-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class APopupMenu extends java.awt.PopupMenu\r
-{\r
- Menu groupMenu = new Menu();\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
-\r
- AlignmentPanel ap;\r
- Menu sequenceMenu = new Menu();\r
- MenuItem sequenceName = new MenuItem();\r
- Sequence sequence;\r
- MenuItem unGroupMenuItem = new MenuItem();\r
- MenuItem nucleotideMenuItem = new MenuItem();\r
-\r
- public APopupMenu(AlignmentPanel ap, Sequence seq)\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 = ap;\r
- sequence = seq;\r
-\r
- try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
-\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
- groupMenu.remove(unGroupMenuItem);\r
-\r
- if(seq==null)\r
- remove(sequenceMenu);\r
-\r
-\r
- }\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Define");\r
-\r
- sequenceMenu.setLabel("Sequence");\r
- sequenceName.setLabel("Edit name");\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
- add(groupMenu);\r
- this.add(sequenceMenu);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(noColourmenuItem);\r
- groupMenu.add(clustalColour);\r
- groupMenu.add(BLOSUM62Colour);\r
- groupMenu.add(PIDColour);\r
-\r
- groupMenu.add(zappoColour);\r
- groupMenu.add(taylorColour);\r
- groupMenu.add(hydrophobicityColour);\r
- groupMenu.add(helixColour);\r
- groupMenu.add(strandColour);\r
- groupMenu.add(turnColour);\r
- groupMenu.add(buriedColour);\r
- groupMenu.add(nucleotideMenuItem);\r
-\r
- groupMenu.add(userDefinedColour);\r
-\r
- groupMenu.addSeparator();\r
- groupMenu.add(abovePIDColour);\r
- groupMenu.add(conservationMenuItem);\r
-\r
- sequenceMenu.add(sequenceName);\r
-\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
- clustalColour.setLabel("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setLabel("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setLabel("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setLabel("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- abovePIDColour.setLabel("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setLabel("User Defined");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setLabel("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setLabel("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
-\r
- }\r
-\r
- void refresh()\r
- {\r
- SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
-\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
-\r
-\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (abovePIDColour.getState())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
-\r
- SliderPanel.showPIDSlider();\r
-\r
-\r
- }\r
- else // remove PIDColouring\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
- }\r
-\r
- refresh();\r
-\r
- }\r
-\r
-\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
- }\r
-\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
-\r
- refresh();\r
- }\r
-\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if(conservationMenuItem.getState())\r
- {\r
-\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
-\r
- sg.cs = ccs;\r
-\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
-\r
- refresh();\r
- }\r
-\r
-\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.elementAt(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
-\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
- ap.av.alignment.addGroup(sg);\r
-\r
- return sg;\r
- }\r
-\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.bin.JalviewLite;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+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.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+public class APopupMenu extends java.awt.PopupMenu
+ implements ActionListener, ItemListener
+{
+ Menu groupMenu = new Menu();
+
+ MenuItem editGroupName = new MenuItem();
+
+ CheckboxMenuItem noColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem clustalColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem zappoColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem taylorColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem helixColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem strandColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem turnColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
+
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
+
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
+
+ protected MenuItem userDefinedColour = new MenuItem();
+
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
+ MenuItem modifyPID = new MenuItem();
+
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+
+ MenuItem modifyConservation = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
+ final AlignmentPanel ap;
+
+ MenuItem unGroupMenuItem = new MenuItem();
+
+ MenuItem createGroupMenuItem = 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,
+ List<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 (String ff : FileFormats.getInstance().getWritableFormats(true))
+ {
+ MenuItem item = new MenuItem(ff);
+
+ item.addActionListener(this);
+ outputmenu.add(item);
+ }
+
+ buildAnnotationSubmenus();
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null && sg.getSize() > 0)
+ {
+ if (sg.isNucleotide())
+ {
+ conservationColour.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
+ }
+ else
+ {
+ purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
+ }
+ 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);
+ if (sg.cs != null)
+ {
+ abovePIDColour.setState(sg.cs.getThreshold() > 0);
+ conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
+ }
+ }
+ setSelectedColour(sg.cs);
+ }
+ else
+ {
+ remove(hideSeqs);
+ remove(groupMenu);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+ addFeatureLinks(seq, links);
+ }
+
+ // 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);
+ }
+ }
+ }
+
+ /**
+ * Select the menu item (if any) matching the current colour scheme. This
+ * works by matching the menu item name (not display text) to the canonical
+ * name of the colour scheme.
+ *
+ * @param cs
+ */
+ protected void setSelectedColour(ResidueShaderI cs)
+ {
+ if (cs == null || cs.getColourScheme() == null)
+ {
+ noColour.setState(true);
+ }
+ else
+ {
+ String name = cs.getColourScheme().getSchemeName();
+ for (int i = 0; i < colourMenu.getItemCount(); i++)
+ {
+ MenuItem item = colourMenu.getItem(i);
+ if (item instanceof CheckboxMenuItem)
+ {
+ if (name.equals(item.getName()))
+ {
+ ((CheckboxMenuItem) item).setState(true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ *
+ * @param seq
+ * @param links
+ */
+ void addFeatureLinks(final SequenceI seq, List<String> links)
+ {
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
+
+ for (String link : links)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + link + "': "
+ + foo.getMessage());
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ addshowLinks(linkMenu, linkset.values());
+
+ // disable link menu if there are no valid entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ linkMenu.setEnabled(true);
+ }
+ else
+ {
+ linkMenu.setEnabled(false);
+ }
+
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+
+ }
+
+ private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
+ /**
+ * 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.
+ */
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+ 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.showURL(url, target);
+ }
+ });
+ linkMenu.add(item);
+ }
+
+ /**
+ * Actions on selecting / unselecting a checkbox menu item
+ */
+ @Override
+ public void itemStateChanged(ItemEvent evt)
+ {
+ Object source = evt.getSource();
+ if (source == noColour)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ else if (source == clustalColour)
+ {
+ clustalColour_actionPerformed();
+ }
+ else if (source == BLOSUM62Colour)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ else if (evt.getSource() == PIDColour)
+ {
+ PIDColour_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 == nucleotideColour)
+ {
+ nucleotideMenuItem_actionPerformed();
+ }
+ else if (source == purinePyrimidineColour)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ else if (source == abovePIDColour)
+ {
+ abovePIDColour_itemStateChanged();
+ }
+ else if (source == conservationColour)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == showColourText)
+ {
+ showColourText_itemStateChanged();
+ }
+ else if (source == showText)
+ {
+ showText_itemStateChanged();
+ }
+ else if (source == showBoxes)
+ {
+ showBoxes_itemStateChanged();
+ }
+ else if (source == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
+ }
+
+ /**
+ * Actions on clicking a menu item
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+ if (source == userDefinedColour)
+ {
+ userDefinedColour_actionPerformed();
+ }
+ else if (source == modifyConservation)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_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 gSize = sg.getSize();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+
+ 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.add(sg.getSequenceAt(i));
+ features.add(new SequenceFeature(null, null, start, end,
+ "Jalview"));
+ }
+ }
+
+ if (!seqs.isEmpty())
+ {
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ ap.av.setShowSequenceFeatures(true);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
+ }
+ }
+ }
+ else
+ {
+ outputText(evt);
+ }
+
+ }
+
+ void outputText(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+ Frame frame = new Frame();
+ frame.add(cap);
+ 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
+
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
+ 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);
+
+ StringBuilder contents = new StringBuilder(128);
+ 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, ap.seqPanel.seqCanvas.fr);
+ 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, false);
+ }
+ }
+
+ void addPDB()
+ {
+ Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+ if (pdbs != null && !pdbs.isEmpty())
+ {
+ PDBEntry entry = pdbs.firstElement();
+
+ if (ap.av.applet.jmolAvailable)
+ {
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
+ }
+ else
+ {
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.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);
+ 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);
+
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
+ 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_conserved"));
+ 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(noColour);
+ 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(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+
+ noColour.setLabel(MessageManager.getString("label.none"));
+ noColour.addItemListener(this);
+
+ /*
+ * setName allows setSelectedColour to do its thing
+ */
+ clustalColour.setLabel(
+ MessageManager.getString("label.colourScheme_clustal"));
+ clustalColour.setName(JalviewColourScheme.Clustal.toString());
+ clustalColour.addItemListener(this);
+ BLOSUM62Colour.setLabel(
+ MessageManager.getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
+ BLOSUM62Colour.addItemListener(this);
+ PIDColour.setLabel(
+ MessageManager.getString("label.colourScheme_%_identity"));
+ PIDColour.setName(JalviewColourScheme.PID.toString());
+ PIDColour.addItemListener(this);
+ zappoColour
+ .setLabel(MessageManager.getString("label.colourScheme_zappo"));
+ zappoColour.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
+ taylorColour.setLabel(
+ MessageManager.getString("label.colourScheme_taylor"));
+ taylorColour.setName(JalviewColourScheme.Taylor.toString());
+ taylorColour.addItemListener(this);
+ hydrophobicityColour.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
+ helixColour.setName(JalviewColourScheme.Helix.toString());
+ helixColour.addItemListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.colourScheme_strand_propensity"));
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turn_propensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buried_index"));
+ buriedColour.setName(JalviewColourScheme.Buried.toString());
+ buriedColour.addItemListener(this);
+ nucleotideColour.setLabel(
+ MessageManager.getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
+ nucleotideColour.addItemListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.colourScheme_purine/pyrimidine"));
+ purinePyrimidineColour
+ .setName(JalviewColourScheme.PurinePyrimidine.toString());
+ purinePyrimidineColour.addItemListener(this);
+
+ userDefinedColour
+ .setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+
+ abovePIDColour.setLabel(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
+ conservationColour
+ .setLabel(MessageManager.getString("action.by_conservation"));
+ conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.addActionListener(this);
+
+ 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, true);
+ }
+
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ResidueShader(
+ new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()));
+ refresh();
+ }
+
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
+ refresh();
+ }
+
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
+ refresh();
+ }
+
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
+ refresh();
+ }
+
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
+ refresh();
+ }
+
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
+ refresh();
+ }
+
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
+ refresh();
+ }
+
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
+ refresh();
+ }
+
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
+ refresh();
+ }
+
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new PurinePyrimidineColourScheme());
+ 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
+ {
+ SliderPanel.hidePIDSlider();
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ }
+ modifyPID.setEnabled(abovePIDColour.getState());
+ refresh();
+ }
+
+ protected void userDefinedColour_actionPerformed()
+ {
+ new UserDefinedColours(ap, getGroup());
+ }
+
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ResidueShader(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 ResidueShader(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 (conservationColour.getState())
+ {
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth(), false,
+ ap.av.getConsPercGaps(), false);
+ sg.getGroupColourScheme().setConservation(conservation);
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ SliderPanel.hideConservationSlider();
+ sg.cs.setConservation(null);
+ }
+ modifyConservation.setEnabled(conservationColour.getState());
+ 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, 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)
+ {
+ ap.av.hideSequences(seq, representGroup);
+ }
+
+ /**
+ * 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(new String[]
+ { MessageManager.getString("label.all") });
+ 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<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
+ 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);
+ }
+
+}