.getString ("action.undefine_groups")); -this.deleteGroups.addActionListener (this); -this.grpsFromSelection.setLabel (jalview.util.MessageManager.getString ("action.make_groups_selection")); -this.grpsFromSelection.addActionListener (this); -this.createGroup.setLabel (jalview.util.MessageManager.getString ("action.create_group")); -this.unGroup.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); -this.annotationColumnSelection.setLabel ("Select by Annotation"); -this.annotationColumnSelection.addActionListener (this); -this.$newView.setLabel (jalview.util.MessageManager.getString ("action.new_view")); -this.$newView.addActionListener (this); -var showMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.show")); -this.showColumns.setLabel (jalview.util.MessageManager.getString ("label.all_columns")); -this.showSeqs.setLabel (jalview.util.MessageManager.getString ("label.all_sequences")); -var hideMenu = 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")); -this.showColumns.addActionListener (this); -this.showSeqs.addActionListener (this); -this.hideColumns.addActionListener (this); -this.hideSequences.addActionListener (this); -this.hideAllButSelection.addActionListener (this); -this.hideAllSelection.addActionListener (this); -this.showAllHidden.addActionListener (this); -this.featureSettings.setLabel (jalview.util.MessageManager.getString ("label.feature_settings")); -this.featureSettings.addActionListener (this); -this.sequenceFeatures.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_features")); -this.sequenceFeatures.addItemListener (this); -this.sequenceFeatures.setState (false); -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 (true); -var autoAnnMenu = 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 (true); -this.scaleAbove.setEnabled (false); -this.scaleAbove.addItemListener (this); -this.scaleLeft.setEnabled (false); -this.scaleLeft.setState (true); -this.scaleLeft.setLabel (jalview.util.MessageManager.getString ("action.scale_left")); -this.scaleLeft.addItemListener (this); -this.scaleRight.setEnabled (false); -this.scaleRight.setState (true); -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 (true); -this.viewBoxesMenuItem.addItemListener (this); -this.viewTextMenuItem.setLabel (jalview.util.MessageManager.getString ("action.text")); -this.viewTextMenuItem.setState (true); -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 (true); -this.renderGapsMenuItem.addItemListener (this); -this.centreColumnLabelFlag.setLabel (jalview.util.MessageManager.getString ("label.centre_column_labels")); -this.centreColumnLabelFlag.addItemListener (this); -this.seqLimits.setState (true); -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 (true); -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 (false); -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"), true); -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 sortMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.sort")); -var calculateTreeMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate_tree")); -this.autoCalculate.addItemListener (this); -this.$sortByTree.addItemListener (this); -var helpMenu = 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 editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); -this.alignFrameMenuBar.add (editMenu); -var selectMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.select")); -this.alignFrameMenuBar.add (selectMenu); -var viewMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.view")); -this.alignFrameMenuBar.add (viewMenu); -var annotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.annotations")); -this.alignFrameMenuBar.add (annotationsMenu); -var formatMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.format")); -this.alignFrameMenuBar.add (formatMenu); -var colourMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.colour")); -this.alignFrameMenuBar.add (colourMenu); -var calculateMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate")); -this.alignFrameMenuBar.add (calculateMenu); -this.alignFrameMenuBar.add (helpMenu); -this.fileMenu.add (this.inputText); -this.fileMenu.add (this.$loadTree); -this.fileMenu.add (this.$loadAnnotations); -this.fileMenu.addSeparator (); -this.fileMenu.add (outputTextboxMenu); -this.fileMenu.add (this.$outputFeatures); -this.fileMenu.add (this.$outputAnnotations); -if (this.jalviewServletURL != null) { -this.fileMenu.add (this.loadApplication); -}this.fileMenu.addSeparator (); -this.fileMenu.add (this.closeMenuItem); -editMenu.add (this.undoMenuItem); -editMenu.add (this.redoMenuItem); -editMenu.add (this.cut); -editMenu.add (this.copy); -this.pasteMenu.add (this.pasteNew); -this.pasteMenu.add (this.pasteThis); -editMenu.add (this.pasteMenu); -editMenu.add (this.$delete); -editMenu.addSeparator (); -editMenu.add (this.remove2LeftMenuItem); -editMenu.add (this.remove2RightMenuItem); -editMenu.add (this.removeGappedColumnMenuItem); -editMenu.add (this.removeAllGapsMenuItem); -editMenu.add (this.removeRedundancyMenuItem); -selectMenu.add (this.findMenuItem); -selectMenu.addSeparator (); -selectMenu.add (this.selectAllSequenceMenuItem); -selectMenu.add (this.deselectAllSequenceMenuItem); -selectMenu.add (this.invertSequenceMenuItem); -selectMenu.add (this.invertColSel); -selectMenu.add (this.createGroup); -selectMenu.add (this.unGroup); -selectMenu.add (this.grpsFromSelection); -selectMenu.add (this.deleteGroups); -selectMenu.add (this.annotationColumnSelection); -viewMenu.add (this.$newView); -viewMenu.addSeparator (); -showMenu.add (this.showColumns); -showMenu.add (this.showSeqs); -showMenu.add (this.showAllHidden); -viewMenu.add (showMenu); -hideMenu.add (this.hideColumns); -hideMenu.add (this.hideSequences); -hideMenu.add (this.hideAllSelection); -hideMenu.add (this.hideAllButSelection); -viewMenu.add (hideMenu); -viewMenu.addSeparator (); -viewMenu.add (this.followMouseOverFlag); -viewMenu.addSeparator (); -viewMenu.add (this.sequenceFeatures); -viewMenu.add (this.featureSettings); -viewMenu.addSeparator (); -viewMenu.add (this.alProperties); -viewMenu.addSeparator (); -viewMenu.add (this.overviewMenuItem); -annotationsMenu.add (this.annotationPanelMenuItem); -annotationsMenu.addSeparator (); -annotationsMenu.add (this.showAlignmentAnnotations); -annotationsMenu.add (this.showSequenceAnnotations); -annotationsMenu.add (this.sortAnnBySequence); -annotationsMenu.add (this.sortAnnByLabel); -annotationsMenu.addSeparator (); -autoAnnMenu.add (this.showAutoFirst); -autoAnnMenu.add (this.showAutoLast); -autoAnnMenu.addSeparator (); -autoAnnMenu.add (this.applyAutoAnnotationSettings); -autoAnnMenu.add (this.showConsensusHistogram); -autoAnnMenu.add (this.showSequenceLogo); -autoAnnMenu.add (this.normSequenceLogo); -autoAnnMenu.addSeparator (); -autoAnnMenu.add (this.showGroupConservation); -autoAnnMenu.add (this.showGroupConsensus); -annotationsMenu.add (autoAnnMenu); -formatMenu.add (this.$font); -formatMenu.add (this.seqLimits); -formatMenu.add (this.wrapMenuItem); -formatMenu.add (this.scaleAbove); -formatMenu.add (this.scaleLeft); -formatMenu.add (this.scaleRight); -formatMenu.add (this.viewBoxesMenuItem); -formatMenu.add (this.viewTextMenuItem); -formatMenu.add (this.colourTextMenuItem); -formatMenu.add (this.displayNonconservedMenuItem); -formatMenu.add (this.renderGapsMenuItem); -formatMenu.add (this.centreColumnLabelFlag); -colourMenu.add (this.applyToAllGroups); -colourMenu.addSeparator (); -colourMenu.add (this.noColourmenuItem); -colourMenu.add (this.clustalColour); -colourMenu.add (this.BLOSUM62Colour); -colourMenu.add (this.PIDColour); -colourMenu.add (this.zappoColour); -colourMenu.add (this.taylorColour); -colourMenu.add (this.hydrophobicityColour); -colourMenu.add (this.helixColour); -colourMenu.add (this.strandColour); -colourMenu.add (this.turnColour); -colourMenu.add (this.buriedColour); -colourMenu.add (this.nucleotideColour); -colourMenu.add (this.purinePyrimidineColour); -colourMenu.add (this.tcoffeeColour); -colourMenu.add (this.userDefinedColour); -colourMenu.addSeparator (); -colourMenu.add (this.conservationMenuItem); -colourMenu.add (this.modifyConservation); -colourMenu.add (this.abovePIDThreshold); -colourMenu.add (this.modifyPID); -colourMenu.add (this.annotationColour); -colourMenu.add (this.RNAHelixColour); -sortMenu.add (this.sortIDMenuItem); -sortMenu.add (this.sortLengthMenuItem); -sortMenu.add (this.sortByTreeMenu); -sortMenu.add (this.sortGroupMenuItem); -sortMenu.add (this.sortPairwiseMenuItem); -calculateMenu.add (sortMenu); -calculateTreeMenu.add (this.averageDistanceTreeMenuItem); -calculateTreeMenu.add (this.neighbourTreeMenuItem); -calculateTreeMenu.add (this.avDistanceTreeBlosumMenuItem); -calculateTreeMenu.add (this.njTreeBlosumMenuItem); -calculateMenu.add (calculateTreeMenu); -calculateMenu.addSeparator (); -calculateMenu.add (this.pairwiseAlignmentMenuItem); -calculateMenu.add (this.PCAMenuItem); -calculateMenu.add (this.autoCalculate); -calculateMenu.add (this.$sortByTree); -helpMenu.add (this.documentation); -helpMenu.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"); -}); -Clazz.overrideMethod (c$, "setStatus", -function (string) { -this.statusBar.setText (string); -}, "~S"); -Clazz.defineMethod (c$, "createAlignFrameWindow", -function (reallyEmbedded) { -if (reallyEmbedded) { -this.embedAlignFrameInApplet (this.viewport.applet); -} else { -if (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"); -Clazz.defineMethod (c$, "embedAlignFrameInApplet", -function (theApplet) { -this.fileMenu.remove (this.closeMenuItem); -this.fileMenu.remove (3); -this.embeddedMenu = this.makeEmbeddedPopupMenu (this.alignFrameMenuBar, false, false); -theApplet.setLayout ( new java.awt.BorderLayout ()); -theApplet.add (this.embeddedMenu, "North"); -theApplet.add (this.statusBar, "South"); -this.alignPanel.setSize (theApplet.getSize ().width, theApplet.getSize ().height - this.embeddedMenu.getHeight () - this.statusBar.getHeight ()); -theApplet.add (this.alignPanel, "Center"); -var me = this; -theApplet.addFocusListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$5") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$5, this, Clazz.cloneFinals ("theApplet", theApplet, "me", me)))); -theApplet.validate (); -}, "jalview.bin.JalviewLite"); -Clazz.defineMethod (c$, "addStructureViewInstance", -function (jmolviewer, sequenceIds) { -return null; -}, "~O,~A"); -Clazz.defineMethod (c$, "addPdbFile", -function (sequenceId, pdbEntryString, pdbFile) { -var toaddpdb = this.viewport.getAlignment ().findName (sequenceId); -var needtoadd = false; -if (toaddpdb != null) { -var pdbe = toaddpdb.getPDBId (); -var pdbentry = null; -if (pdbe != null && pdbe.size () > 0) { -for (var pe = 0, peSize = pdbe.size (); pe < peSize; pe++) { -pdbentry = pdbe.elementAt (pe); -if (!pdbentry.getId ().equals (pdbEntryString) && !pdbentry.getFile ().equals (pdbFile)) { -pdbentry = null; -} else { -continue; -}} -}if (pdbentry == null) { -pdbentry = new jalview.datamodel.PDBEntry (); -pdbentry.setId (pdbEntryString); -pdbentry.setFile (pdbFile); -needtoadd = true; -}var protocol = jalview.io.AppletFormatAdapter.resolveProtocol (pdbFile, "PDB"); -if (protocol == null) { -return false; -}if (needtoadd) { -if (pdbentry.getProperty () == null) { -pdbentry.setProperty ( new java.util.Hashtable ()); -}pdbentry.getProperty ().put ("protocol", protocol); -toaddpdb.addPDBId (pdbentry); -this.alignPanel.getStructureSelectionManager ().registerPDBEntry (pdbentry); -}}return true; -}, "~S,~S,~S"); -Clazz.defineMethod (c$, "cleanSeqChainArrays", - function (seqs, chains) { -if (seqs != null) { -var sequences = new java.util.Vector (); -for (var i = 0; i < seqs.length; i++) { -if (seqs[i] != null) { -sequences.addElement ( Clazz.newArray (-1, [seqs[i], (chains != null) ? chains[i] : null])); -}} -seqs = new Array (sequences.size ()); -chains = new Array (sequences.size ()); -for (var i = 0, isize = sequences.size (); i < isize; i++) { -var oj = sequences.elementAt (i); -seqs[i] = oj[0]; -chains[i] = oj[1]; -} -}return Clazz.newArray (-1, [seqs, chains]); -}, "~A,~A"); -Clazz.defineMethod (c$, "newStructureView", -function (applet, pdb, seqs, chains, protocol) { -var sqch = this.cleanSeqChainArrays (seqs, chains); -seqs = sqch[0]; -chains = sqch[1]; -if (seqs == null || seqs.length == 0) { -System.err.println ("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); -}if (protocol == null || protocol.trim ().length == 0 || protocol.equals ("null")) { -protocol = pdb.getProperty ().get ("protocol"); -if (protocol == null) { -System.err.println ("Couldn't work out protocol to open structure: " + pdb.getId ()); -return; -}}if (applet.useXtrnalSviewer) { -if (jalview.structure.StructureSelectionManager.getStructureSelectionManager (applet).setMapping (seqs, chains, pdb.getFile (), protocol) == null) { -System.err.println ("Failed to map " + pdb.getFile () + " (" + protocol + ") to any sequences"); -}return; -}if (applet.isAlignPdbStructures () && applet.jmolAvailable) { -var ajm = null; -var tajm; -var jmols = applet.getAppletWindow (jalview.appletgui.AppletJmol); -for (var i = 0, iSize = jmols.size (); i < iSize; i++) { -tajm = jmols.elementAt (i); -if (tajm.ap.alignFrame === this) { -ajm = tajm; -break; -}} -if (ajm != null) { -System.err.println ("Incremental adding and aligning structure to existing Jmol view not yet implemented."); -ajm = null; -}} new jalview.appletgui.AppletJmol (pdb, seqs, chains, this.alignPanel, protocol); -jalview.bin.JalviewLite.lastFrameX += 40; -jalview.bin.JalviewLite.lastFrameY += 40; -}, "jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S"); -Clazz.defineMethod (c$, "alignedStructureView", -function (applet, pdb, seqs, chains, protocols) { -System.err.println ("Aligned Structure View: Not yet implemented."); -}, "jalview.bin.JalviewLite,~A,~A,~A,~A"); -Clazz.defineMethod (c$, "select", -function (sel, csel) { -this.alignPanel.seqPanel.selection (sel, csel, null); -}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection"); -Clazz.defineMethod (c$, "scrollTo", -function (row, column) { -this.alignPanel.seqPanel.scrollTo (row, column); -}, "~N,~N"); -Clazz.defineMethod (c$, "scrollToRow", -function (row) { -this.alignPanel.seqPanel.scrollToRow (row); -}, "~N"); -Clazz.defineMethod (c$, "scrollToColumn", -function (column) { -this.alignPanel.seqPanel.scrollToColumn (column); -}, "~N"); -Clazz.defineMethod (c$, "getSequenceSetId", -function () { -return this.viewport.getSequenceSetId (); -}); -Clazz.defineMethod (c$, "loadScoreFile", -function (inFile) { -var file = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [inFile, jalview.io.AppletFormatAdapter.checkProtocol (inFile)]); -if (!file.isValid ()) { -System.err.println ("Problems parsing T-Coffee scores: " + file.getWarningMessage ()); -System.err.println ("Origin was:\n" + inFile); -return false; -}var aln; -if ((aln = this.viewport.getAlignment ()) != null && (aln.getHeight () != file.getHeight () || aln.getWidth () != file.getWidth ())) { -System.err.println ("The scores matrix does not match the alignment dimensions"); -}if (file.annotateAlignment (this.alignPanel.getAlignment (), false)) { -this.alignPanel.fontChanged (); -this.tcoffeeColour.setEnabled (true); -this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); -return true; -} else { -System.err.println ("Problems resolving T-Coffee scores:"); -if (file.getWarningMessage () != null) { -System.err.println (file.getWarningMessage ()); -}}return false; -}, "~S"); -Clazz.defineMethod (c$, "getSplitFrame", -function () { -return this.splitFrame; -}); -Clazz.defineMethod (c$, "setSplitFrame", -function (sf) { -this.splitFrame = sf; -}, "jalview.appletgui.SplitFrame"); -Clazz.overrideMethod (c$, "setShowSeqFeatures", -function (b) { -this.viewport.setShowSequenceFeatures (b); -}, "~B"); -Clazz.overrideMethod (c$, "setMenusForViewport", -function () { -}); -Clazz.overrideMethod (c$, "refreshFeatureUI", -function (enableIfNecessary) { -if (enableIfNecessary) { -this.sequenceFeatures.setState (true); -this.alignPanel.av.setShowSequenceFeatures (true); -}}, "~B"); -Clazz.overrideMethod (c$, "getFeatureSettingsUI", -function () { -return this.alignPanel.av.featureSettings; -}); -c$.$AlignFrame$1$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$1", java.awt.event.WindowAdapter); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -if (this.f$.ap != null) { -this.f$.ap.setOverviewPanel (null); -}}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$2$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$2", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (evt) { -this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$3$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$3", java.awt.event.WindowAdapter); -Clazz.defineMethod (c$, "windowOpened", -function (e) { -if (this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree) { -this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); -}Clazz.superCall (this, jalview.appletgui.AlignFrame$3, "windowOpened", [e]); -}, "java.awt.event.WindowEvent"); -Clazz.overrideMethod (c$, "windowClosing", -function (e) { -this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove (this.f$.item); -}, "java.awt.event.WindowEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$1AboutPanel$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.decorateAsClass (function () { -Clazz.prepareCallback (this, arguments); -this.version = null; -this.builddate = null; -Clazz.instantialize (this, arguments); -}, jalview.appletgui, "AlignFrame$1AboutPanel", awt2swing.Canvas); -Clazz.makeConstructor (c$, -function (a, b) { -Clazz.superConstructor (this, jalview.appletgui.AlignFrame$1AboutPanel, []); -this.version = a; -this.builddate = b; -}, "~S,~S"); -Clazz.overrideMethod (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 (); -var c = b.getHeight (); -var d = 5; -var e = 7; -a.setColor (java.awt.Color.black); -a.setFont ( new java.awt.Font ("Helvetica", 1, 14)); -a.drawString (jalview.util.MessageManager.formatMessage ("label.jalviewLite_release", Clazz.newArray (-1, [this.version])), e, d += c); -a.setFont ( new java.awt.Font ("Helvetica", 1, 12)); -a.drawString (jalview.util.MessageManager.formatMessage ("label.jaview_build_date", Clazz.newArray (-1, [this.builddate])), e, d += c); -a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_1"), e, d += c * 1.5); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_2"), e + 50, d += c + 8); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_dev_managers"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_distribution_lists"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_please_cite"), e, d += c + 8); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_authors"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_title"), e, d += c); -a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_ref"), e, d += c); -}, "java.awt.Graphics"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$4$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$4", null, java.awt.event.ActionListener); -Clazz.overrideMethod (c$, "actionPerformed", -function (e) { -this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed (e); -}, "java.awt.event.ActionEvent"); -c$ = Clazz.p0p (); -}; -c$.$AlignFrame$5$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$5", null, java.awt.event.FocusListener); -Clazz.overrideMethod (c$, "focusLost", -function (e) { -if (this.f$.theApplet.currentAlignFrame === this.f$.me) { -this.f$.theApplet.currentAlignFrame = null; -}}, "java.awt.event.FocusEvent"); -Clazz.overrideMethod (c$, "focusGained", -function (e) { -this.f$.theApplet.currentAlignFrame = this.f$.me; -}, "java.awt.event.FocusEvent"); -c$ = Clazz.p0p (); -}; -Clazz.defineStatics (c$, -"copiedSequences", null, -"copiedHiddenColumns", null); -}); +Clazz.declarePackage ("jalview.appletgui"); +Clazz.load (["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"], "jalview.appletgui.AlignFrame", ["awt2swing.Frame", "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"], function () { +c$ = Clazz.decorateAsClass (function () { +this.avc = null; +this.alignPanel = null; +this.viewport = null; +this.frameWidth = 700; +this.frameHeight = 500; +this.jalviewServletURL = null; +this.showAutoCalculatedAbove = false; +this.annotationSortOrder = null; +this.alignFrameMenuBar = null; +this.fileMenu = null; +this.loadApplication = null; +this.$loadTree = null; +this.$loadAnnotations = null; +this.$outputFeatures = null; +this.$outputAnnotations = null; +this.closeMenuItem = null; +this.selectAllSequenceMenuItem = null; +this.deselectAllSequenceMenuItem = null; +this.invertSequenceMenuItem = null; +this.remove2LeftMenuItem = null; +this.remove2RightMenuItem = null; +this.removeGappedColumnMenuItem = null; +this.removeAllGapsMenuItem = null; +this.viewBoxesMenuItem = null; +this.viewTextMenuItem = null; +this.sortPairwiseMenuItem = null; +this.sortIDMenuItem = null; +this.sortLengthMenuItem = null; +this.sortGroupMenuItem = null; +this.removeRedundancyMenuItem = null; +this.pairwiseAlignmentMenuItem = null; +this.PCAMenuItem = null; +this.averageDistanceTreeMenuItem = null; +this.neighbourTreeMenuItem = null; +this.borderLayout1 = null; +this.statusBar = null; +this.clustalColour = null; +this.zappoColour = null; +this.taylorColour = null; +this.hydrophobicityColour = null; +this.helixColour = null; +this.strandColour = null; +this.turnColour = null; +this.buriedColour = null; +this.purinePyrimidineColour = null; +this.RNAInteractionColour = null; +this.RNAHelixColour = null; +this.userDefinedColour = null; +this.PIDColour = null; +this.BLOSUM62Colour = null; +this.tcoffeeColour = null; +this.njTreeBlosumMenuItem = null; +this.avDistanceTreeBlosumMenuItem = null; +this.annotationPanelMenuItem = null; +this.colourTextMenuItem = null; +this.displayNonconservedMenuItem = null; +this.alProperties = null; +this.overviewMenuItem = null; +this.undoMenuItem = null; +this.redoMenuItem = null; +this.conservationMenuItem = null; +this.noColourmenuItem = null; +this.wrapMenuItem = null; +this.renderGapsMenuItem = null; +this.findMenuItem = null; +this.abovePIDThreshold = null; +this.nucleotideColour = null; +this.deleteGroups = null; +this.grpsFromSelection = null; +this.createGroup = null; +this.unGroup = null; +this.$delete = null; +this.copy = null; +this.cut = null; +this.pasteMenu = null; +this.pasteNew = null; +this.pasteThis = null; +this.applyToAllGroups = null; +this.$font = null; +this.scaleAbove = null; +this.scaleLeft = null; +this.scaleRight = null; +this.modifyPID = null; +this.modifyConservation = null; +this.autoCalculate = null; +this.$sortByTree = null; +this.sortByTreeMenu = null; +this.inputText = null; +this.documentation = null; +this.about = null; +this.seqLimits = null; +this.centreColumnLabelFlag = null; +this.followMouseOverFlag = null; +this.showSequenceLogo = null; +this.applyAutoAnnotationSettings = null; +this.showConsensusHistogram = null; +this.showGroupConsensus = null; +this.showGroupConservation = null; +this.normSequenceLogo = null; +this.featureSettings = null; +this.sequenceFeatures = null; +this.annotationColour = null; +this.annotationColumnSelection = null; +this.invertColSel = null; +this.showColumns = null; +this.showSeqs = null; +this.hideColumns = null; +this.hideSequences = null; +this.hideAllButSelection = null; +this.hideAllSelection = null; +this.showAllHidden = null; +this.$newView = null; +this.showAlignmentAnnotations = null; +this.showSequenceAnnotations = null; +this.sortAnnBySequence = null; +this.sortAnnByLabel = null; +this.showAutoFirst = null; +this.showAutoLast = null; +this.splitFrame = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignFrame", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.KeyListener, jalview.api.AlignViewControllerGuiI]); +Clazz.prepareFields (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", true); +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 (); +}); +Clazz.makeConstructor (c$, +function (al, applet, title, embedded) { +this.construct (al, applet, title, embedded, true); +}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B"); +Clazz.makeConstructor (c$, +function (al, applet, title, embedded, addToDisplay) { +this.construct (al, null, null, applet, title, embedded, addToDisplay); +}, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B"); +Clazz.makeConstructor (c$, +function (al, hiddenSeqs, columnSelection, applet, title, embedded) { +this.construct (al, hiddenSeqs, columnSelection, applet, title, embedded, true); +}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B"); +Clazz.makeConstructor (c$, +function (al, hiddenSeqs, columnSelection, applet, title, embedded, addToDisplay) { +Clazz.superConstructor (this, jalview.appletgui.AlignFrame, []); +if (applet != null) { +this.jalviewServletURL = applet.jalviewServletURL; +}try { +this.jbInit (); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (applet != null) { +var param; +try { +param = applet.windowWidth; +if (param != null) { +var width = Integer.parseInt (param); +this.frameWidth = width; +}param = applet.windowHeight; +if (param != null) { +var height = Integer.parseInt (param); +this.frameHeight = height; +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}this.viewport = new jalview.appletgui.AlignViewport (al, applet); +if (hiddenSeqs != null && hiddenSeqs.length > 0) { +this.viewport.hideSequence (hiddenSeqs); +}if (columnSelection != null) { +this.viewport.setColumnSelection (columnSelection); +}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 ()); +if (applet != null) { +var param = applet.sortBy; +if (param != null) { +if (param.equalsIgnoreCase ("Id")) { +this.sortIDMenuItem_actionPerformed (); +} else if (param.equalsIgnoreCase ("Pairwise Identity")) { +this.sortPairwiseMenuItem_actionPerformed (); +} else if (param.equalsIgnoreCase ("Length")) { +this.sortLengthMenuItem_actionPerformed (); +}}param = applet.wrap; +if (param != null) { +if (param.equalsIgnoreCase ("true")) { +this.wrapMenuItem.setState (true); +this.wrapMenuItem_actionPerformed (); +}}param = applet.centrecolumnlabels; +if (param != null) { +this.centreColumnLabelFlag.setState (true); +this.centreColumnLabelFlag_stateChanged (); +}}if (this.viewport.getAlignment ().isNucleotide ()) { +this.viewport.updateStrucConsensus (this.alignPanel); +if (this.viewport.getAlignment ().hasRNAStructure ()) { +this.RNAHelixColour.setEnabled (true); +} else { +this.RNAHelixColour.setEnabled (false); +}} else { +this.RNAHelixColour.setEnabled (false); +this.purinePyrimidineColour.setEnabled (false); +}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); +if (addToDisplay) { +this.addToDisplay (embedded); +}}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B"); +Clazz.defineMethod (c$, "addToDisplay", +function (embedded) { +this.createAlignFrameWindow (embedded); +this.validate (); +this.alignPanel.adjustAnnotationHeight (); +this.alignPanel.paintAlignment (true); +}, "~B"); +Clazz.defineMethod (c$, "getAlignViewport", +function () { +return this.viewport; +}); +Clazz.defineMethod (c$, "getSeqcanvas", +function () { +return this.alignPanel.seqPanel.seqCanvas; +}); +Clazz.defineMethod (c$, "parseFeaturesFile", +function (file, type) { +return this.parseFeaturesFile (file, type, true); +}, "~S,~S"); +Clazz.defineMethod (c$, "parseFeaturesFile", +function (file, type, autoenabledisplay) { +var featureLinks = new java.util.Hashtable (); +var featuresFile = false; +try { +featuresFile = new jalview.io.FeaturesFile (file, type).parse (this.viewport.getAlignment (), this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().getFeatureColours (), featureLinks, true, this.viewport.applet.getDefaultParameter ("relaxedidmatch", false)); +} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +ex.printStackTrace (); +} else { +throw ex; +} +} +if (featuresFile) { +if (featureLinks.size () > 0) { +this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().featureLinks = featureLinks; +}if (autoenabledisplay) { +this.viewport.setShowSequenceFeatures (true); +this.sequenceFeatures.setState (true); +}if (this.alignPanel.seqPanel.seqCanvas.fr != null) { +this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures (true); +}if (this.viewport.featureSettings != null) { +this.viewport.featureSettings.refreshTable (); +}this.alignPanel.paintAlignment (true); +this.setStatus (jalview.util.MessageManager.getString ("label.successfully_added_features_alignment")); +}return featuresFile; +}, "~S,~S,~B"); +Clazz.overrideMethod (c$, "keyPressed", +function (evt) { +if (this.viewport.cursorMode && ((evt.getKeyCode () >= 48 && evt.getKeyCode () <= 57) || (evt.getKeyCode () >= 96 && evt.getKeyCode () <= 105)) && Character.isDigit (evt.getKeyChar ())) { +this.alignPanel.seqPanel.numberPressed (evt.getKeyChar ()); +}switch (evt.getKeyCode ()) { +case 27: +this.deselectAllSequenceMenuItem_actionPerformed (); +this.alignPanel.alabels.cancelDrag (); +break; +case 88: +if (evt.isControlDown () || evt.isMetaDown ()) { +this.cut_actionPerformed (); +}break; +case 67: +if (this.viewport.cursorMode && !evt.isControlDown ()) { +this.alignPanel.seqPanel.setCursorColumn (); +}if (evt.isControlDown () || evt.isMetaDown ()) { +this.copy_actionPerformed (); +}break; +case 86: +if (evt.isControlDown ()) { +this.paste (evt.isShiftDown ()); +}break; +case 65: +if (evt.isControlDown () || evt.isMetaDown ()) { +this.selectAllSequenceMenuItem_actionPerformed (); +}break; +case 40: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (0, 1); +} else { +this.moveSelectedSequences (false); +}break; +case 38: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (0, -1); +} else { +this.moveSelectedSequences (true); +}break; +case 37: +if (evt.isAltDown () || !this.viewport.cursorMode) { +this.slideSequences (false, this.alignPanel.seqPanel.getKeyboardNo1 ()); +} else { +this.alignPanel.seqPanel.moveCursor (-1, 0); +}break; +case 39: +if (evt.isAltDown () || !this.viewport.cursorMode) { +this.slideSequences (true, this.alignPanel.seqPanel.getKeyboardNo1 ()); +} else { +this.alignPanel.seqPanel.moveCursor (1, 0); +}break; +case 32: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.insertGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); +}break; +case 127: +case 8: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.deleteGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ()); +} else { +this.cut_actionPerformed (); +this.alignPanel.seqPanel.seqCanvas.repaint (); +}break; +case 83: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorRow (); +}break; +case 80: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorPosition (); +}break; +case 10: +case 44: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setCursorRowAndColumn (); +}break; +case 81: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setSelectionAreaAtCursor (true); +}break; +case 77: +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.setSelectionAreaAtCursor (false); +}break; +case 113: +this.viewport.cursorMode = !this.viewport.cursorMode; +this.setStatus (jalview.util.MessageManager.formatMessage ("label.keyboard_editing_mode", Clazz.newArray (-1, [(this.viewport.cursorMode ? "on" : "off")]))); +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.seqCanvas.cursorX = this.viewport.startRes; +this.alignPanel.seqPanel.seqCanvas.cursorY = this.viewport.startSeq; +}break; +case 70: +if (evt.isControlDown ()) { +this.findMenuItem_actionPerformed (); +}break; +case 72: +{ +var toggleSeqs = !evt.isControlDown (); +var toggleCols = !evt.isShiftDown (); +this.toggleHiddenRegions (toggleSeqs, toggleCols); +break; +}case 33: +if (this.viewport.getWrapAlignment ()) { +this.alignPanel.scrollUp (true); +} else { +this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq - this.viewport.endSeq + this.viewport.startSeq); +}break; +case 34: +if (this.viewport.getWrapAlignment ()) { +this.alignPanel.scrollUp (false); +} else { +this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq + this.viewport.endSeq - this.viewport.startSeq); +}break; +case 90: +if (evt.isControlDown ()) { +this.undoMenuItem_actionPerformed (); +}break; +case 89: +if (evt.isControlDown ()) { +this.redoMenuItem_actionPerformed (); +}break; +case 76: +if (evt.isControlDown ()) { +this.trimAlignment (true); +}break; +case 82: +if (evt.isControlDown ()) { +this.trimAlignment (false); +}break; +case 69: +if (evt.isControlDown ()) { +if (evt.isShiftDown ()) { +this.removeAllGapsMenuItem_actionPerformed (); +} else { +this.removeGappedColumnMenuItem_actionPerformed (); +}}break; +case 73: +if (evt.isControlDown ()) { +if (evt.isAltDown ()) { +this.invertColSel_actionPerformed (); +} else { +this.invertSequenceMenuItem_actionPerformed (); +}}break; +case 71: +if (evt.isControlDown ()) { +if (evt.isShiftDown ()) { +this.unGroup_actionPerformed (); +} else { +this.createGroup_actionPerformed (); +}}break; +case 85: +if (evt.isControlDown ()) { +this.deleteGroups_actionPerformed (); +}break; +case 84: +if (evt.isControlDown ()) { +this.newView (null); +}break; +} +this.alignPanel.paintAlignment (true); +}, "java.awt.event.KeyEvent"); +Clazz.defineMethod (c$, "toggleHiddenRegions", + function (toggleSeqs, toggleCols) { +var hide = false; +var sg = this.viewport.getSelectionGroup (); +if (!toggleSeqs && !toggleCols) { +if ((this.viewport.getColumnSelection () != null && this.viewport.getColumnSelection ().getSelected () != null && this.viewport.getColumnSelection ().getSelected ().size () > 0) || (sg != null && sg.getSize () > 0 && sg.getStartRes () <= sg.getEndRes ())) { +if (sg != null) { +this.invertSequenceMenuItem_actionPerformed (); +sg = this.viewport.getSelectionGroup (); +toggleSeqs = true; +}this.viewport.expandColSelection (sg, true); +this.invertColSel_actionPerformed (); +toggleCols = true; +}}if (toggleSeqs) { +if (sg != null && sg.getSize () != this.viewport.getAlignment ().getHeight ()) { +hide = true; +this.viewport.hideAllSelectedSeqs (); +} else if (!(toggleCols && this.viewport.getColumnSelection ().getSelected ().size () > 0)) { +this.viewport.showAllHiddenSeqs (); +}}if (toggleCols) { +if (this.viewport.getColumnSelection ().getSelected ().size () > 0) { +this.viewport.hideSelectedColumns (); +if (!toggleSeqs) { +this.viewport.setSelectionGroup (sg); +}} else if (!hide) { +this.viewport.showAllHiddenColumns (); +}}}, "~B,~B"); +Clazz.overrideMethod (c$, "keyReleased", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "keyTyped", +function (evt) { +}, "java.awt.event.KeyEvent"); +Clazz.overrideMethod (c$, "itemStateChanged", +function (evt) { +var source = evt.getSource (); +if (source === this.displayNonconservedMenuItem) { +this.displayNonconservedMenuItem_actionPerformed (); +} else if (source === this.colourTextMenuItem) { +this.colourTextMenuItem_actionPerformed (); +} else if (source === this.wrapMenuItem) { +this.wrapMenuItem_actionPerformed (); +} else if (source === this.scaleAbove) { +this.viewport.setScaleAboveWrapped (this.scaleAbove.getState ()); +} else if (source === this.scaleLeft) { +this.viewport.setScaleLeftWrapped (this.scaleLeft.getState ()); +} else if (source === this.scaleRight) { +this.viewport.setScaleRightWrapped (this.scaleRight.getState ()); +} else if (source === this.seqLimits) { +this.seqLimits_itemStateChanged (); +} else if (source === this.viewBoxesMenuItem) { +this.viewport.setShowBoxes (this.viewBoxesMenuItem.getState ()); +} else if (source === this.viewTextMenuItem) { +this.viewport.setShowText (this.viewTextMenuItem.getState ()); +} else if (source === this.renderGapsMenuItem) { +this.viewport.setRenderGaps (this.renderGapsMenuItem.getState ()); +} else if (source === this.annotationPanelMenuItem) { +this.viewport.setShowAnnotation (this.annotationPanelMenuItem.getState ()); +this.alignPanel.setAnnotationVisible (this.annotationPanelMenuItem.getState ()); +} else if (source === this.sequenceFeatures) { +this.viewport.setShowSequenceFeatures (this.sequenceFeatures.getState ()); +this.alignPanel.seqPanel.seqCanvas.repaint (); +} else if (source === this.showAlignmentAnnotations) { +this.setAnnotationsVisibility (); +} else if (source === this.showSequenceAnnotations) { +this.setAnnotationsVisibility (); +} else if (source === this.sortAnnBySequence) { +var newState = this.sortAnnBySequence.getState (); +this.sortAnnByLabel.setState (false); +this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); +this.setViewportAnnotationOrder (); +} else if (source === this.sortAnnByLabel) { +var newState = this.sortAnnByLabel.getState (); +this.sortAnnBySequence.setState (false); +this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE); +this.setViewportAnnotationOrder (); +} else if (source === this.showAutoFirst) { +this.showAutoLast.setState (!this.showAutoFirst.getState ()); +this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); +this.setViewportAnnotationOrder (); +} else if (source === this.showAutoLast) { +this.showAutoFirst.setState (!this.showAutoLast.getState ()); +this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ()); +this.setViewportAnnotationOrder (); +} else if (source === this.conservationMenuItem) { +this.conservationMenuItem_actionPerformed (); +} else if (source === this.abovePIDThreshold) { +this.abovePIDThreshold_actionPerformed (); +} else if (source === this.applyToAllGroups) { +this.viewport.setColourAppliesToAllGroups (this.applyToAllGroups.getState ()); +} else if (source === this.autoCalculate) { +this.viewport.autoCalculateConsensus = this.autoCalculate.getState (); +} else if (source === this.$sortByTree) { +this.viewport.sortByTree = this.$sortByTree.getState (); +} else if (source === this.centreColumnLabelFlag) { +this.centreColumnLabelFlag_stateChanged (); +} else if (source === this.followMouseOverFlag) { +this.mouseOverFlag_stateChanged (); +} else if (source === this.showGroupConsensus) { +this.showGroupConsensus_actionPerformed (); +} else if (source === this.showGroupConservation) { +this.showGroupConservation_actionPerformed (); +} else if (source === this.showSequenceLogo) { +this.showSequenceLogo_actionPerformed (); +} else if (source === this.normSequenceLogo) { +this.normSequenceLogo_actionPerformed (); +} else if (source === this.showConsensusHistogram) { +this.showConsensusHistogram_actionPerformed (); +} else if (source === this.applyAutoAnnotationSettings) { +this.applyAutoAnnotationSettings_actionPerformed (); +}this.alignPanel.paintAlignment (true); +}, "java.awt.event.ItemEvent"); +Clazz.defineMethod (c$, "setAnnotationsVisibility", + function () { +var showForAlignment = this.showAlignmentAnnotations.getState (); +var showForSequences = this.showSequenceAnnotations.getState (); +for (var aa, $aa = 0, $$aa = this.alignPanel.getAlignment ().getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) { +var visible = (aa.sequenceRef == null ? showForAlignment : showForSequences); +aa.visible = visible; +} +this.alignPanel.validateAnnotationDimensions (true); +this.validate (); +this.repaint (); +}); +Clazz.defineMethod (c$, "setAnnotationSortOrder", + function (order) { +this.annotationSortOrder = order; +}, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder"); +Clazz.defineMethod (c$, "setViewportAnnotationOrder", + function () { +this.alignPanel.av.setSortAnnotationsBy (this.annotationSortOrder); +this.alignPanel.av.setShowAutocalculatedAbove (this.showAutoCalculatedAbove); +}); +Clazz.defineMethod (c$, "setShowAutoCalculatedAbove", + function (showAbove) { +this.showAutoCalculatedAbove = showAbove; +}, "~B"); +Clazz.defineMethod (c$, "mouseOverFlag_stateChanged", + function () { +this.viewport.setFollowHighlight (this.followMouseOverFlag.getState ()); +}); +Clazz.defineMethod (c$, "centreColumnLabelFlag_stateChanged", + function () { +this.viewport.centreColumnLabels = this.centreColumnLabelFlag.getState (); +this.alignPanel.annotationPanel.repaint (); +}); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +var source = evt.getSource (); +if (source === this.inputText) { +this.inputText_actionPerformed (); +} else if (source === this.$loadTree) { +this.loadTree_actionPerformed (); +} else if (source === this.loadApplication) { +this.launchFullApplication (); +} else if (source === this.$loadAnnotations) { +this.loadAnnotations (); +} else if (source === this.$outputAnnotations) { +this.outputAnnotations (true); +} else if (source === this.$outputFeatures) { +this.outputFeatures (true, "Jalview"); +} else if (source === this.closeMenuItem) { +this.closeMenuItem_actionPerformed (); +} else if (source === this.copy) { +this.copy_actionPerformed (); +} else if (source === this.undoMenuItem) { +this.undoMenuItem_actionPerformed (); +} else if (source === this.redoMenuItem) { +this.redoMenuItem_actionPerformed (); +} else if (source === this.inputText) { +this.inputText_actionPerformed (); +} else if (source === this.closeMenuItem) { +this.closeMenuItem_actionPerformed (); +} else if (source === this.undoMenuItem) { +this.undoMenuItem_actionPerformed (); +} else if (source === this.redoMenuItem) { +this.redoMenuItem_actionPerformed (); +} else if (source === this.copy) { +this.copy_actionPerformed (); +} else if (source === this.pasteNew) { +this.pasteNew_actionPerformed (); +} else if (source === this.pasteThis) { +this.pasteThis_actionPerformed (); +} else if (source === this.cut) { +this.cut_actionPerformed (); +} else if (source === this.$delete) { +this.delete_actionPerformed (); +} else if (source === this.grpsFromSelection) { +this.makeGrpsFromSelection_actionPerformed (); +} else if (source === this.deleteGroups) { +this.deleteGroups_actionPerformed (); +} else if (source === this.selectAllSequenceMenuItem) { +this.selectAllSequenceMenuItem_actionPerformed (); +} else if (source === this.deselectAllSequenceMenuItem) { +this.deselectAllSequenceMenuItem_actionPerformed (); +} else if (source === this.invertSequenceMenuItem) { +this.invertSequenceMenuItem_actionPerformed (); +} else if (source === this.invertColSel) { +this.viewport.invertColumnSelection (); +this.alignPanel.paintAlignment (true); +} else if (source === this.remove2LeftMenuItem) { +this.trimAlignment (true); +} else if (source === this.remove2RightMenuItem) { +this.trimAlignment (false); +} else if (source === this.removeGappedColumnMenuItem) { +this.removeGappedColumnMenuItem_actionPerformed (); +} else if (source === this.removeAllGapsMenuItem) { +this.removeAllGapsMenuItem_actionPerformed (); +} else if (source === this.findMenuItem) { +this.findMenuItem_actionPerformed (); +} else if (source === this.$font) { + new jalview.appletgui.FontChooser (this.alignPanel); +} else if (source === this.$newView) { +this.newView (null); +} else if (source === this.showColumns) { +this.viewport.showAllHiddenColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showSeqs) { +this.viewport.showAllHiddenSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideColumns) { +this.viewport.hideSelectedColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideSequences && this.viewport.getSelectionGroup () != null) { +this.viewport.hideAllSelectedSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideAllButSelection) { +this.toggleHiddenRegions (false, false); +this.alignPanel.paintAlignment (true); +} else if (source === this.hideAllSelection) { +var sg = this.viewport.getSelectionGroup (); +this.viewport.expandColSelection (sg, false); +this.viewport.hideAllSelectedSeqs (); +this.viewport.hideSelectedColumns (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showAllHidden) { +this.viewport.showAllHiddenColumns (); +this.viewport.showAllHiddenSeqs (); +this.alignPanel.paintAlignment (true); +} else if (source === this.showGroupConsensus) { +this.showGroupConsensus_actionPerformed (); +} else if (source === this.showGroupConservation) { +this.showGroupConservation_actionPerformed (); +} else if (source === this.showSequenceLogo) { +this.showSequenceLogo_actionPerformed (); +} else if (source === this.normSequenceLogo) { +this.normSequenceLogo_actionPerformed (); +} else if (source === this.showConsensusHistogram) { +this.showConsensusHistogram_actionPerformed (); +} else if (source === this.applyAutoAnnotationSettings) { +this.applyAutoAnnotationSettings_actionPerformed (); +} else if (source === this.featureSettings) { + new jalview.appletgui.FeatureSettings (this.alignPanel); +} else if (source === this.alProperties) { +var contents = new jalview.io.AlignmentProperties (this.viewport.getAlignment ()).formatAsString (); +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); +cap.setText (contents.toString ()); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_properties", Clazz.newArray (-1, [this.getTitle ()])), 400, 250); +} else if (source === this.overviewMenuItem) { +this.overviewMenuItem_actionPerformed (); +} else if (source === this.noColourmenuItem) { +this.changeColour (null); +} else if (source === this.clustalColour) { +this.abovePIDThreshold.setState (false); +this.changeColour ( new jalview.schemes.ClustalxColourScheme (this.viewport.getAlignment (), null)); +} else if (source === this.zappoColour) { +this.changeColour ( new jalview.schemes.ZappoColourScheme ()); +} else if (source === this.taylorColour) { +this.changeColour ( new jalview.schemes.TaylorColourScheme ()); +} else if (source === this.hydrophobicityColour) { +this.changeColour ( new jalview.schemes.HydrophobicColourScheme ()); +} else if (source === this.helixColour) { +this.changeColour ( new jalview.schemes.HelixColourScheme ()); +} else if (source === this.strandColour) { +this.changeColour ( new jalview.schemes.StrandColourScheme ()); +} else if (source === this.turnColour) { +this.changeColour ( new jalview.schemes.TurnColourScheme ()); +} else if (source === this.buriedColour) { +this.changeColour ( new jalview.schemes.BuriedColourScheme ()); +} else if (source === this.nucleotideColour) { +this.changeColour ( new jalview.schemes.NucleotideColourScheme ()); +} else if (source === this.purinePyrimidineColour) { +this.changeColour ( new jalview.schemes.PurinePyrimidineColourScheme ()); +} else if (source === this.RNAInteractionColour) { +this.changeColour ( new jalview.schemes.RNAInteractionColourScheme ()); +} else if (source === this.RNAHelixColour) { + new jalview.schemes.RNAHelicesColourChooser (this.viewport, this.alignPanel); +} else if (source === this.modifyPID) { +this.modifyPID_actionPerformed (); +} else if (source === this.modifyConservation) { +this.modifyConservation_actionPerformed (); +} else if (source === this.userDefinedColour) { + new jalview.appletgui.UserDefinedColours (this.alignPanel, null); +} else if (source === this.PIDColour) { +this.changeColour ( new jalview.schemes.PIDColourScheme ()); +} else if (source === this.BLOSUM62Colour) { +this.changeColour ( new jalview.schemes.Blosum62ColourScheme ()); +} else if (source === this.tcoffeeColour) { +this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); +} else if (source === this.annotationColour) { + new jalview.appletgui.AnnotationColourChooser (this.viewport, this.alignPanel); +} else if (source === this.annotationColumnSelection) { + new jalview.appletgui.AnnotationColumnChooser (this.viewport, this.alignPanel); +} else if (source === this.sortPairwiseMenuItem) { +this.sortPairwiseMenuItem_actionPerformed (); +} else if (source === this.sortIDMenuItem) { +this.sortIDMenuItem_actionPerformed (); +} else if (source === this.sortLengthMenuItem) { +this.sortLengthMenuItem_actionPerformed (); +} else if (source === this.sortGroupMenuItem) { +this.sortGroupMenuItem_actionPerformed (); +} else if (source === this.removeRedundancyMenuItem) { +this.removeRedundancyMenuItem_actionPerformed (); +} else if (source === this.pairwiseAlignmentMenuItem) { +this.pairwiseAlignmentMenuItem_actionPerformed (); +} else if (source === this.PCAMenuItem) { +this.PCAMenuItem_actionPerformed (); +} else if (source === this.averageDistanceTreeMenuItem) { +this.averageDistanceTreeMenuItem_actionPerformed (); +} else if (source === this.neighbourTreeMenuItem) { +this.neighbourTreeMenuItem_actionPerformed (); +} else if (source === this.njTreeBlosumMenuItem) { +this.njTreeBlosumMenuItem_actionPerformed (); +} else if (source === this.avDistanceTreeBlosumMenuItem) { +this.avTreeBlosumMenuItem_actionPerformed (); +} else if (source === this.documentation) { +this.documentation_actionPerformed (); +} else if (source === this.about) { +this.about_actionPerformed (); +}}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "inputText_actionPerformed", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.input_cut_paste"), 500, 500); +}); +Clazz.defineMethod (c$, "outputText_actionPerformed", +function (e) { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500); +var fr = this.alignPanel.cloneFeatureRenderer (); +cap.setText ( new jalview.io.AppletFormatAdapter (this.alignPanel).formatSequences (e.getActionCommand (), this.viewport.getAlignment (), this.viewport.getShowJVSuffix ())); +}, "java.awt.event.ActionEvent"); +Clazz.defineMethod (c$, "loadAnnotations", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +cap.setText (jalview.util.MessageManager.getString ("label.paste_features_annotations_Tcoffee_here")); +cap.setAnnotationImport (); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.paste_annotations"), 400, 300); +}); +Clazz.defineMethod (c$, "outputAnnotations", +function (displayTextbox) { +var annotation = new jalview.io.AnnotationFile ().printAnnotationsForView (this.viewport); +if (displayTextbox) { +var cap = new jalview.appletgui.CutAndPasteTransfer (false, this); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.annotations"), 600, 500); +cap.setText (annotation); +}return annotation; +}, "~B"); +Clazz.defineMethod (c$, "getDisplayedFeatureCols", + function () { +if (this.alignPanel.getFeatureRenderer () != null && this.viewport.getFeaturesDisplayed () != null) { +return this.alignPanel.getFeatureRenderer ().getDisplayedFeatureCols (); +}return null; +}); +Clazz.defineMethod (c$, "outputFeatures", +function (displayTextbox, format) { +var features; +if (format.equalsIgnoreCase ("Jalview")) { +features = new jalview.io.FeaturesFile ().printJalviewFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); +} else { +features = new jalview.io.FeaturesFile ().printGFFFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ()); +}if (displayTextbox) { +var frimport = false; +if (features == null || features.equals ("No Features Visible")) { +features = "# No features visible - paste some and import them here."; +frimport = true; +}var cap = new jalview.appletgui.CutAndPasteTransfer (frimport, this); +if (frimport) { +cap.setAnnotationImport (); +}var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.features"), 600, 500); +cap.setText (features); +} else { +if (features == null) { +features = ""; +}}return features; +}, "~B,~S"); +Clazz.defineMethod (c$, "launchFullApplication", +function () { +var url = new StringBuffer (this.jalviewServletURL); +var firstSep = url.lastIndexOf ("?") > url.lastIndexOf ("/") ? "&" : "?"; +url.append (firstSep); +var applet = this.viewport.applet; +var s = applet.startupFile; +url.append ("open=" + this.appendProtocol (s)); +if (this.viewport.applet.features != null) { +url.append ("&features="); +url.append (this.appendProtocol (applet.features)); +}if (applet.annotations != null) { +url.append ("&annotations="); +url.append (this.appendProtocol (applet.annotations)); +}if (applet.jnetFile != null) { +url.append ("&annotations="); +url.append (this.appendProtocol (applet.jnetFile)); +}if (applet.defaultColour != null) { +url.append ("&colour=" + this.removeWhiteSpace (applet.defaultColour)); +}if (applet.userDefinedColour != null) { +url.append ("&colour=" + this.removeWhiteSpace (applet.userDefinedColour)); +}if (applet.treeFile != null) { +url.append ("&tree=" + this.appendProtocol (applet.treeFile)); +}this.showURL (url.toString (), "FULL_APP"); +}); +Clazz.defineMethod (c$, "removeWhiteSpace", +function (colour) { +var sb = new StringBuffer (); +for (var i = 0; i < colour.length; i++) { +if (Character.isWhitespace (colour.charAt (i))) { +sb.append ("%20"); +} else { +sb.append (colour.charAt (i)); +}} +return sb.toString (); +}, "~S"); +Clazz.defineMethod (c$, "appendProtocol", +function (url) { +try { + new java.net.URL (url); +url = java.net.URLEncoder.encode (url); +} catch (ex) { +if (Clazz.exceptionOf (ex, java.net.MalformedURLException)) { +url = this.viewport.applet.getCodeBase () + url; +} else { +throw ex; +} +} +return url; +}, "~S"); +Clazz.defineMethod (c$, "closeMenuItem_actionPerformed", +function () { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel); +if (this.alignPanel.seqPanel != null && this.alignPanel.seqPanel.seqCanvas != null) { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.seqPanel.seqCanvas); +}if (this.alignPanel.idPanel != null && this.alignPanel.idPanel.idCanvas != null) { +jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.idPanel.idCanvas); +}if (jalview.appletgui.PaintRefresher.components.size () == 0 && this.viewport.applet == null) { +System.exit (0); +} else { +}this.viewport = null; +this.alignPanel = null; +this.dispose (); +}); +Clazz.defineMethod (c$, "updateEditMenuBar", +function () { +if (this.viewport.getHistoryList ().size () > 0) { +this.undoMenuItem.setEnabled (true); +var command = this.viewport.getHistoryList ().peek (); +this.undoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.undo_command", Clazz.newArray (-1, [command.getDescription ()]))); +} else { +this.undoMenuItem.setEnabled (false); +this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); +}if (this.viewport.getRedoList ().size () > 0) { +this.redoMenuItem.setEnabled (true); +var command = this.viewport.getRedoList ().peek (); +this.redoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.redo_command", Clazz.newArray (-1, [command.getDescription ()]))); +} else { +this.redoMenuItem.setEnabled (false); +this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); +}}); +Clazz.overrideMethod (c$, "addHistoryItem", +function (command) { +if (command.getSize () > 0) { +this.viewport.addToHistoryList (command); +this.viewport.clearRedoList (); +this.updateEditMenuBar (); +this.viewport.updateHiddenColumns (); +}}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "undoMenuItem_actionPerformed", +function () { +if (this.viewport.getHistoryList ().isEmpty ()) { +return; +}var command = this.viewport.getHistoryList ().pop (); +this.viewport.addToRedoList (command); +command.undoCommand (null); +var originalSource = this.getOriginatingSource (command); +if (originalSource !== this.viewport) { +System.err.println ("Warning: Viewport object mismatch whilst undoing"); +}originalSource.updateHiddenColumns (); +this.updateEditMenuBar (); +originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "redoMenuItem_actionPerformed", +function () { +if (this.viewport.getRedoList ().isEmpty ()) { +return; +}var command = this.viewport.getRedoList ().pop (); +this.viewport.addToHistoryList (command); +command.doCommand (null); +var originalSource = this.getOriginatingSource (command); +if (originalSource !== this.viewport) { +System.err.println ("Warning: Viewport object mismatch whilst re-doing"); +}originalSource.updateHiddenColumns (); +this.updateEditMenuBar (); +originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "getOriginatingSource", +function (command) { +var originalSource = null; +var al = null; +if (Clazz.instanceOf (command, jalview.commands.EditCommand)) { +var editCommand = command; +al = editCommand.getAlignment (); +var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); +for (var i = 0; i < comps.size (); i++) { +if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { +if (al === (comps.elementAt (i)).av.getAlignment ()) { +originalSource = (comps.elementAt (i)).av; +break; +}}} +}if (originalSource == null) { +if (al != null) { +jalview.appletgui.PaintRefresher.validateSequences (al, this.viewport.getAlignment ()); +}originalSource = this.viewport; +}return originalSource; +}, "jalview.commands.CommandI"); +Clazz.defineMethod (c$, "moveSelectedSequences", +function (up) { +var sg = this.viewport.getSelectionGroup (); +if (sg == null) { +return; +}this.viewport.getAlignment ().moveSelectedSequencesByOne (sg, up ? null : this.viewport.getHiddenRepSequences (), up); +this.alignPanel.paintAlignment (true); +var complement = this.viewport.getCodingComplement (); +if (complement != null) { +var mappedSelection = jalview.util.MappingUtils.mapSequenceGroup (sg, this.viewport, complement); +complement.getAlignment ().moveSelectedSequencesByOne (mappedSelection, up ? null : complement.getHiddenRepSequences (), up); +}}, "~B"); +Clazz.defineMethod (c$, "slideSequences", +function (right, size) { +var sg = new java.util.Vector (); +if (this.viewport.cursorMode) { +sg.add (this.viewport.getAlignment ().getSequenceAt (this.alignPanel.seqPanel.seqCanvas.cursorY)); +} else if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () != this.viewport.getAlignment ().getHeight ()) { +sg = this.viewport.getSelectionGroup ().getSequences (this.viewport.getHiddenRepSequences ()); +}if (sg.size () < 1) { +return; +}var invertGroup = new java.util.Vector (); +for (var i = 0; i < this.viewport.getAlignment ().getHeight (); i++) { +if (!sg.contains (this.viewport.getAlignment ().getSequenceAt (i))) { +invertGroup.addElement (this.viewport.getAlignment ().getSequenceAt (i)); +}} +var seqs1 = sg.toArray ( new Array (sg.size ())); +var seqs2 = invertGroup.toArray ( new Array (invertGroup.size ())); +for (var i = 0; i < invertGroup.size (); i++) { +seqs2[i] = invertGroup.elementAt (i); +} +var ssc; +if (right) { +ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs2, seqs1, size, this.viewport.getGapCharacter ()); +} else { +ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs1, seqs2, size, this.viewport.getGapCharacter ()); +}var groupAdjustment = 0; +if (ssc.getGapsInsertedBegin () && right) { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (size, 0); +} else { +groupAdjustment = size; +}} else if (!ssc.getGapsInsertedBegin () && !right) { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.moveCursor (-size, 0); +} else { +groupAdjustment = -size; +}}if (groupAdjustment != 0) { +this.viewport.getSelectionGroup ().setStartRes (this.viewport.getSelectionGroup ().getStartRes () + groupAdjustment); +this.viewport.getSelectionGroup ().setEndRes (this.viewport.getSelectionGroup ().getEndRes () + groupAdjustment); +}var appendHistoryItem = false; +var historyList = this.viewport.getHistoryList (); +if (historyList != null && historyList.size () > 0 && Clazz.instanceOf (historyList.peek (), jalview.commands.SlideSequencesCommand)) { +appendHistoryItem = ssc.appendSlideCommand (historyList.peek ()); +}if (!appendHistoryItem) { +this.addHistoryItem (ssc); +}this.repaint (); +}, "~B,~N"); +Clazz.defineMethod (c$, "copy_actionPerformed", +function () { +if (this.viewport.getSelectionGroup () == null) { +return; +}var sg = this.viewport.getSelectionGroup (); +jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer (); +var orderedSeqs = new java.util.HashMap (); +for (var i = 0; i < sg.getSize (); i++) { +var seq = sg.getSequenceAt (i); +var index = this.viewport.getAlignment ().findIndex (seq); +orderedSeqs.put (new Integer (index), seq); +} +var index = 0; +var startRes; +var endRes; +var ch; +if (this.viewport.hasHiddenColumns () && this.viewport.getSelectionGroup () != null) { +jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector (); +var hiddenOffset = this.viewport.getSelectionGroup ().getStartRes (); +for (var region, $region = this.viewport.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) { +jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0] - hiddenOffset, region[1] - hiddenOffset])); +} +} else { +jalview.appletgui.AlignFrame.copiedHiddenColumns = null; +}for (var i = 0; i < sg.getSize (); i++) { +var seq = null; +while (seq == null) { +if (orderedSeqs.containsKey (new Integer (index))) { +seq = orderedSeqs.get (new Integer (index)); +index++; +break; +} else { +index++; +}} +startRes = seq.findPosition (sg.getStartRes ()); +endRes = 0; +for (var j = 0; j < sg.getEndRes () + 1 && j < seq.getLength (); j++) { +ch = seq.getCharAt (j); +if (!jalview.util.Comparison.isGap ((ch))) { +endRes++; +}} +if (endRes > 0) { +endRes += seq.getStart () - 1; +}jalview.appletgui.AlignFrame.copiedSequences.append (seq.getName () + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1) + "\n"); +} +}); +Clazz.defineMethod (c$, "pasteNew_actionPerformed", +function () { +this.paste (true); +}); +Clazz.defineMethod (c$, "pasteThis_actionPerformed", +function () { +this.paste (false); +}); +Clazz.defineMethod (c$, "paste", +function (newAlignment) { +try { +if (jalview.appletgui.AlignFrame.copiedSequences == null) { +return; +}var st = new java.util.StringTokenizer (jalview.appletgui.AlignFrame.copiedSequences.toString ()); +var seqs = new java.util.Vector (); +while (st.hasMoreElements ()) { +var name = st.nextToken (); +var start = Integer.parseInt (st.nextToken ()); +var end = Integer.parseInt (st.nextToken ()); +seqs.addElement ( new jalview.datamodel.Sequence (name, st.nextToken (), start, end)); +} +var newSeqs = new Array (seqs.size ()); +for (var i = 0; i < seqs.size (); i++) { +newSeqs[i] = seqs.elementAt (i); +} +if (newAlignment) { +var newtitle = jalview.util.MessageManager.getString ("label.copied_sequences"); +if (this.getTitle ().startsWith (jalview.util.MessageManager.getString ("label.copied_sequences"))) { +newtitle = this.getTitle (); +} else { +newtitle = newtitle.concat (jalview.util.MessageManager.formatMessage ("label.from_msname", Clazz.newArray (-1, [this.getTitle ()]))); +}var af = new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (newSeqs), this.viewport.applet, newtitle, false); +if (jalview.appletgui.AlignFrame.copiedHiddenColumns != null) { +for (var i = 0; i < jalview.appletgui.AlignFrame.copiedHiddenColumns.size (); i++) { +var region = jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt (i); +af.viewport.hideColumns (region[0], region[1]); +} +}jalview.bin.JalviewLite.addFrame (af, newtitle, this.frameWidth, this.frameHeight); +} else { +this.addSequences (newSeqs); +}} catch (ex) { +if (Clazz.exceptionOf (ex, Exception)) { +} else { +throw ex; +} +} +}, "~B"); +Clazz.defineMethod (c$, "addSequences", +function (seqs) { +for (var i = 0; i < seqs.length; i++) { +this.viewport.getAlignment ().addSequence (seqs[i]); +} +this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.add_sequences"), jalview.commands.EditCommand.Action.PASTE, seqs, 0, this.viewport.getAlignment ().getWidth (), this.viewport.getAlignment ())); +this.viewport.setEndSeq (this.viewport.getAlignment ().getHeight ()); +this.viewport.getAlignment ().getWidth (); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}, "~A"); +Clazz.defineMethod (c$, "cut_actionPerformed", +function () { +this.copy_actionPerformed (); +this.delete_actionPerformed (); +}); +Clazz.defineMethod (c$, "delete_actionPerformed", +function () { +var sg = this.viewport.getSelectionGroup (); +if (sg == null) { +return; +}var seqs = new java.util.Vector (); +var seq; +for (var i = 0; i < sg.getSize (); i++) { +seq = sg.getSequenceAt (i); +seqs.addElement (seq); +} +if (sg.getSize () == this.viewport.getAlignment ().getHeight ()) { +this.viewport.getColumnSelection ().removeElements (sg.getStartRes (), sg.getEndRes () + 1); +}var cut = new Array (seqs.size ()); +for (var i = 0; i < seqs.size (); i++) { +cut[i] = seqs.elementAt (i); +} +this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.cut_sequences"), jalview.commands.EditCommand.Action.CUT, cut, sg.getStartRes (), sg.getEndRes () - sg.getStartRes () + 1, this.viewport.getAlignment ())); +this.viewport.setSelectionGroup (null); +this.viewport.getAlignment ().deleteGroup (sg); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +if (this.viewport.getAlignment ().getHeight () < 1) { +this.setVisible (false); +}this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "showGroupConsensus_actionPerformed", +function () { +this.viewport.setShowGroupConsensus (this.showGroupConsensus.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showGroupConservation_actionPerformed", +function () { +this.viewport.setShowGroupConservation (this.showGroupConservation.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showConsensusHistogram_actionPerformed", +function () { +this.viewport.setShowConsensusHistogram (this.showConsensusHistogram.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "showSequenceLogo_actionPerformed", +function () { +this.viewport.setShowSequenceLogo (this.showSequenceLogo.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "normSequenceLogo_actionPerformed", +function () { +this.showSequenceLogo.setState (true); +this.viewport.setShowSequenceLogo (true); +this.viewport.setNormaliseSequenceLogo (this.normSequenceLogo.getState ()); +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "applyAutoAnnotationSettings_actionPerformed", +function () { +this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ()); +}); +Clazz.defineMethod (c$, "makeGrpsFromSelection_actionPerformed", +function () { +if (this.avc.makeGroupsFromSelection ()) { +jalview.appletgui.PaintRefresher.Refresh (this, this.viewport.getSequenceSetId ()); +this.alignPanel.updateAnnotation (); +this.alignPanel.paintAlignment (true); +}}); +Clazz.defineMethod (c$, "createGroup_actionPerformed", +function () { +this.avc.createGroup (); +}); +Clazz.defineMethod (c$, "unGroup_actionPerformed", +function () { +if (this.avc.unGroup ()) { +this.alignPanel.alignmentChanged (); +}}); +Clazz.defineMethod (c$, "deleteGroups_actionPerformed", +function () { +if (this.avc.deleteGroups ()) { +this.alignPanel.alignmentChanged (); +}}); +Clazz.defineMethod (c$, "selectAllSequenceMenuItem_actionPerformed", +function () { +var sg = new jalview.datamodel.SequenceGroup (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +sg.addSequence (this.viewport.getAlignment ().getSequenceAt (i), false); +} +sg.setEndRes (this.viewport.getAlignment ().getWidth () - 1); +this.viewport.setSelectionGroup (sg); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "deselectAllSequenceMenuItem_actionPerformed", +function () { +if (this.viewport.cursorMode) { +this.alignPanel.seqPanel.keyboardNo1 = null; +this.alignPanel.seqPanel.keyboardNo2 = null; +}this.viewport.setSelectionGroup (null); +this.viewport.getColumnSelection ().clear (); +this.viewport.setSelectionGroup (null); +this.alignPanel.idPanel.idCanvas.searchResults = null; +this.alignPanel.seqPanel.seqCanvas.highlightSearchResults (null); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "invertSequenceMenuItem_actionPerformed", +function () { +var sg = this.viewport.getSelectionGroup (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +sg.addOrRemove (this.viewport.getAlignment ().getSequenceAt (i), false); +} +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "invertColSel_actionPerformed", +function () { +this.viewport.invertColumnSelection (); +this.alignPanel.paintAlignment (true); +jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ()); +this.viewport.sendSelection (); +}); +Clazz.defineMethod (c$, "trimAlignment", +function (trimLeft) { +var colSel = this.viewport.getColumnSelection (); +var column; +if (colSel.size () > 0) { +if (trimLeft) { +column = colSel.getMin (); +} else { +column = colSel.getMax (); +}var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var trimRegion; +if (trimLeft) { +trimRegion = new jalview.commands.TrimRegionCommand ("Remove Left", jalview.commands.TrimRegionCommand.TRIM_LEFT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); +this.viewport.setStartRes (0); +} else { +trimRegion = new jalview.commands.TrimRegionCommand ("Remove Right", jalview.commands.TrimRegionCommand.TRIM_RIGHT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ()); +}this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_columns", Clazz.newArray (-1, [Integer.$valueOf (trimRegion.getSize ()).toString ()]))); +this.addHistoryItem (trimRegion); +for (var sg, $sg = this.viewport.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) { +if ((trimLeft && !sg.adjustForRemoveLeft (column)) || (!trimLeft && !sg.adjustForRemoveRight (column))) { +this.viewport.getAlignment ().deleteGroup (sg); +}} +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}}, "~B"); +Clazz.defineMethod (c$, "removeGappedColumnMenuItem_actionPerformed", +function () { +var start = 0; +var end = this.viewport.getAlignment ().getWidth () - 1; +var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +start = this.viewport.getSelectionGroup ().getStartRes (); +end = this.viewport.getSelectionGroup ().getEndRes (); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var removeGapCols = new jalview.commands.RemoveGapColCommand ("Remove Gapped Columns", seqs, start, end, this.viewport.getAlignment ()); +this.addHistoryItem (removeGapCols); +this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_empty_columns", Clazz.newArray (-1, [Integer.$valueOf (removeGapCols.getSize ()).toString ()]))); +var seq = this.viewport.getAlignment ().getSequenceAt (0); +var startRes = seq.findPosition (this.viewport.startRes); +this.viewport.setStartRes (seq.findIndex (startRes) - 1); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "removeAllGapsMenuItem_actionPerformed", +function () { +var start = 0; +var end = this.viewport.getAlignment ().getWidth () - 1; +var seqs; +if (this.viewport.getSelectionGroup () != null) { +seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ()); +start = this.viewport.getSelectionGroup ().getStartRes (); +end = this.viewport.getSelectionGroup ().getEndRes (); +} else { +seqs = this.viewport.getAlignment ().getSequencesArray (); +}var seq = this.viewport.getAlignment ().getSequenceAt (0); +var startRes = seq.findPosition (this.viewport.startRes); +this.addHistoryItem ( new jalview.commands.RemoveGapsCommand ("Remove Gaps", seqs, start, end, this.viewport.getAlignment ())); +this.viewport.setStartRes (seq.findIndex (startRes) - 1); +this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ()); +}); +Clazz.defineMethod (c$, "findMenuItem_actionPerformed", +function () { + new jalview.appletgui.Finder (this.alignPanel); +}); +Clazz.defineMethod (c$, "newView", +function (viewtitle) { +var newal; +if (this.viewport.hasHiddenRows ()) { +newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getHiddenSequences ().getFullAlignment ().getSequencesArray ()); +} else { +newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getSequencesArray ()); +}if (this.viewport.getAlignment ().getAlignmentAnnotation () != null) { +for (var i = 0; i < this.viewport.getAlignment ().getAlignmentAnnotation ().length; i++) { +if (!this.viewport.getAlignment ().getAlignmentAnnotation ()[i].autoCalculated) { +newal.addAnnotation (this.viewport.getAlignment ().getAlignmentAnnotation ()[i]); +}} +}var newaf = new jalview.appletgui.AlignFrame (newal, this.viewport.applet, "", false); +newaf.viewport.setSequenceSetId (this.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (this.alignPanel, this.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId ()); +jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId ()); +var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ()); +var viewSize = -1; +for (var i = 0; i < comps.size (); i++) { +if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) { +viewSize++; +}} +var title = String.instantialize (this.getTitle ()); +if (viewtitle != null) { +title = viewtitle + " ( " + title + ")"; +} else { +if (title.indexOf ("(View") > -1) { +title = title.substring (0, title.indexOf ("(View")); +}title += "(View " + viewSize + ")"; +}newaf.setTitle (title.toString ()); +newaf.viewport.setHistoryList (this.viewport.getHistoryList ()); +newaf.viewport.setRedoList (this.viewport.getRedoList ()); +return newaf; +}, "~S"); +Clazz.defineMethod (c$, "getFeatureGroups", +function () { +var fr = null; +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +var gps = fr.getFeatureGroups (); +var _gps = gps.toArray ( new Array (gps.size ())); +return _gps; +}return null; +}); +Clazz.defineMethod (c$, "getFeatureGroupsOfState", +function (visible) { +var fr = null; +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +var gps = fr.getGroups (visible); +var _gps = gps.toArray ( new Array (gps.size ())); +return _gps; +}return null; +}, "~B"); +Clazz.defineMethod (c$, "setFeatureGroupState", +function (groups, state) { +var fr = null; +this.sequenceFeatures.setState (true); +this.viewport.setShowSequenceFeatures (true); +if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) { +fr.setGroupVisibility (java.util.Arrays.asList (groups), state); +this.alignPanel.seqPanel.seqCanvas.repaint (); +if (this.alignPanel.overviewPanel != null) { +this.alignPanel.overviewPanel.updateOverviewImage (); +}}}, "~A,~B"); +Clazz.defineMethod (c$, "seqLimits_itemStateChanged", +function () { +this.viewport.setShowJVSuffix (this.seqLimits.getState ()); +this.alignPanel.fontChanged (); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "colourTextMenuItem_actionPerformed", +function () { +this.viewport.setColourText (this.colourTextMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "displayNonconservedMenuItem_actionPerformed", +function () { +this.viewport.setShowUnconserved (this.displayNonconservedMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "wrapMenuItem_actionPerformed", +function () { +this.viewport.setWrapAlignment (this.wrapMenuItem.getState ()); +this.alignPanel.setWrapAlignment (this.wrapMenuItem.getState ()); +this.scaleAbove.setEnabled (this.wrapMenuItem.getState ()); +this.scaleLeft.setEnabled (this.wrapMenuItem.getState ()); +this.scaleRight.setEnabled (this.wrapMenuItem.getState ()); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "overviewMenuItem_actionPerformed", +function () { +if (this.alignPanel.overviewPanel != null) { +return; +}var frame = new awt2swing.Frame (); +var overview = new jalview.appletgui.OverviewPanel (this.alignPanel); +frame.add (overview); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.overview_params", Clazz.newArray (-1, [this.getTitle ()])), overview.getPreferredSize ().width, overview.getPreferredSize ().height + 50); +frame.pack (); +var ap = this.alignPanel; +frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1, this, Clazz.cloneFinals ("ap", ap)))); +this.alignPanel.setOverviewPanel (overview); +}); +Clazz.overrideMethod (c$, "changeColour", +function (cs) { +var threshold = 0; +if (cs != null) { +if (this.viewport.getAbovePIDThreshold ()) { +this.viewport.setThreshold (jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, cs, "Background")); +}if (this.viewport.getConservationSelected ()) { +cs.setConservationApplied (true); +this.viewport.setIncrement (jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, cs, "Background")); +} else { +cs.setConservationApplied (false); +}}this.viewport.setGlobalColourScheme (cs); +if (this.alignPanel.getOverviewPanel () != null) { +this.alignPanel.getOverviewPanel ().updateOverviewImage (); +}jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.viewport.applet).sequenceColoursChanged (this.alignPanel); +this.alignPanel.paintAlignment (true); +}, "jalview.schemes.ColourSchemeI"); +Clazz.defineMethod (c$, "modifyPID_actionPerformed", +function () { +if (this.viewport.getAbovePIDThreshold () && this.viewport.getGlobalColourScheme () != null) { +jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); +jalview.appletgui.SliderPanel.showPIDSlider (); +}}); +Clazz.defineMethod (c$, "modifyConservation_actionPerformed", +function () { +if (this.viewport.getConservationSelected () && this.viewport.getGlobalColourScheme () != null) { +jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background"); +jalview.appletgui.SliderPanel.showConservationSlider (); +}}); +Clazz.defineMethod (c$, "conservationMenuItem_actionPerformed", +function () { +this.viewport.setConservationSelected (this.conservationMenuItem.getState ()); +this.viewport.setAbovePIDThreshold (false); +this.abovePIDThreshold.setState (false); +this.changeColour (this.viewport.getGlobalColourScheme ()); +this.modifyConservation_actionPerformed (); +}); +Clazz.defineMethod (c$, "abovePIDThreshold_actionPerformed", +function () { +this.viewport.setAbovePIDThreshold (this.abovePIDThreshold.getState ()); +this.conservationMenuItem.setState (false); +this.viewport.setConservationSelected (false); +this.changeColour (this.viewport.getGlobalColourScheme ()); +this.modifyPID_actionPerformed (); +}); +Clazz.defineMethod (c$, "sortPairwiseMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByPID (this.viewport.getAlignment (), this.viewport.getAlignment ().getSequenceAt (0), null); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Pairwise Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortIDMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByID (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("ID Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortLengthMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByLength (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Length Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "sortGroupMenuItem_actionPerformed", +function () { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByGroup (this.viewport.getAlignment ()); +this.addHistoryItem ( new jalview.commands.OrderCommand ("Group Sort", oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}); +Clazz.defineMethod (c$, "removeRedundancyMenuItem_actionPerformed", +function () { + new jalview.appletgui.RedundancyPanel (this.alignPanel); +}); +Clazz.defineMethod (c$, "pairwiseAlignmentMenuItem_actionPerformed", +function () { +if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) { +var frame = new awt2swing.Frame (); +frame.add ( new jalview.appletgui.PairwiseAlignPanel (this.alignPanel)); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.pairwise_alignment"), 600, 500); +}}); +Clazz.defineMethod (c$, "PCAMenuItem_actionPerformed", +function () { +if (!this.viewport.getAlignment ().isAligned (false)) { +var current; +var Width = this.viewport.getAlignment ().getWidth (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +current = this.viewport.getAlignment ().getSequenceAt (i); +if (current.getLength () < Width) { +current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); +}} +this.alignPanel.paintAlignment (true); +}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () < 4 && this.viewport.getSelectionGroup ().getSize () > 0) || this.viewport.getAlignment ().getHeight () < 4) { +return; +}try { + new jalview.appletgui.PCAPanel (this.viewport); +} catch (ex) { +if (Clazz.exceptionOf (ex, OutOfMemoryError)) { +} else { +throw ex; +} +} +}); +Clazz.defineMethod (c$, "averageDistanceTreeMenuItem_actionPerformed", +function () { +this.NewTreePanel ("AV", "PID", "Average distance tree using PID"); +}); +Clazz.defineMethod (c$, "neighbourTreeMenuItem_actionPerformed", +function () { +this.NewTreePanel ("NJ", "PID", "Neighbour joining tree using PID"); +}); +Clazz.defineMethod (c$, "njTreeBlosumMenuItem_actionPerformed", +function () { +this.NewTreePanel ("NJ", "BL", "Neighbour joining tree using BLOSUM62"); +}); +Clazz.defineMethod (c$, "avTreeBlosumMenuItem_actionPerformed", +function () { +this.NewTreePanel ("AV", "BL", "Average distance tree using BLOSUM62"); +}); +Clazz.defineMethod (c$, "NewTreePanel", +function (type, pwType, title) { +if (!this.viewport.getAlignment ().isAligned (false)) { +var current; +var Width = this.viewport.getAlignment ().getWidth (); +for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) { +current = this.viewport.getAlignment ().getSequenceAt (i); +if (current.getLength () < Width) { +current.insertCharAt (Width - 1, this.viewport.getGapCharacter ()); +}} +this.alignPanel.paintAlignment (true); +}if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) || (this.viewport.getAlignment ().getHeight () > 1)) { +var tp = new jalview.appletgui.TreePanel (this.alignPanel, type, pwType); +this.addTreeMenuItem (tp, title); +jalview.bin.JalviewLite.addFrame (tp, title, 600, 500); +}}, "~S,~S,~S"); +Clazz.defineMethod (c$, "loadTree_actionPerformed", +function () { +var cap = new jalview.appletgui.CutAndPasteTransfer (true, this); +cap.setText (jalview.util.MessageManager.getString ("label.paste_newick_tree_file")); +cap.setTreeImport (); +var frame = new awt2swing.Frame (); +frame.add (cap); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.paste_newick_file"), 400, 300); +}); +Clazz.defineMethod (c$, "loadTree", +function (tree, treeFile) { +var tp = new jalview.appletgui.TreePanel (this.alignPanel, treeFile, jalview.util.MessageManager.getString ("label.load_tree_from_file"), tree); +jalview.bin.JalviewLite.addFrame (tp, treeFile, 600, 500); +this.addTreeMenuItem (tp, treeFile); +}, "jalview.io.NewickFile,~S"); +Clazz.defineMethod (c$, "sortByTree", +function (treePanel, title) { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +jalview.analysis.AlignmentSorter.sortByTree (this.viewport.getAlignment (), treePanel.getTree ()); +this.addHistoryItem ( new jalview.commands.OrderCommand (jalview.util.MessageManager.formatMessage ("label.order_by_params", Clazz.newArray (-1, [title])), oldOrder, this.viewport.getAlignment ())); +this.alignPanel.paintAlignment (true); +}, "jalview.appletgui.TreePanel,~S"); +Clazz.defineMethod (c$, "addTreeMenuItem", +function (treePanel, title) { +var item = new awt2swing.MenuItem (title); +this.sortByTreeMenu.add (item); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$2") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$2, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title)))); +treePanel.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$3") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$3, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title, "item", item)))); +}, "jalview.appletgui.TreePanel,~S"); +Clazz.defineMethod (c$, "sortBy", +function (alorder, undoname) { +var oldOrder = this.viewport.getAlignment ().getSequencesArray (); +if ((this.viewport.applet, jalview.bin.JalviewLite).debug) { +System.err.println ("Sorting " + alorder.getOrder ().size () + " in alignment '" + this.getTitle () + "'"); +}jalview.analysis.AlignmentSorter.sortBy (this.viewport.getAlignment (), alorder); +if (undoname != null) { +this.addHistoryItem ( new jalview.commands.OrderCommand (undoname, oldOrder, this.viewport.getAlignment ())); +}this.alignPanel.paintAlignment (true); +return true; +}, "jalview.datamodel.AlignmentOrder,~S"); +Clazz.defineMethod (c$, "documentation_actionPerformed", +function () { +this.alignPanel.av.applet.openJalviewHelpUrl (); +}); +Clazz.defineMethod (c$, "about_actionPerformed", +function () { +if (!Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1AboutPanel")) { +jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$ (); +} +var frame = new awt2swing.Frame (); +frame.add (Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1AboutPanel, this, null, jalview.bin.JalviewLite.getVersion (), jalview.bin.JalviewLite.getBuildDate ())); +jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.jalview"), 580, 220); +}); +Clazz.defineMethod (c$, "showURL", +function (url, target) { +if (this.viewport.applet == null) { +System.out.println ("Not running as applet - no browser available."); +} else { +this.viewport.applet.showURL (url, target); +}}, "~S,~S"); +Clazz.defineMethod (c$, "jbInit", + function () { +this.setMenuBar (this.alignFrameMenuBar); +this.inputText.setLabel (jalview.util.MessageManager.getString ("label.input_from_textbox")); +this.inputText.addActionListener (this); +var outputTextboxMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.out_to_textbox")); +for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { +var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); +item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$4") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$4, this, null))); +outputTextboxMenu.add (item); +} +this.closeMenuItem.addActionListener (this); +this.loadApplication.addActionListener (this); +this.$loadTree.addActionListener (this); +this.$loadAnnotations.addActionListener (this); +this.$outputFeatures.addActionListener (this); +this.$outputAnnotations.addActionListener (this); +this.undoMenuItem.setEnabled (false); +this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo")); +this.undoMenuItem.addActionListener (this); +this.redoMenuItem.setEnabled (false); +this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo")); +this.redoMenuItem.addActionListener (this); +this.copy.setLabel (jalview.util.MessageManager.getString ("action.copy")); +this.copy.addActionListener (this); +this.cut.setLabel (jalview.util.MessageManager.getString ("action.cut")); +this.cut.addActionListener (this); +this.$delete.setLabel (jalview.util.MessageManager.getString ("action.delete")); +this.$delete.addActionListener (this); +this.pasteMenu.setLabel (jalview.util.MessageManager.getString ("action.paste")); +this.pasteNew.setLabel (jalview.util.MessageManager.getString ("label.to_new_alignment")); +this.pasteNew.addActionListener (this); +this.pasteThis.setLabel (jalview.util.MessageManager.getString ("label.to_this_alignment")); +this.pasteThis.addActionListener (this); +this.remove2LeftMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_left")); +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")); +this.invertSequenceMenuItem.addActionListener (this); +this.invertColSel.setLabel (jalview.util.MessageManager.getString ("action.invert_column_selection")); +this.invertColSel.addActionListener (this); +this.deleteGroups.setLabel (jalview.util.MessageManager.getString ("action.undefine_groups")); +this.deleteGroups.addActionListener (this); +this.grpsFromSelection.setLabel (jalview.util.MessageManager.getString ("action.make_groups_selection")); +this.grpsFromSelection.addActionListener (this); +this.createGroup.setLabel (jalview.util.MessageManager.getString ("action.create_group")); +this.unGroup.setLabel (jalview.util.MessageManager.getString ("action.remove_group")); +this.annotationColumnSelection.setLabel ("Select by Annotation"); +this.annotationColumnSelection.addActionListener (this); +this.$newView.setLabel (jalview.util.MessageManager.getString ("action.new_view")); +this.$newView.addActionListener (this); +var showMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.show")); +this.showColumns.setLabel (jalview.util.MessageManager.getString ("label.all_columns")); +this.showSeqs.setLabel (jalview.util.MessageManager.getString ("label.all_sequences")); +var hideMenu = 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")); +this.showColumns.addActionListener (this); +this.showSeqs.addActionListener (this); +this.hideColumns.addActionListener (this); +this.hideSequences.addActionListener (this); +this.hideAllButSelection.addActionListener (this); +this.hideAllSelection.addActionListener (this); +this.showAllHidden.addActionListener (this); +this.featureSettings.setLabel (jalview.util.MessageManager.getString ("label.feature_settings")); +this.featureSettings.addActionListener (this); +this.sequenceFeatures.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_features")); +this.sequenceFeatures.addItemListener (this); +this.sequenceFeatures.setState (false); +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 (true); +var autoAnnMenu = 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 (true); +this.scaleAbove.setEnabled (false); +this.scaleAbove.addItemListener (this); +this.scaleLeft.setEnabled (false); +this.scaleLeft.setState (true); +this.scaleLeft.setLabel (jalview.util.MessageManager.getString ("action.scale_left")); +this.scaleLeft.addItemListener (this); +this.scaleRight.setEnabled (false); +this.scaleRight.setState (true); +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 (true); +this.viewBoxesMenuItem.addItemListener (this); +this.viewTextMenuItem.setLabel (jalview.util.MessageManager.getString ("action.text")); +this.viewTextMenuItem.setState (true); +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 (true); +this.renderGapsMenuItem.addItemListener (this); +this.centreColumnLabelFlag.setLabel (jalview.util.MessageManager.getString ("label.centre_column_labels")); +this.centreColumnLabelFlag.addItemListener (this); +this.seqLimits.setState (true); +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 (true); +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 (false); +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"), true); +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 sortMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.sort")); +var calculateTreeMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate_tree")); +this.autoCalculate.addItemListener (this); +this.$sortByTree.addItemListener (this); +var helpMenu = 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 editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit")); +this.alignFrameMenuBar.add (editMenu); +var selectMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.select")); +this.alignFrameMenuBar.add (selectMenu); +var viewMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.view")); +this.alignFrameMenuBar.add (viewMenu); +var annotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.annotations")); +this.alignFrameMenuBar.add (annotationsMenu); +var formatMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.format")); +this.alignFrameMenuBar.add (formatMenu); +var colourMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.colour")); +this.alignFrameMenuBar.add (colourMenu); +var calculateMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate")); +this.alignFrameMenuBar.add (calculateMenu); +this.alignFrameMenuBar.add (helpMenu); +this.fileMenu.add (this.inputText); +this.fileMenu.add (this.$loadTree); +this.fileMenu.add (this.$loadAnnotations); +this.fileMenu.addSeparator (); +this.fileMenu.add (outputTextboxMenu); +this.fileMenu.add (this.$outputFeatures); +this.fileMenu.add (this.$outputAnnotations); +if (this.jalviewServletURL != null) { +this.fileMenu.add (this.loadApplication); +}this.fileMenu.addSeparator (); +this.fileMenu.add (this.closeMenuItem); +editMenu.add (this.undoMenuItem); +editMenu.add (this.redoMenuItem); +editMenu.add (this.cut); +editMenu.add (this.copy); +this.pasteMenu.add (this.pasteNew); +this.pasteMenu.add (this.pasteThis); +editMenu.add (this.pasteMenu); +editMenu.add (this.$delete); +editMenu.addSeparator (); +editMenu.add (this.remove2LeftMenuItem); +editMenu.add (this.remove2RightMenuItem); +editMenu.add (this.removeGappedColumnMenuItem); +editMenu.add (this.removeAllGapsMenuItem); +editMenu.add (this.removeRedundancyMenuItem); +selectMenu.add (this.findMenuItem); +selectMenu.addSeparator (); +selectMenu.add (this.selectAllSequenceMenuItem); +selectMenu.add (this.deselectAllSequenceMenuItem); +selectMenu.add (this.invertSequenceMenuItem); +selectMenu.add (this.invertColSel); +selectMenu.add (this.createGroup); +selectMenu.add (this.unGroup); +selectMenu.add (this.grpsFromSelection); +selectMenu.add (this.deleteGroups); +selectMenu.add (this.annotationColumnSelection); +viewMenu.add (this.$newView); +viewMenu.addSeparator (); +showMenu.add (this.showColumns); +showMenu.add (this.showSeqs); +showMenu.add (this.showAllHidden); +viewMenu.add (showMenu); +hideMenu.add (this.hideColumns); +hideMenu.add (this.hideSequences); +hideMenu.add (this.hideAllSelection); +hideMenu.add (this.hideAllButSelection); +viewMenu.add (hideMenu); +viewMenu.addSeparator (); +viewMenu.add (this.followMouseOverFlag); +viewMenu.addSeparator (); +viewMenu.add (this.sequenceFeatures); +viewMenu.add (this.featureSettings); +viewMenu.addSeparator (); +viewMenu.add (this.alProperties); +viewMenu.addSeparator (); +viewMenu.add (this.overviewMenuItem); +annotationsMenu.add (this.annotationPanelMenuItem); +annotationsMenu.addSeparator (); +annotationsMenu.add (this.showAlignmentAnnotations); +annotationsMenu.add (this.showSequenceAnnotations); +annotationsMenu.add (this.sortAnnBySequence); +annotationsMenu.add (this.sortAnnByLabel); +annotationsMenu.addSeparator (); +autoAnnMenu.add (this.showAutoFirst); +autoAnnMenu.add (this.showAutoLast); +autoAnnMenu.addSeparator (); +autoAnnMenu.add (this.applyAutoAnnotationSettings); +autoAnnMenu.add (this.showConsensusHistogram); +autoAnnMenu.add (this.showSequenceLogo); +autoAnnMenu.add (this.normSequenceLogo); +autoAnnMenu.addSeparator (); +autoAnnMenu.add (this.showGroupConservation); +autoAnnMenu.add (this.showGroupConsensus); +annotationsMenu.add (autoAnnMenu); +formatMenu.add (this.$font); +formatMenu.add (this.seqLimits); +formatMenu.add (this.wrapMenuItem); +formatMenu.add (this.scaleAbove); +formatMenu.add (this.scaleLeft); +formatMenu.add (this.scaleRight); +formatMenu.add (this.viewBoxesMenuItem); +formatMenu.add (this.viewTextMenuItem); +formatMenu.add (this.colourTextMenuItem); +formatMenu.add (this.displayNonconservedMenuItem); +formatMenu.add (this.renderGapsMenuItem); +formatMenu.add (this.centreColumnLabelFlag); +colourMenu.add (this.applyToAllGroups); +colourMenu.addSeparator (); +colourMenu.add (this.noColourmenuItem); +colourMenu.add (this.clustalColour); +colourMenu.add (this.BLOSUM62Colour); +colourMenu.add (this.PIDColour); +colourMenu.add (this.zappoColour); +colourMenu.add (this.taylorColour); +colourMenu.add (this.hydrophobicityColour); +colourMenu.add (this.helixColour); +colourMenu.add (this.strandColour); +colourMenu.add (this.turnColour); +colourMenu.add (this.buriedColour); +colourMenu.add (this.nucleotideColour); +colourMenu.add (this.purinePyrimidineColour); +colourMenu.add (this.tcoffeeColour); +colourMenu.add (this.userDefinedColour); +colourMenu.addSeparator (); +colourMenu.add (this.conservationMenuItem); +colourMenu.add (this.modifyConservation); +colourMenu.add (this.abovePIDThreshold); +colourMenu.add (this.modifyPID); +colourMenu.add (this.annotationColour); +colourMenu.add (this.RNAHelixColour); +sortMenu.add (this.sortIDMenuItem); +sortMenu.add (this.sortLengthMenuItem); +sortMenu.add (this.sortByTreeMenu); +sortMenu.add (this.sortGroupMenuItem); +sortMenu.add (this.sortPairwiseMenuItem); +calculateMenu.add (sortMenu); +calculateTreeMenu.add (this.averageDistanceTreeMenuItem); +calculateTreeMenu.add (this.neighbourTreeMenuItem); +calculateTreeMenu.add (this.avDistanceTreeBlosumMenuItem); +calculateTreeMenu.add (this.njTreeBlosumMenuItem); +calculateMenu.add (calculateTreeMenu); +calculateMenu.addSeparator (); +calculateMenu.add (this.pairwiseAlignmentMenuItem); +calculateMenu.add (this.PCAMenuItem); +calculateMenu.add (this.autoCalculate); +calculateMenu.add (this.$sortByTree); +helpMenu.add (this.documentation); +helpMenu.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"); +}); +Clazz.overrideMethod (c$, "setStatus", +function (string) { +this.statusBar.setText (string); +}, "~S"); +Clazz.defineMethod (c$, "createAlignFrameWindow", +function (reallyEmbedded) { +if (reallyEmbedded) { +this.embedAlignFrameInApplet (this.viewport.applet); +} else { +if (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"); +Clazz.defineMethod (c$, "embedAlignFrameInApplet", +function (theApplet) { +this.fileMenu.remove (this.closeMenuItem); +this.fileMenu.remove (3); +this.embeddedMenu = this.makeEmbeddedPopupMenu (this.alignFrameMenuBar, false, false); +theApplet.setLayout ( new java.awt.BorderLayout ()); +theApplet.add (this.embeddedMenu, "North"); +theApplet.add (this.statusBar, "South"); +this.alignPanel.setSize (theApplet.getSize ().width, theApplet.getSize ().height - this.embeddedMenu.getHeight () - this.statusBar.getHeight ()); +theApplet.add (this.alignPanel, "Center"); +var me = this; +theApplet.addFocusListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$5") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$5, this, Clazz.cloneFinals ("theApplet", theApplet, "me", me)))); +theApplet.validate (); +}, "jalview.bin.JalviewLite"); +Clazz.defineMethod (c$, "addStructureViewInstance", +function (jmolviewer, sequenceIds) { +return null; +}, "~O,~A"); +Clazz.defineMethod (c$, "addPdbFile", +function (sequenceId, pdbEntryString, pdbFile) { +var toaddpdb = this.viewport.getAlignment ().findName (sequenceId); +var needtoadd = false; +if (toaddpdb != null) { +var pdbe = toaddpdb.getPDBId (); +var pdbentry = null; +if (pdbe != null && pdbe.size () > 0) { +for (var pe = 0, peSize = pdbe.size (); pe < peSize; pe++) { +pdbentry = pdbe.elementAt (pe); +if (!pdbentry.getId ().equals (pdbEntryString) && !pdbentry.getFile ().equals (pdbFile)) { +pdbentry = null; +} else { +continue; +}} +}if (pdbentry == null) { +pdbentry = new jalview.datamodel.PDBEntry (); +pdbentry.setId (pdbEntryString); +pdbentry.setFile (pdbFile); +needtoadd = true; +}var protocol = jalview.io.AppletFormatAdapter.resolveProtocol (pdbFile, "PDB"); +if (protocol == null) { +return false; +}if (needtoadd) { +if (pdbentry.getProperty () == null) { +pdbentry.setProperty ( new java.util.Hashtable ()); +}pdbentry.getProperty ().put ("protocol", protocol); +toaddpdb.addPDBId (pdbentry); +this.alignPanel.getStructureSelectionManager ().registerPDBEntry (pdbentry); +}}return true; +}, "~S,~S,~S"); +Clazz.defineMethod (c$, "cleanSeqChainArrays", + function (seqs, chains) { +if (seqs != null) { +var sequences = new java.util.Vector (); +for (var i = 0; i < seqs.length; i++) { +if (seqs[i] != null) { +sequences.addElement ( Clazz.newArray (-1, [seqs[i], (chains != null) ? chains[i] : null])); +}} +seqs = new Array (sequences.size ()); +chains = new Array (sequences.size ()); +for (var i = 0, isize = sequences.size (); i < isize; i++) { +var oj = sequences.elementAt (i); +seqs[i] = oj[0]; +chains[i] = oj[1]; +} +}return Clazz.newArray (-1, [seqs, chains]); +}, "~A,~A"); +Clazz.defineMethod (c$, "newStructureView", +function (applet, pdb, seqs, chains, protocol) { +var sqch = this.cleanSeqChainArrays (seqs, chains); +seqs = sqch[0]; +chains = sqch[1]; +if (seqs == null || seqs.length == 0) { +System.err.println ("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); +}if (protocol == null || protocol.trim ().length == 0 || protocol.equals ("null")) { +protocol = pdb.getProperty ().get ("protocol"); +if (protocol == null) { +System.err.println ("Couldn't work out protocol to open structure: " + pdb.getId ()); +return; +}}if (applet.useXtrnalSviewer) { +if (jalview.structure.StructureSelectionManager.getStructureSelectionManager (applet).setMapping (seqs, chains, pdb.getFile (), protocol) == null) { +System.err.println ("Failed to map " + pdb.getFile () + " (" + protocol + ") to any sequences"); +}return; +}if (applet.isAlignPdbStructures () && applet.jmolAvailable) { +var ajm = null; +var tajm; +var jmols = applet.getAppletWindow (jalview.appletgui.AppletJmol); +for (var i = 0, iSize = jmols.size (); i < iSize; i++) { +tajm = jmols.elementAt (i); +if (tajm.ap.alignFrame === this) { +ajm = tajm; +break; +}} +if (ajm != null) { +System.err.println ("Incremental adding and aligning structure to existing Jmol view not yet implemented."); +ajm = null; +}} new jalview.appletgui.AppletJmol (pdb, seqs, chains, this.alignPanel, protocol); +jalview.bin.JalviewLite.lastFrameX += 40; +jalview.bin.JalviewLite.lastFrameY += 40; +}, "jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S"); +Clazz.defineMethod (c$, "alignedStructureView", +function (applet, pdb, seqs, chains, protocols) { +System.err.println ("Aligned Structure View: Not yet implemented."); +}, "jalview.bin.JalviewLite,~A,~A,~A,~A"); +Clazz.defineMethod (c$, "select", +function (sel, csel) { +this.alignPanel.seqPanel.selection (sel, csel, null); +}, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection"); +Clazz.defineMethod (c$, "scrollTo", +function (row, column) { +this.alignPanel.seqPanel.scrollTo (row, column); +}, "~N,~N"); +Clazz.defineMethod (c$, "scrollToRow", +function (row) { +this.alignPanel.seqPanel.scrollToRow (row); +}, "~N"); +Clazz.defineMethod (c$, "scrollToColumn", +function (column) { +this.alignPanel.seqPanel.scrollToColumn (column); +}, "~N"); +Clazz.defineMethod (c$, "getSequenceSetId", +function () { +return this.viewport.getSequenceSetId (); +}); +Clazz.defineMethod (c$, "loadScoreFile", +function (inFile) { +var file = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [inFile, jalview.io.AppletFormatAdapter.checkProtocol (inFile)]); +if (!file.isValid ()) { +System.err.println ("Problems parsing T-Coffee scores: " + file.getWarningMessage ()); +System.err.println ("Origin was:\n" + inFile); +return false; +}var aln; +if ((aln = this.viewport.getAlignment ()) != null && (aln.getHeight () != file.getHeight () || aln.getWidth () != file.getWidth ())) { +System.err.println ("The scores matrix does not match the alignment dimensions"); +}if (file.annotateAlignment (this.alignPanel.getAlignment (), false)) { +this.alignPanel.fontChanged (); +this.tcoffeeColour.setEnabled (true); +this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ())); +return true; +} else { +System.err.println ("Problems resolving T-Coffee scores:"); +if (file.getWarningMessage () != null) { +System.err.println (file.getWarningMessage ()); +}}return false; +}, "~S"); +Clazz.defineMethod (c$, "getSplitFrame", +function () { +return this.splitFrame; +}); +Clazz.defineMethod (c$, "setSplitFrame", +function (sf) { +this.splitFrame = sf; +}, "jalview.appletgui.SplitFrame"); +Clazz.overrideMethod (c$, "setShowSeqFeatures", +function (b) { +this.viewport.setShowSequenceFeatures (b); +}, "~B"); +Clazz.overrideMethod (c$, "setMenusForViewport", +function () { +}); +Clazz.overrideMethod (c$, "refreshFeatureUI", +function (enableIfNecessary) { +if (enableIfNecessary) { +this.sequenceFeatures.setState (true); +this.alignPanel.av.setShowSequenceFeatures (true); +}}, "~B"); +Clazz.overrideMethod (c$, "getFeatureSettingsUI", +function () { +return this.alignPanel.av.featureSettings; +}); +c$.$AlignFrame$1$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$1", java.awt.event.WindowAdapter); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +if (this.f$.ap != null) { +this.f$.ap.setOverviewPanel (null); +}}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$2$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$2", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (evt) { +this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$3$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$3", java.awt.event.WindowAdapter); +Clazz.defineMethod (c$, "windowOpened", +function (e) { +if (this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree) { +this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title); +}Clazz.superCall (this, jalview.appletgui.AlignFrame$3, "windowOpened", [e]); +}, "java.awt.event.WindowEvent"); +Clazz.overrideMethod (c$, "windowClosing", +function (e) { +this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove (this.f$.item); +}, "java.awt.event.WindowEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$1AboutPanel$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.decorateAsClass (function () { +Clazz.prepareCallback (this, arguments); +this.version = null; +this.builddate = null; +Clazz.instantialize (this, arguments); +}, jalview.appletgui, "AlignFrame$1AboutPanel", awt2swing.Canvas); +Clazz.makeConstructor (c$, +function (a, b) { +Clazz.superConstructor (this, jalview.appletgui.AlignFrame$1AboutPanel, []); +this.version = a; +this.builddate = b; +}, "~S,~S"); +Clazz.overrideMethod (c$, "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 (); +var c = b.getHeight (); +var d = 5; +var e = 7; +a.setColor (java.awt.Color.black); +a.setFont ( new java.awt.Font ("Helvetica", 1, 14)); +a.drawString (jalview.util.MessageManager.formatMessage ("label.jalviewLite_release", Clazz.newArray (-1, [this.version])), e, d += c); +a.setFont ( new java.awt.Font ("Helvetica", 1, 12)); +a.drawString (jalview.util.MessageManager.formatMessage ("label.jaview_build_date", Clazz.newArray (-1, [this.builddate])), e, d += c); +a.setFont ( new java.awt.Font ("Helvetica", 0, 12)); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_1"), e, d += c * 1.5); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_2"), e + 50, d += c + 8); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_dev_managers"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_distribution_lists"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_please_cite"), e, d += c + 8); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_authors"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_title"), e, d += c); +a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_ref"), e, d += c); +}, "java.awt.Graphics"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$4$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$4", null, java.awt.event.ActionListener); +Clazz.overrideMethod (c$, "actionPerformed", +function (e) { +this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed (e); +}, "java.awt.event.ActionEvent"); +c$ = Clazz.p0p (); +}; +c$.$AlignFrame$5$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$5", null, java.awt.event.FocusListener); +Clazz.overrideMethod (c$, "focusLost", +function (e) { +if (this.f$.theApplet.currentAlignFrame === this.f$.me) { +this.f$.theApplet.currentAlignFrame = null; +}}, "java.awt.event.FocusEvent"); +Clazz.overrideMethod (c$, "focusGained", +function (e) { +this.f$.theApplet.currentAlignFrame = this.f$.me; +}, "java.awt.event.FocusEvent"); +c$ = Clazz.p0p (); +}; +Clazz.defineStatics (c$, +"copiedSequences", null, +"copiedHiddenColumns", null); +});