- 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)
- {
- viewport.followSelection = listenToViewSelections.isSelected();