X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=66cafc5f17e9bdbd40894e331a0969e8e02e142d;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=722bad1d4e5b74d8eee4b537507efa4de970d218;hpb=b7c522b6eba60889fb1078f75e83e8e6c97ef7f8;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
old mode 100755
new mode 100644
index 722bad1..66cafc5
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,585 +1,2097 @@
-package jalview.gui;
-
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
-import javax.swing.*;
-import java.awt.event.*;
-
-
-public class PopupMenu extends JPopupMenu
-{
- JMenu groupMenu = new JMenu();
- JMenuItem copyGroup = new JMenuItem();
- JMenuItem moveGroup = new JMenuItem();
- JMenuItem deleteSequences = new JMenuItem();
- JMenuItem analyze = new JMenuItem();
- JMenu defineMenu = new JMenu();
- JMenuItem groupName = new JMenuItem();
- JMenuItem groupAnnotation = 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();
- JMenu residueMenu = new JMenu();
- JMenuItem annotateResidue = new JMenuItem();
-
- SequenceI sequence;
-
- public PopupMenu(AlignmentPanel ap, SequenceI seq)
- {
- ///////////////////////////////////////////////////////////
- // 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);
-
- try
- { jbInit(); }
- catch(Exception e)
- { e.printStackTrace(); }
-
- SequenceGroup sg = ap.av.getRubberbandGroup();
- 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 instanceof ConservationColourScheme)
- conservationMenuItem.setSelected(true);
-
- }
-
- if(seq!=null)
- {
- residueMenu.setVisible(false);
- sequenceName.setText( sequence.getName() );
- }
- else
- sequenceMenu.setVisible(false);
-
- }
- private void jbInit() throws Exception
- {
- groupMenu.setText("Group");
- copyGroup.setText("Copy region to new Alignment");
- copyGroup.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- copyGroup_actionPerformed(e);
- }
- });
- moveGroup.setText("Move sequences to new Alignment");
- moveGroup.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- moveGroup_actionPerformed(e);
- }
- });
- deleteSequences.setText("Delete sequences");
- deleteSequences.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deleteSequences_actionPerformed(e);
- }
- });
- analyze.setText("Analyze");
- analyze.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- analyze_actionPerformed(e);
- }
- });
- defineMenu.setText("Define");
- groupName.setText("Name");
- groupName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupName_actionPerformed(e);
- }
- });
- groupAnnotation.setText("Annotation");
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupAnnotation_actionPerformed(e);
- }
- });
- sequenceMenu.setText("Sequence");
- sequenceName.setText("sequenceName");
- sequenceName.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sequenceName_actionPerformed(e);
- }
- });
- residueMenu.setText("Residue");
- annotateResidue.setText("annotate residue???");
- PIDColour.setFocusPainted(false);
- add(groupMenu);
- this.add(sequenceMenu);
- this.add(residueMenu);
- groupMenu.add(defineMenu);
- groupMenu.addSeparator();
- groupMenu.add(copyGroup);
- groupMenu.add(moveGroup);
- groupMenu.add(deleteSequences);
- groupMenu.addSeparator();
- groupMenu.add(analyze);
- defineMenu.add(groupName);
- defineMenu.add(groupAnnotation);
- defineMenu.addSeparator();
- defineMenu.add(noColourmenuItem);
- defineMenu.add(clustalColour);
- defineMenu.add(zappoColour);
- defineMenu.add(taylorColour);
- defineMenu.add(hydrophobicityColour);
- defineMenu.add(helixColour);
- defineMenu.add(strandColour);
- defineMenu.add(turnColour);
- defineMenu.add(buriedColour);
- defineMenu.add(userDefinedColour);
- defineMenu.add(PIDColour);
- defineMenu.add(BLOSUM62Colour);
- defineMenu.addSeparator();
- defineMenu.add(abovePIDColour);
- defineMenu.add(conservationMenuItem);
-
- sequenceMenu.add(sequenceName);
- residueMenu.add(annotateResidue);
-
- 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 colour scheme");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setText("Taylor colour scheme");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setText("By 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 PID threshold only");
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- abovePIDColour_actionPerformed(e);
- }
- });
- userDefinedColour.setText("User defined colours");
- 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 score");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed(e);
- }
- });
- conservationMenuItem.setText("By conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
-
-
-
- }
-
- void refresh()
- {
- SequenceGroup sg = getGroup();
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
- if( superG !=null)
- superG.setSuperGroupProperties( sg );
-
- ap.seqPanel.seqCanvas.paintFlag=true;
- ap.seqPanel.repaint();
- }
-
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new ClustalxColourScheme();
- refresh();
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
-
-/*
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
-{
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
-JInternalFrame frame = new JInternalFrame();
-frame.setContentPane(cip);
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
-frame.setMaximizable(false);
-
- }*/
-
-
- protected void abovePIDColour_actionPerformed(ActionEvent e)
- {
- SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(sp);
- Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);
- frame.setMaximizable(false);
-
- }
-
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- JInternalFrame frame = new JInternalFrame();
- UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
- frame.setContentPane(chooser);
- Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );
- frame.setResizable(false);
- frame.setIconifiable(false);
- frame.setMaximizable(false);
-
- }
-
- protected void PIDColour_actionPerformed(ActionEvent e)
- {
-
- }
-
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- getGroup().cs = new Blosum62ColourScheme(ap.av);
- refresh();
- }
-
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- getGroup().cs = null;
- refresh();
- }
-
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
- sg.getEndRes() );
-
- c.calculate();
- c.verdict(false, 100);
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
- sg.cs = ccs;
-
- refresh();
- }
-
- protected void groupAnnotation_actionPerformed(ActionEvent e)
- {
-
- }
-
- 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);
- }
-
- protected void copyGroup_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = ap.av.getRubberbandGroup();
-
- SequenceI[] s = new Sequence[sg.sequences.size()];
- for (int i=0; i < sg.sequences.size(); i++)
- {
- s[i] = new Sequence( sg.getSequenceAt(i));
- s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
- }
- AlignFrame af = new AlignFrame(new Alignment(s));
- int newHeight = s.length * af.viewport.getCharHeight() + 200;
- if (newHeight > 500)
- newHeight = 500;
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
- }
-
- protected void moveGroup_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = ap.av.getRubberbandGroup();
-
- SequenceI[] s = new Sequence[sg.sequences.size()];
-
- for (int i=0; i < sg.sequences.size(); i++)
- s[i] = new Sequence( sg.getSequenceAt(i));
-
- AlignFrame af = new AlignFrame(new Alignment(s));
- int newHeight = s.length * af.viewport.getCharHeight() + 200;
- if(newHeight>500)
- newHeight=500;
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
-
-
- for (int i=0; i < sg.sequences.size(); i++)
- ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
-
-
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
- ap.RefreshPanels();
-
-
- }
-
- protected void deleteSequences_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = ap.av.getRubberbandGroup();
- for (int i=0;i < sg.sequences.size(); i++)
- ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
-
- ap.av.alignment.deleteGroup(sg);
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
- ap.seqPanel.parent.RefreshPanels();
-
- }
-
- protected void analyze_actionPerformed(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
- JInternalFrame frame = new JInternalFrame();
- cap.formatForOutput();
- frame.setContentPane(cap);
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
- SequenceGroup sg = getGroup();
- StringBuffer sb = new StringBuffer();
-
- for(int i=0; i" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
+ + "
"); + new SequenceAnnotationReport(null) + .createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + : null); + contents.append("
"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")})) + ,500, 400); + + } + + protected void showNonconserved_actionPerformed() + { + getGroup().setShowNonconserved(displayNonconserved.isSelected()); + refresh(); + } + + /** + * call to refresh view after settings change + */ + void refresh() + { + ap.updateAnnotation(); + ap.paintAlignment(true); + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void clustalColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void zappoColour_actionPerformed() + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + protected void purinePyrimidineColour_actionPerformed() + { + getGroup().cs = new PurinePyrimidineColourScheme(); + refresh(); + } + + /* + * protected void covariationColour_actionPerformed() { getGroup().cs = new + * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } + */ + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + + 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.getSource().equals(userDefinedColour)) + { + new UserDefinedColours(ap, sg); + } + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours + .getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void PIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.isSelected()) + { + // JBPNote: Conservation name shouldn't be i18n translated + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), + sg.getEndRes() + 1); + + c.calculate(); + c.verdict(false, ap.av.getConsPercGaps()); + + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else + // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } + + public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = getGroup(); + if (sg == null) + { + return; + } + + AnnotationColourGradient acg = new AnnotationColourGradient( + sequence.getAnnotation()[0], null, + AnnotationColourGradient.NO_THRESHOLD); + + acg.setPredefinedColours(true); + sg.cs = acg; + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void groupName_actionPerformed() + { + + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), + sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", + MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + + /** + * Get selection group - adding it to the alignment if necessary. + * + * @return sequence group to operate on + */ + SequenceGroup getGroup() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + // this method won't add a new group if it already exists + if (sg != null) + { + ap.av.getAlignment().addGroup(sg); + } + + return sg; + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void sequenceName_actionPerformed() + { + EditNameDialog dialog = new EditNameDialog(sequence.getName(), + sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ", + MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"), + ap.alignFrame); + + if (!dialog.accept) + { + return; + } + + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + MessageManager.getString("label.spaces_converted_to_backslashes"), + MessageManager.getString("label.no_spaces_allowed_sequence_name"), + JOptionPane.WARNING_MESSAGE); + } + + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false); + } + + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.getAlignment().deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } + void createGroupMenuItem_actionPerformed() + { + getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void outline_actionPerformed() + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), + Color.BLUE); + + if (col != null) + { + sg.setOutlineColour(col); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showBoxes_actionPerformed() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + + public void showLink(String url) + { + try + { + jalview.util.BrowserLauncher.openURL(url); + } catch (Exception ex) + { + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); + + ex.printStackTrace(); + } + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg.getSize() < 1) + { + ap.av.hideSequence(new SequenceI[] + { sequence }); + return; + } + + ap.av.setSelectionGroup(null); + + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); + + return; + } + + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); + } + + ap.av.hideSequence(hseqs); + // refresh(); TODO: ? needed ? + ap.av.sendSelection(); + } + + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } + + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + sg.getEndRes() + 1); + + String description; + int caseChange; + + if (source == toggle) + { + description = MessageManager.getString("label.toggle_case"); + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if (source == upperCase) + { + description = MessageManager.getString("label.to_upper_case"); + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = MessageManager.getString("label.to_lower_case"); + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + startEnd, caseChange); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + Desktop.addInternalFrame(cap, + MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); + + String[] omitHidden = null; + + System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens + // or we simply trust the user wants + // wysiwig behaviour + SequenceGroup sg = ap.av.getSelectionGroup(); + ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); + omitHidden = ap.av.getViewAsString(true); + Alignment oal = new Alignment(ap.av.getSequenceSelection()); + AlignmentAnnotation[] nala = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (nala != null) + { + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } + } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + oal, omitHidden, csel, sg)); + oal = null; + } + + public void pdbFromFile_actionPerformed() + { + jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)})); + chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()})); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, + jalview.io.AppletFormatAdapter.FILE, sequence, true); + } + + } + + public void enterPDB_actionPerformed() + { + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE); + + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id.toUpperCase()); + sequence.getDatasetSequence().addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed() + { + + final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[] + { sequence } + : ap.av.getSequenceSelection()); + Thread discpdb = new Thread(new Runnable() + { + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); + } + + public void sequenceFeature_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + return; + } + + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) + { + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); + features[rsize] = new SequenceFeature(null, null, null, start, end, + "Jalview"); + rsize++; + } + } + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs, 0, rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.highlightSearchResults(null); + } + } + + public void textColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg != null) + { + new TextColourChooser().chooseColour(ap, sg); + } + } + + public void colourByStructure(String pdbid) + { + Annotation[] anots = ap.av.getStructureSelectionManager() + .colourSequenceFromStructure(sequence, pdbid); + + AlignmentAnnotation an = new AlignmentAnnotation("Structure", + "Coloured by " + pdbid, anots); + + ap.av.getAlignment().addAnnotation(an); + an.createSequenceMapping(sequence, 0, true); + // an.adjustForAlignment(); + ap.av.getAlignment().setAnnotationIndex(an, 0); + + ap.adjustAnnotationHeight(); + + sequence.addAlignmentAnnotation(an); + + } + + public void editSequence_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + if (sequence == null) + sequence = (Sequence) sg.getSequenceAt(0); + + EditNameDialog dialog = new EditNameDialog( + sequence.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, + MessageManager.getString("label.edit_sequence"), ap.alignFrame); + + if (dialog.accept) + { + EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), + EditCommand.REPLACE, dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); + + ap.alignFrame.addHistoryItem(editCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + } + } + } + +}