import javax.swing.*;\r
\r
import java.util.Vector;\r
+import jalview.io.FormatAdapter;\r
\r
\r
/**\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
\r
/**\r
* Creates a new PopupMenu object.\r
colours.add(PIDColour);\r
colours.add(BLOSUM62Colour);\r
\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
+ elementAt(\r
+ i));\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
+\r
try\r
{\r
jbInit();\r
\r
if (seq != null)\r
{\r
+ int start = Math.max(sequence.getName().length()-15, 0);\r
+ sequenceMenu.setText(sequence.getName().substring(start));\r
+\r
JMenuItem menuItem;\r
if( seq.getDatasetSequence().getPDBId() != null)\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
hideSequences(false);\r
}\r
});\r
- sequenceMenu.add(menuItem);\r
+ add(menuItem);\r
\r
if(ap.av.getSelectionGroup() !=null\r
&& ap.av.getSelectionGroup().getSize(false)>1)\r
if (ap.av.adjustForHiddenSeqs(index) -\r
ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
{\r
- menuItem = new JMenuItem("Reveal");\r
+ menuItem = new JMenuItem("Reveal Sequences");\r
menuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
ap.overviewPanel.updateOverviewImage();\r
}\r
});\r
- sequenceMenu.add(menuItem);\r
+ add(menuItem);\r
}\r
\r
menuItem = new JMenuItem("Reveal All");\r
}\r
});\r
\r
- sequenceMenu.add(menuItem);\r
-\r
-\r
-\r
+ add(menuItem);\r
}\r
\r
\r
{\r
unGroupMenuItem.setVisible(false);\r
}\r
- else\r
- {\r
- groupMenu.insertSeparator(3);\r
- }\r
+\r
\r
if (seq == null)\r
{\r
sequenceMenu.setVisible(false);\r
+ pdbMenu.setVisible(false);\r
}\r
\r
if(links != null && links.size()>0)\r
\r
linkMenu.add(item);\r
}\r
- add(linkMenu);\r
+ sequenceMenu.add(linkMenu);\r
}\r
}\r
\r
private void jbInit() throws Exception\r
{\r
groupMenu.setText("Group");\r
- groupMenu.setText("Group");\r
+ groupMenu.setText("Selection");\r
groupName.setText("Name");\r
groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
toggle_actionPerformed(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(e);\r
+ }\r
+ });\r
+ enterPDB.setText("Enter PDB Id");\r
+ enterPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ enterPDB_actionPerformed(e);\r
+ }\r
+ });\r
+ discoverPDB.setText("Discover PDB ids");\r
+ discoverPDB.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ discoverPDB_actionPerformed(e);\r
+ }\r
+ });\r
+ outputMenu.setText("Output to Textbox...");\r
add(groupMenu);\r
- add(sequenceMenu);\r
- this.add(editMenu);\r
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.addSeparator();\r
groupMenu.add(groupName);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(unGroupMenuItem);\r
groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
+ groupMenu.add(showBoxes);\r
groupMenu.add(showText);\r
groupMenu.add(showColourText);\r
- groupMenu.addSeparator();\r
- groupMenu.add(outline);\r
+ groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
- colourMenu.add(noColourmenuItem);\r
+ sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.add(PIDColour);\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
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
\r
ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
refresh();\r
}\r
\r
ap.repaint();\r
}\r
\r
+ public void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\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
+\r
+ public void pdbFromFile_actionPerformed(ActionEvent e)\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
+ return;\r
+\r
+ entry.setId(reply);\r
+ }\r
+ else\r
+ entry.setId(pdbfile.id);\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(ActionEvent e)\r
+ {\r
+ int size = (ap.av.getSelectionGroup() == null ? 0 :\r
+ ap.av.getSelectionGroup().getSize(false));\r
+\r
+ if (size == 0 || size > 1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(\r
+ Desktop.desktop,\r
+ "Select a single sequence to specify a PDB id for first",\r
+ "Select Single Selected", JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\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);\r
+ ap.av.getSelectionGroup().getSequenceAt(0).getDatasetSequence()\r
+ .addPDBId(entry);\r
+ }\r
+ }\r
+\r
+ public void discoverPDB_actionPerformed(ActionEvent e)\r
+ {\r
+ new jalview.io.DBRefFetcher(\r
+ ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff