-/*\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
-package jalview.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import MCview.*;\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PopupMenu\r
- extends JPopupMenu\r
-{\r
- JMenu groupMenu = new JMenu();\r
- JMenuItem groupName = new JMenuItem();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new\r
- JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- AlignmentPanel ap;\r
- JMenu sequenceMenu = new JMenu();\r
- JMenuItem sequenceName = new JMenuItem();\r
- Sequence sequence;\r
- JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem outline = new JMenuItem();\r
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
- JMenu colourMenu = new JMenu();\r
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
- JMenu editMenu = new JMenu();\r
- JMenuItem cut = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem upperCase = new JMenuItem();\r
- JMenuItem lowerCase = new JMenuItem();\r
- JMenuItem toggle = new JMenuItem();\r
- JMenu pdbMenu = new JMenu();\r
- JMenuItem pdbFromFile = new JMenuItem();\r
- JMenuItem enterPDB = new JMenuItem();\r
- JMenuItem discoverPDB = new JMenuItem();\r
- JMenu outputMenu = new JMenu();\r
- JMenuItem sequenceFeature = new JMenuItem();\r
- JMenuItem textColour = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenu structureMenu = new JMenu();\r
- JMenu viewStructureMenu = new JMenu();\r
- // JMenu colStructureMenu = new JMenu();\r
- JMenuItem editSequence = new JMenuItem();\r
- // JMenuItem annotationMenuItem = new JMenuItem();\r
-\r
- /**\r
- * Creates a new PopupMenu object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- public PopupMenu(final AlignmentPanel ap, 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
- this.ap = ap;\r
- sequence = seq;\r
-\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
-\r
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
- i]);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputMenu.add(item);\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- if (seq != null)\r
- {\r
- sequenceMenu.setText(sequence.getName());\r
-\r
- JMenuItem menuItem;\r
- if (seq.getDatasetSequence().getPDBId() != null\r
- && seq.getDatasetSequence().getPDBId().size()>0)\r
- {\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
- elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- final PDBEntry pdb = (PDBEntry) e.nextElement();\r
-\r
- menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- Vector seqs = new Vector();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
- {\r
- Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
- if(pdbs==null)\r
- continue;\r
-\r
- for(int p=0; p<pdbs.size(); p++)\r
- {\r
- PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
- if(p1.getId().equals(pdb.getId()))\r
- {\r
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
- seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
-\r
- continue;\r
- }\r
- }\r
- }\r
-\r
- SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
- seqs.toArray(seqs2);\r
-\r
- new AppJMol(pdb, seqs2, null, ap);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
-\r
- /* menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- colourByStructure(pdb.getId());\r
- }\r
- });\r
- colStructureMenu.add(menuItem);*/\r
- }\r
- }\r
- else\r
- {\r
- structureMenu.remove(viewStructureMenu);\r
- // structureMenu.remove(colStructureMenu);\r
- }\r
-\r
- menuItem = new JMenuItem("Hide Sequences");\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(false);\r
- }\r
- });\r
- add(menuItem);\r
-\r
- if (ap.av.getSelectionGroup() != null\r
- && ap.av.getSelectionGroup().getSize() > 1)\r
- {\r
- menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(true);\r
- }\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\r
-\r
- if (ap.av.hasHiddenRows)\r
- {\r
- final int index = ap.av.alignment.findIndex(seq);\r
-\r
- if (ap.av.adjustForHiddenSeqs(index) -\r
- ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
- {\r
- menuItem = new JMenuItem("Reveal Sequences");\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showSequence(index);\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
- add(menuItem);\r
- }\r
-\r
- menuItem = new JMenuItem("Reveal All");\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- add(menuItem);\r
- }\r
-\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- groupName.setText(sg.getName());\r
-\r
- if (sg.cs instanceof ZappoColourScheme)\r
- {\r
- zappoColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TaylorColourScheme)\r
- {\r
- taylorColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PIDColourScheme)\r
- {\r
- PIDColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof Blosum62ColourScheme)\r
- {\r
- BLOSUM62Colour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof UserColourScheme)\r
- {\r
- userDefinedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HydrophobicColourScheme)\r
- {\r
- hydrophobicityColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HelixColourScheme)\r
- {\r
- helixColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof StrandColourScheme)\r
- {\r
- strandColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TurnColourScheme)\r
- {\r
- turnColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof BuriedColourScheme)\r
- {\r
- buriedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof ClustalxColourScheme)\r
- {\r
- clustalColour.setSelected(true);\r
- }\r
- else\r
- {\r
- noColourmenuItem.setSelected(true);\r
- }\r
-\r
- if (sg.cs != null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\r
- }\r
-\r
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- }\r
- else\r
- {\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
-\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- unGroupMenuItem.setVisible(false);\r
- }\r
-\r
- if (seq == null)\r
- {\r
- sequenceMenu.setVisible(false);\r
- structureMenu.setVisible(false);\r
- }\r
-\r
- if (links != null && links.size() > 0)\r
- {\r
- JMenu linkMenu = new JMenu("Link");\r
- JMenuItem item;\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- String link = links.elementAt(i).toString();\r
- final String label = link.substring(0, link.indexOf("|"));\r
- item = new JMenuItem(label);\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
- showLink(url);\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
- if (sequence != null)\r
- {\r
- sequenceMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit()\r
- throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- groupMenu.setText("Selection");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed();\r
- }\r
- });\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit Name/Description");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceName_actionPerformed();\r
- }\r
- });\r
- PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- outline.setText("Border colour");\r
- outline.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outline_actionPerformed();\r
- }\r
- });\r
- nucleotideMenuItem.setText("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
- });\r
- colourMenu.setText("Group Colour");\r
- showBoxes.setText("Boxes");\r
- showBoxes.setState(true);\r
- showBoxes.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showBoxes_actionPerformed();\r
- }\r
- });\r
- showText.setText("Text");\r
- showText.setState(true);\r
- showText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showText_actionPerformed();\r
- }\r
- });\r
- showColourText.setText("Colour Text");\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed();\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- cut.setText("Cut");\r
- cut.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed();\r
- }\r
- });\r
- upperCase.setText("To Upper Case");\r
- upperCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed();\r
- }\r
- });\r
- lowerCase.setText("To Lower Case");\r
- lowerCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- toggle.setText("Toggle Case");\r
- toggle.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- pdbMenu.setText("Associate Structure with Sequence");\r
- pdbFromFile.setText("From File");\r
- pdbFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbFromFile_actionPerformed();\r
- }\r
- });\r
- enterPDB.setText("Enter PDB Id");\r
- enterPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- enterPDB_actionPerformed();\r
- }\r
- });\r
- discoverPDB.setText("Discover PDB ids");\r
- discoverPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- discoverPDB_actionPerformed();\r
- }\r
- });\r
- outputMenu.setText("Output to Textbox...");\r
- sequenceFeature.setText("Create Sequence Feature");\r
- sequenceFeature.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceFeature_actionPerformed();\r
- }\r
- });\r
- textColour.setText("Text Colour");\r
- textColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textColour_actionPerformed();\r
- }\r
- });\r
- jMenu1.setText("Group");\r
- structureMenu.setText("Structure");\r
- viewStructureMenu.setText("View Structure");\r
- // colStructureMenu.setText("Colour By Structure");\r
- editSequence.setText("Edit Sequence...");\r
- editSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- editSequence_actionPerformed(actionEvent);\r
- }\r
- });\r
- /* annotationMenuItem.setText("By Annotation");\r
- annotationMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- annotationMenuItem_actionPerformed(actionEvent);\r
- }\r
- });*/\r
-\r
- add(groupMenu);\r
-\r
- add(sequenceMenu);\r
- this.add(structureMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\r
- colourMenu.add(textColour);\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
-\r
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
- {\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- JMenuItem item = new JMenuItem(userColours.\r
- nextElement().toString());\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.add(item);\r
- }\r
- }\r
-\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
- //colourMenu.add(annotationMenuItem);\r
- editMenu.add(copy);\r
- editMenu.add(cut);\r
- editMenu.add(editSequence);\r
- editMenu.add(upperCase);\r
- editMenu.add(lowerCase);\r
- editMenu.add(toggle);\r
- pdbMenu.add(pdbFromFile);\r
- pdbMenu.add(enterPDB);\r
- pdbMenu.add(discoverPDB);\r
- jMenu1.add(groupName);\r
- jMenu1.add(unGroupMenuItem);\r
- jMenu1.add(colourMenu);\r
- jMenu1.add(showBoxes);\r
- jMenu1.add(showText);\r
- jMenu1.add(showColourText);\r
- jMenu1.add(outline);\r
- structureMenu.add(pdbMenu);\r
- structureMenu.add(viewStructureMenu);\r
- // structureMenu.add(colStructureMenu);\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed();\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed();\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed();\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed();\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed();\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed();\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed();\r
- }\r
- });\r
- abovePIDColour.setText("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed();\r
- }\r
- });\r
- userDefinedColour.setText("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.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed();\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- });\r
- conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void refresh()\r
- {\r
- ap.paintAlignment(true);\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void abovePIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\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
- else // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if (e.getActionCommand().equals("User Defined..."))\r
- {\r
- new UserDefinedColours(ap, sg);\r
- }\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
-\r
- sg.cs = udc;\r
- }\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1);\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
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(\r
- sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);\r
-\r
- acg.predefinedColours = true;\r
- sg.cs = acg;\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = getGroup();\r
- EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
- sg.getDescription(),\r
- " Group Name ",\r
- "Group Description ",\r
- "Edit Group Name/Description");\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(),\r
- " Sequence Name ",\r
- "Sequence Description ",\r
- "Edit Sequence Name/Description");\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- if (dialog.getName() != null)\r
- {\r
- if (dialog.getName().indexOf(" ") > -1)\r
- {\r
- JOptionPane.showMessageDialog(ap,\r
- "Spaces have been converted to \"_\"",\r
- "No spaces allowed in Sequence Name",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
- sequence.setName(dialog.getName().replace(' ', '_'));\r
- ap.paintAlignment(false);\r
- }\r
-\r
- sequence.setDescription(dialog.getDescription());\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
- Color.BLUE);\r
-\r
- if (col != null)\r
- {\r
- sg.setOutlineColour(col);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showBoxes_actionPerformed()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showText_actionPerformed()\r
- {\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showColourText_actionPerformed()\r
- {\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
- }\r
-\r
- public void showLink(String url)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher.openURL(url);\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Unixers: Couldn't find default web browser."\r
- +\r
- "\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- ex.printStackTrace();\r
- }\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
- {sequence});\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(sequence, 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
- public void copy_actionPerformed()\r
- {\r
- ap.alignFrame.copy_actionPerformed(null);\r
- }\r
-\r
- public void cut_actionPerformed()\r
- {\r
- ap.alignFrame.cut_actionPerformed(null);\r
- }\r
-\r
- void changeCase(ActionEvent e)\r
- {\r
- Object source = e.getSource();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(\r
- sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggle)\r
- {\r
- description = "Toggle Case";\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == upperCase)\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
-\r
- public void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(null);\r
- Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
-\r
- String[] omitHidden = null;\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = ap.av.getViewAsString(true);\r
- }\r
-\r
- cap.setText(new FormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- ap.av.getSelectionAsNewSequence(),\r
- omitHidden));\r
- }\r
-\r
- public void pdbFromFile_actionPerformed()\r
- {\r
- jalview.io.JalviewFileChooser chooser\r
- = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Select a PDB file");\r
- chooser.setToolTipText("Load a PDB file");\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
- jalview.io.AppletFormatAdapter.FILE);\r
-\r
- if (pdbfile.id == null)\r
- {\r
- String reply = JOptionPane.showInternalInputDialog(\r
- Desktop.desktop,\r
- "Couldn't find a PDB id in the file supplied."\r
- + "Please enter an Id to identify this structure.",\r
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- entry.setId(reply);\r
- }\r
- else\r
- {\r
- entry.setId(pdbfile.id);\r
- }\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- entry.setFile(choice);\r
- sequence.getDatasetSequence().addPDBId(entry);\r
- }\r
-\r
- }\r
-\r
- public void enterPDB_actionPerformed()\r
- {\r
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(id.toUpperCase());\r
- sequence.getDatasetSequence()\r
- .addPDBId(entry);\r
- }\r
- }\r
-\r
- public void discoverPDB_actionPerformed()\r
- {\r
- SequenceI[] sequences =\r
- ap.av.selectionGroup == null ?\r
- new Sequence[]{sequence}\r
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);\r
-\r
- new jalview.io.DBRefFetcher(sequences,\r
- ap.alignFrame).fetchDBRefs(false);\r
- }\r
-\r
- public void sequenceFeature_actionPerformed()\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).getDatasetSequence();\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, "Jalview");\r
- }\r
-\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .amendFeatures(seqs, features, true, ap))\r
- {\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- ap.av.setShowSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
- }\r
-\r
- public void textColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg != null)\r
- {\r
- new TextColourChooser().chooseColour(ap, sg);\r
- }\r
- }\r
-\r
- public void colourByStructure(String pdbid)\r
- {\r
- Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
- .colourSequenceFromStructure(sequence, pdbid);\r
-\r
- AlignmentAnnotation an = new AlignmentAnnotation(\r
- "Structure", "Coloured by "+pdbid, anots);\r
-\r
- ap.av.alignment.addAnnotation(an);\r
- an.createSequenceMapping(sequence, 0, true);\r
- //an.adjustForAlignment();\r
- ap.av.alignment.setAnnotationIndex(an,0);\r
-\r
- ap.adjustAnnotationHeight();\r
-\r
- sequence.addAlignmentAnnotation(an);\r
-\r
- }\r
-\r
- public void editSequence_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if(sg!=null)\r
- {\r
- if (sequence == null)\r
- sequence = (Sequence) sg.getSequenceAt(0);\r
-\r
- EditNameDialog dialog = new EditNameDialog(\r
- sequence.getSequenceAsString(\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1),\r
- null,\r
- "Edit Sequence ",\r
- null,\r
- "Edit Sequence");\r
-\r
- if (dialog.accept)\r
- {\r
- EditCommand editCommand = new EditCommand(\r
- "Edit Sequences", EditCommand.REPLACE,\r
- dialog.getName().replace(' ', ap.av.getGapCharacter()),\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
-\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.gui;
+
+import java.util.Locale;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
+import jalview.bin.Console;
+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.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.Comparison;
+import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+import jalview.util.UrlLink;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
+/**
+ * The popup menu that is displayed on right-click on a sequence id, or in the
+ * sequence alignment.
+ */
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
+{
+ /*
+ * maximum length of feature description to include in popup menu item text
+ */
+ private static final int FEATURE_DESC_MAX = 40;
+
+ /*
+ * true for ID Panel menu, false for alignment panel menu
+ */
+ private final boolean forIdPanel;
+
+ private final AlignmentPanel ap;
+
+ /*
+ * the sequence under the cursor when clicked
+ * (additional sequences may be selected)
+ */
+ private final SequenceI sequence;
+
+ JMenu groupMenu = new JMenu();
+
+ JMenuItem groupName = new JMenuItem();
+
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
+ protected JMenuItem modifyPID = new JMenuItem();
+
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+ protected JRadioButtonMenuItem annotationColour;
+
+ protected JMenuItem modifyConservation = new JMenuItem();
+
+ JMenu sequenceMenu = new JMenu();
+
+ JMenuItem makeReferenceSeq = new JMenuItem();
+
+ JMenuItem createGroupMenuItem = new JMenuItem();
+
+ JMenuItem unGroupMenuItem = new JMenuItem();
+
+ JMenu colourMenu = new JMenu();
+
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
+ JMenu editMenu = new JMenu();
+
+ JMenuItem upperCase = new JMenuItem();
+
+ JMenuItem lowerCase = new JMenuItem();
+
+ JMenuItem toggle = new JMenuItem();
+
+ JMenu outputMenu = new JMenu();
+
+ JMenu seqShowAnnotationsMenu = new JMenu();
+
+ JMenu seqHideAnnotationsMenu = new JMenu();
+
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
+
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ JMenuItem textColour = new JMenuItem();
+
+ JMenu editGroupMenu = new JMenu();
+
+ JMenuItem chooseStructure = new JMenuItem();
+
+ JMenu rnaStructureMenu = new JMenu();
+
+ /**
+ * Constructs a menu with sub-menu items for any hyperlinks for the sequence
+ * and/or features provided. Hyperlinks may include a lookup by sequence id,
+ * or database cross-references, depending on which links are enabled in user
+ * preferences.
+ *
+ * @param seq
+ * @param features
+ * @return
+ */
+ protected static JMenu buildLinkMenu(final SequenceI seq,
+ List<SequenceFeature> features)
+ {
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+
+ List<String> nlinks = null;
+ if (seq != null)
+ {
+ nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ UrlLink.sort(nlinks);
+ }
+ else
+ {
+ nlinks = new ArrayList<>();
+ }
+
+ if (features != null)
+ {
+ for (SequenceFeature sf : features)
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ nlinks.add(link);
+ }
+ }
+ }
+ }
+
+ /*
+ * instantiate the hyperlinklink templates from sequence data;
+ * note the order of the templates is preserved in the map
+ */
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
+ for (String link : nlinks)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ Console.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Console.error(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ /*
+ * construct menu items for the hyperlinks (still preserving
+ * the order of the sorted templates)
+ */
+ addUrlLinks(linkMenu, linkset.values());
+
+ return linkMenu;
+ }
+
+ /**
+ * A helper method that builds menu items from the given links, with action
+ * handlers to open the link URL, and adds them to the linkMenu. Each provided
+ * link should be a list whose second item is the menu text, and whose fourth
+ * item is the URL to open when the menu item is selected.
+ *
+ * @param linkMenu
+ * @param linkset
+ */
+ static private void addUrlLinks(JMenu linkMenu,
+ Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ final String url = linkstrset.get(3);
+ JMenuItem item = new JMenuItem(linkstrset.get(1));
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_param", new Object[]
+ { url }));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ showLink(url);
+ }
+ }).start();
+ }
+ });
+ linkMenu.add(item);
+ }
+ }
+
+ /**
+ * Opens the provided url in the default web browser, or shows an error
+ * message if this fails
+ *
+ * @param url
+ */
+ static void showLink(String url)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ } catch (Exception ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * add a late bound groupURL item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
+ */
+ static void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_seqs_param", new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e2)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * Constructor for a PopupMenu for a click in the alignment panel (on a
+ * residue)
+ *
+ * @param ap
+ * the panel in which the mouse is clicked
+ * @param seq
+ * the sequence under the mouse
+ * @throws NullPointerException
+ * if seq is null
+ */
+ public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
+ {
+ this(false, ap, seq, column, null);
+ }
+
+ /**
+ * Constructor for a PopupMenu for a click in the sequence id panel
+ *
+ * @param alignPanel
+ * the panel in which the mouse is clicked
+ * @param seq
+ * the sequence under the mouse click
+ * @param groupLinks
+ * templates for sequence external links
+ * @throws NullPointerException
+ * if seq is null
+ */
+ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
+ List<String> groupLinks)
+ {
+ this(true, alignPanel, seq, -1, groupLinks);
+ }
+
+ /**
+ * Private constructor that constructs a popup menu for either sequence ID
+ * Panel, or alignment context
+ *
+ * @param fromIdPanel
+ * @param alignPanel
+ * @param seq
+ * @param column
+ * aligned column position (0...)
+ * @param groupLinks
+ */
+ private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
+ final SequenceI seq, final int column, List<String> groupLinks)
+ {
+ Objects.requireNonNull(seq);
+ this.forIdPanel = fromIdPanel;
+ this.ap = alignPanel;
+ sequence = seq;
+
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
+ {
+ JMenuItem item = new JMenuItem(ff);
+
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputMenu.add(item);
+ }
+
+ /*
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment. First for the
+ * currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (forIdPanel && seq != null
+ ? Arrays.asList(seq)
+ : Collections.<SequenceI> emptyList());
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (alignPanel.av
+ .getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ if (forIdPanel)
+ {
+ JMenuItem menuItem;
+ sequenceMenu.setText(sequence.getName());
+ if (seq == alignPanel.av.getAlignment().getSeqrep())
+ {
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.unmark_as_reference"));
+ }
+ else
+ {
+ makeReferenceSeq.setText(
+ MessageManager.getString("action.set_as_reference"));
+ }
+
+ if (!alignPanel.av.getAlignment().isNucleotide())
+ {
+ remove(rnaStructureMenu);
+ }
+ else
+ {
+ int origCount = rnaStructureMenu.getItemCount();
+ /*
+ * add menu items to 2D-render any alignment or sequence secondary
+ * structure annotation
+ */
+ AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (aas != null)
+ {
+ for (final AlignmentAnnotation aa : aas)
+ {
+ if (aa.isValidStruc() && aa.sequenceRef == null)
+ {
+ /*
+ * valid alignment RNA secondary structure annotation
+ */
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new Object[]
+ { aa.label }));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new AppVarna(seq, aa, alignPanel);
+ }
+ });
+ rnaStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+ for (final AlignmentAnnotation aa : seqAnns)
+ {
+ if (aa.isValidStruc())
+ {
+ /*
+ * valid sequence RNA secondary structure annotation
+ */
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new Object[]
+ { seq.getName() }));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: VARNA does'nt print gaps in the sequence
+ new AppVarna(seq, aa, alignPanel);
+ }
+ });
+ rnaStructureMenu.add(menuItem);
+ }
+ }
+ }
+ if (rnaStructureMenu.getItemCount() == origCount)
+ {
+ remove(rnaStructureMenu);
+ }
+ }
+
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(false);
+ }
+ });
+ add(menuItem);
+
+ if (alignPanel.av.getSelectionGroup() != null
+ && alignPanel.av.getSelectionGroup().getSize() > 1)
+ {
+ menuItem = new JMenuItem(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(true);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+
+ if (alignPanel.av.hasHiddenRows())
+ {
+ final int index = alignPanel.av.getAlignment().findIndex(seq);
+
+ if (alignPanel.av.adjustForHiddenSeqs(index)
+ - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ alignPanel.av.showSequence(index);
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ add(menuItem);
+ }
+ }
+ }
+
+ /*
+ * offer 'Reveal All'
+ * - in the IdPanel (seq not null) if any sequence is hidden
+ * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
+ */
+ if (alignPanel.av.hasHiddenRows())
+ {
+ boolean addOption = seq != null;
+ if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
+ {
+ addOption = true;
+ }
+ if (addOption)
+ {
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ alignPanel.av.showAllHiddenSeqs();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ add(menuItem);
+ }
+ }
+
+ SequenceGroup sg = alignPanel.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg != null)
+ ? alignPanel.av.getAlignment().getGroups().contains(sg)
+ : false;
+
+ if (sg != null && sg.getSize() > 0)
+ {
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
+
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
+
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
+
+ if (sg.cs != null)
+ {
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
+ }
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
+ modifyPID.setEnabled(abovePIDColour.isSelected());
+ displayNonconserved.setSelected(sg.getShowNonconserved());
+ showText.setSelected(sg.getDisplayText());
+ showColourText.setSelected(sg.getColourText());
+ showBoxes.setSelected(sg.getDisplayBoxes());
+ // add any groupURLs to the groupURL submenu and make it visible
+ if (groupLinks != null && groupLinks.size() > 0)
+ {
+ buildGroupURLMenu(sg, groupLinks);
+ }
+ // Add a 'show all structures' for the current selection
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+ reppdb = new Hashtable<>();
+
+ SequenceI sqass = null;
+ for (SequenceI sq : alignPanel.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
+ if (pes != null && pes.size() > 0)
+ {
+ reppdb.put(pes.get(0).getId(), pes.get(0));
+ for (PDBEntry pe : pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ if (pdbe.size() > 0)
+ {
+ final PDBEntry[] pe = pdbe.values()
+ .toArray(new PDBEntry[pdbe.size()]),
+ pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
+ }
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!isDefinedGroup)
+ {
+ createGroupMenuItem.setVisible(true);
+ unGroupMenuItem.setVisible(false);
+ editGroupMenu
+ .setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ editGroupMenu.setText(MessageManager.getString("action.edit_group"));
+ }
+
+ if (!forIdPanel)
+ {
+ sequenceMenu.setVisible(false);
+ chooseStructure.setVisible(false);
+ rnaStructureMenu.setVisible(false);
+ }
+
+ addLinksAndFeatures(seq, column);
+ }
+
+ /**
+ * Adds
+ * <ul>
+ * <li>configured sequence database links (ID panel popup menu)</li>
+ * <li>non-positional feature links (ID panel popup menu)</li>
+ * <li>positional feature links (alignment panel popup menu)</li>
+ * <li>feature details links (alignment panel popup menu)</li>
+ * </ul>
+ * If this panel is also showed complementary (CDS/protein) features, then
+ * links to their feature details are also added.
+ *
+ * @param seq
+ * @param column
+ */
+ void addLinksAndFeatures(final SequenceI seq, final int column)
+ {
+ List<SequenceFeature> features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
+ {
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
+ }
+
+ addLinks(seq, features);
+
+ if (!forIdPanel)
+ {
+ addFeatureDetails(features, seq, column);
+ }
+ }
+
+ /**
+ * Add a menu item to show feature details for each sequence feature. Any
+ * linked 'virtual' features (CDS/protein) are also optionally found and
+ * included.
+ *
+ * @param features
+ * @param seq
+ * @param column
+ */
+ protected void addFeatureDetails(List<SequenceFeature> features,
+ final SequenceI seq, final int column)
+ {
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ MappedFeatures mf = null;
+ if (ap.av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
+ {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ int seqPos = sequence.findPosition(column);
+ mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
+ }
+ }
+
+ if (features.isEmpty() && mf == null)
+ {
+ /*
+ * no features to show at this position
+ */
+ return;
+ }
+
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
+
+ String name = seq.getName();
+ for (final SequenceFeature sf : features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, null);
+ }
+
+ if (mf != null)
+ {
+ for (final SequenceFeature sf : mf.features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, mf);
+ }
+ }
+ }
+
+ /**
+ * A helper method to add one menu item whose action is to show details for
+ * one feature. The menu text includes feature description, but this may be
+ * truncated.
+ *
+ * @param details
+ * @param seqName
+ * @param sf
+ * @param mf
+ */
+ void addFeatureDetailsMenuItem(JMenu details, final String seqName,
+ final SequenceFeature sf, MappedFeatures mf)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ if (mf != null)
+ {
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
+ }
+ StringBuilder desc = new StringBuilder();
+ desc.append(sf.getType()).append(" ").append(String.valueOf(start));
+ if (start != end)
+ {
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ desc.append(" ");
+ description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * truncate overlong descriptions unless they contain an href
+ * (as truncation could leave corrupted html)
+ */
+ boolean hasLink = description.indexOf("a href") > -1;
+ if (description.length() > FEATURE_DESC_MAX && !hasLink)
+ {
+ description = description.substring(0, FEATURE_DESC_MAX) + "...";
+ }
+ desc.append(description);
+ }
+ String featureGroup = sf.getFeatureGroup();
+ if (featureGroup != null)
+ {
+ desc.append(" (").append(featureGroup).append(")");
+ }
+ String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
+ JMenuItem item = new JMenuItem(htmlText);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showFeatureDetails(sf, seqName, mf);
+ }
+ });
+ details.add(item);
+ }
+
+ /**
+ * Opens a panel showing a text report of feature details
+ *
+ * @param sf
+ * @param seqName
+ * @param mf
+ */
+ protected void showFeatureDetails(SequenceFeature sf, String seqName,
+ MappedFeatures mf)
+ {
+ JInternalFrame details;
+ if (Platform.isJS())
+ {
+ details = new JInternalFrame();
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.setOpaque(true);
+ panel.setBackground(Color.white);
+ // TODO JAL-3026 set style of table correctly for feature details
+ JLabel reprt = new JLabel(MessageManager
+ .formatMessage("label.html_content", new Object[]
+ { sf.getDetailsReport(seqName, mf) }));
+ reprt.setBackground(Color.WHITE);
+ reprt.setOpaque(true);
+ panel.add(reprt, BorderLayout.CENTER);
+ details.setContentPane(panel);
+ details.pack();
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ // it appears Java's CSS does not support border-collapse :-(
+ cap.addStylesheetRule("table { border-collapse: collapse;}");
+ cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
+ cap.setText(sf.getDetailsReport(seqName, mf));
+ details = cap;
+ }
+ Desktop.addInternalFrame(details,
+ MessageManager.getString("label.feature_details"), 500, 500);
+ }
+
+ /**
+ * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
+ * When seq is not null, these are links for the sequence id, which may be to
+ * external web sites for the sequence accession, and/or links embedded in
+ * non-positional features. When seq is null, only links embedded in the
+ * provided features are added. If no links are found, the menu is not added.
+ *
+ * @param seq
+ * @param features
+ */
+ void addLinks(final SequenceI seq, List<SequenceFeature> features)
+ {
+ JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
+
+ // only add link menu if it has entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (forIdPanel)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ /**
+ * 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(JMenu showMenu, JMenu 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());
+ }
+
+ /**
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
+ *
+ * @param seq
+ * @return
+ */
+ protected List<SequenceI> getSequenceScope(SequenceI seq)
+ {
+ List<SequenceI> forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
+ {
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq);
+ }
+ return forSequences;
+ }
+
+ /**
+ * 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(JMenu 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); // a, b, c
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
+ {
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
+ // sequence only URLs
+ // ID/regex match URLs
+ JMenu groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ // three types of url that might be created.
+ JMenu[] linkMenus = new JMenu[] { null,
+ new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+ Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
+
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
+ // just collect ids from dataset sequence
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
+ SequenceI sqi = seqs[sq];
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
+ List<DBRefEntry> dbr = sqi.getDBRefs();
+ int nd;
+ if (dbr != null && (nd = dbr.size()) > 0)
+ {
+ for (int d = 0; d < nd; d++)
+ {
+ DBRefEntry e = dbr.get(d);
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
+ Object[] sarray = commonDbrefs.get(src);
+ if (sarray == null)
+ {
+ sarray = new Object[2];
+ sarray[0] = new int[] { 0 };
+ sarray[1] = new String[seqs.length];
+
+ commonDbrefs.put(src, sarray);
+ }
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!e.hasMap()
+ || (e.getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = e.getAccessionId();
+ ((int[]) sarray[0])[0]++;
+ }
+ }
+ }
+ }
+ }
+ // now create group links for all distinct ID/sequence sets.
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (String link : groupLinks)
+ {
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
+ continue;
+ }
+ if (!urlLink.isValid())
+ {
+ Console.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
+ {
+ if (allids[sq] != null)
+ {
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
+ }
+ }
+ }
+ else
+ {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
+ }
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
+ {
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
+ urlLink, urlset);
+ addMenu = true;
+ }
+ }
+ if (addMenu)
+ {
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ for (int m = 0; m < linkMenus.length; m++)
+ {
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
+ {
+ groupLinksMenu.add(linkMenus[m]);
+ }
+ }
+
+ groupMenu.add(groupLinksMenu);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
+ groupName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed();
+ }
+ });
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+
+ JMenuItem sequenceName = new JMenuItem(
+ MessageManager.getString("label.edit_name_description"));
+ sequenceName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed();
+ }
+ });
+ JMenuItem chooseAnnotations = new JMenuItem(
+ MessageManager.getString("action.choose_annotations"));
+ chooseAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
+ JMenuItem sequenceDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSequenceDetailsReport(new SequenceI[] { sequence });
+ }
+ });
+ JMenuItem sequenceSelDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+ });
+
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+ });
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
+
+ JMenuItem outline = new JMenuItem(
+ MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed();
+ }
+ });
+ showBoxes.setText(MessageManager.getString("action.boxes"));
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed();
+ }
+ });
+ showText.setText(MessageManager.getString("action.text"));
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed();
+ }
+ });
+ showColourText.setText(MessageManager.getString("label.colour_text"));
+ showColourText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed();
+ }
+ });
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
+ editMenu.setText(MessageManager.getString("action.edit"));
+ JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
+ cut.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed();
+ }
+ });
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
+ upperCase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
+ copy.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed();
+ }
+ });
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
+ lowerCase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ toggle.setText(MessageManager.getString("label.toggle_case"));
+ toggle.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ JMenuItem sequenceFeature = new JMenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
+ sequenceFeature.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceFeature_actionPerformed();
+ }
+ });
+ editGroupMenu.setText(MessageManager.getString("label.group"));
+ chooseStructure.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ chooseStructure.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
+
+ // colStructureMenu.setText("Colour By Structure");
+ JMenuItem editSequence = new JMenuItem(
+ MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ editSequence_actionPerformed();
+ }
+ });
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
+ makeReferenceSeq.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ makeReferenceSeq_actionPerformed(actionEvent);
+
+ }
+ });
+
+ groupMenu.add(sequenceSelDetails);
+ add(groupMenu);
+ add(sequenceMenu);
+ add(rnaStructureMenu);
+ add(chooseStructure);
+ if (forIdPanel)
+ {
+ JMenuItem hideInsertions = new JMenuItem(
+ MessageManager.getString("label.hide_insertions"));
+ hideInsertions.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
+ add(hideInsertions);
+ }
+ // annotations configuration panel suppressed for now
+ // groupMenu.add(chooseAnnotations);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ 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(editGroupMenu);
+ sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
+ sequenceMenu.add(makeReferenceSeq);
+
+ initColourMenu();
+ buildColourMenu();
+
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ editGroupMenu.add(groupName);
+ editGroupMenu.add(colourMenu);
+ editGroupMenu.add(showBoxes);
+ editGroupMenu.add(showText);
+ editGroupMenu.add(showColourText);
+ editGroupMenu.add(outline);
+ editGroupMenu.add(displayNonconserved);
+ }
+
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
+ }
+ });
+
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
+ }
+ });
+
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.setEnabled(false);
+ annotationColour.setToolTipText(
+ MessageManager.getString("label.by_annotation_tooltip"));
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+ }
+
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
+ *
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
+ *
+ * @param menuItem
+ * @param forSequences
+ */
+ protected void configureReferenceAnnotationsMenu(JMenuItem 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 tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ 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();
+ }
+
+ protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
+ {
+ 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(sequence);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == sequence)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ }
+ refresh();
+ }
+
+ protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
+ {
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
+
+ boolean markedPopup = false;
+ // mark inserts in current selection
+ if (ap.av.getSelectionGroup() != null)
+ {
+ // mark just the columns in the selection group to be hidden
+ inserts.set(ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
+
+ // now clear columns without gaps
+ for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
+ {
+ if (sq == sequence)
+ {
+ markedPopup = true;
+ }
+ inserts.and(sq.getInsertionsAsBits());
+ }
+ hidden.clearAndHideColumns(inserts,
+ ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
+ }
+
+ // now mark for sequence under popup if we haven't already done it
+ else if (!markedPopup && sequence != null)
+ {
+ inserts.or(sequence.getInsertionsAsBits());
+
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
+ refresh();
+ }
+
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ StringBuilder contents = new StringBuilder(128);
+ contents.append("<html><body>");
+ for (SequenceI seq : sequences)
+ {
+ contents.append("<p><h2>" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
+ contents.append("</p>");
+ }
+ contents.append("</body></html>");
+ String report = contents.toString();
+
+ JInternalFrame frame;
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(report);
+ textLabel.setBackground(Color.WHITE);
+ JPanel pane = new JPanel(new BorderLayout());
+ pane.setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ pane.add(textLabel, BorderLayout.NORTH);
+ frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(pane));
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ cap.setText(report);
+ frame = cap;
+ }
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
+ }
+
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
+ refresh();
+ }
+
+ /**
+ * call to refresh view after settings change
+ */
+ void refresh()
+ {
+ ap.updateAnnotation();
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param selected
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void abovePIDColour_actionPerformed(boolean selected)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (selected)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+ }
+ else
+ // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
+ }
+ modifyPID.setEnabled(selected);
+
+ refresh();
+ }
+
+ /**
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
+ *
+ * @param e
+ */
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
+ {
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void conservationMenuItem_actionPerformed(boolean selected)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (selected)
+ {
+ // JBPNote: Conservation name shouldn't be i18n translated
+ Conservation c = new Conservation("Group",
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
+ }
+ modifyConservation.setEnabled(selected);
+
+ refresh();
+ }
+
+ /**
+ * Shows a dialog where group name and description may be edited
+ */
+ protected void groupName_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
+ sg.getDescription(),
+ MessageManager.getString("label.group_name"),
+ MessageManager.getString("label.group_description"));
+ dialog.showDialog(ap.alignFrame,
+ MessageManager.getString("label.edit_group_name_description"),
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ }
+ });
+ }
+
+ /**
+ * Get selection group - adding it to the alignment if necessary.
+ *
+ * @return sequence group to operate on
+ */
+ 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;
+ }
+
+ /**
+ * Shows a dialog where the sequence name and description may be edited. If a
+ * name containing spaces is entered, these are converted to underscores, with
+ * a warning message.
+ */
+ void sequenceName_actionPerformed()
+ {
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(),
+ MessageManager.getString("label.sequence_name"),
+ MessageManager.getString("label.sequence_description"));
+ dialog.showDialog(ap.alignFrame, MessageManager.getString(
+ "label.edit_sequence_name_description"), new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager.getString(
+ "label.spaces_converted_to_underscores"),
+ MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
+ }
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.getAlignment().deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
+ /**
+ * Offers a colour chooser and sets the selected colour as the group outline
+ */
+ protected void outline_actionPerformed()
+ {
+ String title = MessageManager.getString("label.select_outline_colour");
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ getGroup().setOutlineColour(c);
+ refresh();
+ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
+ Color.BLUE, listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showBoxes_actionPerformed()
+ {
+ getGroup().setDisplayBoxes(showBoxes.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showText_actionPerformed()
+ {
+ getGroup().setDisplayText(showText.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void showColourText_actionPerformed()
+ {
+ getGroup().setColourText(showColourText.isSelected());
+ refresh();
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ ap.av.hideSequences(sequence, representGroup);
+ }
+
+ public void copy_actionPerformed()
+ {
+ ap.alignFrame.copy_actionPerformed();
+ }
+
+ public void cut_actionPerformed()
+ {
+ ap.alignFrame.cut_actionPerformed();
+ }
+
+ void changeCase(ActionEvent e)
+ {
+ Object source = e.getSource();
+ 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 == toggle)
+ {
+ description = MessageManager.getString("label.toggle_case");
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == upperCase)
+ {
+ description = MessageManager.getString("label.to_upper_case");
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
+ description = MessageManager.getString("label.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());
+
+ }
+ }
+
+ public void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
+
+ String[] omitHidden = null;
+
+ System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+ // or we simply trust the user wants
+ // wysiwig behaviour
+
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
+ }
+
+ public void sequenceFeature_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ int gSize = sg.getSize();
+ 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).getDatasetSequence());
+ features.add(new SequenceFeature(null, null, start, end, null));
+ }
+ }
+
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
+ {
+ new FeatureEditor(ap, seqs, features, true).showDialog();
+ }
+ }
+
+ public void textColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg != null)
+ {
+ new TextColourChooser().chooseColour(ap, sg);
+ }
+ }
+
+ /**
+ * Shows a dialog where sequence characters may be edited. Any changes are
+ * applied, and added as an available 'Undo' item in the edit commands
+ * history.
+ */
+ public void editSequence_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ SequenceI seq = sequence;
+ if (sg != null)
+ {
+ if (seq == null)
+ {
+ seq = sg.getSequenceAt(0);
+ }
+
+ EditNameDialog dialog = new EditNameDialog(
+ seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null);
+ dialog.showDialog(ap.alignFrame,
+ MessageManager.getString("label.edit_sequence"),
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ 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());
+ }
+ });
+ }
+ }
+
+ /**
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
+ *
+ * @return
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ SequenceGroup sg = getGroup();
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, ap.av, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
+
+ refresh();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff