--- /dev/null
+package jalview.gui;
+
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
+import jalview.datamodel.AlignmentI;
+import jalview.jbgui.GAlignFrame;
+import jalview.jbgui.GSplitFrame;
+import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Component;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.beans.PropertyVetoException;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.InputMap;
+import javax.swing.JComponent;
+import javax.swing.JMenuItem;
+import javax.swing.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * An internal frame on the desktop that hosts a horizontally split view of
+ * linked DNA and Protein alignments. Additional views can be created in linked
+ * pairs, expanded to separate split frames, or regathered into a single frame.
+ * <p>
+ * (Some) operations on each alignment are automatically mirrored on the other.
+ * These include mouseover (highlighting), sequence and column selection,
+ * sequence ordering and sorting, and grouping, colouring and sorting by tree.
+ *
+ * @author gmcarstairs
+ *
+ */
+public class SplitFrame extends GSplitFrame implements SplitContainerI
+{
+ private static final long serialVersionUID = 1L;
+
+ public SplitFrame(GAlignFrame top, GAlignFrame bottom)
+ {
+ super(top, bottom);
+ init();
+ }
+
+ /**
+ * Initialise this frame.
+ */
+ protected void init()
+ {
+ getTopFrame().setSplitFrame(this);
+ getBottomFrame().setSplitFrame(this);
+ getTopFrame().setVisible(true);
+ getBottomFrame().setVisible(true);
+
+ ((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
+ ((AlignFrame) getBottomFrame()).getViewport());
+
+ setSize(AlignFrame.DEFAULT_WIDTH, Desktop.instance.getHeight() - 20);
+
+ adjustLayout();
+
+ addCloseFrameListener();
+
+ addKeyListener();
+
+ addKeyBindings();
+
+ addCommandListeners();
+ }
+
+ /**
+ * Set the top and bottom frames to listen to each others Commands (e.g. Edit,
+ * Order).
+ */
+ protected void addCommandListeners()
+ {
+ // TODO if CommandListener is only ever 1:1 for complementary views,
+ // may change broadcast pattern to direct messaging (more efficient)
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
+ ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
+ }
+
+ /**
+ * Do any tweaking and twerking of the layout wanted.
+ */
+ private void adjustLayout()
+ {
+ /*
+ * Ensure sequence ids are the same width for good alignment.
+ */
+ int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
+ int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
+ int w3 = Math.max(w1, w2);
+ if (w1 != w3)
+ {
+ ((AlignFrame) getTopFrame()).getViewport().setIdWidth(w3);
+ }
+ if (w2 != w3)
+ {
+ ((AlignFrame) getBottomFrame()).getViewport().setIdWidth(w3);
+ }
+
+ /*
+ * Set the character width for protein to 3 times that for dna.
+ */
+ final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
+ final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
+ final AlignmentI topAlignment = topViewport.getAlignment();
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();
+ AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
+ : (bottomAlignment.isNucleotide() ? bottomViewport : null);
+ AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
+ : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
+ if (protein != null && cdna != null)
+ {
+ ViewStyleI vs = cdna.getViewStyle();
+ vs.setCharWidth(3 * vs.getCharWidth());
+ protein.setViewStyle(vs);
+ }
+ }
+
+ /**
+ * Add a listener to tidy up when the frame is closed.
+ */
+ protected void addCloseFrameListener()
+ {
+ addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
+ if (getTopFrame() instanceof AlignFrame)
+ {
+ ((AlignFrame) getTopFrame())
+ .closeMenuItem_actionPerformed(true);
+ }
+ if (getBottomFrame() instanceof AlignFrame)
+ {
+ ((AlignFrame) getBottomFrame())
+ .closeMenuItem_actionPerformed(true);
+ }
+ };
+ });
+ }
+
+ /**
+ * Add a key listener that delegates to whichever split component the mouse is
+ * in (or does nothing if neither).
+ */
+ protected void addKeyListener()
+ {
+ addKeyListener(new KeyAdapter() {
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ AlignFrame af = (AlignFrame) getFrameAtMouse();
+
+ /*
+ * Intercept and override any keys here if wanted.
+ */
+ if (!overrideKey(e, af))
+ {
+ if (af != null)
+ {
+ for (KeyListener kl : af.getKeyListeners())
+ {
+ kl.keyPressed(e);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ Component c = getFrameAtMouse();
+ if (c != null)
+ {
+ for (KeyListener kl : c.getKeyListeners())
+ {
+ kl.keyReleased(e);
+ }
+ }
+ }
+
+ });
+ }
+
+ /**
+ * Returns true if the key event is overriden and actioned (or ignored) here,
+ * else returns false, indicating it should be delegated to the AlignFrame's
+ * usual handler.
+ * <p>
+ * We can't handle Cmd-Key combinations here, instead this is done by
+ * overriding key bindings.
+ *
+ * @see addKeyOverrides
+ * @param e
+ * @param af
+ * @return
+ */
+ protected boolean overrideKey(KeyEvent e, AlignFrame af)
+ {
+ boolean actioned = false;
+ int keyCode = e.getKeyCode();
+ switch (keyCode)
+ {
+ case KeyEvent.VK_DOWN:
+ if (e.isAltDown() || !af.viewport.cursorMode)
+ {
+ /*
+ * Key down (or Alt-key-down in cursor mode) - move selected sequences
+ */
+ ((AlignFrame) getTopFrame()).moveSelectedSequences(false);
+ ((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
+ actioned = true;
+ e.consume();
+ }
+ break;
+ case KeyEvent.VK_UP:
+ if (e.isAltDown() || !af.viewport.cursorMode)
+ {
+ /*
+ * Key up (or Alt-key-up in cursor mode) - move selected sequences
+ */
+ ((AlignFrame) getTopFrame()).moveSelectedSequences(true);
+ ((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
+ actioned = true;
+ e.consume();
+ }
+ default:
+ }
+ return actioned;
+ }
+
+ /**
+ * Set key bindings (recommended for Swing over key accelerators).
+ */
+ private void addKeyBindings()
+ {
+ overrideDelegatedKeyBindings();
+
+ overrideImplementedKeyBindings();
+ }
+
+ /**
+ * Override key bindings with alternative action methods implemented in this
+ * class.
+ */
+ protected void overrideImplementedKeyBindings()
+ {
+ overrideNewView();
+ overrideCloseView();
+ overrideExpandViews();
+ overrideGatherViews();
+ }
+
+ /**
+ * Replace Cmd-W close view action with our version.
+ */
+ protected void overrideCloseView()
+ {
+ AbstractAction action;
+ /*
+ * Ctrl-W / Cmd-W - close view or window
+ */
+ KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ closeView_actionPerformed();
+ }
+ };
+ overrideKeyBinding(key_cmdW, action);
+ }
+
+ /**
+ * Replace Cmd-T new view action with our version.
+ */
+ protected void overrideNewView()
+ {
+ /*
+ * Ctrl-T / Cmd-T open new view
+ */
+ KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed();
+ }
+ };
+ overrideKeyBinding(key_cmdT, action);
+ }
+
+ /**
+ * For now, delegates key events to the corresponding key accelerator for the
+ * AlignFrame that the mouse is in. Hopefully can be simplified in future if
+ * AlignFrame is changed to use key bindings rather than accelerators.
+ */
+ protected void overrideDelegatedKeyBindings()
+ {
+ if (getTopFrame() instanceof AlignFrame)
+ {
+ /*
+ * Get all accelerator keys in the top frame (the bottom should be
+ * identical) and override each one.
+ */
+ for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
+ .getAccelerators().entrySet())
+ {
+ overrideKeyBinding(acc);
+ }
+ }
+ }
+
+ /**
+ * Overrides an AlignFrame key accelerator with our version which delegates to
+ * the action listener in whichever frame has the mouse (and does nothing if
+ * neither has).
+ *
+ * @param acc
+ */
+ private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)
+ {
+ final KeyStroke ks = acc.getKey();
+ InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
+ inputMap.put(ks, ks);
+ this.getActionMap().put(ks, new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Component c = getFrameAtMouse();
+ if (c != null && c instanceof AlignFrame)
+ {
+ for (ActionListener a : ((AlignFrame) c).getAccelerators()
+ .get(ks).getActionListeners())
+ {
+ a.actionPerformed(null);
+ }
+ }
+ }
+ });
+ }
+
+ /**
+ * Replace an accelerator key's action with the specified action.
+ *
+ * @param ks
+ */
+ protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)
+ {
+ this.getActionMap().put(ks, action);
+ overrideMenuItem(ks, action);
+ }
+
+ /**
+ * Create and link new views (with matching names) in both panes.
+ * <p>
+ * Note this is _not_ multiple tabs, each hosting a split pane view, rather it
+ * is a single split pane with each split holding multiple tabs which are
+ * linked in pairs.
+ * <p>
+ * TODO implement instead with a tabbed holder in the SplitView, each tab
+ * holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
+ * some additional coding.
+ */
+ protected void newView_actionPerformed()
+ {
+ AlignFrame topFrame = (AlignFrame) getTopFrame();
+ AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
+
+ AlignmentPanel newTopPanel = topFrame.newView(null, true);
+ AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
+
+ /*
+ * This currently (for the first new view only) leaves the top pane on tab 0
+ * but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
+ * from the bottom back to the first frame. Next line is a fudge to work
+ * around this. TODO find a better way.
+ */
+ if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
+ {
+ topFrame.setDisplayedView(newTopPanel);
+ }
+
+ newBottomPanel.av.viewName = newTopPanel.av.viewName;
+ newTopPanel.av.setCodingComplement(newBottomPanel.av);
+
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.addCommandListener(newTopPanel.av);
+ ssm.addCommandListener(newBottomPanel.av);
+ }
+
+ /**
+ * Close the currently selected view in both panes. If there is only one view,
+ * close this split frame.
+ */
+ protected void closeView_actionPerformed()
+ {
+ int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
+ if (viewCount < 2)
+ {
+ close();
+ return;
+ }
+
+ AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
+ AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
+
+ ((AlignFrame) getTopFrame()).closeView(topPanel);
+ ((AlignFrame) getBottomFrame()).closeView(bottomPanel);
+
+ }
+
+ /**
+ * Close child frames and this split frame.
+ */
+ public void close()
+ {
+ ((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
+ ((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
+ try
+ {
+ this.setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ // ignore
+ }
+ }
+
+ /**
+ * Replace AlignFrame 'expand views' action with SplitFrame version.
+ */
+ protected void overrideExpandViews()
+ {
+ KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed();
+ }
+ };
+ overrideMenuItem(key_X, action);
+ }
+
+ /**
+ * Replace AlignFrame 'gather views' action with SplitFrame version.
+ */
+ protected void overrideGatherViews()
+ {
+ KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ AbstractAction action = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed();
+ }
+ };
+ overrideMenuItem(key_G, action);
+ }
+
+ /**
+ * Override the menu action associated with the keystroke in the child frames,
+ * replacing it with the given action.
+ *
+ * @param ks
+ * @param action
+ */
+ private void overrideMenuItem(KeyStroke ks, AbstractAction action)
+ {
+ overrideMenuItem(ks, action, getTopFrame());
+ overrideMenuItem(ks, action, getBottomFrame());
+ }
+
+ /**
+ * Override the menu action associated with the keystroke in one child frame,
+ * replacing it with the given action. Mwahahahaha.
+ *
+ * @param key
+ * @param action
+ * @param comp
+ */
+ private void overrideMenuItem(KeyStroke key, final AbstractAction action,
+ JComponent comp)
+ {
+ if (comp instanceof AlignFrame)
+ {
+ JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
+ if (mi != null)
+ {
+ for (ActionListener al : mi.getActionListeners())
+ {
+ mi.removeActionListener(al);
+ }
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ action.actionPerformed(e);
+ }
+ });
+ }
+ }
+ }
+
+ /**
+ * Expand any multiple views (which are always in pairs) into separate split
+ * frames.
+ */
+ protected void expandViews_actionPerformed()
+ {
+ Desktop.instance.explodeViews(this);
+ }
+
+ /**
+ * Gather any other SplitFrame views of this alignment back in as multiple
+ * (pairs of) views in this SplitFrame.
+ */
+ protected void gatherViews_actionPerformed()
+ {
+ Desktop.instance.gatherViews(this);
+ }
+
+ /**
+ * Returns the alignment in the complementary frame to the one given.
+ */
+ @Override
+ public AlignmentI getComplement(Object alignFrame)
+ {
+ if (alignFrame == this.getTopFrame())
+ {
+ return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
+ }
+ else if (alignFrame == this.getBottomFrame())
+ {
+ return ((AlignFrame) getTopFrame()).viewport.getAlignment();
+ }
+ return null;
+ }
+
+ /**
+ * Returns the title of the complementary frame to the one given.
+ */
+ @Override
+ public String getComplementTitle(Object alignFrame)
+ {
+ if (alignFrame == this.getTopFrame())
+ {
+ return ((AlignFrame) getBottomFrame()).getTitle();
+ }
+ else if (alignFrame == this.getBottomFrame())
+ {
+ return ((AlignFrame) getTopFrame()).getTitle();
+ }
+ return null;
+ }
+}
+
git://source.jalview.org / jalview.git / blobdiff