2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.SplitContainerI;
24 import jalview.datamodel.AlignmentI;
25 import jalview.jbgui.GAlignFrame;
26 import jalview.jbgui.GSplitFrame;
27 import jalview.structure.StructureSelectionManager;
28 import jalview.util.Platform;
29 import jalview.viewmodel.AlignmentViewport;
31 import java.awt.Component;
32 import java.awt.Toolkit;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.KeyAdapter;
36 import java.awt.event.KeyEvent;
37 import java.awt.event.KeyListener;
38 import java.beans.PropertyVetoException;
39 import java.util.Arrays;
40 import java.util.List;
41 import java.util.Map.Entry;
43 import javax.swing.AbstractAction;
44 import javax.swing.InputMap;
45 import javax.swing.JComponent;
46 import javax.swing.JMenuItem;
47 import javax.swing.KeyStroke;
48 import javax.swing.event.InternalFrameAdapter;
49 import javax.swing.event.InternalFrameEvent;
52 * An internal frame on the desktop that hosts a horizontally split view of
53 * linked DNA and Protein alignments. Additional views can be created in linked
54 * pairs, expanded to separate split frames, or regathered into a single frame.
56 * (Some) operations on each alignment are automatically mirrored on the other.
57 * These include mouseover (highlighting), sequence and column selection,
58 * sequence ordering and sorting, and grouping, colouring and sorting by tree.
63 public class SplitFrame extends GSplitFrame implements SplitContainerI
65 private static final int WINDOWS_INSETS_WIDTH = 28; // tbc
67 private static final int MAC_INSETS_WIDTH = 28;
69 private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc
71 private static final int MAC_INSETS_HEIGHT = 50;
73 private static final int DESKTOP_DECORATORS_HEIGHT = 65;
75 private static final long serialVersionUID = 1L;
77 public SplitFrame(GAlignFrame top, GAlignFrame bottom)
84 * Initialise this frame.
88 getTopFrame().setSplitFrame(this);
89 getBottomFrame().setSplitFrame(this);
90 getTopFrame().setVisible(true);
91 getBottomFrame().setVisible(true);
93 ((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
94 ((AlignFrame) getBottomFrame()).getViewport());
97 * estimate width and height of SplitFrame; this.getInsets() doesn't seem to
98 * give the full additional size (a few pixels short)
100 int widthFudge = Platform.isAMac() ? MAC_INSETS_WIDTH
101 : WINDOWS_INSETS_WIDTH;
102 int heightFudge = Platform.isAMac() ? MAC_INSETS_HEIGHT
103 : WINDOWS_INSETS_HEIGHT;
104 int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
105 int height = ((AlignFrame) getTopFrame()).getHeight()
106 + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
108 height = fitHeightToDesktop(height);
109 setSize(width, height);
113 addCloseFrameListener();
119 addCommandListeners();
123 * Reduce the height if too large to fit in the Desktop. Also adjust the
124 * divider location in proportion.
128 * @return original or reduced height
130 public int fitHeightToDesktop(int height)
132 // allow about 65 pixels for Desktop decorators on Windows
134 int newHeight = Math.min(height, Desktop.instance.getHeight()
135 - DESKTOP_DECORATORS_HEIGHT);
136 if (newHeight != height)
138 int oldDividerLocation = getDividerLocation();
139 setDividerLocation(oldDividerLocation * newHeight / height);
145 * Set the top and bottom frames to listen to each others Commands (e.g. Edit,
148 protected void addCommandListeners()
150 // TODO if CommandListener is only ever 1:1 for complementary views,
151 // may change broadcast pattern to direct messaging (more efficient)
152 final StructureSelectionManager ssm = StructureSelectionManager
153 .getStructureSelectionManager(Desktop.instance);
154 ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
155 ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
159 * Do any tweaking and twerking of the layout wanted.
161 public void adjustLayout()
164 * Ensure sequence ids are the same width so sequences line up
166 int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
167 int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
168 int w3 = Math.max(w1, w2);
171 ((AlignFrame) getTopFrame()).getViewport().setIdWidth(w3);
175 ((AlignFrame) getBottomFrame()).getViewport().setIdWidth(w3);
179 * Scale protein to either 1 or 3 times character width of dna
181 final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
182 final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
183 final AlignmentI topAlignment = topViewport.getAlignment();
184 final AlignmentI bottomAlignment = bottomViewport.getAlignment();
185 AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
186 : (bottomAlignment.isNucleotide() ? bottomViewport : null);
187 AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
188 : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
189 if (protein != null && cdna != null)
191 // if (protein.isProteinFontAsCdna())
193 // TODO handle different fonts
194 int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
195 protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
201 * Adjust the divider for a sensible split of the real estate (for example,
202 * when many transcripts are shown with a single protein). This should only be
203 * called after the split pane has been laid out (made visible) so it has a
206 protected void adjustDivider()
208 final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
209 final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
210 final AlignmentI topAlignment = topViewport.getAlignment();
211 final AlignmentI bottomAlignment = bottomViewport.getAlignment();
212 boolean topAnnotations = topViewport.isShowAnnotation();
213 boolean bottomAnnotations = bottomViewport.isShowAnnotation();
214 // TODO need number of visible sequences here, not #sequences - how?
215 int topCount = topAlignment.getHeight();
216 int bottomCount = bottomAlignment.getHeight();
217 int topCharHeight = topViewport.getViewStyle().getCharHeight();
218 int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
221 * estimate ratio of (topFrameContent / bottomFrameContent)
223 int insets = Platform.isAMac() ? MAC_INSETS_HEIGHT
224 : WINDOWS_INSETS_HEIGHT;
225 // allow 3 'rows' for scale, scrollbar, status bar
226 int topHeight = insets + (3 + topCount) * topCharHeight
227 + (topAnnotations ? topViewport.calcPanelHeight() : 0);
228 int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
229 + (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
230 double ratio = ((double) topHeight) / (topHeight + bottomHeight);
233 * limit to 0.2 <= ratio <= 0.8 to avoid concealing all sequences
235 ratio = Math.min(ratio, 0.8d);
236 ratio = Math.max(ratio, 0.2d);
237 setRelativeDividerLocation(ratio);
241 * Add a listener to tidy up when the frame is closed.
243 protected void addCloseFrameListener()
245 addInternalFrameListener(new InternalFrameAdapter()
248 public void internalFrameClosed(InternalFrameEvent evt)
256 * Add a key listener that delegates to whichever split component the mouse is
257 * in (or does nothing if neither).
259 protected void addKeyListener()
261 addKeyListener(new KeyAdapter()
265 public void keyPressed(KeyEvent e)
267 AlignFrame af = (AlignFrame) getFrameAtMouse();
270 * Intercept and override any keys here if wanted.
272 if (!overrideKey(e, af))
276 for (KeyListener kl : af.getKeyListeners())
285 public void keyReleased(KeyEvent e)
287 Component c = getFrameAtMouse();
290 for (KeyListener kl : c.getKeyListeners())
301 * Returns true if the key event is overriden and actioned (or ignored) here,
302 * else returns false, indicating it should be delegated to the AlignFrame's
305 * We can't handle Cmd-Key combinations here, instead this is done by
306 * overriding key bindings.
308 * @see addKeyOverrides
313 protected boolean overrideKey(KeyEvent e, AlignFrame af)
315 boolean actioned = false;
316 int keyCode = e.getKeyCode();
319 case KeyEvent.VK_DOWN:
320 if (e.isAltDown() || !af.viewport.cursorMode)
323 * Key down (or Alt-key-down in cursor mode) - move selected sequences
325 ((AlignFrame) getTopFrame()).moveSelectedSequences(false);
326 ((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
332 if (e.isAltDown() || !af.viewport.cursorMode)
335 * Key up (or Alt-key-up in cursor mode) - move selected sequences
337 ((AlignFrame) getTopFrame()).moveSelectedSequences(true);
338 ((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
349 * Set key bindings (recommended for Swing over key accelerators).
351 private void addKeyBindings()
353 overrideDelegatedKeyBindings();
355 overrideImplementedKeyBindings();
359 * Override key bindings with alternative action methods implemented in this
362 protected void overrideImplementedKeyBindings()
367 overrideExpandViews();
368 overrideGatherViews();
372 * Replace Cmd-W close view action with our version.
374 protected void overrideCloseView()
376 AbstractAction action;
378 * Ctrl-W / Cmd-W - close view or window
380 KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
381 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
382 action = new AbstractAction()
385 public void actionPerformed(ActionEvent e)
387 closeView_actionPerformed();
390 overrideKeyBinding(key_cmdW, action);
394 * Replace Cmd-T new view action with our version.
396 protected void overrideNewView()
399 * Ctrl-T / Cmd-T open new view
401 KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
402 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
403 AbstractAction action = new AbstractAction()
406 public void actionPerformed(ActionEvent e)
408 newView_actionPerformed();
411 overrideKeyBinding(key_cmdT, action);
415 * For now, delegates key events to the corresponding key accelerator for the
416 * AlignFrame that the mouse is in. Hopefully can be simplified in future if
417 * AlignFrame is changed to use key bindings rather than accelerators.
419 protected void overrideDelegatedKeyBindings()
421 if (getTopFrame() instanceof AlignFrame)
424 * Get all accelerator keys in the top frame (the bottom should be
425 * identical) and override each one.
427 for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
428 .getAccelerators().entrySet())
430 overrideKeyBinding(acc);
436 * Overrides an AlignFrame key accelerator with our version which delegates to
437 * the action listener in whichever frame has the mouse (and does nothing if
442 private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)
444 final KeyStroke ks = acc.getKey();
445 InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
446 inputMap.put(ks, ks);
447 this.getActionMap().put(ks, new AbstractAction()
450 public void actionPerformed(ActionEvent e)
452 Component c = getFrameAtMouse();
453 if (c != null && c instanceof AlignFrame)
455 for (ActionListener a : ((AlignFrame) c).getAccelerators()
456 .get(ks).getActionListeners())
458 a.actionPerformed(null);
466 * Replace an accelerator key's action with the specified action.
470 protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)
472 this.getActionMap().put(ks, action);
473 overrideMenuItem(ks, action);
477 * Create and link new views (with matching names) in both panes.
479 * Note this is _not_ multiple tabs, each hosting a split pane view, rather it
480 * is a single split pane with each split holding multiple tabs which are
483 * TODO implement instead with a tabbed holder in the SplitView, each tab
484 * holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
485 * some additional coding.
487 protected void newView_actionPerformed()
489 AlignFrame topFrame = (AlignFrame) getTopFrame();
490 AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
491 final boolean scaleProteinAsCdna = topFrame.viewport
492 .isScaleProteinAsCdna();
494 AlignmentPanel newTopPanel = topFrame.newView(null, true);
495 AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
498 * This currently (for the first new view only) leaves the top pane on tab 0
499 * but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
500 * from the bottom back to the first frame. Next line is a fudge to work
501 * around this. TODO find a better way.
503 if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
505 topFrame.setDisplayedView(newTopPanel);
508 newBottomPanel.av.viewName = newTopPanel.av.viewName;
509 newTopPanel.av.setCodingComplement(newBottomPanel.av);
512 * These lines can be removed once scaleProteinAsCdna is added to element
513 * Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
516 newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
517 newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
520 * Line up id labels etc
524 final StructureSelectionManager ssm = StructureSelectionManager
525 .getStructureSelectionManager(Desktop.instance);
526 ssm.addCommandListener(newTopPanel.av);
527 ssm.addCommandListener(newBottomPanel.av);
531 * Close the currently selected view in both panes. If there is only one view,
532 * close this split frame.
534 protected void closeView_actionPerformed()
536 int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
543 AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
544 AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
546 ((AlignFrame) getTopFrame()).closeView(topPanel);
547 ((AlignFrame) getBottomFrame()).closeView(bottomPanel);
552 * Close child frames and this split frame.
556 ((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
557 ((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
560 this.setClosed(true);
561 } catch (PropertyVetoException e)
568 * Replace AlignFrame 'expand views' action with SplitFrame version.
570 protected void overrideExpandViews()
572 KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
573 AbstractAction action = new AbstractAction()
576 public void actionPerformed(ActionEvent e)
578 expandViews_actionPerformed();
581 overrideMenuItem(key_X, action);
585 * Replace AlignFrame 'gather views' action with SplitFrame version.
587 protected void overrideGatherViews()
589 KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
590 AbstractAction action = new AbstractAction()
593 public void actionPerformed(ActionEvent e)
595 gatherViews_actionPerformed();
598 overrideMenuItem(key_G, action);
602 * Override the menu action associated with the keystroke in the child frames,
603 * replacing it with the given action.
608 private void overrideMenuItem(KeyStroke ks, AbstractAction action)
610 overrideMenuItem(ks, action, getTopFrame());
611 overrideMenuItem(ks, action, getBottomFrame());
615 * Override the menu action associated with the keystroke in one child frame,
616 * replacing it with the given action. Mwahahahaha.
622 private void overrideMenuItem(KeyStroke key, final AbstractAction action,
625 if (comp instanceof AlignFrame)
627 JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
630 for (ActionListener al : mi.getActionListeners())
632 mi.removeActionListener(al);
634 mi.addActionListener(new ActionListener()
637 public void actionPerformed(ActionEvent e)
639 action.actionPerformed(e);
647 * Expand any multiple views (which are always in pairs) into separate split
650 protected void expandViews_actionPerformed()
652 Desktop.instance.explodeViews(this);
656 * Gather any other SplitFrame views of this alignment back in as multiple
657 * (pairs of) views in this SplitFrame.
659 protected void gatherViews_actionPerformed()
661 Desktop.instance.gatherViews(this);
665 * Returns the alignment in the complementary frame to the one given.
668 public AlignmentI getComplement(Object alignFrame)
670 if (alignFrame == this.getTopFrame())
672 return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
674 else if (alignFrame == this.getBottomFrame())
676 return ((AlignFrame) getTopFrame()).viewport.getAlignment();
682 * Returns the title of the complementary frame to the one given.
685 public String getComplementTitle(Object alignFrame)
687 if (alignFrame == this.getTopFrame())
689 return ((AlignFrame) getBottomFrame()).getTitle();
691 else if (alignFrame == this.getBottomFrame())
693 return ((AlignFrame) getTopFrame()).getTitle();
699 * Set the 'other half' to hidden / revealed.
702 public void setComplementVisible(Object alignFrame, boolean show)
705 * Hiding the AlignPanel suppresses unnecessary repaints
707 if (alignFrame == getTopFrame())
709 ((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
711 else if (alignFrame == getBottomFrame())
713 ((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
715 super.setComplementVisible(alignFrame, show);
719 * return the AlignFrames held by this container
721 * @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
724 public List<AlignFrame> getAlignFrames()
726 return Arrays.asList(new AlignFrame[] { (AlignFrame) getTopFrame(),
727 (AlignFrame) getBottomFrame() });
731 * Replace Cmd-F Find action with our version. This is necessary because the
732 * 'default' Finder searches in the first AlignFrame it finds. We need it to
733 * search in the half of the SplitFrame that has the mouse.
735 protected void overrideFind()
738 * Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
740 KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
741 .getDefaultToolkit().getMenuShortcutKeyMask(), false);
742 AbstractAction action = new AbstractAction()
745 public void actionPerformed(ActionEvent e)
747 Component c = getFrameAtMouse();
748 if (c != null && c instanceof AlignFrame)
750 AlignFrame af = (AlignFrame) c;
751 new Finder(af.viewport, af.alignPanel);
755 overrideKeyBinding(key_cmdF, action);