/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
\r
import jalview.datamodel.*;\r
\r
-import jalview.io.*;\r
\r
import jalview.schemes.*;\r
\r
\r
import javax.swing.*;\r
\r
+import java.util.Vector;\r
+import jalview.io.FormatAdapter;\r
+\r
\r
/**\r
* DOCUMENT ME!\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
+ 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
*\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, Vector links)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\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[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
+\r
try\r
{\r
jbInit();\r
e.printStackTrace();\r
}\r
\r
- if ((seq == null) || (seq.getPDBId() == null))\r
+\r
+ if (seq != null)\r
{\r
- pdbMenuItem.setVisible(false);\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
+\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
+ add(menuItem);\r
+\r
+ if(ap.av.getSelectionGroup() !=null\r
+ && ap.av.getSelectionGroup().getSize(false)>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
+ ap.overviewPanel.updateOverviewImage();\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
+ ap.overviewPanel.updateOverviewImage();\r
+ }\r
+ });\r
+\r
+ 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
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
- else\r
- {\r
- java.util.Vector links = Preferences.sequenceURLLinks;\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
- item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
-\r
- final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
- + sequence.getName() +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+ {\r
+ String id = seq.getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\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
+ url = link.substring(link.lastIndexOf("|")+1);\r
\r
\r
item.addActionListener(new java.awt.event.ActionListener()\r
\r
linkMenu.add(item);\r
}\r
- add(linkMenu);\r
+ if(sequence!=null)\r
+ sequenceMenu.add(linkMenu);\r
+ else\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("Selection");\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
- add(sequenceMenu);\r
- groupMenu.add(groupName);\r
- groupMenu.addSeparator();\r
- groupMenu.add(unGroupMenuItem);\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
+ 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
+\r
+ add(sequenceMenu);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputMenu);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(groupName);\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
- sequenceMenu.add(pdbMenuItem);\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
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
+ 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
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
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
}\r
\r
/**\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences,\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
ap.av.alignment.getWidth());\r
refresh();\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
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\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
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
ap.av.alignment.getWidth()));\r
\r
refresh();\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
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(true), 0,\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\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
SequenceGroup sg = getGroup();\r
StringBuffer sb = new StringBuffer();\r
\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
- Sequence tmp = (Sequence) sg.sequences.get(i);\r
+ Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
sb.append("\n");\r
}\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
ex.printStackTrace();\r
}\r
}\r
+\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null || sg.getSize(false)<1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]{sequence});\r
+ return;\r
+ }\r
+\r
+ int gsize = sg.getSize(false);\r
+ SequenceI [] hseqs;\r
+\r
+ hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
+ int index = 0;\r
+ while(index < gsize)\r
+ {\r
+ if(representGroup && sg.getSequenceAt(index)!=sequence)\r
+ {\r
+ sequence.addHiddenSequence(sg.getSequenceAt(index));\r
+ hseqs[index] = sg.getSequenceAt(index);\r
+ }\r
+ else if(!representGroup)\r
+ {\r
+ hseqs[index] = sg.getSequenceAt(index);\r
+ }\r
+ index ++;\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+\r
+ ap.av.setSelectionGroup(null);\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
+ changeCase(e.getSource());\r
+ }\r
+\r
+ public void lowerCase_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
+\r
+ public void toggle_actionPerformed(ActionEvent e)\r
+ {\r
+ changeCase(e.getSource());\r
+ }\r
+\r
+ void changeCase(Object source)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\r
+ for (int g = 0; g < sg.getSize(true); g++)\r
+ {\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ end = sg.getEndRes() + 1;\r
+ if (end > sg.getEndRes())\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+\r
+ if (source == toggle)\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .toggleCase(start, end);\r
+ else\r
+ ( (SequenceI) sg.getSequences(true).elementAt(g))\r
+ .changeCase(source == upperCase, start, end);\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+\r
+ }\r
+ while (end < sg.getEndRes());\r
+ }\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+ }\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
+ 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
+ sequence.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