-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.io.AppletFormatAdapter;\r
-\r
-public class APopupMenu\r
- extends java.awt.PopupMenu implements ActionListener, ItemListener\r
-{\r
- Menu groupMenu = new Menu();\r
- MenuItem editGroupName = new MenuItem();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
-\r
- final AlignmentPanel ap;\r
- MenuItem unGroupMenuItem = new MenuItem();\r
- MenuItem nucleotideMenuItem = new MenuItem();\r
- Menu colourMenu = new Menu();\r
- CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
- CheckboxMenuItem showText = new CheckboxMenuItem();\r
- CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
- Menu editMenu = new Menu("Edit");\r
- MenuItem copy = new MenuItem("Copy (Jalview Only)");\r
- MenuItem cut = new MenuItem("Cut (Jalview Only)");\r
- MenuItem toUpper = new MenuItem("To Upper Case");\r
- MenuItem toLower = new MenuItem("To Lower Case");\r
- MenuItem toggleCase = new MenuItem("Toggle Case");\r
- Menu outputmenu = new Menu();\r
- Menu seqMenu = new Menu();\r
- MenuItem pdb = new MenuItem();\r
- MenuItem hideSeqs = new MenuItem();\r
- MenuItem repGroup = new MenuItem();\r
- MenuItem sequenceName = new MenuItem("Edit Name/Description");\r
- MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");\r
- MenuItem editSequence = new MenuItem("Edit Sequence");\r
-\r
- Sequence seq;\r
- MenuItem revealAll = new MenuItem();\r
- Menu menu1 = new Menu();\r
-\r
- public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
- {\r
- ///////////////////////////////////////////////////////////\r
- // If this is activated from the sequence panel, the user may want to\r
- // edit or annotate a particular residue. Therefore display the residue menu\r
- //\r
- // If from the IDPanel, we must display the sequence menu\r
- //////////////////////////////////////////////////////////\r
-\r
- this.ap = apanel;\r
- this.seq = seq;\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
- i++)\r
- {\r
- MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.\r
- WRITEABLE_FORMATS[i]);\r
-\r
- item.addActionListener(this);\r
- outputmenu.add(item);\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null && sg.getSize() > 0)\r
- {\r
- editGroupName.setLabel(sg.getName());\r
- showText.setState(sg.getDisplayText());\r
- showColourText.setState(sg.getColourText());\r
- showBoxes.setState(sg.getDisplayBoxes());\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- groupMenu.remove(unGroupMenuItem);\r
- }\r
-\r
- }\r
- else\r
- {\r
- remove(hideSeqs);\r
- remove(groupMenu);\r
- }\r
-\r
- if (links != null)\r
- {\r
- Menu linkMenu = new Menu("Link");\r
- MenuItem item;\r
- String link;\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- link = links.elementAt(i).toString();\r
- final String target = link.substring(0, link.indexOf("|"));\r
- item = new MenuItem(target);\r
-\r
- final String url;\r
-\r
- if (link.indexOf("$SEQUENCE_ID$") > -1)\r
- {\r
- String id = seq.getName();\r
- if (id.indexOf("|") > -1)\r
- {\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
- }\r
-\r
- url = link.substring(link.indexOf("|") + 1,\r
- link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
- }\r
- else\r
- {\r
- url = link.substring(link.lastIndexOf("|") + 1);\r
- }\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.alignFrame.showURL(url, target);\r
- }\r
- });\r
- linkMenu.add(item);\r
- }\r
- if (seq != null)\r
- {\r
- seqMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- if (seq != null)\r
- {\r
- seqMenu.setLabel(seq.getName());\r
- repGroup.setLabel("Represent Group with " + seq.getName());\r
- }\r
- else\r
- {\r
- remove(seqMenu);\r
- }\r
-\r
- if (!ap.av.hasHiddenRows)\r
- {\r
- remove(revealAll);\r
- }\r
- }\r
-\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (evt.getSource() == abovePIDColour)\r
- {\r
- abovePIDColour_itemStateChanged();\r
- }\r
- else if (evt.getSource() == showColourText)\r
- {\r
- showColourText_itemStateChanged();\r
- }\r
- else if (evt.getSource() == showText)\r
- {\r
- showText_itemStateChanged();\r
- }\r
- else if (evt.getSource() == showBoxes)\r
- {\r
- showBoxes_itemStateChanged();\r
- }\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- Object source = evt.getSource();\r
- if (source == clustalColour)\r
- {\r
- clustalColour_actionPerformed();\r
- }\r
- else if (source == zappoColour)\r
- {\r
- zappoColour_actionPerformed();\r
- }\r
- else if (source == taylorColour)\r
- {\r
- taylorColour_actionPerformed();\r
- }\r
- else if (source == hydrophobicityColour)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- else if (source == helixColour)\r
- {\r
- helixColour_actionPerformed();\r
- }\r
- else if (source == strandColour)\r
- {\r
- strandColour_actionPerformed();\r
- }\r
- else if (source == turnColour)\r
- {\r
- turnColour_actionPerformed();\r
- }\r
- else if (source == buriedColour)\r
- {\r
- buriedColour_actionPerformed();\r
- }\r
- else if (source == nucleotideMenuItem)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
-\r
- else if (source == userDefinedColour)\r
- {\r
- userDefinedColour_actionPerformed();\r
- }\r
- else if (source == PIDColour)\r
- {\r
- PIDColour_actionPerformed();\r
- }\r
- else if (source == BLOSUM62Colour)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- else if (source == noColourmenuItem)\r
- {\r
- noColourmenuItem_actionPerformed();\r
- }\r
- else if (source == conservationMenuItem)\r
- {\r
- conservationMenuItem_itemStateChanged();\r
- }\r
- else if (source == unGroupMenuItem)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
-\r
- else if (source == sequenceName)\r
- {\r
- editName();\r
- }\r
- else if (source == pdb)\r
- {\r
- addPDB();\r
- }\r
- else if (source == hideSeqs)\r
- {\r
- hideSequences(false);\r
- }\r
- else if (source == repGroup)\r
- {\r
- hideSequences(true);\r
- }\r
- else if (source == revealAll)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- }\r
-\r
- else if (source == editGroupName)\r
- {\r
- EditNameDialog dialog = new EditNameDialog(\r
- getGroup().getName(),\r
- getGroup().getDescription(),\r
- " Group Name",\r
- "Group Description",\r
- ap.alignFrame,\r
- "Edit Group Name / Description",\r
- 500,100, true);\r
-\r
- if (dialog.accept)\r
- {\r
- getGroup().setName(dialog.getName().replace(' ', '_'));\r
- getGroup().setDescription(dialog.getDescription());\r
- }\r
-\r
- }\r
- else if (source == copy)\r
- {\r
- ap.alignFrame.copy_actionPerformed();\r
- }\r
- else if (source == cut)\r
- {\r
- ap.alignFrame.cut_actionPerformed();\r
- }\r
- else if(source == editSequence)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if(sg!=null)\r
- {\r
- if (seq == null)\r
- seq = (Sequence) sg.getSequenceAt(0);\r
-\r
- EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1),\r
- null,\r
- "Edit Sequence ",\r
- null,\r
-\r
- ap.alignFrame,\r
- "Edit Sequence",\r
- 500, 100, true);\r
-\r
- if (dialog.accept)\r
- {\r
- EditCommand editCommand = new EditCommand(\r
- "Edit Sequences", EditCommand.REPLACE,\r
- dialog.getName(),\r
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(editCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- }\r
- }\r
- }\r
- else if (source == toUpper || source == toLower || source == toggleCase)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- Vector regions = new Vector();\r
- if (sg != null)\r
- {\r
- int start = sg.getStartRes();\r
- int end = sg.getEndRes() + 1;\r
-\r
- do\r
- {\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- if (start == 0)\r
- {\r
- start = ap.av.colSel.adjustForHiddenColumns(start);\r
- }\r
-\r
- end = ap.av.colSel.getHiddenBoundaryRight(start);\r
- if (start == end)\r
- {\r
- end = sg.getEndRes() + 1;\r
- }\r
- if (end > sg.getEndRes())\r
- {\r
- end = sg.getEndRes() + 1;\r
- }\r
- }\r
-\r
- regions.addElement(new int[]\r
- {start, end});\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- start = ap.av.colSel.adjustForHiddenColumns(end);\r
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
- }\r
- }\r
- while (end < sg.getEndRes());\r
-\r
- int[][] startEnd = new int[regions.size()][2];\r
- for (int i = 0; i < regions.size(); i++)\r
- {\r
- startEnd[i] = (int[]) regions.elementAt(i);\r
- }\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggleCase)\r
- {\r
- description = "Toggle Case";\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == toUpper)\r
- {\r
- description = "To Upper Case";\r
- caseChange = ChangeCaseCommand.TO_UPPER;\r
- }\r
- else\r
- {\r
- description = "To Lower Case";\r
- caseChange = ChangeCaseCommand.TO_LOWER;\r
- }\r
-\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- startEnd, caseChange\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(caseCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
-\r
- }\r
- }\r
- else if(source == sequenceFeature)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- int gSize = sg.getSize();\r
- SequenceI[] seqs = new SequenceI[gSize];\r
- SequenceFeature[] features = new SequenceFeature[gSize];\r
-\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- seqs[i] = sg.getSequenceAt(i);\r
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
- int end = sg.findEndRes(sg.getSequenceAt(i));\r
- features[i] = new SequenceFeature(null, null, null, start, end,\r
- "Jalview");\r
- }\r
-\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .amendFeatures(seqs, features, true, ap))\r
- {\r
- ap.alignFrame.sequenceFeatures.setState(true);\r
- ap.av.showSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
- }\r
- else\r
- {\r
- outputText(evt);\r
- }\r
-\r
- }\r
-\r
- void outputText(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
-\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Selection output - " + e.getActionCommand(),\r
- 600, 500);\r
-\r
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- new Alignment(ap.av.getSelectionAsNewSequence()),\r
- ap.av.showJVSuffix));\r
-\r
- }\r
-\r
- void editName()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(\r
- seq.getName(),\r
- seq.getDescription(),\r
- " Sequence Name",\r
- "Sequence Description",\r
- ap.alignFrame,\r
- "Edit Sequence Name / Description",\r
- 500,100, true);\r
-\r
- if (dialog.accept)\r
- {\r
- seq.setName(dialog.getName());\r
- seq.setDescription(dialog.getDescription());\r
- ap.paintAlignment(false);\r
- }\r
- }\r
-\r
- void addPDB()\r
- {\r
- if(seq.getPDBId()!=null)\r
- {\r
- PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();\r
-\r
- if ( ap.av.applet.jmolAvailable )\r
- new jalview.appletgui.AppletJmol(entry,\r
- new Sequence[]{seq},\r
- null,\r
- ap,\r
- AppletFormatAdapter.URL);\r
- else\r
- new MCview.AppletPDBViewer(entry,\r
- new Sequence[]{seq},\r
- null,\r
- ap,\r
- AppletFormatAdapter.URL);\r
-\r
- }\r
- else\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
- cap.setText("Paste your PDB file here.");\r
- cap.setPDBImport(seq);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Selection");\r
- sequenceFeature.addActionListener(this);\r
-\r
- editGroupName.addActionListener(this);\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(this);\r
-\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(this);\r
- conservationMenuItem.addItemListener(this);\r
- abovePIDColour.addItemListener(this);\r
- colourMenu.setLabel("Group Colour");\r
- showBoxes.setLabel("Boxes");\r
- showBoxes.setState(true);\r
- showBoxes.addItemListener(this);\r
- sequenceName.addActionListener(this);\r
-\r
- showText.setLabel("Text");\r
- showText.addItemListener(this);\r
- showColourText.setLabel("Colour Text");\r
- showColourText.addItemListener(this);\r
- outputmenu.setLabel("Output to Textbox...");\r
- seqMenu.setLabel("Sequence");\r
- pdb.setLabel("View PDB Structure");\r
- hideSeqs.setLabel("Hide Sequences");\r
- repGroup.setLabel("Represent Group with");\r
- revealAll.setLabel("Reveal All");\r
- menu1.setLabel("Group");\r
- add(groupMenu);\r
- this.add(seqMenu);\r
- this.add(hideSeqs);\r
- this.add(revealAll);\r
- groupMenu.add(editGroupName);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputmenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(menu1);\r
-\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideMenuItem);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
-\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(this);\r
-\r
- clustalColour.setLabel("Clustalx colours");\r
- clustalColour.addActionListener(this);\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(this);\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(this);\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(this);\r
- helixColour.setLabel("Helix propensity");\r
- helixColour.addActionListener(this);\r
- strandColour.setLabel("Strand propensity");\r
- strandColour.addActionListener(this);\r
- turnColour.setLabel("Turn propensity");\r
- turnColour.addActionListener(this);\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(this);\r
- abovePIDColour.setLabel("Above % Identity");\r
-\r
- userDefinedColour.setLabel("User Defined");\r
- userDefinedColour.addActionListener(this);\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(this);\r
- BLOSUM62Colour.setLabel("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(this);\r
- conservationMenuItem.setLabel("Conservation");\r
-\r
- editMenu.add(copy);\r
- copy.addActionListener(this);\r
- editMenu.add(cut);\r
- cut.addActionListener(this);\r
-\r
- editMenu.add(editSequence);\r
- editSequence.addActionListener(this);\r
-\r
- editMenu.add(toUpper);\r
- toUpper.addActionListener(this);\r
- editMenu.add(toLower);\r
- toLower.addActionListener(this);\r
- editMenu.add(toggleCase);\r
- seqMenu.add(sequenceName);\r
- seqMenu.add(pdb);\r
- seqMenu.add(repGroup);\r
- menu1.add(unGroupMenuItem);\r
- menu1.add(colourMenu);\r
- menu1.add(showBoxes);\r
- menu1.add(showText);\r
- menu1.add(showColourText);\r
- toggleCase.addActionListener(this);\r
- pdb.addActionListener(this);\r
- hideSeqs.addActionListener(this);\r
- repGroup.addActionListener(this);\r
- revealAll.addActionListener(this);\r
- }\r
-\r
- void refresh()\r
- {\r
- ap.paintAlignment(true);\r
- }\r
-\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
- ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void abovePIDColour_itemStateChanged()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (abovePIDColour.getState())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences), 0,\r
- ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
-\r
- }\r
- else // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
-\r
- }\r
-\r
- protected void userDefinedColour_actionPerformed()\r
- {\r
- new UserDefinedColours(ap, getGroup());\r
- }\r
-\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences), 0,\r
- ap.av.alignment.getWidth()));\r
- refresh();\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences), 0,\r
- ap.av.alignment.getWidth()));\r
-\r
- refresh();\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- protected void conservationMenuItem_itemStateChanged()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (conservationMenuItem.getState())\r
- {\r
-\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.\r
- hiddenRepSequences), 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- // this method won't add a new group if it already exists\r
- if (sg != null)\r
- {\r
- ap.av.alignment.addGroup(sg);\r
- }\r
-\r
- return sg;\r
- }\r
-\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.paintAlignment(true);\r
- }\r
-\r
- public void showColourText_itemStateChanged()\r
- {\r
- getGroup().setColourText(showColourText.getState());\r
- refresh();\r
- }\r
-\r
- public void showText_itemStateChanged()\r
- {\r
- getGroup().setDisplayText(showText.getState());\r
- refresh();\r
- }\r
-\r
- public void showBoxes_itemStateChanged()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.getState());\r
- refresh();\r
- }\r
-\r
- void hideSequences(boolean representGroup)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null || sg.getSize() < 1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]\r
- {seq});\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(seq, sg);\r
-\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize();\r
- SequenceI[] hseqs;\r
-\r
- hseqs = new SequenceI[gsize];\r
-\r
- int index = 0;\r
- for (int i = 0; i < gsize; i++)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
-\r
- ap.av.hideSequence(hseqs);\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
+
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+public class APopupMenu extends java.awt.PopupMenu implements
+ ActionListener, ItemListener
+{
+ private static final String ALL_ANNOTATIONS = "All";
+
+ Menu groupMenu = new Menu();
+
+ MenuItem editGroupName = new MenuItem();
+
+ protected MenuItem clustalColour = new MenuItem();
+
+ protected MenuItem zappoColour = new MenuItem();
+
+ protected MenuItem taylorColour = new MenuItem();
+
+ protected MenuItem hydrophobicityColour = new MenuItem();
+
+ protected MenuItem helixColour = new MenuItem();
+
+ protected MenuItem strandColour = new MenuItem();
+
+ protected MenuItem turnColour = new MenuItem();
+
+ protected MenuItem buriedColour = new MenuItem();
+
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
+ protected MenuItem userDefinedColour = new MenuItem();
+
+ protected MenuItem PIDColour = new MenuItem();
+
+ protected MenuItem BLOSUM62Colour = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+
+ final AlignmentPanel ap;
+
+ MenuItem unGroupMenuItem = new MenuItem();
+
+ MenuItem createGroupMenuItem = new MenuItem();
+
+ MenuItem nucleotideMenuItem = new MenuItem();
+
+ Menu colourMenu = new Menu();
+
+ CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+
+ CheckboxMenuItem showText = new CheckboxMenuItem();
+
+ CheckboxMenuItem showColourText = new CheckboxMenuItem();
+
+ CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+
+ Menu seqShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu seqHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem seqAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu groupShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu groupHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem groupAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
+
+ MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
+
+ MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
+
+ MenuItem toUpper = new MenuItem(
+ MessageManager.getString("label.to_upper_case"));
+
+ MenuItem toLower = new MenuItem(
+ MessageManager.getString("label.to_lower_case"));
+
+ MenuItem toggleCase = new MenuItem(
+ MessageManager.getString("label.toggle_case"));
+
+ Menu outputmenu = new Menu();
+
+ Menu seqMenu = new Menu();
+
+ MenuItem pdb = new MenuItem();
+
+ MenuItem hideSeqs = new MenuItem();
+
+ MenuItem repGroup = new MenuItem();
+
+ MenuItem sequenceName = new MenuItem(
+ MessageManager.getString("label.edit_name_description"));
+
+ MenuItem sequenceFeature = new MenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
+
+ MenuItem editSequence = new MenuItem(
+ MessageManager.getString("label.edit_sequence"));
+
+ MenuItem sequenceDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details"));
+
+ MenuItem selSeqDetails = new MenuItem(
+ MessageManager.getString("label.sequence_details"));
+
+ MenuItem makeReferenceSeq = new MenuItem();
+
+ SequenceI seq;
+
+ MenuItem revealAll = new MenuItem();
+
+ MenuItem revealSeq = new MenuItem();
+
+ /**
+ * index of sequence to be revealed
+ */
+ int revealSeq_index = -1;
+
+ Menu menu1 = new Menu();
+
+ public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
+ Vector<String> links)
+ {
+ // /////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ // ////////////////////////////////////////////////////////
+
+ this.ap = apanel;
+ this.seq = seq;
+
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ MenuItem item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+
+ item.addActionListener(this);
+ outputmenu.add(item);
+ }
+
+ buildAnnotationSubmenus();
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null && sg.getSize() > 0)
+ {
+ editGroupName.setLabel(MessageManager.formatMessage(
+ "label.name_param", new Object[] { sg.getName() }));
+ showText.setState(sg.getDisplayText());
+ showColourText.setState(sg.getColourText());
+ showBoxes.setState(sg.getDisplayBoxes());
+ displayNonconserved.setState(sg.getShowNonconserved());
+ if (!ap.av.getAlignment().getGroups().contains(sg))
+ {
+ menu1.setLabel(MessageManager.getString("action.edit_new_group"));
+ groupMenu.remove(unGroupMenuItem);
+ }
+ else
+ {
+ menu1.setLabel(MessageManager.getString("action.edit_group"));
+ groupMenu.remove(createGroupMenuItem);
+ }
+
+ }
+ else
+ {
+ remove(hideSeqs);
+ remove(groupMenu);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+ for (int i = 0; i < links.size(); i++)
+ {
+ String link = links.elementAt(i);
+ UrlLink urlLink = new UrlLink(link);
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String target = urlLink.getTarget(); // link.substring(0,
+ // link.indexOf("|"));
+ final String label = urlLink.getLabel();
+ if (seq != null && urlLink.isDynamic())
+ {
+
+ // collect matching db-refs
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[] { target });
+ // collect id string too
+ String id = seq.getName();
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
+ {
+ descr = null;
+ }
+ if (dbr != null)
+ {
+ for (int r = 0; r < dbr.length; r++)
+ {
+ if (id != null && dbr[r].getAccessionId().equals(id))
+ {
+ // suppress duplicate link creation for the bare sequence ID
+ // string with this link
+ id = null;
+ }
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ }
+ }
+ }
+ }
+ if (id != null)
+ {
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);
+ }
+ // Now construct URLs from description but only try to do it for regex
+ // URL links
+ if (descr != null && urlLink.getRegexReplace() != null)
+ {
+ // create link for this URL from description only if regex matches
+ String[] urls = urlLink.makeUrls(descr, true);
+ if (urls != null)
+ {
+ for (int u = 0; u < urls.length; u += 2)
+ {
+ addshowLink(linkMenu, label, urls[u + 1]);
+ }
+ }
+ }
+ }
+ else
+ {
+ addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
+ }
+ /*
+ * final String url;
+ *
+ * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
+ * string and any matching database reference accessions String url_pref
+ * = link.substring(link.indexOf("|") + 1,
+ * link.indexOf("$SEQUENCE_ID$"));
+ *
+ * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ * // collect matching db-refs DBRefEntry[] dbr =
+ * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
+ * String[]{target}); // collect id string too String id =
+ * seq.getName(); if (id.indexOf("|") > -1) { id =
+ * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
+ * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
+ * suppress duplicate link creation for the bare sequence ID string with
+ * this link id = null; } addshowLink(linkMenu,
+ * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
+ * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
+ * create Bare ID link for this RUL addshowLink(linkMenu, target,
+ * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
+ * link.substring(link.lastIndexOf("|")+1)); }
+ */
+ }
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+ // TODO: add group link menu entry here
+ if (seq != null)
+ {
+ seqMenu.setLabel(seq.getName());
+ if (seq == ap.av.getAlignment().getSeqrep())
+ {
+ makeReferenceSeq.setLabel(MessageManager
+ .getString("action.unmark_as_reference"));// Unmark
+ // representative");
+ }
+ else
+ {
+ makeReferenceSeq.setLabel(MessageManager
+ .getString("action.set_as_reference")); // );
+ }
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new Object[] { seq.getName() }));
+ }
+ else
+ {
+ remove(seqMenu);
+ }
+
+ if (!ap.av.hasHiddenRows())
+ {
+ remove(revealAll);
+ remove(revealSeq);
+ }
+ else
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ revealSeq_index = index;
+ }
+ else
+ {
+ remove(revealSeq);
+ }
+ }
+ }
+
+ /**
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment.
+ */
+ private void buildAnnotationSubmenus()
+ {
+ /*
+ * First for the currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * and repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()
+ .getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+ }
+
+ /**
+ * Determine whether or not to enable 'add reference annotations' menu item.
+ * It is enable if there are any annotations, on any of the selected
+ * sequences, which are not yet on the alignment (visible or not).
+ *
+ * @param menu
+ * @param forSequences
+ */
+ private void configureReferenceAnnotationsMenu(MenuItem menuItem,
+ List<SequenceI> forSequences)
+ {
+ menuItem.setEnabled(false);
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ Map<String, String> tipEntries = new TreeMap<String, String>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its action.
+ */
+ menuItem.setEnabled(true);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
+ refresh();
+ }
+
+ /**
+ * add a show URL menu item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param target
+ * - menu label string
+ * @param url
+ * - url to open
+ */
+ private void addshowLink(Menu linkMenu, final String target,
+ final String url)
+ {
+ addshowLink(linkMenu, target, target, url);
+ }
+
+ /**
+ * add a show URL menu item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param target
+ * - URL target window
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
+ */
+ private void addshowLink(Menu linkMenu, final String target,
+ final String label, final String url)
+ {
+ MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.showURL(url, target);
+ }
+ });
+ linkMenu.add(item);
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == abovePIDColour)
+ {
+ abovePIDColour_itemStateChanged();
+ }
+ else if (evt.getSource() == showColourText)
+ {
+ showColourText_itemStateChanged();
+ }
+ else if (evt.getSource() == showText)
+ {
+ showText_itemStateChanged();
+ }
+ else if (evt.getSource() == showBoxes)
+ {
+ showBoxes_itemStateChanged();
+ }
+ else if (evt.getSource() == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+ if (source == clustalColour)
+ {
+ clustalColour_actionPerformed();
+ }
+ else if (source == zappoColour)
+ {
+ zappoColour_actionPerformed();
+ }
+ else if (source == taylorColour)
+ {
+ taylorColour_actionPerformed();
+ }
+ else if (source == hydrophobicityColour)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ else if (source == helixColour)
+ {
+ helixColour_actionPerformed();
+ }
+ else if (source == strandColour)
+ {
+ strandColour_actionPerformed();
+ }
+ else if (source == turnColour)
+ {
+ turnColour_actionPerformed();
+ }
+ else if (source == buriedColour)
+ {
+ buriedColour_actionPerformed();
+ }
+ else if (source == nucleotideMenuItem)
+ {
+ nucleotideMenuItem_actionPerformed();
+ }
+
+ else if (source == userDefinedColour)
+ {
+ userDefinedColour_actionPerformed();
+ }
+ else if (source == PIDColour)
+ {
+ PIDColour_actionPerformed();
+ }
+ else if (source == BLOSUM62Colour)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ else if (source == noColourmenuItem)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ else if (source == conservationMenuItem)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == unGroupMenuItem)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
+ else if (source == sequenceName)
+ {
+ editName();
+ }
+ else if (source == makeReferenceSeq)
+ {
+ makeReferenceSeq_actionPerformed();
+ }
+ else if (source == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
+ else if (source == pdb)
+ {
+ addPDB();
+ }
+ else if (source == hideSeqs)
+ {
+ hideSequences(false);
+ }
+ else if (source == repGroup)
+ {
+ hideSequences(true);
+ }
+ else if (source == revealSeq)
+ {
+ ap.av.showSequence(revealSeq_index);
+ }
+ else if (source == revealAll)
+ {
+ ap.av.showAllHiddenSeqs();
+ }
+
+ else if (source == editGroupName)
+ {
+ EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+ getGroup().getDescription(), " Group Name",
+ "Group Description", ap.alignFrame,
+ "Edit Group Name / Description", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ getGroup().setName(dialog.getName().replace(' ', '_'));
+ getGroup().setDescription(dialog.getDescription());
+ }
+
+ }
+ else if (source == copy)
+ {
+ ap.alignFrame.copy_actionPerformed();
+ }
+ else if (source == cut)
+ {
+ ap.alignFrame.cut_actionPerformed();
+ }
+ else if (source == editSequence)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ if (seq == null)
+ {
+ seq = sg.getSequenceAt(0);
+ }
+
+ EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
+ sg.getStartRes(), sg.getEndRes() + 1), null,
+ "Edit Sequence ", null,
+
+ ap.alignFrame, "Edit Sequence", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE, dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+ }
+ }
+ }
+ else if (source == toUpper || source == toLower || source == toggleCase)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
+ {
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ String description;
+ int caseChange;
+
+ if (source == toggleCase)
+ {
+ description = "Toggle Case";
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == toUpper)
+ {
+ description = "To Upper Case";
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
+ description = "To Lower Case";
+ caseChange = ChangeCaseCommand.TO_LOWER;
+ }
+
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
+
+ ap.alignFrame.addHistoryItem(caseCommand);
+
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
+
+ }
+ }
+ else if (source == sequenceFeature)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
+ for (int i = 0; i < gSize; i++)
+ {
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+ int end = sg.findEndRes(sg.getSequenceAt(i));
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i);
+ features[rsize] = new SequenceFeature(null, null, null, start,
+ end, "Jalview");
+ rsize++;
+ }
+ }
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ ap.av.setShowSequenceFeatures(true);
+ ;
+ ap.highlightSearchResults(null);
+ }
+ }
+ else
+ {
+ outputText(evt);
+ }
+
+ }
+
+ void outputText(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.selection_output_command",
+ new Object[] { e.getActionCommand() }), 600, 500);
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
+ // now returns a full copy of sequence data
+ // TODO consider using getSequenceSelection instead here
+
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
+
+ }
+
+ protected void showSequenceSelectionDetails()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void showSequenceDetails()
+ {
+ createSequenceDetailsReport(new SequenceI[] { seq });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append(MessageManager.formatMessage(
+ "label.annotation_for_displayid",
+ new Object[] { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+ .getMinMax() : null);
+ contents.append("</p>");
+ }
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 600, 500);
+ cap.setText(MessageManager.formatMessage("label.html_content",
+ new Object[] { contents.toString() }));
+ }
+
+ void editName()
+ {
+ EditNameDialog dialog = new EditNameDialog(seq.getName(),
+ seq.getDescription(), " Sequence Name",
+ "Sequence Description", ap.alignFrame,
+ "Edit Sequence Name / Description", 500, 100, true);
+
+ if (dialog.accept)
+ {
+ seq.setName(dialog.getName());
+ seq.setDescription(dialog.getDescription());
+ ap.paintAlignment(false);
+ }
+ }
+
+ void addPDB()
+ {
+ if (seq.getAllPDBEntries() != null)
+ {
+ PDBEntry entry = seq.getAllPDBEntries().firstElement();
+
+ if (ap.av.applet.jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+ null, ap, AppletFormatAdapter.URL);
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, AppletFormatAdapter.URL);
+ }
+
+ }
+ else
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));
+ cap.setPDBImport(seq);
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence",
+ new Object[] { seq.getName() }), 400, 300);
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ groupMenu.setLabel(MessageManager.getString("label.selection"));
+ sequenceFeature.addActionListener(this);
+
+ editGroupName.addActionListener(this);
+ unGroupMenuItem.setLabel(MessageManager
+ .getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(this);
+
+ createGroupMenuItem.setLabel(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
+ nucleotideMenuItem.setLabel(MessageManager
+ .getString("label.nucleotide"));
+ nucleotideMenuItem.addActionListener(this);
+ conservationMenuItem.addItemListener(this);
+ abovePIDColour.addItemListener(this);
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
+ showBoxes.setState(true);
+ showBoxes.addItemListener(this);
+ sequenceName.addActionListener(this);
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
+ displayNonconserved.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
+ displayNonconserved.setState(false);
+ displayNonconserved.addItemListener(this);
+ showText.setLabel(MessageManager.getString("action.text"));
+ showText.addItemListener(this);
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));
+ showColourText.addItemListener(this);
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
+ repGroup.setLabel(MessageManager.formatMessage(
+ "label.represent_group_with", new Object[] { "" }));
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
+ menu1.setLabel(MessageManager.getString("label.group") + ":");
+ add(groupMenu);
+ this.add(seqMenu);
+ this.add(hideSeqs);
+ this.add(revealSeq);
+ this.add(revealAll);
+ // groupMenu.add(selSeqDetails);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputmenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
+ groupMenu.add(menu1);
+
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(this);
+
+ clustalColour.setLabel(MessageManager
+ .getString("label.clustalx_colours"));
+ clustalColour.addActionListener(this);
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(this);
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(this);
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(this);
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(this);
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(this);
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(this);
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_percentage"));
+
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.setLabel("BLOSUM62");
+ BLOSUM62Colour.addActionListener(this);
+ conservationMenuItem.setLabel(MessageManager
+ .getString("label.conservation"));
+
+ editMenu.add(copy);
+ copy.addActionListener(this);
+ editMenu.add(cut);
+ cut.addActionListener(this);
+
+ editMenu.add(editSequence);
+ editSequence.addActionListener(this);
+
+ editMenu.add(toUpper);
+ toUpper.addActionListener(this);
+ editMenu.add(toLower);
+ toLower.addActionListener(this);
+ editMenu.add(toggleCase);
+ seqMenu.add(seqShowAnnotationsMenu);
+ seqMenu.add(seqHideAnnotationsMenu);
+ seqMenu.add(seqAddReferenceAnnotations);
+ seqMenu.add(sequenceName);
+ seqMenu.add(makeReferenceSeq);
+ // seqMenu.add(sequenceDetails);
+
+ if (!ap.av.applet.useXtrnalSviewer)
+ {
+ seqMenu.add(pdb);
+ }
+ seqMenu.add(repGroup);
+ menu1.add(editGroupName);
+ menu1.add(colourMenu);
+ menu1.add(showBoxes);
+ menu1.add(showText);
+ menu1.add(showColourText);
+ menu1.add(displayNonconserved);
+ toggleCase.addActionListener(this);
+ pdb.addActionListener(this);
+ hideSeqs.addActionListener(this);
+ repGroup.addActionListener(this);
+ revealAll.addActionListener(this);
+ revealSeq.addActionListener(this);
+ makeReferenceSeq.addActionListener(this);
+ }
+
+ void refresh()
+ {
+ ap.paintAlignment(true);
+ }
+
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+ refresh();
+ }
+
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ZappoColourScheme();
+ refresh();
+ }
+
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new TaylorColourScheme();
+ refresh();
+ }
+
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new HydrophobicColourScheme();
+ refresh();
+ }
+
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new HelixColourScheme();
+ refresh();
+ }
+
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new StrandColourScheme();
+ refresh();
+ }
+
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new TurnColourScheme();
+ refresh();
+ }
+
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new BuriedColourScheme();
+ refresh();
+ }
+
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new NucleotideColourScheme();
+ refresh();
+ }
+
+ protected void abovePIDColour_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (abovePIDColour.getState())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
+
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+
+ }
+ else
+ // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ }
+
+ refresh();
+
+ }
+
+ protected void userDefinedColour_actionPerformed()
+ {
+ new UserDefinedColours(ap, getGroup());
+ }
+
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ refresh();
+ }
+
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+
+ refresh();
+ }
+
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ protected void conservationMenuItem_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (conservationMenuItem.getState())
+ {
+
+ sg.cs.setConservation(Conservation.calculateConservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment()
+ .getWidth(), false, ap.av.getConsPercGaps(), false));
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ // this method won't add a new group if it already exists
+ if (sg != null)
+ {
+ ap.av.getAlignment().addGroup(sg);
+ }
+
+ return sg;
+ }
+
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.getAlignment().deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ ap.paintAlignment(true);
+ }
+
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly create group
+ refresh();
+ }
+
+ public void showColourText_itemStateChanged()
+ {
+ getGroup().setColourText(showColourText.getState());
+ refresh();
+ }
+
+ public void showText_itemStateChanged()
+ {
+ getGroup().setDisplayText(showText.getState());
+ refresh();
+ }
+
+ public void makeReferenceSeq_actionPerformed()
+ {
+ if (!ap.av.getAlignment().hasSeqrep())
+ {
+ // initialise the display flags so the user sees something happen
+ ap.av.setDisplayReferenceSeq(true);
+ ap.av.setColourByReferenceSeq(true);
+ ap.av.getAlignment().setSeqrep(seq);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == seq)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(seq);
+ }
+ }
+ refresh();
+ }
+
+ public void showNonconserved_itemStateChanged()
+ {
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());
+ refresh();
+ }
+
+ public void showBoxes_itemStateChanged()
+ {
+ getGroup().setDisplayBoxes(showBoxes.getState());
+ refresh();
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null || sg.getSize() < 1)
+ {
+ ap.av.hideSequence(new SequenceI[] { seq });
+ return;
+ }
+
+ ap.av.setSelectionGroup(null);
+
+ if (representGroup)
+ {
+ ap.av.hideRepSequences(seq, sg);
+
+ return;
+ }
+
+ int gsize = sg.getSize();
+ SequenceI[] hseqs;
+
+ hseqs = new SequenceI[gsize];
+
+ int index = 0;
+ for (int i = 0; i < gsize; i++)
+ {
+ hseqs[index++] = sg.getSequenceAt(i);
+ }
+
+ ap.av.hideSequence(hseqs);
+ ap.av.sendSelection();
+ }
+
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ * <p>
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff