-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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 MCview.*;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PopupMenu 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 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
-\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)\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
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
-\r
- if (seq != null)\r
- {\r
- JMenuItem menuItem;\r
- if( seq.getDatasetSequence().getPDBId() != null)\r
- {\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
- elements();\r
- while (e.hasMoreElements())\r
- {\r
- final PDBEntry pdb = (PDBEntry) e.nextElement();\r
-\r
- menuItem = new JMenuItem();\r
- menuItem.setText("View PDB entry: " + pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
- }\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\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
- sequenceMenu.add(menuItem);\r
-\r
- if(ap.av.getSelectionGroup() !=null && 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
-\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
-\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- unGroupMenuItem.setVisible(false);\r
- }\r
- else\r
- {\r
- groupMenu.insertSeparator(3);\r
- }\r
-\r
- if (seq == null)\r
- {\r
- sequenceMenu.setVisible(false);\r
- }\r
- else\r
- {\r
- java.util.Vector links = Preferences.sequenceURLLinks;\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
-\r
- item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
- String id = sequence.getName();\r
- if(id.indexOf("|")>-1)\r
- id = id.substring(id.lastIndexOf("|")+1);\r
-\r
- final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\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
- add(linkMenu);\r
- }\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit() throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- groupMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed(e);\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(e);\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(e);\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(e);\r
- }\r
- });\r
- nucleotideMenuItem.setText("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed(e);\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(e);\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(e);\r
- }\r
- });\r
- showColourText.setText("Colour Text");\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed(e);\r
- }\r
- });\r
- add(groupMenu);\r
- add(sequenceMenu);\r
- groupMenu.add(groupName);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- groupMenu.addSeparator();\r
- groupMenu.add(outline);\r
- sequenceMenu.add(sequenceName);\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
-\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- abovePIDColour.setText("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.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(e);\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(e);\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(e);\r
- }\r
- });\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void refresh()\r
- {\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
-\r
- ap.seqPanel.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences,\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
-\r
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\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
- new UserDefinedColours(ap, sg);\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
-\r
- sg.cs = udc;\r
- }\r
- }\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\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(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if(sg.cs==null)\r
- return;\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter new group name", "Edit group name",\r
- JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(reply);\r
- groupName.setText(reply);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
-\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence) sg.sequences.get(i);\r
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
- }\r
-\r
- /**\r
- * 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
- ap.av.alignment.addGroup(sg);\r
-\r
- return sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed(ActionEvent e)\r
- {\r
- JLabel idlabel = new JLabel( " Sequence Name ");\r
- JLabel desclabel = new JLabel("Sequence Description ");\r
- idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
- desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
- JTextField id = new JTextField(sequence.getName(), 40);\r
- JTextField description = new JTextField(sequence.getDescription(), 40);\r
- JPanel panel = new JPanel(new BorderLayout());\r
- JPanel panel2 = new JPanel(new BorderLayout());\r
- panel2.add(idlabel, BorderLayout.WEST);\r
- panel2.add(id, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.NORTH);\r
- panel2 = new JPanel(new BorderLayout());\r
- panel2.add(desclabel, BorderLayout.WEST);\r
- panel2.add(description, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.SOUTH);\r
-\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- panel, "Edit Sequence Name/Description",\r
- JOptionPane.OK_CANCEL_OPTION );\r
-\r
-\r
- if (reply != JOptionPane.OK_OPTION )\r
- {\r
- return;\r
- }\r
-\r
- String s = id.getText();\r
-\r
- if (s != null)\r
- {\r
- if (s.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
- s = s.replace(' ', '_');\r
- sequence.getDatasetSequence().setName(s);\r
- sequence.setName(s);\r
- ap.repaint();\r
- }\r
-\r
- sequence.getDatasetSequence().setDescription(description.getText());\r
- sequence.setDescription(description.getText());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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(ActionEvent e)\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
- +"\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found", JOptionPane.WARNING_MESSAGE );\r
-\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(sequence);\r
- return;\r
- }\r
-\r
- int index = 0;\r
- while(index < sg.sequences.size())\r
- {\r
- if(representGroup && sg.getSequenceAt(index)!=sequence)\r
- {\r
- sequence.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- else if(!representGroup)\r
- {\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- index ++;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import MCview.*;
+
+import jalview.analysis.*;
+
+import jalview.datamodel.*;
+
+
+import jalview.schemes.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import java.util.Vector;
+import jalview.io.FormatAdapter;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PopupMenu extends JPopupMenu
+{
+ JMenu groupMenu = new JMenu();
+ JMenuItem groupName = new JMenuItem();
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ AlignmentPanel ap;
+ JMenu sequenceMenu = new JMenu();
+ JMenuItem sequenceName = new JMenuItem();
+ Sequence sequence;
+ JMenuItem unGroupMenuItem = new JMenuItem();
+ JMenuItem outline = new JMenuItem();
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+ JMenu colourMenu = new JMenu();
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+ JMenu editMenu = new JMenu();
+ JMenuItem cut = new JMenuItem();
+ JMenuItem copy = new JMenuItem();
+ JMenuItem upperCase = new JMenuItem();
+ JMenuItem lowerCase = new JMenuItem();
+ JMenuItem toggle = new JMenuItem();
+ JMenu pdbMenu = new JMenu();
+ JMenuItem pdbFromFile = new JMenuItem();
+ JMenuItem enterPDB = new JMenuItem();
+ JMenuItem discoverPDB = new JMenuItem();
+ JMenu outputMenu = new JMenu();
+
+ /**
+ * Creates a new PopupMenu object.
+ *
+ * @param ap DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ {
+ ///////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ //////////////////////////////////////////////////////////
+ this.ap = ap;
+ sequence = seq;
+
+ ButtonGroup colours = new ButtonGroup();
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(abovePIDColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputMenu.add(item);
+ }
+
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+
+ if (seq != null)
+ {
+ int start = Math.max(sequence.getName().length()-15, 0);
+ sequenceMenu.setText(sequence.getName().substring(start));
+
+ JMenuItem menuItem;
+ if( seq.getDatasetSequence().getPDBId() != null)
+ {
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+ elements();
+
+ while (e.hasMoreElements())
+ {
+ final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+ menuItem = new JMenuItem();
+ menuItem.setText("View PDB entry: " + pdb.getId());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+ }
+
+ menuItem = new JMenuItem("Hide Sequences");
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(false);
+ }
+ });
+ add(menuItem);
+
+ if(ap.av.getSelectionGroup() !=null
+ && ap.av.getSelectionGroup().getSize(false)>1)
+ {
+ menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(true);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+
+ if (ap.av.hasHiddenRows)
+ {
+ final int index = ap.av.alignment.findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index) -
+ ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ menuItem = new JMenuItem("Reveal Sequences");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showSequence(index);
+ if (ap.overviewPanel != null)
+ ap.overviewPanel.updateOverviewImage();
+ }
+ });
+ add(menuItem);
+ }
+
+ menuItem = new JMenuItem("Reveal All");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showAllHiddenSeqs();
+ if (ap.overviewPanel != null)
+ ap.overviewPanel.updateOverviewImage();
+ }
+ });
+
+ add(menuItem);
+ }
+
+
+ }
+
+
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ groupName.setText(sg.getName());
+
+ if (sg.cs instanceof ZappoColourScheme)
+ {
+ zappoColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TaylorColourScheme)
+ {
+ taylorColour.setSelected(true);
+ }
+ else if (sg.cs instanceof PIDColourScheme)
+ {
+ PIDColour.setSelected(true);
+ }
+ else if (sg.cs instanceof Blosum62ColourScheme)
+ {
+ BLOSUM62Colour.setSelected(true);
+ }
+ else if (sg.cs instanceof UserColourScheme)
+ {
+ userDefinedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HydrophobicColourScheme)
+ {
+ hydrophobicityColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HelixColourScheme)
+ {
+ helixColour.setSelected(true);
+ }
+ else if (sg.cs instanceof StrandColourScheme)
+ {
+ strandColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TurnColourScheme)
+ {
+ turnColour.setSelected(true);
+ }
+ else if (sg.cs instanceof BuriedColourScheme)
+ {
+ buriedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof ClustalxColourScheme)
+ {
+ clustalColour.setSelected(true);
+ }
+ else
+ {
+ noColourmenuItem.setSelected(true);
+ }
+
+ if (sg.cs!=null && sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+
+ showText.setSelected(sg.getDisplayText());
+ showColourText.setSelected(sg.getColourText());
+ showBoxes.setSelected(sg.getDisplayBoxes());
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!ap.av.alignment.getGroups().contains(sg))
+ {
+ unGroupMenuItem.setVisible(false);
+ }
+
+
+ if (seq == null)
+ {
+ sequenceMenu.setVisible(false);
+ pdbMenu.setVisible(false);
+ }
+
+ if(links != null && links.size()>0)
+ {
+ JMenu linkMenu = new JMenu("Link");
+ JMenuItem item;
+ for(int i=0; i<links.size(); i++)
+ {
+ String link = links.elementAt(i).toString();
+ final String label = link.substring(0, link.indexOf("|"));
+ item = new JMenuItem(label);
+ final String url;
+
+ if (link.indexOf("$SEQUENCE_ID$") > -1)
+ {
+ String id = seq.getName();
+ if (id.indexOf("|") > -1)
+ id = id.substring(id.lastIndexOf("|") + 1);
+
+ url = link.substring(link.indexOf("|") + 1,
+ link.indexOf("$SEQUENCE_ID$"))
+ + id +
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ }
+ else
+ url = link.substring(link.lastIndexOf("|")+1);
+
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showLink(url);
+ }
+ });
+
+ linkMenu.add(item);
+ }
+ if(sequence!=null)
+ sequenceMenu.add(linkMenu);
+ else
+ add(linkMenu);
+ }
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ groupMenu.setText("Group");
+ groupMenu.setText("Selection");
+ groupName.setText("Name");
+ groupName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed(e);
+ }
+ });
+ sequenceMenu.setText("Sequence");
+ sequenceName.setText("Edit Name/Description");
+ sequenceName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed(e);
+ }
+ });
+ PIDColour.setFocusPainted(false);
+ unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed(e);
+ }
+ });
+
+ outline.setText("Border colour");
+ outline.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed(e);
+ }
+ });
+ nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideMenuItem_actionPerformed(e);
+ }
+ });
+ colourMenu.setText("Group Colour");
+ showBoxes.setText("Boxes");
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed(e);
+ }
+ });
+ showText.setText("Text");
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed(e);
+ }
+ });
+ showColourText.setText("Colour Text");
+ showColourText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed(e);
+ }
+ });
+ editMenu.setText("Edit");
+ cut.setText("Cut");
+ cut.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed(e);
+ }
+ });
+ upperCase.setText("To Upper Case");
+ upperCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ upperCase_actionPerformed(e);
+ }
+ });
+ copy.setText("Copy");
+ copy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(e);
+ }
+ });
+ lowerCase.setText("To Lower Case");
+ lowerCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ lowerCase_actionPerformed(e);
+ }
+ });
+ toggle.setText("Toggle Case");
+ toggle.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ toggle_actionPerformed(e);
+ }
+ });
+ pdbMenu.setText("Associate Structure with Sequence");
+ pdbFromFile.setText("From File");
+ pdbFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pdbFromFile_actionPerformed(e);
+ }
+ });
+ enterPDB.setText("Enter PDB Id");
+ enterPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ enterPDB_actionPerformed(e);
+ }
+ });
+ discoverPDB.setText("Discover PDB ids");
+ discoverPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ discoverPDB_actionPerformed(e);
+ }
+ });
+ outputMenu.setText("Output to Textbox...");
+ add(groupMenu);
+
+ add(sequenceMenu);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputMenu);
+ groupMenu.addSeparator();
+ groupMenu.add(groupName);
+ groupMenu.add(unGroupMenuItem);
+ groupMenu.add(colourMenu);
+ groupMenu.add(showBoxes);
+ groupMenu.add(showText);
+ groupMenu.add(showColourText);
+ groupMenu.add(outline);
+ sequenceMenu.add(sequenceName);
+ sequenceMenu.add(pdbMenu);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(userDefinedColour);
+
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ JMenuItem item = new JMenuItem(userColours.
+ nextElement().toString());
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.add(item);
+ }
+ }
+
+
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ pdbMenu.add(pdbFromFile);
+ pdbMenu.add(enterPDB);
+ pdbMenu.add(discoverPDB);
+ noColourmenuItem.setText("None");
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed(e);
+ }
+ });
+
+ clustalColour.setText("Clustalx colours");
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed(e);
+ }
+ });
+ zappoColour.setText("Zappo");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed(e);
+ }
+ });
+ taylorColour.setText("Taylor");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed(e);
+ }
+ });
+ hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed(e);
+ }
+ });
+ helixColour.setText("Helix propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed(e);
+ }
+ });
+ strandColour.setText("Strand propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed(e);
+ }
+ });
+ turnColour.setText("Turn propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed(e);
+ }
+ });
+ buriedColour.setText("Buried Index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed(e);
+ }
+ });
+ abovePIDColour.setText("Above % Identity");
+ abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed(e);
+ }
+ });
+ userDefinedColour.setText("User Defined...");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed(e);
+ }
+ });
+ BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed(e);
+ }
+ });
+ conservationMenuItem.setText("Conservation");
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(e);
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void refresh()
+ {
+ if (ap.overviewPanel != null)
+ ap.overviewPanel.updateOverviewImage();
+
+ ap.seqPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true),
+ ap.av.alignment.getWidth());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new ZappoColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new TaylorColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new HydrophobicColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new HelixColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void strandColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new StrandColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new TurnColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new BuriedColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = new NucleotideColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void abovePIDColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ if(sg.cs==null)
+ return;
+
+ if (abovePIDColour.isSelected())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+ }
+ else // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+
+ if (e.getActionCommand().equals("User Defined..."))
+ new UserDefinedColours(ap, sg);
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ sg.cs = udc;
+ }
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+ ap.av.alignment.getWidth()));
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ if(sg.cs==null)
+ return;
+
+ if (conservationMenuItem.isSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(true), 0,
+ ap.av.alignment.getWidth());
+
+ c.calculate();
+ c.verdict(false, ap.av.ConsPercGaps);
+
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void groupName_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter new group name", "Edit group name",
+ JOptionPane.QUESTION_MESSAGE);
+
+ if (reply == null)
+ {
+ return;
+ }
+
+ sg.setName(reply);
+ groupName.setText(reply);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void analyze_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ JInternalFrame frame = new JInternalFrame();
+ frame.setContentPane(cap);
+ Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
+
+ SequenceGroup sg = getGroup();
+ StringBuffer sb = new StringBuffer();
+
+ for (int i = 0; i < sg.getSize(false); i++)
+ {
+ Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
+ sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
+ sb.append("\n");
+ }
+
+ sb.append("Something amazing will happen soon");
+ cap.setText(sb.toString());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ // this method won't add a new group if it already exists
+ if(sg!=null)
+ ap.av.alignment.addGroup(sg);
+
+ return sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ void sequenceName_actionPerformed(ActionEvent e)
+ {
+ JLabel idlabel = new JLabel( " Sequence Name ");
+ JLabel desclabel = new JLabel("Sequence Description ");
+ idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+ desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+ JTextField id = new JTextField(sequence.getName(), 40);
+ JTextField description = new JTextField(sequence.getDescription(), 40);
+ JPanel panel = new JPanel(new BorderLayout());
+ JPanel panel2 = new JPanel(new BorderLayout());
+ panel2.add(idlabel, BorderLayout.WEST);
+ panel2.add(id, BorderLayout.CENTER);
+ panel.add(panel2, BorderLayout.NORTH);
+ panel2 = new JPanel(new BorderLayout());
+ panel2.add(desclabel, BorderLayout.WEST);
+ panel2.add(description, BorderLayout.CENTER);
+ panel.add(panel2, BorderLayout.SOUTH);
+
+
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ panel, "Edit Sequence Name/Description",
+ JOptionPane.OK_CANCEL_OPTION );
+
+
+ if (reply != JOptionPane.OK_OPTION )
+ {
+ return;
+ }
+
+ String s = id.getText();
+
+ if (s != null)
+ {
+ if (s.indexOf(" ") > -1)
+ {
+ JOptionPane.showMessageDialog(ap,
+ "Spaces have been converted to \"_\"",
+ "No spaces allowed in Sequence Name",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ s = s.replace(' ', '_');
+ sequence.getDatasetSequence().setName(s);
+ sequence.setName(s);
+ ap.repaint();
+ }
+
+ sequence.getDatasetSequence().setDescription(description.getText());
+ sequence.setDescription(description.getText());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ void unGroupMenuItem_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.alignment.deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void outline_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color.BLUE);
+
+ if (col != null)
+ {
+ sg.setOutlineColour(col);
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showBoxes_actionPerformed(ActionEvent e)
+ {
+ getGroup().setDisplayBoxes(showBoxes.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showText_actionPerformed(ActionEvent e)
+ {
+ getGroup().setDisplayText(showText.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showColourText_actionPerformed(ActionEvent e)
+ {
+ getGroup().setColourText(showColourText.isSelected());
+ refresh();
+ }
+
+ public void showLink(String url)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Unixers: Couldn't find default web browser."
+ +"\nAdd the full path to your browser in Preferences.",
+ "Web browser not found", JOptionPane.WARNING_MESSAGE );
+
+
+ ex.printStackTrace();
+ }
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if(sg==null || sg.getSize(false)<1)
+ {
+ ap.av.hideSequence(sequence);
+ return;
+ }
+
+ int index = 0;
+ while(index < sg.getSize(false))
+ {
+ if(representGroup && sg.getSequenceAt(index)!=sequence)
+ {
+ sequence.addHiddenSequence(sg.getSequenceAt(index));
+ ap.av.hideSequence(sg.getSequenceAt(index));
+ }
+ else if(!representGroup)
+ {
+ ap.av.hideSequence(sg.getSequenceAt(index));
+ }
+ index ++;
+ }
+
+ ap.av.setSelectionGroup(null);
+ }
+
+ public void copy_actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.copy_actionPerformed(null);
+ }
+
+ public void cut_actionPerformed(ActionEvent e)
+ {
+ ap.alignFrame.cut_actionPerformed(null);
+ }
+
+ public void upperCase_actionPerformed(ActionEvent e)
+ {
+ changeCase(e.getSource());
+ }
+
+ public void lowerCase_actionPerformed(ActionEvent e)
+ {
+ changeCase(e.getSource());
+ }
+
+ public void toggle_actionPerformed(ActionEvent e)
+ {
+ changeCase(e.getSource());
+ }
+
+ void changeCase(Object source)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg != null)
+ {
+ for (int g = 0; g < sg.getSize(true); g++)
+ {
+ int start = sg.getStartRes();
+ int end = sg.getEndRes() + 1;
+
+ do
+ {
+ if (ap.av.hasHiddenColumns)
+ {
+ end = ap.av.colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ end = sg.getEndRes() + 1;
+ if (end > sg.getEndRes())
+ end = sg.getEndRes() + 1;
+ }
+
+ if (source == toggle)
+ ( (SequenceI) sg.getSequences(true).elementAt(g))
+ .toggleCase(start, end);
+ else
+ ( (SequenceI) sg.getSequences(true).elementAt(g))
+ .changeCase(source == upperCase, start, end);
+
+ if (ap.av.hasHiddenColumns)
+ {
+ start = ap.av.colSel.adjustForHiddenColumns(end);
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+
+ }
+ while (end < sg.getEndRes());
+ }
+ ap.repaint();
+ }
+ }
+
+ public void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600,
+ 500);
+
+ String [] omitHidden = null;
+
+ if(ap.av.hasHiddenColumns)
+ {
+ System.out.println("PROMPT USER HERE");
+ omitHidden = ap.av.getViewAsString(true);
+ }
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ ap.av.getSelectionAsNewSequence(),
+ omitHidden));
+ }
+
+
+ public void pdbFromFile_actionPerformed(ActionEvent e)
+ {
+ jalview.io.JalviewFileChooser chooser
+ = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Select a PDB file");
+ chooser.setToolTipText("Load a PDB file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ PDBEntry entry = new PDBEntry();
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ try
+ {
+ MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ if (pdbfile.id == null)
+ {
+ String reply = JOptionPane.showInternalInputDialog(
+ Desktop.desktop,
+ "Couldn't find a PDB id in the file supplied."
+ + "Please enter an Id to identify this structure.",
+ "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+ if (reply == null)
+ return;
+
+ entry.setId(reply);
+ }
+ else
+ entry.setId(pdbfile.id);
+ }
+ catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ }
+
+ }
+
+ public void enterPDB_actionPerformed(ActionEvent e)
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+ if (id != null && id.length() > 0)
+ {
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ sequence.getDatasetSequence()
+ .addPDBId(entry);
+ }
+ }
+
+ public void discoverPDB_actionPerformed(ActionEvent e)
+ {
+ new jalview.io.DBRefFetcher(
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff