\r
import jalview.datamodel.*;\r
\r
-import jalview.io.*;\r
\r
import jalview.schemes.*;\r
\r
JMenuItem sequenceName = new JMenuItem();\r
Sequence sequence;\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem pdbMenuItem = 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
+ 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
+\r
+ /**\r
* Creates a new PopupMenu object.\r
*\r
* @param ap DOCUMENT ME!\r
* @param seq DOCUMENT ME!\r
*/\r
- public PopupMenu(AlignmentPanel ap, Sequence seq)\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
e.printStackTrace();\r
}\r
\r
- if ((seq == null) || (seq.getPDBId() == null))\r
+\r
+ if (seq != null)\r
{\r
- pdbMenuItem.setVisible(false);\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
noColourmenuItem.setSelected(true);\r
}\r
\r
- if (sg.cs instanceof ConservationColourScheme)\r
+ if (sg.cs!=null && sg.cs.conservationApplied())\r
{\r
conservationMenuItem.setSelected(true);\r
}\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
{\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
private void jbInit() throws Exception\r
{\r
groupMenu.setText("Group");\r
- groupMenu.setText("Define");\r
+ groupMenu.setText("Group");\r
groupName.setText("Name");\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit name");\r
+ sequenceName.setText("Edit Name/Description");\r
sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- pdbMenuItem.setText("View PDB structure");\r
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbMenuItem_actionPerformed(e);\r
- }\r
- });\r
+\r
outline.setText("Border colour");\r
outline.addActionListener(new java.awt.event.ActionListener()\r
{\r
showColourText_actionPerformed(e);\r
}\r
});\r
- add(groupMenu);\r
+ editMenu.setText("Edit");\r
+ cut.setText("Cut");\r
+ cut.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ upperCase.setText("To Upper Case");\r
+ upperCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ upperCase_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setText("Copy");\r
+ copy.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ lowerCase.setText("To Lower Case");\r
+ lowerCase.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ lowerCase_actionPerformed(e);\r
+ }\r
+ });\r
+ toggle.setText("Toggle Case");\r
+ toggle.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ toggle_actionPerformed(e);\r
+ }\r
+ });\r
+ add(groupMenu);\r
add(sequenceMenu);\r
- groupMenu.add(groupName);\r
+ this.add(editMenu);\r
+ groupMenu.add(groupName);\r
groupMenu.addSeparator();\r
groupMenu.add(unGroupMenuItem);\r
groupMenu.add(colourMenu);\r
groupMenu.addSeparator();\r
groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(pdbMenuItem);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\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
+ editMenu.add(copy);\r
+ editMenu.add(cut);\r
+ editMenu.add(upperCase);\r
+ editMenu.add(lowerCase);\r
+ editMenu.add(toggle);\r
+ noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDColour_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User Defined");\r
+ userDefinedColour.setText("User Defined...");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
*/\r
void refresh()\r
{\r
- SequenceGroup sg = getGroup();\r
- if(sg!=null)\r
- {\r
- SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
\r
- if (superG != null)\r
- {\r
- superG.setSuperGroupProperties(sg);\r
- }\r
- }\r
ap.seqPanel.repaint();\r
}\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
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
SliderPanel.showPIDSlider();\r
}\r
else // remove PIDColouring\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
refresh();\r
*/\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours(ap, getGroup());\r
- }\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
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
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ sg.cs.setConservation(c);\r
\r
- sg.cs = ccs;\r
-\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
- sg.cs = ccs.cs;\r
+ sg.cs.setConservation(null);\r
}\r
\r
refresh();\r
*/\r
void sequenceName_actionPerformed(ActionEvent e)\r
{\r
- String id = sequence.getName();\r
- String s = (String) JOptionPane.showInternalInputDialog(ap,\r
- "Edit sequence name",\r
- "Edit sequence name (" + sequence.getName() + ")",\r
- JOptionPane.PLAIN_MESSAGE, null, null, id);\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
}\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
refresh();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void pdbMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (sequence.getPDBId() == null)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
- null);\r
-\r
- PDBfile pdb = new PDBfile(result);\r
-\r
- rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame,\r
- sequence.getName() + " " + sequence.getPDBId(), 400, 400);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
\r
/**\r
* DOCUMENT ME!\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
+ public void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed(null);\r
+ }\r
+\r
+ public void cut_actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed(null);\r
+ }\r
+\r
+ public void upperCase_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ for(int g=0; g<sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
+ }\r
+ ap.repaint();\r
+ }\r
+\r
+ public void lowerCase_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ for(int g=0; g<sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
+ }\r
+ ap.repaint();\r
+ }\r
+\r
+ public void toggle_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null)\r
+ return;\r
+\r
+ for (int g = 0; g < sg.getSize(); g++)\r
+ {\r
+ sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
+ }\r
+\r
+ ap.repaint();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff