-Clazz.declarePackage ("jalview.appletgui");\r
-Clazz.load (["awt2swing.PopupMenu", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuItem", "jalview.util.MessageManager"], "jalview.appletgui.APopupMenu", ["awt2swing.Frame", "jalview.analysis.AAFrequency", "$.AlignmentAnnotationUtils", "$.AlignmentUtils", "$.Conservation", "jalview.appletgui.AppletJmol", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.SliderPanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.ChangeCaseCommand", "$.EditCommand", "jalview.datamodel.SequenceFeature", "jalview.io.AppletFormatAdapter", "$.SequenceAnnotationReport", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "$.StrandColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.util.DBRefUtils", "$.UrlLink", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.LinkedHashMap", "$.TreeMap"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.groupMenu = null;\r
-this.editGroupName = null;\r
-this.clustalColour = null;\r
-this.zappoColour = null;\r
-this.taylorColour = null;\r
-this.hydrophobicityColour = null;\r
-this.helixColour = null;\r
-this.strandColour = null;\r
-this.turnColour = null;\r
-this.buriedColour = null;\r
-this.abovePIDColour = null;\r
-this.userDefinedColour = null;\r
-this.PIDColour = null;\r
-this.BLOSUM62Colour = null;\r
-this.noColourmenuItem = null;\r
-this.conservationMenuItem = null;\r
-this.ap = null;\r
-this.unGroupMenuItem = null;\r
-this.createGroupMenuItem = null;\r
-this.nucleotideMenuItem = null;\r
-this.colourMenu = null;\r
-this.showBoxes = null;\r
-this.showText = null;\r
-this.showColourText = null;\r
-this.displayNonconserved = null;\r
-this.seqShowAnnotationsMenu = null;\r
-this.seqHideAnnotationsMenu = null;\r
-this.seqAddReferenceAnnotations = null;\r
-this.groupShowAnnotationsMenu = null;\r
-this.groupHideAnnotationsMenu = null;\r
-this.groupAddReferenceAnnotations = null;\r
-this.editMenu = null;\r
-this.copy = null;\r
-this.cut = null;\r
-this.toUpper = null;\r
-this.toLower = null;\r
-this.toggleCase = null;\r
-this.outputmenu = null;\r
-this.seqMenu = null;\r
-this.pdb = null;\r
-this.hideSeqs = null;\r
-this.repGroup = null;\r
-this.sequenceName = null;\r
-this.sequenceFeature = null;\r
-this.editSequence = null;\r
-this.sequenceDetails = null;\r
-this.selSeqDetails = null;\r
-this.makeReferenceSeq = null;\r
-this.seq = null;\r
-this.revealAll = null;\r
-this.revealSeq = null;\r
-this.revealSeq_index = -1;\r
-this.menu1 = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.appletgui, "APopupMenu", awt2swing.PopupMenu, [java.awt.event.ActionListener, java.awt.event.ItemListener]);\r
-Clazz.prepareFields (c$, function () {\r
-this.groupMenu = new awt2swing.Menu ();\r
-this.editGroupName = new awt2swing.MenuItem ();\r
-this.clustalColour = new awt2swing.MenuItem ();\r
-this.zappoColour = new awt2swing.MenuItem ();\r
-this.taylorColour = new awt2swing.MenuItem ();\r
-this.hydrophobicityColour = new awt2swing.MenuItem ();\r
-this.helixColour = new awt2swing.MenuItem ();\r
-this.strandColour = new awt2swing.MenuItem ();\r
-this.turnColour = new awt2swing.MenuItem ();\r
-this.buriedColour = new awt2swing.MenuItem ();\r
-this.abovePIDColour = new awt2swing.CheckboxMenuItem ();\r
-this.userDefinedColour = new awt2swing.MenuItem ();\r
-this.PIDColour = new awt2swing.MenuItem ();\r
-this.BLOSUM62Colour = new awt2swing.MenuItem ();\r
-this.noColourmenuItem = new awt2swing.MenuItem ();\r
-this.conservationMenuItem = new awt2swing.CheckboxMenuItem ();\r
-this.unGroupMenuItem = new awt2swing.MenuItem ();\r
-this.createGroupMenuItem = new awt2swing.MenuItem ();\r
-this.nucleotideMenuItem = new awt2swing.MenuItem ();\r
-this.colourMenu = new awt2swing.Menu ();\r
-this.showBoxes = new awt2swing.CheckboxMenuItem ();\r
-this.showText = new awt2swing.CheckboxMenuItem ();\r
-this.showColourText = new awt2swing.CheckboxMenuItem ();\r
-this.displayNonconserved = new awt2swing.CheckboxMenuItem ();\r
-this.seqShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations"));\r
-this.seqHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations"));\r
-this.seqAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations"));\r
-this.groupShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations"));\r
-this.groupHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations"));\r
-this.groupAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations"));\r
-this.editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit"));\r
-this.copy = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.copy"));\r
-this.cut = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.cut"));\r
-this.toUpper = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_upper_case"));\r
-this.toLower = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_lower_case"));\r
-this.toggleCase = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.toggle_case"));\r
-this.outputmenu = new awt2swing.Menu ();\r
-this.seqMenu = new awt2swing.Menu ();\r
-this.pdb = new awt2swing.MenuItem ();\r
-this.hideSeqs = new awt2swing.MenuItem ();\r
-this.repGroup = new awt2swing.MenuItem ();\r
-this.sequenceName = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_name_description"));\r
-this.sequenceFeature = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.create_sequence_feature"));\r
-this.editSequence = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_sequence"));\r
-this.sequenceDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "...");\r
-this.selSeqDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "...");\r
-this.makeReferenceSeq = new awt2swing.MenuItem ();\r
-this.revealAll = new awt2swing.MenuItem ();\r
-this.revealSeq = new awt2swing.MenuItem ();\r
-this.menu1 = new awt2swing.Menu ();\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (apanel, seq, links) {\r
-Clazz.superConstructor (this, jalview.appletgui.APopupMenu, []);\r
-this.ap = apanel;\r
-this.seq = seq;\r
-try {\r
-this.jbInit ();\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, Exception)) {\r
-e.printStackTrace ();\r
-} else {\r
-throw e;\r
-}\r
-}\r
-for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) {\r
-var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
-item.addActionListener (this);\r
-this.outputmenu.add (item);\r
-}\r
-this.buildAnnotationSubmenus ();\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg != null && sg.getSize () > 0) {\r
-this.editGroupName.setLabel (jalview.util.MessageManager.formatMessage ("label.name_param", Clazz.newArray (-1, [sg.getName ()])));\r
-this.showText.setState (sg.getDisplayText ());\r
-this.showColourText.setState (sg.getColourText ());\r
-this.showBoxes.setState (sg.getDisplayBoxes ());\r
-this.displayNonconserved.setState (sg.getShowNonconserved ());\r
-if (!this.ap.av.getAlignment ().getGroups ().contains (sg)) {\r
-this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_new_group"));\r
-this.groupMenu.remove (this.unGroupMenuItem);\r
-} else {\r
-this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_group"));\r
-this.groupMenu.remove (this.createGroupMenuItem);\r
-}} else {\r
-this.remove (this.hideSeqs);\r
-this.remove (this.groupMenu);\r
-}if (links != null && links.size () > 0) {\r
-var linkMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.link"));\r
-for (var i = 0; i < links.size (); i++) {\r
-var link = links.elementAt (i);\r
-var urlLink = new jalview.util.UrlLink (link);\r
-if (!urlLink.isValid ()) {\r
-System.err.println (urlLink.getInvalidMessage ());\r
-continue;\r
-}var target = urlLink.getTarget ();\r
-var label = urlLink.getLabel ();\r
-if (seq != null && urlLink.isDynamic ()) {\r
-var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target]));\r
-var id = seq.getName ();\r
-var descr = seq.getDescription ();\r
-if (descr != null && descr.length < 1) {\r
-descr = null;\r
-}if (dbr != null) {\r
-for (var r = 0; r < dbr.length; r++) {\r
-if (id != null && dbr[r].getAccessionId ().equals (id)) {\r
-id = null;\r
-}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true);\r
-if (urls != null) {\r
-for (var u = 0; u < urls.length; u += 2) {\r
-this.addshowLink (linkMenu, label + "|" + urls[u], urls[u + 1]);\r
-}\r
-}}\r
-}if (id != null) {\r
-var urls = urlLink.makeUrls (id, true);\r
-if (urls != null) {\r
-for (var u = 0; u < urls.length; u += 2) {\r
-this.addshowLink (linkMenu, label, urls[u + 1]);\r
-}\r
-}}if (descr != null && urlLink.getRegexReplace () != null) {\r
-var urls = urlLink.makeUrls (descr, true);\r
-if (urls != null) {\r
-for (var u = 0; u < urls.length; u += 2) {\r
-this.addshowLink (linkMenu, label, urls[u + 1]);\r
-}\r
-}}} else {\r
-this.addshowLink (linkMenu, target, urlLink.getUrl_prefix ());\r
-}}\r
-if (linkMenu.getItemCount () > 0) {\r
-if (seq != null) {\r
-this.seqMenu.add (linkMenu);\r
-} else {\r
-this.add (linkMenu);\r
-}}}if (seq != null) {\r
-this.seqMenu.setLabel (seq.getName ());\r
-if (seq === this.ap.av.getAlignment ().getSeqrep ()) {\r
-this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.unmark_as_reference"));\r
-} else {\r
-this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.set_as_reference"));\r
-}this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [seq.getName ()])));\r
-} else {\r
-this.remove (this.seqMenu);\r
-}if (!this.ap.av.hasHiddenRows ()) {\r
-this.remove (this.revealAll);\r
-this.remove (this.revealSeq);\r
-} else {\r
-var index = this.ap.av.getAlignment ().findIndex (seq);\r
-if (this.ap.av.adjustForHiddenSeqs (index) - this.ap.av.adjustForHiddenSeqs (index - 1) > 1) {\r
-this.revealSeq_index = index;\r
-} else {\r
-this.remove (this.revealSeq);\r
-}}}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceI,java.util.Vector");\r
-Clazz.defineMethod (c$, "buildAnnotationSubmenus", \r
- function () {\r
-var selectedSequence = (this.seq == null ? java.util.Collections.emptyList () : java.util.Arrays.asList ([this.seq]));\r
-this.buildAnnotationTypesMenus (this.seqShowAnnotationsMenu, this.seqHideAnnotationsMenu, selectedSequence);\r
-this.configureReferenceAnnotationsMenu (this.seqAddReferenceAnnotations, selectedSequence);\r
-var selectedGroup = (this.ap.av.getSelectionGroup () == null ? java.util.Collections.emptyList () : this.ap.av.getSelectionGroup ().getSequences ());\r
-this.buildAnnotationTypesMenus (this.groupShowAnnotationsMenu, this.groupHideAnnotationsMenu, selectedGroup);\r
-this.configureReferenceAnnotationsMenu (this.groupAddReferenceAnnotations, selectedGroup);\r
-});\r
-Clazz.defineMethod (c$, "configureReferenceAnnotationsMenu", \r
- function (menuItem, forSequences) {\r
-menuItem.setEnabled (false);\r
-var tipEntries = new java.util.TreeMap ();\r
-var candidates = new java.util.LinkedHashMap ();\r
-var al = this.ap.av.getAlignment ();\r
-jalview.analysis.AlignmentUtils.findAddableReferenceAnnotations (forSequences, tipEntries, candidates, al);\r
-if (!candidates.isEmpty ()) {\r
-var tooltip = new StringBuilder (64);\r
-tooltip.append (jalview.util.MessageManager.getString ("label.add_annotations_for"));\r
-menuItem.setEnabled (true);\r
-menuItem.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$1") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$1, this, Clazz.cloneFinals ("candidates", candidates))));\r
-}}, "awt2swing.MenuItem,java.util.List");\r
-Clazz.defineMethod (c$, "addReferenceAnnotations_actionPerformed", \r
-function (candidates) {\r
-var selectionGroup = this.ap.av.getSelectionGroup ();\r
-var alignment = this.ap.getAlignment ();\r
-jalview.analysis.AlignmentUtils.addReferenceAnnotations (candidates, alignment, selectionGroup);\r
-this.refresh ();\r
-}, "java.util.Map");\r
-Clazz.defineMethod (c$, "addshowLink", \r
- function (linkMenu, target, url) {\r
-this.addshowLink (linkMenu, target, target, url);\r
-}, "awt2swing.Menu,~S,~S");\r
-Clazz.defineMethod (c$, "addshowLink", \r
- function (linkMenu, target, label, url) {\r
-var item = new awt2swing.MenuItem (label);\r
-item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$2") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$2, this, Clazz.cloneFinals ("url", url, "target", target))));\r
-linkMenu.add (item);\r
-}, "awt2swing.Menu,~S,~S,~S");\r
-Clazz.overrideMethod (c$, "itemStateChanged", \r
-function (evt) {\r
-if (evt.getSource () === this.abovePIDColour) {\r
-this.abovePIDColour_itemStateChanged ();\r
-} else if (evt.getSource () === this.showColourText) {\r
-this.showColourText_itemStateChanged ();\r
-} else if (evt.getSource () === this.showText) {\r
-this.showText_itemStateChanged ();\r
-} else if (evt.getSource () === this.showBoxes) {\r
-this.showBoxes_itemStateChanged ();\r
-} else if (evt.getSource () === this.displayNonconserved) {\r
-this.showNonconserved_itemStateChanged ();\r
-}}, "java.awt.event.ItemEvent");\r
-Clazz.overrideMethod (c$, "actionPerformed", \r
-function (evt) {\r
-var source = evt.getSource ();\r
-if (source === this.clustalColour) {\r
-this.clustalColour_actionPerformed ();\r
-} else if (source === this.zappoColour) {\r
-this.zappoColour_actionPerformed ();\r
-} else if (source === this.taylorColour) {\r
-this.taylorColour_actionPerformed ();\r
-} else if (source === this.hydrophobicityColour) {\r
-this.hydrophobicityColour_actionPerformed ();\r
-} else if (source === this.helixColour) {\r
-this.helixColour_actionPerformed ();\r
-} else if (source === this.strandColour) {\r
-this.strandColour_actionPerformed ();\r
-} else if (source === this.turnColour) {\r
-this.turnColour_actionPerformed ();\r
-} else if (source === this.buriedColour) {\r
-this.buriedColour_actionPerformed ();\r
-} else if (source === this.nucleotideMenuItem) {\r
-this.nucleotideMenuItem_actionPerformed ();\r
-} else if (source === this.userDefinedColour) {\r
-this.userDefinedColour_actionPerformed ();\r
-} else if (source === this.PIDColour) {\r
-this.PIDColour_actionPerformed ();\r
-} else if (source === this.BLOSUM62Colour) {\r
-this.BLOSUM62Colour_actionPerformed ();\r
-} else if (source === this.noColourmenuItem) {\r
-this.noColourmenuItem_actionPerformed ();\r
-} else if (source === this.conservationMenuItem) {\r
-this.conservationMenuItem_itemStateChanged ();\r
-} else if (source === this.unGroupMenuItem) {\r
-this.unGroupMenuItem_actionPerformed ();\r
-} else if (source === this.createGroupMenuItem) {\r
-this.createGroupMenuItem_actionPerformed ();\r
-} else if (source === this.sequenceName) {\r
-this.editName ();\r
-} else if (source === this.makeReferenceSeq) {\r
-this.makeReferenceSeq_actionPerformed ();\r
-} else if (source === this.sequenceDetails) {\r
-this.showSequenceDetails ();\r
-} else if (source === this.selSeqDetails) {\r
-this.showSequenceSelectionDetails ();\r
-} else if (source === this.pdb) {\r
-this.addPDB ();\r
-} else if (source === this.hideSeqs) {\r
-this.hideSequences (false);\r
-} else if (source === this.repGroup) {\r
-this.hideSequences (true);\r
-} else if (source === this.revealSeq) {\r
-this.ap.av.showSequence (this.revealSeq_index);\r
-} else if (source === this.revealAll) {\r
-this.ap.av.showAllHiddenSeqs ();\r
-} else if (source === this.editGroupName) {\r
-var dialog = new jalview.appletgui.EditNameDialog (this.getGroup ().getName (), this.getGroup ().getDescription (), " Group Name", "Group Description", this.ap.alignFrame, "Edit Group Name / Description", 500, 100, true);\r
-if (dialog.accept) {\r
-this.getGroup ().setName (dialog.getName ().$replace (' ', '_'));\r
-this.getGroup ().setDescription (dialog.getDescription ());\r
-}} else if (source === this.copy) {\r
-this.ap.alignFrame.copy_actionPerformed ();\r
-} else if (source === this.cut) {\r
-this.ap.alignFrame.cut_actionPerformed ();\r
-} else if (source === this.editSequence) {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg != null) {\r
-if (this.seq == null) {\r
-this.seq = sg.getSequenceAt (0);\r
-}var dialog = new jalview.appletgui.EditNameDialog (this.seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1), null, "Edit Sequence ", null, this.ap.alignFrame, "Edit Sequence", 500, 100, true);\r
-if (dialog.accept) {\r
-var editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.edit_sequences"), jalview.commands.EditCommand.Action.REPLACE, dialog.getName ().$replace (' ', this.ap.av.getGapCharacter ()), sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), sg.getStartRes (), sg.getEndRes () + 1, this.ap.av.getAlignment ());\r
-this.ap.alignFrame.addHistoryItem (editCommand);\r
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());\r
-}}} else if (source === this.toUpper || source === this.toLower || source === this.toggleCase) {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg != null) {\r
-var startEnd = this.ap.av.getVisibleRegionBoundaries (sg.getStartRes (), sg.getEndRes () + 1);\r
-var description;\r
-var caseChange;\r
-if (source === this.toggleCase) {\r
-description = "Toggle Case";\r
-caseChange = jalview.commands.ChangeCaseCommand.TOGGLE_CASE;\r
-} else if (source === this.toUpper) {\r
-description = "To Upper Case";\r
-caseChange = jalview.commands.ChangeCaseCommand.TO_UPPER;\r
-} else {\r
-description = "To Lower Case";\r
-caseChange = jalview.commands.ChangeCaseCommand.TO_LOWER;\r
-}var caseCommand = new jalview.commands.ChangeCaseCommand (description, sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), startEnd, caseChange);\r
-this.ap.alignFrame.addHistoryItem (caseCommand);\r
-this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());\r
-}} else if (source === this.sequenceFeature) {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg == null) {\r
-return;\r
-}var rsize = 0;\r
-var gSize = sg.getSize ();\r
-var rseqs;\r
-var seqs = new Array (gSize);\r
-var tfeatures;\r
-var features = new Array (gSize);\r
-for (var i = 0; i < gSize; i++) {\r
-var start = sg.getSequenceAt (i).findPosition (sg.getStartRes ());\r
-var end = sg.findEndRes (sg.getSequenceAt (i));\r
-if (start <= end) {\r
-seqs[rsize] = sg.getSequenceAt (i);\r
-features[rsize] = new jalview.datamodel.SequenceFeature (null, null, null, start, end, "Jalview");\r
-rsize++;\r
-}}\r
-rseqs = new Array (rsize);\r
-tfeatures = new Array (rsize);\r
-System.arraycopy (seqs, 0, rseqs, 0, rsize);\r
-System.arraycopy (features, 0, tfeatures, 0, rsize);\r
-features = tfeatures;\r
-seqs = rseqs;\r
-if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) {\r
-this.ap.alignFrame.sequenceFeatures.setState (true);\r
-this.ap.av.setShowSequenceFeatures (true);\r
-;this.ap.highlightSearchResults (null);\r
-}} else {\r
-this.outputText (evt);\r
-}}, "java.awt.event.ActionEvent");\r
-Clazz.defineMethod (c$, "outputText", \r
-function (e) {\r
-var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame);\r
-var frame = new awt2swing.Frame ();\r
-frame.add (cap);\r
-jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.selection_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500);\r
-cap.setText ( new jalview.io.AppletFormatAdapter ().formatSequences (e.getActionCommand (), this.ap.av.getShowJVSuffix (), this.ap, true));\r
-}, "java.awt.event.ActionEvent");\r
-Clazz.defineMethod (c$, "showSequenceSelectionDetails", \r
-function () {\r
-this.createSequenceDetailsReport (this.ap.av.getSequenceSelection ());\r
-});\r
-Clazz.defineMethod (c$, "showSequenceDetails", \r
-function () {\r
-this.createSequenceDetailsReport ( Clazz.newArray (-1, [this.seq]));\r
-});\r
-Clazz.defineMethod (c$, "createSequenceDetailsReport", \r
-function (sequences) {\r
-var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame);\r
-var contents = new StringBuffer ();\r
-for (var seq, $seq = 0, $$seq = sequences; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {\r
-contents.append (jalview.util.MessageManager.formatMessage ("label.annotation_for_displayid", Clazz.newArray (-1, [seq.getDisplayId (true)])));\r
- new jalview.io.SequenceAnnotationReport (null).createSequenceAnnotationReport (contents, seq, true, true, false, (this.ap.seqPanel.seqCanvas.fr != null) ? this.ap.seqPanel.seqCanvas.fr.getMinMax () : null);\r
-contents.append ("</p>");\r
-}\r
-var frame = new awt2swing.Frame ();\r
-frame.add (cap);\r
-jalview.bin.JalviewLite.addFrame (frame, "Sequence Details for " + (sequences.length == 1 ? sequences[0].getDisplayId (true) : "Selection"), 600, 500);\r
-cap.setText (jalview.util.MessageManager.formatMessage ("label.html_content", Clazz.newArray (-1, [contents.toString ()])));\r
-}, "~A");\r
-Clazz.defineMethod (c$, "editName", \r
-function () {\r
-var dialog = new jalview.appletgui.EditNameDialog (this.seq.getName (), this.seq.getDescription (), " Sequence Name", "Sequence Description", this.ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true);\r
-if (dialog.accept) {\r
-this.seq.setName (dialog.getName ());\r
-this.seq.setDescription (dialog.getDescription ());\r
-this.ap.paintAlignment (false);\r
-}});\r
-Clazz.defineMethod (c$, "addPDB", \r
-function () {\r
-if (this.seq.getPDBId () != null) {\r
-var entry = this.seq.getPDBId ().firstElement ();\r
-if (this.ap.av.applet.jmolAvailable) {\r
- new jalview.appletgui.AppletJmol (entry, Clazz.newArray (-1, [this.seq]), null, this.ap, jalview.io.AppletFormatAdapter.URL);\r
-}} else {\r
-var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame);\r
-cap.setText (jalview.util.MessageManager.getString ("label.paste_pdb_file"));\r
-cap.setPDBImport (this.seq);\r
-var frame = new awt2swing.Frame ();\r
-frame.add (cap);\r
-jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.paste_pdb_file_for_sequence", Clazz.newArray (-1, [this.seq.getName ()])), 400, 300);\r
-}});\r
-Clazz.defineMethod (c$, "jbInit", \r
- function () {\r
-this.groupMenu.setLabel (jalview.util.MessageManager.getString ("label.selection"));\r
-this.sequenceFeature.addActionListener (this);\r
-this.editGroupName.addActionListener (this);\r
-this.unGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_group"));\r
-this.unGroupMenuItem.addActionListener (this);\r
-this.createGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.create_group"));\r
-this.createGroupMenuItem.addActionListener (this);\r
-this.nucleotideMenuItem.setLabel (jalview.util.MessageManager.getString ("label.nucleotide"));\r
-this.nucleotideMenuItem.addActionListener (this);\r
-this.conservationMenuItem.addItemListener (this);\r
-this.abovePIDColour.addItemListener (this);\r
-this.colourMenu.setLabel (jalview.util.MessageManager.getString ("label.group_colour"));\r
-this.showBoxes.setLabel (jalview.util.MessageManager.getString ("action.boxes"));\r
-this.showBoxes.setState (true);\r
-this.showBoxes.addItemListener (this);\r
-this.sequenceName.addActionListener (this);\r
-this.sequenceDetails.addActionListener (this);\r
-this.selSeqDetails.addActionListener (this);\r
-this.displayNonconserved.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed"));\r
-this.displayNonconserved.setState (false);\r
-this.displayNonconserved.addItemListener (this);\r
-this.showText.setLabel (jalview.util.MessageManager.getString ("action.text"));\r
-this.showText.addItemListener (this);\r
-this.showColourText.setLabel (jalview.util.MessageManager.getString ("label.colour_text"));\r
-this.showColourText.addItemListener (this);\r
-this.outputmenu.setLabel (jalview.util.MessageManager.getString ("label.out_to_textbox"));\r
-this.seqMenu.setLabel (jalview.util.MessageManager.getString ("label.sequence"));\r
-this.pdb.setLabel (jalview.util.MessageManager.getString ("label.view_pdb_structure"));\r
-this.hideSeqs.setLabel (jalview.util.MessageManager.getString ("action.hide_sequences"));\r
-this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [""])));\r
-this.revealAll.setLabel (jalview.util.MessageManager.getString ("action.reveal_all"));\r
-this.revealSeq.setLabel (jalview.util.MessageManager.getString ("action.reveal_sequences"));\r
-this.menu1.setLabel (jalview.util.MessageManager.getString ("label.group") + ":");\r
-this.add (this.groupMenu);\r
-this.add (this.seqMenu);\r
-this.add (this.hideSeqs);\r
-this.add (this.revealSeq);\r
-this.add (this.revealAll);\r
-this.groupMenu.add (this.groupShowAnnotationsMenu);\r
-this.groupMenu.add (this.groupHideAnnotationsMenu);\r
-this.groupMenu.add (this.groupAddReferenceAnnotations);\r
-this.groupMenu.add (this.editMenu);\r
-this.groupMenu.add (this.outputmenu);\r
-this.groupMenu.add (this.sequenceFeature);\r
-this.groupMenu.add (this.createGroupMenuItem);\r
-this.groupMenu.add (this.unGroupMenuItem);\r
-this.groupMenu.add (this.menu1);\r
-this.colourMenu.add (this.noColourmenuItem);\r
-this.colourMenu.add (this.clustalColour);\r
-this.colourMenu.add (this.BLOSUM62Colour);\r
-this.colourMenu.add (this.PIDColour);\r
-this.colourMenu.add (this.zappoColour);\r
-this.colourMenu.add (this.taylorColour);\r
-this.colourMenu.add (this.hydrophobicityColour);\r
-this.colourMenu.add (this.helixColour);\r
-this.colourMenu.add (this.strandColour);\r
-this.colourMenu.add (this.turnColour);\r
-this.colourMenu.add (this.buriedColour);\r
-this.colourMenu.add (this.nucleotideMenuItem);\r
-this.colourMenu.add (this.userDefinedColour);\r
-this.colourMenu.addSeparator ();\r
-this.colourMenu.add (this.abovePIDColour);\r
-this.colourMenu.add (this.conservationMenuItem);\r
-this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none"));\r
-this.noColourmenuItem.addActionListener (this);\r
-this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx_colours"));\r
-this.clustalColour.addActionListener (this);\r
-this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo"));\r
-this.zappoColour.addActionListener (this);\r
-this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor"));\r
-this.taylorColour.addActionListener (this);\r
-this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity"));\r
-this.hydrophobicityColour.addActionListener (this);\r
-this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity"));\r
-this.helixColour.addActionListener (this);\r
-this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity"));\r
-this.strandColour.addActionListener (this);\r
-this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity"));\r
-this.turnColour.addActionListener (this);\r
-this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index"));\r
-this.buriedColour.addActionListener (this);\r
-this.abovePIDColour.setLabel (jalview.util.MessageManager.getString ("label.above_identity_percentage"));\r
-this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined"));\r
-this.userDefinedColour.addActionListener (this);\r
-this.PIDColour.setLabel (jalview.util.MessageManager.getString ("action.percentage_identity"));\r
-this.PIDColour.addActionListener (this);\r
-this.BLOSUM62Colour.setLabel ("BLOSUM62");\r
-this.BLOSUM62Colour.addActionListener (this);\r
-this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("label.conservation"));\r
-this.editMenu.add (this.copy);\r
-this.copy.addActionListener (this);\r
-this.editMenu.add (this.cut);\r
-this.cut.addActionListener (this);\r
-this.editMenu.add (this.editSequence);\r
-this.editSequence.addActionListener (this);\r
-this.editMenu.add (this.toUpper);\r
-this.toUpper.addActionListener (this);\r
-this.editMenu.add (this.toLower);\r
-this.toLower.addActionListener (this);\r
-this.editMenu.add (this.toggleCase);\r
-this.seqMenu.add (this.seqShowAnnotationsMenu);\r
-this.seqMenu.add (this.seqHideAnnotationsMenu);\r
-this.seqMenu.add (this.seqAddReferenceAnnotations);\r
-this.seqMenu.add (this.sequenceName);\r
-this.seqMenu.add (this.makeReferenceSeq);\r
-if (!this.ap.av.applet.useXtrnalSviewer) {\r
-this.seqMenu.add (this.pdb);\r
-}this.seqMenu.add (this.repGroup);\r
-this.menu1.add (this.editGroupName);\r
-this.menu1.add (this.colourMenu);\r
-this.menu1.add (this.showBoxes);\r
-this.menu1.add (this.showText);\r
-this.menu1.add (this.showColourText);\r
-this.menu1.add (this.displayNonconserved);\r
-this.toggleCase.addActionListener (this);\r
-this.pdb.addActionListener (this);\r
-this.hideSeqs.addActionListener (this);\r
-this.repGroup.addActionListener (this);\r
-this.revealAll.addActionListener (this);\r
-this.revealSeq.addActionListener (this);\r
-this.makeReferenceSeq.addActionListener (this);\r
-});\r
-Clazz.defineMethod (c$, "refresh", \r
-function () {\r
-this.ap.paintAlignment (true);\r
-});\r
-Clazz.defineMethod (c$, "clustalColour_actionPerformed", \r
-function () {\r
-var sg = this.getGroup ();\r
-sg.cs = new jalview.schemes.ClustalxColourScheme (sg, this.ap.av.getHiddenRepSequences ());\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "zappoColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.ZappoColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "taylorColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.TaylorColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "hydrophobicityColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.HydrophobicColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "helixColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.HelixColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "strandColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.StrandColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "turnColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.TurnColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "buriedColour_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.BuriedColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "nucleotideMenuItem_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = new jalview.schemes.NucleotideColourScheme ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "abovePIDColour_itemStateChanged", \r
-function () {\r
-var sg = this.getGroup ();\r
-if (sg.cs == null) {\r
-return;\r
-}if (this.abovePIDColour.getState ()) {\r
-sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));\r
-var threshold = jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, sg.cs, this.getGroup ().getName ());\r
-sg.cs.setThreshold (threshold, this.ap.av.isIgnoreGapsConsensus ());\r
-jalview.appletgui.SliderPanel.showPIDSlider ();\r
-} else {\r
-sg.cs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ());\r
-}this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "userDefinedColour_actionPerformed", \r
-function () {\r
- new jalview.appletgui.UserDefinedColours (this.ap, this.getGroup ());\r
-});\r
-Clazz.defineMethod (c$, "PIDColour_actionPerformed", \r
-function () {\r
-var sg = this.getGroup ();\r
-sg.cs = new jalview.schemes.PIDColourScheme ();\r
-sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "BLOSUM62Colour_actionPerformed", \r
-function () {\r
-var sg = this.getGroup ();\r
-sg.cs = new jalview.schemes.Blosum62ColourScheme ();\r
-sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "noColourmenuItem_actionPerformed", \r
-function () {\r
-this.getGroup ().cs = null;\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "conservationMenuItem_itemStateChanged", \r
-function () {\r
-var sg = this.getGroup ();\r
-if (sg.cs == null) {\r
-return;\r
-}if (this.conservationMenuItem.getState ()) {\r
-sg.cs.setConservation (jalview.analysis.Conservation.calculateConservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth (), false, this.ap.av.getConsPercGaps (), false));\r
-jalview.appletgui.SliderPanel.setConservationSlider (this.ap, sg.cs, sg.getName ());\r
-jalview.appletgui.SliderPanel.showConservationSlider ();\r
-} else {\r
-sg.cs.setConservation (null);\r
-}this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "getGroup", \r
-function () {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg != null) {\r
-this.ap.av.getAlignment ().addGroup (sg);\r
-}return sg;\r
-});\r
-Clazz.defineMethod (c$, "unGroupMenuItem_actionPerformed", \r
-function () {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-this.ap.av.getAlignment ().deleteGroup (sg);\r
-this.ap.av.setSelectionGroup (null);\r
-this.ap.paintAlignment (true);\r
-});\r
-Clazz.defineMethod (c$, "createGroupMenuItem_actionPerformed", \r
-function () {\r
-this.getGroup ();\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "showColourText_itemStateChanged", \r
-function () {\r
-this.getGroup ().setColourText (this.showColourText.getState ());\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "showText_itemStateChanged", \r
-function () {\r
-this.getGroup ().setDisplayText (this.showText.getState ());\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "makeReferenceSeq_actionPerformed", \r
-function () {\r
-if (!this.ap.av.getAlignment ().hasSeqrep ()) {\r
-this.ap.av.setDisplayReferenceSeq (true);\r
-this.ap.av.setColourByReferenceSeq (true);\r
-this.ap.av.getAlignment ().setSeqrep (this.seq);\r
-} else {\r
-if (this.ap.av.getAlignment ().getSeqrep () === this.seq) {\r
-this.ap.av.getAlignment ().setSeqrep (null);\r
-} else {\r
-this.ap.av.getAlignment ().setSeqrep (this.seq);\r
-}}this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "showNonconserved_itemStateChanged", \r
-function () {\r
-this.getGroup ().setShowNonconserved (this.displayNonconserved.getState ());\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "showBoxes_itemStateChanged", \r
-function () {\r
-this.getGroup ().setDisplayBoxes (this.showBoxes.getState ());\r
-this.refresh ();\r
-});\r
-Clazz.defineMethod (c$, "hideSequences", \r
-function (representGroup) {\r
-var sg = this.ap.av.getSelectionGroup ();\r
-if (sg == null || sg.getSize () < 1) {\r
-this.ap.av.hideSequence ( Clazz.newArray (-1, [this.seq]));\r
-return;\r
-}this.ap.av.setSelectionGroup (null);\r
-if (representGroup) {\r
-this.ap.av.hideRepSequences (this.seq, sg);\r
-return;\r
-}var gsize = sg.getSize ();\r
-var hseqs;\r
-hseqs = new Array (gsize);\r
-var index = 0;\r
-for (var i = 0; i < gsize; i++) {\r
-hseqs[index++] = sg.getSequenceAt (i);\r
-}\r
-this.ap.av.hideSequence (hseqs);\r
-this.ap.av.sendSelection ();\r
-}, "~B");\r
-Clazz.defineMethod (c$, "buildAnnotationTypesMenus", \r
-function (showMenu, hideMenu, forSequences) {\r
-showMenu.removeAll ();\r
-hideMenu.removeAll ();\r
-var all = java.util.Arrays.asList (["All"]);\r
-this.addAnnotationTypeToShowHide (showMenu, forSequences, "", all, true, true);\r
-this.addAnnotationTypeToShowHide (hideMenu, forSequences, "", all, true, false);\r
-showMenu.addSeparator ();\r
-hideMenu.addSeparator ();\r
-var annotations = this.ap.getAlignment ().getAlignmentAnnotation ();\r
-var shownTypes = new java.util.LinkedHashMap ();\r
-var hiddenTypes = new java.util.LinkedHashMap ();\r
-jalview.analysis.AlignmentAnnotationUtils.getShownHiddenTypes (shownTypes, hiddenTypes, jalview.analysis.AlignmentAnnotationUtils.asList (annotations), forSequences);\r
-for (var calcId, $calcId = hiddenTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {\r
-for (var type, $type = hiddenTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) {\r
-this.addAnnotationTypeToShowHide (showMenu, forSequences, calcId, type, false, true);\r
-}\r
-}\r
-showMenu.setEnabled (!hiddenTypes.isEmpty ());\r
-for (var calcId, $calcId = shownTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {\r
-for (var type, $type = shownTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) {\r
-this.addAnnotationTypeToShowHide (hideMenu, forSequences, calcId, type, false, false);\r
-}\r
-}\r
-hideMenu.setEnabled (!shownTypes.isEmpty ());\r
-}, "awt2swing.Menu,awt2swing.Menu,java.util.List");\r
-Clazz.defineMethod (c$, "addAnnotationTypeToShowHide", \r
-function (showOrHideMenu, forSequences, calcId, types, allTypes, actionIsShow) {\r
-var label = types.toString ();\r
-label = label.substring (1, label.length - 1);\r
-var item = new awt2swing.MenuItem (label);\r
-item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$3") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$3, this, Clazz.cloneFinals ("types", types, "forSequences", forSequences, "allTypes", allTypes, "actionIsShow", actionIsShow))));\r
-showOrHideMenu.add (item);\r
-}, "awt2swing.Menu,java.util.List,~S,java.util.List,~B,~B");\r
-c$.$APopupMenu$1$ = function () {\r
-Clazz.pu$h(self.c$);\r
-c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$1", null, java.awt.event.ActionListener);\r
-Clazz.overrideMethod (c$, "actionPerformed", \r
-function (e) {\r
-this.b$["jalview.appletgui.APopupMenu"].addReferenceAnnotations_actionPerformed (this.f$.candidates);\r
-}, "java.awt.event.ActionEvent");\r
-c$ = Clazz.p0p ();\r
-};\r
-c$.$APopupMenu$2$ = function () {\r
-Clazz.pu$h(self.c$);\r
-c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$2", null, java.awt.event.ActionListener);\r
-Clazz.overrideMethod (c$, "actionPerformed", \r
-function (e) {\r
-this.b$["jalview.appletgui.APopupMenu"].ap.alignFrame.showURL (this.f$.url, this.f$.target);\r
-}, "java.awt.event.ActionEvent");\r
-c$ = Clazz.p0p ();\r
-};\r
-c$.$APopupMenu$3$ = function () {\r
-Clazz.pu$h(self.c$);\r
-c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$3", null, java.awt.event.ActionListener);\r
-Clazz.overrideMethod (c$, "actionPerformed", \r
-function (e) {\r
-jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.APopupMenu"].ap.getAlignment (), this.f$.types, this.f$.forSequences, this.f$.allTypes, this.f$.actionIsShow);\r
-this.b$["jalview.appletgui.APopupMenu"].refresh ();\r
-}, "java.awt.event.ActionEvent");\r
-c$ = Clazz.p0p ();\r
-};\r
-Clazz.defineStatics (c$,\r
-"ALL_ANNOTATIONS", "All");\r
-});\r
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.PopupMenu", "java.awt.event.ActionListener", "$.ItemListener", "awt2swing.CheckboxMenuItem", "$.Menu", "$.MenuItem", "jalview.util.MessageManager"], "jalview.appletgui.APopupMenu", ["awt2swing.Frame", "jalview.analysis.AAFrequency", "$.AlignmentAnnotationUtils", "$.AlignmentUtils", "$.Conservation", "jalview.appletgui.AppletJmol", "$.CutAndPasteTransfer", "$.EditNameDialog", "$.SliderPanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.ChangeCaseCommand", "$.EditCommand", "jalview.datamodel.SequenceFeature", "jalview.io.AppletFormatAdapter", "$.SequenceAnnotationReport", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.ResidueProperties", "$.StrandColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.util.DBRefUtils", "$.UrlLink", "java.lang.StringBuffer", "$.StringBuilder", "java.util.Arrays", "$.Collections", "$.LinkedHashMap", "$.TreeMap"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.groupMenu = null;
+this.editGroupName = 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.abovePIDColour = null;
+this.userDefinedColour = null;
+this.PIDColour = null;
+this.BLOSUM62Colour = null;
+this.noColourmenuItem = null;
+this.conservationMenuItem = null;
+this.ap = null;
+this.unGroupMenuItem = null;
+this.createGroupMenuItem = null;
+this.nucleotideMenuItem = null;
+this.colourMenu = null;
+this.showBoxes = null;
+this.showText = null;
+this.showColourText = null;
+this.displayNonconserved = null;
+this.seqShowAnnotationsMenu = null;
+this.seqHideAnnotationsMenu = null;
+this.seqAddReferenceAnnotations = null;
+this.groupShowAnnotationsMenu = null;
+this.groupHideAnnotationsMenu = null;
+this.groupAddReferenceAnnotations = null;
+this.editMenu = null;
+this.copy = null;
+this.cut = null;
+this.toUpper = null;
+this.toLower = null;
+this.toggleCase = null;
+this.outputmenu = null;
+this.seqMenu = null;
+this.pdb = null;
+this.hideSeqs = null;
+this.repGroup = null;
+this.sequenceName = null;
+this.sequenceFeature = null;
+this.editSequence = null;
+this.sequenceDetails = null;
+this.selSeqDetails = null;
+this.makeReferenceSeq = null;
+this.seq = null;
+this.revealAll = null;
+this.revealSeq = null;
+this.revealSeq_index = -1;
+this.menu1 = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "APopupMenu", awt2swing.PopupMenu, [java.awt.event.ActionListener, java.awt.event.ItemListener]);
+Clazz.prepareFields (c$, function () {
+this.groupMenu = new awt2swing.Menu ();
+this.editGroupName = new awt2swing.MenuItem ();
+this.clustalColour = new awt2swing.MenuItem ();
+this.zappoColour = new awt2swing.MenuItem ();
+this.taylorColour = new awt2swing.MenuItem ();
+this.hydrophobicityColour = new awt2swing.MenuItem ();
+this.helixColour = new awt2swing.MenuItem ();
+this.strandColour = new awt2swing.MenuItem ();
+this.turnColour = new awt2swing.MenuItem ();
+this.buriedColour = new awt2swing.MenuItem ();
+this.abovePIDColour = new awt2swing.CheckboxMenuItem ();
+this.userDefinedColour = new awt2swing.MenuItem ();
+this.PIDColour = new awt2swing.MenuItem ();
+this.BLOSUM62Colour = new awt2swing.MenuItem ();
+this.noColourmenuItem = new awt2swing.MenuItem ();
+this.conservationMenuItem = new awt2swing.CheckboxMenuItem ();
+this.unGroupMenuItem = new awt2swing.MenuItem ();
+this.createGroupMenuItem = new awt2swing.MenuItem ();
+this.nucleotideMenuItem = new awt2swing.MenuItem ();
+this.colourMenu = new awt2swing.Menu ();
+this.showBoxes = new awt2swing.CheckboxMenuItem ();
+this.showText = new awt2swing.CheckboxMenuItem ();
+this.showColourText = new awt2swing.CheckboxMenuItem ();
+this.displayNonconserved = new awt2swing.CheckboxMenuItem ();
+this.seqShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations"));
+this.seqHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations"));
+this.seqAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations"));
+this.groupShowAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.show_annotations"));
+this.groupHideAnnotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.hide_annotations"));
+this.groupAddReferenceAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.add_reference_annotations"));
+this.editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit"));
+this.copy = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.copy"));
+this.cut = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.cut"));
+this.toUpper = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_upper_case"));
+this.toLower = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.to_lower_case"));
+this.toggleCase = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.toggle_case"));
+this.outputmenu = new awt2swing.Menu ();
+this.seqMenu = new awt2swing.Menu ();
+this.pdb = new awt2swing.MenuItem ();
+this.hideSeqs = new awt2swing.MenuItem ();
+this.repGroup = new awt2swing.MenuItem ();
+this.sequenceName = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_name_description"));
+this.sequenceFeature = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.create_sequence_feature"));
+this.editSequence = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.edit_sequence"));
+this.sequenceDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "...");
+this.selSeqDetails = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.sequence_details") + "...");
+this.makeReferenceSeq = new awt2swing.MenuItem ();
+this.revealAll = new awt2swing.MenuItem ();
+this.revealSeq = new awt2swing.MenuItem ();
+this.menu1 = new awt2swing.Menu ();
+});
+Clazz.makeConstructor (c$,
+function (apanel, seq, links) {
+Clazz.superConstructor (this, jalview.appletgui.APopupMenu, []);
+this.ap = apanel;
+this.seq = seq;
+try {
+this.jbInit ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+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 (this);
+this.outputmenu.add (item);
+}
+this.buildAnnotationSubmenus ();
+var sg = this.ap.av.getSelectionGroup ();
+if (sg != null && sg.getSize () > 0) {
+this.editGroupName.setLabel (jalview.util.MessageManager.formatMessage ("label.name_param", Clazz.newArray (-1, [sg.getName ()])));
+this.showText.setState (sg.getDisplayText ());
+this.showColourText.setState (sg.getColourText ());
+this.showBoxes.setState (sg.getDisplayBoxes ());
+this.displayNonconserved.setState (sg.getShowNonconserved ());
+if (!this.ap.av.getAlignment ().getGroups ().contains (sg)) {
+this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_new_group"));
+this.groupMenu.remove (this.unGroupMenuItem);
+} else {
+this.menu1.setLabel (jalview.util.MessageManager.getString ("action.edit_group"));
+this.groupMenu.remove (this.createGroupMenuItem);
+}} else {
+this.remove (this.hideSeqs);
+this.remove (this.groupMenu);
+}if (links != null && links.size () > 0) {
+var linkMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.link"));
+for (var i = 0; i < links.size (); i++) {
+var link = links.elementAt (i);
+var urlLink = new jalview.util.UrlLink (link);
+if (!urlLink.isValid ()) {
+System.err.println (urlLink.getInvalidMessage ());
+continue;
+}var target = urlLink.getTarget ();
+var label = urlLink.getLabel ();
+if (seq != null && urlLink.isDynamic ()) {
+var dbr = jalview.util.DBRefUtils.selectRefs (seq.getDBRef (), Clazz.newArray (-1, [target]));
+var id = seq.getName ();
+var descr = seq.getDescription ();
+if (descr != null && descr.length < 1) {
+descr = null;
+}if (dbr != null) {
+for (var r = 0; r < dbr.length; r++) {
+if (id != null && dbr[r].getAccessionId ().equals (id)) {
+id = null;
+}var urls = urlLink.makeUrls (dbr[r].getAccessionId (), true);
+if (urls != null) {
+for (var u = 0; u < urls.length; u += 2) {
+this.addshowLink (linkMenu, label + "|" + urls[u], urls[u + 1]);
+}
+}}
+}if (id != null) {
+var urls = urlLink.makeUrls (id, true);
+if (urls != null) {
+for (var u = 0; u < urls.length; u += 2) {
+this.addshowLink (linkMenu, label, urls[u + 1]);
+}
+}}if (descr != null && urlLink.getRegexReplace () != null) {
+var urls = urlLink.makeUrls (descr, true);
+if (urls != null) {
+for (var u = 0; u < urls.length; u += 2) {
+this.addshowLink (linkMenu, label, urls[u + 1]);
+}
+}}} else {
+this.addshowLink (linkMenu, target, urlLink.getUrl_prefix ());
+}}
+if (linkMenu.getItemCount () > 0) {
+if (seq != null) {
+this.seqMenu.add (linkMenu);
+} else {
+this.add (linkMenu);
+}}}if (seq != null) {
+this.seqMenu.setLabel (seq.getName ());
+if (seq === this.ap.av.getAlignment ().getSeqrep ()) {
+this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.unmark_as_reference"));
+} else {
+this.makeReferenceSeq.setLabel (jalview.util.MessageManager.getString ("action.set_as_reference"));
+}this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [seq.getName ()])));
+} else {
+this.remove (this.seqMenu);
+}if (!this.ap.av.hasHiddenRows ()) {
+this.remove (this.revealAll);
+this.remove (this.revealSeq);
+} else {
+var index = this.ap.av.getAlignment ().findIndex (seq);
+if (this.ap.av.adjustForHiddenSeqs (index) - this.ap.av.adjustForHiddenSeqs (index - 1) > 1) {
+this.revealSeq_index = index;
+} else {
+this.remove (this.revealSeq);
+}}}, "jalview.appletgui.AlignmentPanel,jalview.datamodel.SequenceI,java.util.Vector");
+Clazz.defineMethod (c$, "buildAnnotationSubmenus",
+ function () {
+var selectedSequence = (this.seq == null ? java.util.Collections.emptyList () : java.util.Arrays.asList ([this.seq]));
+this.buildAnnotationTypesMenus (this.seqShowAnnotationsMenu, this.seqHideAnnotationsMenu, selectedSequence);
+this.configureReferenceAnnotationsMenu (this.seqAddReferenceAnnotations, selectedSequence);
+var selectedGroup = (this.ap.av.getSelectionGroup () == null ? java.util.Collections.emptyList () : this.ap.av.getSelectionGroup ().getSequences ());
+this.buildAnnotationTypesMenus (this.groupShowAnnotationsMenu, this.groupHideAnnotationsMenu, selectedGroup);
+this.configureReferenceAnnotationsMenu (this.groupAddReferenceAnnotations, selectedGroup);
+});
+Clazz.defineMethod (c$, "configureReferenceAnnotationsMenu",
+ function (menuItem, forSequences) {
+menuItem.setEnabled (false);
+var tipEntries = new java.util.TreeMap ();
+var candidates = new java.util.LinkedHashMap ();
+var al = this.ap.av.getAlignment ();
+jalview.analysis.AlignmentUtils.findAddableReferenceAnnotations (forSequences, tipEntries, candidates, al);
+if (!candidates.isEmpty ()) {
+var tooltip = new StringBuilder (64);
+tooltip.append (jalview.util.MessageManager.getString ("label.add_annotations_for"));
+menuItem.setEnabled (true);
+menuItem.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$1") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$1, this, Clazz.cloneFinals ("candidates", candidates))));
+}}, "awt2swing.MenuItem,java.util.List");
+Clazz.defineMethod (c$, "addReferenceAnnotations_actionPerformed",
+function (candidates) {
+var selectionGroup = this.ap.av.getSelectionGroup ();
+var alignment = this.ap.getAlignment ();
+jalview.analysis.AlignmentUtils.addReferenceAnnotations (candidates, alignment, selectionGroup);
+this.refresh ();
+}, "java.util.Map");
+Clazz.defineMethod (c$, "addshowLink",
+ function (linkMenu, target, url) {
+this.addshowLink (linkMenu, target, target, url);
+}, "awt2swing.Menu,~S,~S");
+Clazz.defineMethod (c$, "addshowLink",
+ function (linkMenu, target, label, url) {
+var item = new awt2swing.MenuItem (label);
+item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$2") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$2, this, Clazz.cloneFinals ("url", url, "target", target))));
+linkMenu.add (item);
+}, "awt2swing.Menu,~S,~S,~S");
+Clazz.overrideMethod (c$, "itemStateChanged",
+function (evt) {
+if (evt.getSource () === this.abovePIDColour) {
+this.abovePIDColour_itemStateChanged ();
+} else if (evt.getSource () === this.showColourText) {
+this.showColourText_itemStateChanged ();
+} else if (evt.getSource () === this.showText) {
+this.showText_itemStateChanged ();
+} else if (evt.getSource () === this.showBoxes) {
+this.showBoxes_itemStateChanged ();
+} else if (evt.getSource () === this.displayNonconserved) {
+this.showNonconserved_itemStateChanged ();
+}}, "java.awt.event.ItemEvent");
+Clazz.overrideMethod (c$, "actionPerformed",
+function (evt) {
+var source = evt.getSource ();
+if (source === this.clustalColour) {
+this.clustalColour_actionPerformed ();
+} else if (source === this.zappoColour) {
+this.zappoColour_actionPerformed ();
+} else if (source === this.taylorColour) {
+this.taylorColour_actionPerformed ();
+} else if (source === this.hydrophobicityColour) {
+this.hydrophobicityColour_actionPerformed ();
+} else if (source === this.helixColour) {
+this.helixColour_actionPerformed ();
+} else if (source === this.strandColour) {
+this.strandColour_actionPerformed ();
+} else if (source === this.turnColour) {
+this.turnColour_actionPerformed ();
+} else if (source === this.buriedColour) {
+this.buriedColour_actionPerformed ();
+} else if (source === this.nucleotideMenuItem) {
+this.nucleotideMenuItem_actionPerformed ();
+} else if (source === this.userDefinedColour) {
+this.userDefinedColour_actionPerformed ();
+} else if (source === this.PIDColour) {
+this.PIDColour_actionPerformed ();
+} else if (source === this.BLOSUM62Colour) {
+this.BLOSUM62Colour_actionPerformed ();
+} else if (source === this.noColourmenuItem) {
+this.noColourmenuItem_actionPerformed ();
+} else if (source === this.conservationMenuItem) {
+this.conservationMenuItem_itemStateChanged ();
+} else if (source === this.unGroupMenuItem) {
+this.unGroupMenuItem_actionPerformed ();
+} else if (source === this.createGroupMenuItem) {
+this.createGroupMenuItem_actionPerformed ();
+} else if (source === this.sequenceName) {
+this.editName ();
+} else if (source === this.makeReferenceSeq) {
+this.makeReferenceSeq_actionPerformed ();
+} else if (source === this.sequenceDetails) {
+this.showSequenceDetails ();
+} else if (source === this.selSeqDetails) {
+this.showSequenceSelectionDetails ();
+} else if (source === this.pdb) {
+this.addPDB ();
+} else if (source === this.hideSeqs) {
+this.hideSequences (false);
+} else if (source === this.repGroup) {
+this.hideSequences (true);
+} else if (source === this.revealSeq) {
+this.ap.av.showSequence (this.revealSeq_index);
+} else if (source === this.revealAll) {
+this.ap.av.showAllHiddenSeqs ();
+} else if (source === this.editGroupName) {
+var dialog = new jalview.appletgui.EditNameDialog (this.getGroup ().getName (), this.getGroup ().getDescription (), " Group Name", "Group Description", this.ap.alignFrame, "Edit Group Name / Description", 500, 100, true);
+if (dialog.accept) {
+this.getGroup ().setName (dialog.getName ().$replace (' ', '_'));
+this.getGroup ().setDescription (dialog.getDescription ());
+}} else if (source === this.copy) {
+this.ap.alignFrame.copy_actionPerformed ();
+} else if (source === this.cut) {
+this.ap.alignFrame.cut_actionPerformed ();
+} else if (source === this.editSequence) {
+var sg = this.ap.av.getSelectionGroup ();
+if (sg != null) {
+if (this.seq == null) {
+this.seq = sg.getSequenceAt (0);
+}var dialog = new jalview.appletgui.EditNameDialog (this.seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1), null, "Edit Sequence ", null, this.ap.alignFrame, "Edit Sequence", 500, 100, true);
+if (dialog.accept) {
+var editCommand = new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.edit_sequences"), jalview.commands.EditCommand.Action.REPLACE, dialog.getName ().$replace (' ', this.ap.av.getGapCharacter ()), sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), sg.getStartRes (), sg.getEndRes () + 1, this.ap.av.getAlignment ());
+this.ap.alignFrame.addHistoryItem (editCommand);
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}}} else if (source === this.toUpper || source === this.toLower || source === this.toggleCase) {
+var sg = this.ap.av.getSelectionGroup ();
+if (sg != null) {
+var startEnd = this.ap.av.getVisibleRegionBoundaries (sg.getStartRes (), sg.getEndRes () + 1);
+var description;
+var caseChange;
+if (source === this.toggleCase) {
+description = "Toggle Case";
+caseChange = jalview.commands.ChangeCaseCommand.TOGGLE_CASE;
+} else if (source === this.toUpper) {
+description = "To Upper Case";
+caseChange = jalview.commands.ChangeCaseCommand.TO_UPPER;
+} else {
+description = "To Lower Case";
+caseChange = jalview.commands.ChangeCaseCommand.TO_LOWER;
+}var caseCommand = new jalview.commands.ChangeCaseCommand (description, sg.getSequencesAsArray (this.ap.av.getHiddenRepSequences ()), startEnd, caseChange);
+this.ap.alignFrame.addHistoryItem (caseCommand);
+this.ap.av.firePropertyChange ("alignment", null, this.ap.av.getAlignment ().getSequences ());
+}} else if (source === this.sequenceFeature) {
+var sg = this.ap.av.getSelectionGroup ();
+if (sg == null) {
+return;
+}var rsize = 0;
+var gSize = sg.getSize ();
+var rseqs;
+var seqs = new Array (gSize);
+var tfeatures;
+var features = new Array (gSize);
+for (var i = 0; i < gSize; i++) {
+var start = sg.getSequenceAt (i).findPosition (sg.getStartRes ());
+var end = sg.findEndRes (sg.getSequenceAt (i));
+if (start <= end) {
+seqs[rsize] = sg.getSequenceAt (i);
+features[rsize] = new jalview.datamodel.SequenceFeature (null, null, null, start, end, "Jalview");
+rsize++;
+}}
+rseqs = new Array (rsize);
+tfeatures = new Array (rsize);
+System.arraycopy (seqs, 0, rseqs, 0, rsize);
+System.arraycopy (features, 0, tfeatures, 0, rsize);
+features = tfeatures;
+seqs = rseqs;
+if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) {
+this.ap.alignFrame.sequenceFeatures.setState (true);
+this.ap.av.setShowSequenceFeatures (true);
+;this.ap.highlightSearchResults (null);
+}} else {
+this.outputText (evt);
+}}, "java.awt.event.ActionEvent");
+Clazz.defineMethod (c$, "outputText",
+function (e) {
+var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame);
+var frame = new awt2swing.Frame ();
+frame.add (cap);
+jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.selection_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500);
+cap.setText ( new jalview.io.AppletFormatAdapter ().formatSequences (e.getActionCommand (), this.ap.av.getShowJVSuffix (), this.ap, true));
+}, "java.awt.event.ActionEvent");
+Clazz.defineMethod (c$, "showSequenceSelectionDetails",
+function () {
+this.createSequenceDetailsReport (this.ap.av.getSequenceSelection ());
+});
+Clazz.defineMethod (c$, "showSequenceDetails",
+function () {
+this.createSequenceDetailsReport ( Clazz.newArray (-1, [this.seq]));
+});
+Clazz.defineMethod (c$, "createSequenceDetailsReport",
+function (sequences) {
+var cap = new jalview.appletgui.CutAndPasteTransfer (false, this.ap.alignFrame);
+var contents = new StringBuffer ();
+for (var seq, $seq = 0, $$seq = sequences; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {
+contents.append (jalview.util.MessageManager.formatMessage ("label.annotation_for_displayid", Clazz.newArray (-1, [seq.getDisplayId (true)])));
+ new jalview.io.SequenceAnnotationReport (null).createSequenceAnnotationReport (contents, seq, true, true, false, (this.ap.seqPanel.seqCanvas.fr != null) ? this.ap.seqPanel.seqCanvas.fr.getMinMax () : null);
+contents.append ("</p>");
+}
+var frame = new awt2swing.Frame ();
+frame.add (cap);
+jalview.bin.JalviewLite.addFrame (frame, "Sequence Details for " + (sequences.length == 1 ? sequences[0].getDisplayId (true) : "Selection"), 600, 500);
+cap.setText (jalview.util.MessageManager.formatMessage ("label.html_content", Clazz.newArray (-1, [contents.toString ()])));
+}, "~A");
+Clazz.defineMethod (c$, "editName",
+function () {
+var dialog = new jalview.appletgui.EditNameDialog (this.seq.getName (), this.seq.getDescription (), " Sequence Name", "Sequence Description", this.ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true);
+if (dialog.accept) {
+this.seq.setName (dialog.getName ());
+this.seq.setDescription (dialog.getDescription ());
+this.ap.paintAlignment (false);
+}});
+Clazz.defineMethod (c$, "addPDB",
+function () {
+if (this.seq.getPDBId () != null) {
+var entry = this.seq.getPDBId ().firstElement ();
+if (this.ap.av.applet.jmolAvailable) {
+ new jalview.appletgui.AppletJmol (entry, Clazz.newArray (-1, [this.seq]), null, this.ap, jalview.io.AppletFormatAdapter.URL);
+}} else {
+var cap = new jalview.appletgui.CutAndPasteTransfer (true, this.ap.alignFrame);
+cap.setText (jalview.util.MessageManager.getString ("label.paste_pdb_file"));
+cap.setPDBImport (this.seq);
+var frame = new awt2swing.Frame ();
+frame.add (cap);
+jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.paste_pdb_file_for_sequence", Clazz.newArray (-1, [this.seq.getName ()])), 400, 300);
+}});
+Clazz.defineMethod (c$, "jbInit",
+ function () {
+this.groupMenu.setLabel (jalview.util.MessageManager.getString ("label.selection"));
+this.sequenceFeature.addActionListener (this);
+this.editGroupName.addActionListener (this);
+this.unGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_group"));
+this.unGroupMenuItem.addActionListener (this);
+this.createGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.create_group"));
+this.createGroupMenuItem.addActionListener (this);
+this.nucleotideMenuItem.setLabel (jalview.util.MessageManager.getString ("label.nucleotide"));
+this.nucleotideMenuItem.addActionListener (this);
+this.conservationMenuItem.addItemListener (this);
+this.abovePIDColour.addItemListener (this);
+this.colourMenu.setLabel (jalview.util.MessageManager.getString ("label.group_colour"));
+this.showBoxes.setLabel (jalview.util.MessageManager.getString ("action.boxes"));
+this.showBoxes.setState (true);
+this.showBoxes.addItemListener (this);
+this.sequenceName.addActionListener (this);
+this.sequenceDetails.addActionListener (this);
+this.selSeqDetails.addActionListener (this);
+this.displayNonconserved.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed"));
+this.displayNonconserved.setState (false);
+this.displayNonconserved.addItemListener (this);
+this.showText.setLabel (jalview.util.MessageManager.getString ("action.text"));
+this.showText.addItemListener (this);
+this.showColourText.setLabel (jalview.util.MessageManager.getString ("label.colour_text"));
+this.showColourText.addItemListener (this);
+this.outputmenu.setLabel (jalview.util.MessageManager.getString ("label.out_to_textbox"));
+this.seqMenu.setLabel (jalview.util.MessageManager.getString ("label.sequence"));
+this.pdb.setLabel (jalview.util.MessageManager.getString ("label.view_pdb_structure"));
+this.hideSeqs.setLabel (jalview.util.MessageManager.getString ("action.hide_sequences"));
+this.repGroup.setLabel (jalview.util.MessageManager.formatMessage ("label.represent_group_with", Clazz.newArray (-1, [""])));
+this.revealAll.setLabel (jalview.util.MessageManager.getString ("action.reveal_all"));
+this.revealSeq.setLabel (jalview.util.MessageManager.getString ("action.reveal_sequences"));
+this.menu1.setLabel (jalview.util.MessageManager.getString ("label.group") + ":");
+this.add (this.groupMenu);
+this.add (this.seqMenu);
+this.add (this.hideSeqs);
+this.add (this.revealSeq);
+this.add (this.revealAll);
+this.groupMenu.add (this.groupShowAnnotationsMenu);
+this.groupMenu.add (this.groupHideAnnotationsMenu);
+this.groupMenu.add (this.groupAddReferenceAnnotations);
+this.groupMenu.add (this.editMenu);
+this.groupMenu.add (this.outputmenu);
+this.groupMenu.add (this.sequenceFeature);
+this.groupMenu.add (this.createGroupMenuItem);
+this.groupMenu.add (this.unGroupMenuItem);
+this.groupMenu.add (this.menu1);
+this.colourMenu.add (this.noColourmenuItem);
+this.colourMenu.add (this.clustalColour);
+this.colourMenu.add (this.BLOSUM62Colour);
+this.colourMenu.add (this.PIDColour);
+this.colourMenu.add (this.zappoColour);
+this.colourMenu.add (this.taylorColour);
+this.colourMenu.add (this.hydrophobicityColour);
+this.colourMenu.add (this.helixColour);
+this.colourMenu.add (this.strandColour);
+this.colourMenu.add (this.turnColour);
+this.colourMenu.add (this.buriedColour);
+this.colourMenu.add (this.nucleotideMenuItem);
+this.colourMenu.add (this.userDefinedColour);
+this.colourMenu.addSeparator ();
+this.colourMenu.add (this.abovePIDColour);
+this.colourMenu.add (this.conservationMenuItem);
+this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none"));
+this.noColourmenuItem.addActionListener (this);
+this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx_colours"));
+this.clustalColour.addActionListener (this);
+this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo"));
+this.zappoColour.addActionListener (this);
+this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor"));
+this.taylorColour.addActionListener (this);
+this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity"));
+this.hydrophobicityColour.addActionListener (this);
+this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity"));
+this.helixColour.addActionListener (this);
+this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity"));
+this.strandColour.addActionListener (this);
+this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity"));
+this.turnColour.addActionListener (this);
+this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index"));
+this.buriedColour.addActionListener (this);
+this.abovePIDColour.setLabel (jalview.util.MessageManager.getString ("label.above_identity_percentage"));
+this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined"));
+this.userDefinedColour.addActionListener (this);
+this.PIDColour.setLabel (jalview.util.MessageManager.getString ("action.percentage_identity"));
+this.PIDColour.addActionListener (this);
+this.BLOSUM62Colour.setLabel ("BLOSUM62");
+this.BLOSUM62Colour.addActionListener (this);
+this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("label.conservation"));
+this.editMenu.add (this.copy);
+this.copy.addActionListener (this);
+this.editMenu.add (this.cut);
+this.cut.addActionListener (this);
+this.editMenu.add (this.editSequence);
+this.editSequence.addActionListener (this);
+this.editMenu.add (this.toUpper);
+this.toUpper.addActionListener (this);
+this.editMenu.add (this.toLower);
+this.toLower.addActionListener (this);
+this.editMenu.add (this.toggleCase);
+this.seqMenu.add (this.seqShowAnnotationsMenu);
+this.seqMenu.add (this.seqHideAnnotationsMenu);
+this.seqMenu.add (this.seqAddReferenceAnnotations);
+this.seqMenu.add (this.sequenceName);
+this.seqMenu.add (this.makeReferenceSeq);
+if (!this.ap.av.applet.useXtrnalSviewer) {
+this.seqMenu.add (this.pdb);
+}this.seqMenu.add (this.repGroup);
+this.menu1.add (this.editGroupName);
+this.menu1.add (this.colourMenu);
+this.menu1.add (this.showBoxes);
+this.menu1.add (this.showText);
+this.menu1.add (this.showColourText);
+this.menu1.add (this.displayNonconserved);
+this.toggleCase.addActionListener (this);
+this.pdb.addActionListener (this);
+this.hideSeqs.addActionListener (this);
+this.repGroup.addActionListener (this);
+this.revealAll.addActionListener (this);
+this.revealSeq.addActionListener (this);
+this.makeReferenceSeq.addActionListener (this);
+});
+Clazz.defineMethod (c$, "refresh",
+function () {
+this.ap.paintAlignment (true);
+});
+Clazz.defineMethod (c$, "clustalColour_actionPerformed",
+function () {
+var sg = this.getGroup ();
+sg.cs = new jalview.schemes.ClustalxColourScheme (sg, this.ap.av.getHiddenRepSequences ());
+this.refresh ();
+});
+Clazz.defineMethod (c$, "zappoColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.ZappoColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "taylorColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.TaylorColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "hydrophobicityColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.HydrophobicColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "helixColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.HelixColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "strandColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.StrandColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "turnColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.TurnColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "buriedColour_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.BuriedColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "nucleotideMenuItem_actionPerformed",
+function () {
+this.getGroup ().cs = new jalview.schemes.NucleotideColourScheme ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "abovePIDColour_itemStateChanged",
+function () {
+var sg = this.getGroup ();
+if (sg.cs == null) {
+return;
+}if (this.abovePIDColour.getState ()) {
+sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));
+var threshold = jalview.appletgui.SliderPanel.setPIDSliderSource (this.ap, sg.cs, this.getGroup ().getName ());
+sg.cs.setThreshold (threshold, this.ap.av.isIgnoreGapsConsensus ());
+jalview.appletgui.SliderPanel.showPIDSlider ();
+} else {
+sg.cs.setThreshold (0, this.ap.av.isIgnoreGapsConsensus ());
+}this.refresh ();
+});
+Clazz.defineMethod (c$, "userDefinedColour_actionPerformed",
+function () {
+ new jalview.appletgui.UserDefinedColours (this.ap, this.getGroup ());
+});
+Clazz.defineMethod (c$, "PIDColour_actionPerformed",
+function () {
+var sg = this.getGroup ();
+sg.cs = new jalview.schemes.PIDColourScheme ();
+sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));
+this.refresh ();
+});
+Clazz.defineMethod (c$, "BLOSUM62Colour_actionPerformed",
+function () {
+var sg = this.getGroup ();
+sg.cs = new jalview.schemes.Blosum62ColourScheme ();
+sg.cs.setConsensus (jalview.analysis.AAFrequency.calculate (sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth ()));
+this.refresh ();
+});
+Clazz.defineMethod (c$, "noColourmenuItem_actionPerformed",
+function () {
+this.getGroup ().cs = null;
+this.refresh ();
+});
+Clazz.defineMethod (c$, "conservationMenuItem_itemStateChanged",
+function () {
+var sg = this.getGroup ();
+if (sg.cs == null) {
+return;
+}if (this.conservationMenuItem.getState ()) {
+sg.cs.setConservation (jalview.analysis.Conservation.calculateConservation ("Group", jalview.schemes.ResidueProperties.propHash, 3, sg.getSequences (this.ap.av.getHiddenRepSequences ()), 0, this.ap.av.getAlignment ().getWidth (), false, this.ap.av.getConsPercGaps (), false));
+jalview.appletgui.SliderPanel.setConservationSlider (this.ap, sg.cs, sg.getName ());
+jalview.appletgui.SliderPanel.showConservationSlider ();
+} else {
+sg.cs.setConservation (null);
+}this.refresh ();
+});
+Clazz.defineMethod (c$, "getGroup",
+function () {
+var sg = this.ap.av.getSelectionGroup ();
+if (sg != null) {
+this.ap.av.getAlignment ().addGroup (sg);
+}return sg;
+});
+Clazz.defineMethod (c$, "unGroupMenuItem_actionPerformed",
+function () {
+var sg = this.ap.av.getSelectionGroup ();
+this.ap.av.getAlignment ().deleteGroup (sg);
+this.ap.av.setSelectionGroup (null);
+this.ap.paintAlignment (true);
+});
+Clazz.defineMethod (c$, "createGroupMenuItem_actionPerformed",
+function () {
+this.getGroup ();
+this.refresh ();
+});
+Clazz.defineMethod (c$, "showColourText_itemStateChanged",
+function () {
+this.getGroup ().setColourText (this.showColourText.getState ());
+this.refresh ();
+});
+Clazz.defineMethod (c$, "showText_itemStateChanged",
+function () {
+this.getGroup ().setDisplayText (this.showText.getState ());
+this.refresh ();
+});
+Clazz.defineMethod (c$, "makeReferenceSeq_actionPerformed",
+function () {
+if (!this.ap.av.getAlignment ().hasSeqrep ()) {
+this.ap.av.setDisplayReferenceSeq (true);
+this.ap.av.setColourByReferenceSeq (true);
+this.ap.av.getAlignment ().setSeqrep (this.seq);
+} else {
+if (this.ap.av.getAlignment ().getSeqrep () === this.seq) {
+this.ap.av.getAlignment ().setSeqrep (null);
+} else {
+this.ap.av.getAlignment ().setSeqrep (this.seq);
+}}this.refresh ();
+});
+Clazz.defineMethod (c$, "showNonconserved_itemStateChanged",
+function () {
+this.getGroup ().setShowNonconserved (this.displayNonconserved.getState ());
+this.refresh ();
+});
+Clazz.defineMethod (c$, "showBoxes_itemStateChanged",
+function () {
+this.getGroup ().setDisplayBoxes (this.showBoxes.getState ());
+this.refresh ();
+});
+Clazz.defineMethod (c$, "hideSequences",
+function (representGroup) {
+var sg = this.ap.av.getSelectionGroup ();
+if (sg == null || sg.getSize () < 1) {
+this.ap.av.hideSequence ( Clazz.newArray (-1, [this.seq]));
+return;
+}this.ap.av.setSelectionGroup (null);
+if (representGroup) {
+this.ap.av.hideRepSequences (this.seq, sg);
+return;
+}var gsize = sg.getSize ();
+var hseqs;
+hseqs = new Array (gsize);
+var index = 0;
+for (var i = 0; i < gsize; i++) {
+hseqs[index++] = sg.getSequenceAt (i);
+}
+this.ap.av.hideSequence (hseqs);
+this.ap.av.sendSelection ();
+}, "~B");
+Clazz.defineMethod (c$, "buildAnnotationTypesMenus",
+function (showMenu, hideMenu, forSequences) {
+showMenu.removeAll ();
+hideMenu.removeAll ();
+var all = java.util.Arrays.asList (["All"]);
+this.addAnnotationTypeToShowHide (showMenu, forSequences, "", all, true, true);
+this.addAnnotationTypeToShowHide (hideMenu, forSequences, "", all, true, false);
+showMenu.addSeparator ();
+hideMenu.addSeparator ();
+var annotations = this.ap.getAlignment ().getAlignmentAnnotation ();
+var shownTypes = new java.util.LinkedHashMap ();
+var hiddenTypes = new java.util.LinkedHashMap ();
+jalview.analysis.AlignmentAnnotationUtils.getShownHiddenTypes (shownTypes, hiddenTypes, jalview.analysis.AlignmentAnnotationUtils.asList (annotations), forSequences);
+for (var calcId, $calcId = hiddenTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {
+for (var type, $type = hiddenTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) {
+this.addAnnotationTypeToShowHide (showMenu, forSequences, calcId, type, false, true);
+}
+}
+showMenu.setEnabled (!hiddenTypes.isEmpty ());
+for (var calcId, $calcId = shownTypes.keySet ().iterator (); $calcId.hasNext () && ((calcId = $calcId.next ()) || true);) {
+for (var type, $type = shownTypes.get (calcId).iterator (); $type.hasNext () && ((type = $type.next ()) || true);) {
+this.addAnnotationTypeToShowHide (hideMenu, forSequences, calcId, type, false, false);
+}
+}
+hideMenu.setEnabled (!shownTypes.isEmpty ());
+}, "awt2swing.Menu,awt2swing.Menu,java.util.List");
+Clazz.defineMethod (c$, "addAnnotationTypeToShowHide",
+function (showOrHideMenu, forSequences, calcId, types, allTypes, actionIsShow) {
+var label = types.toString ();
+label = label.substring (1, label.length - 1);
+var item = new awt2swing.MenuItem (label);
+item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.APopupMenu$3") ? 0 : jalview.appletgui.APopupMenu.$APopupMenu$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.APopupMenu$3, this, Clazz.cloneFinals ("types", types, "forSequences", forSequences, "allTypes", allTypes, "actionIsShow", actionIsShow))));
+showOrHideMenu.add (item);
+}, "awt2swing.Menu,java.util.List,~S,java.util.List,~B,~B");
+c$.$APopupMenu$1$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$1", null, java.awt.event.ActionListener);
+Clazz.overrideMethod (c$, "actionPerformed",
+function (e) {
+this.b$["jalview.appletgui.APopupMenu"].addReferenceAnnotations_actionPerformed (this.f$.candidates);
+}, "java.awt.event.ActionEvent");
+c$ = Clazz.p0p ();
+};
+c$.$APopupMenu$2$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$2", null, java.awt.event.ActionListener);
+Clazz.overrideMethod (c$, "actionPerformed",
+function (e) {
+this.b$["jalview.appletgui.APopupMenu"].ap.alignFrame.showURL (this.f$.url, this.f$.target);
+}, "java.awt.event.ActionEvent");
+c$ = Clazz.p0p ();
+};
+c$.$APopupMenu$3$ = function () {
+Clazz.pu$h(self.c$);
+c$ = Clazz.declareAnonymous (jalview.appletgui, "APopupMenu$3", null, java.awt.event.ActionListener);
+Clazz.overrideMethod (c$, "actionPerformed",
+function (e) {
+jalview.analysis.AlignmentUtils.showOrHideSequenceAnnotations (this.b$["jalview.appletgui.APopupMenu"].ap.getAlignment (), this.f$.types, this.f$.forSequences, this.f$.allTypes, this.f$.actionIsShow);
+this.b$["jalview.appletgui.APopupMenu"].refresh ();
+}, "java.awt.event.ActionEvent");
+c$ = Clazz.p0p ();
+};
+Clazz.defineStatics (c$,
+"ALL_ANNOTATIONS", "All");
+});
git://source.jalview.org / jalviewjs.git / blobdiff