- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
- /*
- * public void covariationColour_actionPerformed(ActionEvent e) {
- * changeColour(new
- * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
- * ()[0])); }
- */
- @Override
- public void annotationColour_actionPerformed(ActionEvent e)
- {
- new AnnotationColourChooser(viewport, alignPanel);
- }
-
- @Override
- public void annotationColumn_actionPerformed(ActionEvent e)
- {
- new AnnotationColumnChooser(viewport, alignPanel);
- }
-
- @Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
- {
- new RNAHelicesColourChooser(viewport, alignPanel);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
- {
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cs
- * DOCUMENT ME!
- */
- @Override
- public void changeColour(ColourSchemeI cs)
- {
- // TODO: pull up to controller method
-
- if (cs != null)
- {
- // Make sure viewport is up to date w.r.t. any sliders
- if (viewport.getAbovePIDThreshold())
- {
- int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
- "Background");
- viewport.setThreshold(threshold);
- }
-
- if (viewport.getConservationSelected())
- {
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
- cs, "Background"));
- }
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
- }
-
- viewport.setGlobalColourScheme(cs);
-
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void modifyPID_actionPerformed(ActionEvent e)
- {
- if (viewport.getAbovePIDThreshold()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setPIDSliderSource(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showPIDSlider();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
- {
- if (viewport.getConservationSelected()
- && viewport.getGlobalColourScheme() != null)
- {
- SliderPanel.setConservationSlider(alignPanel,
- viewport.getGlobalColourScheme(), "Background");
- SliderPanel.showConservationSlider();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
- {
- viewport.setConservationSelected(conservationMenuItem.isSelected());
-
- viewport.setAbovePIDThreshold(false);
- abovePIDThreshold.setSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyConservation_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
- {
- viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
- conservationMenuItem.setSelected(false);
- viewport.setConservationSelected(false);
-
- changeColour(viewport.getGlobalColourScheme());
-
- modifyPID_actionPerformed(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
- {
- new UserDefinedColours(alignPanel, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
- }
- }
-
- public void updateUserColourMenu()
- {
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
- addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortIDMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByID(viewport.getAlignment());
- addHistoryItem(new OrderCommand("ID Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortLengthMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByLength(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Length Sort", oldOrder,
- viewport.getAlignment()));
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)
- {
- SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByGroup(viewport.getAlignment());
- addHistoryItem(new OrderCommand("Group Sort", oldOrder,
- viewport.getAlignment()));
-
- alignPanel.paintAlignment(true);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
- {
- new RedundancyPanel(alignPanel, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
- {
- if ((viewport.getSelectionGroup() == null)
- || (viewport.getSelectionGroup().getSize() < 2))
- {
- JOptionPane.showInternalMessageDialog(this, MessageManager
- .getString("label.you_must_select_least_two_sequences"),
- MessageManager.getString("label.invalid_selection"),
- JOptionPane.WARNING_MESSAGE);
- }
- else
- {
- JInternalFrame frame = new JInternalFrame();
- frame.setContentPane(new PairwiseAlignPanel(viewport));
- Desktop.addInternalFrame(frame,
- MessageManager.getString("action.pairwise_alignment"), 600,
- 500);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < 4) && (viewport
- .getSelectionGroup().getSize() > 0))
- || (viewport.getAlignment().getHeight() < 4))
- {
- JOptionPane
- .showInternalMessageDialog(
- this,
- MessageManager
- .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
- MessageManager
- .getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- new PCAPanel(alignPanel);
- }
-
- @Override
- public void autoCalculate_actionPerformed(ActionEvent e)
- {
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
- {
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- }
-
- @Override
- public void sortByTreeOption_actionPerformed(ActionEvent e)
- {
- viewport.sortByTree = sortByTree.isSelected();
- }
-
- @Override
- protected void listenToViewSelections_actionPerformed(ActionEvent e)