* (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 int WINDOWS_INSETS_WIDTH = 28; // tbc private static final int MAC_INSETS_WIDTH = 28; private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc private static final int MAC_INSETS_HEIGHT = 50; private static final int DESKTOP_DECORATORS_HEIGHT = 65; private static final long serialVersionUID = 1L; /** * geometry for Feature Settings Holder */ private static final int FS_MIN_WIDTH = 400; private static final int FS_MIN_HEIGHT = 400; 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()); /* * estimate width and height of SplitFrame; this.getInsets() doesn't seem to * give the full additional size (a few pixels short) */ int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH : WINDOWS_INSETS_WIDTH; int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT : WINDOWS_INSETS_HEIGHT; int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge; int height = ((AlignFrame) getTopFrame()).getHeight() + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE + heightFudge; height = fitHeightToDesktop(height); setSize(width, height); adjustLayout(); addCloseFrameListener(); addKeyListener(); addKeyBindings(); addCommandListeners(); } /** * Reduce the height if too large to fit in the Desktop. Also adjust the * divider location in proportion. * * @param height * in pixels * @return original or reduced height */ public int fitHeightToDesktop(int height) { // allow about 65 pixels for Desktop decorators on Windows int newHeight = Math.min(height, Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT); if (newHeight != height) { int oldDividerLocation = getDividerLocation(); setDividerLocation(oldDividerLocation * newHeight / height); } return newHeight; } /** * 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. */ public void adjustLayout() { final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport; final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport; /* * Ensure sequence ids are the same width so sequences line up */ int w1 = topViewport.getIdWidth(); int w2 = bottomViewport.getIdWidth(); int w3 = Math.max(w1, w2); topViewport.setIdWidth(w3); bottomViewport.setIdWidth(w3); /* * Scale protein to either 1 or 3 times character width of dna */ 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) { int scale = protein.isScaleProteinAsCdna() ? 3 : 1; protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth()); } } /** * Adjusts the divider for a sensible split of the real estate (for example, * when many transcripts are shown with a single protein). This should only be * called after the split pane has been laid out (made visible) so it has a * height. The aim is to avoid unnecessary vertical scroll bars, while * ensuring that at least 2 sequences are visible in each panel. *
* Once laid out, the user may choose to customise as they wish, so this * method is not called again after the initial layout. */ protected void adjustInitialLayout() { AlignFrame topFrame = (AlignFrame) getTopFrame(); AlignFrame bottomFrame = (AlignFrame) getBottomFrame(); /* * recompute layout of top and bottom panels to reflect their * actual (rather than requested) height */ topFrame.alignPanel.adjustAnnotationHeight(); bottomFrame.alignPanel.adjustAnnotationHeight(); final AlignViewport topViewport = topFrame.viewport; final AlignViewport bottomViewport = bottomFrame.viewport; final AlignmentI topAlignment = topViewport.getAlignment(); final AlignmentI bottomAlignment = bottomViewport.getAlignment(); boolean topAnnotations = topViewport.isShowAnnotation(); boolean bottomAnnotations = bottomViewport.isShowAnnotation(); // TODO need number of visible sequences here, not #sequences - how? int topCount = topAlignment.getHeight(); int bottomCount = bottomAlignment.getHeight(); int topCharHeight = topViewport.getViewStyle().getCharHeight(); int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight(); /* * calculate the minimum ratio that leaves at least the height * of two sequences (after rounding) visible in the top panel */ int topPanelHeight = topFrame.getHeight(); int bottomPanelHeight = bottomFrame.getHeight(); int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas .getHeight(); int topPanelMinHeight = topPanelHeight - Math.max(0, topSequencesHeight - 3 * topCharHeight); double totalHeight = (double) topPanelHeight + bottomPanelHeight; double minRatio = topPanelMinHeight / totalHeight; /* * calculate the maximum ratio that leaves at least the height * of two sequences (after rounding) visible in the bottom panel */ int bottomSequencesHeight = bottomFrame.alignPanel .getSeqPanel().seqCanvas.getHeight(); int bottomPanelMinHeight = bottomPanelHeight - Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight); double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight; /* * estimate ratio of (topFrameContent / bottomFrameContent) */ int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT : WINDOWS_INSETS_HEIGHT; // allow 3 'rows' for scale, scrollbar, status bar int topHeight = insets + (3 + topCount) * topCharHeight + (topAnnotations ? topViewport.calcPanelHeight() : 0); int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight + (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0); double ratio = ((double) topHeight) / (double) (topHeight + bottomHeight); /* * limit ratio to avoid concealing all sequences */ ratio = Math.min(ratio, maxRatio); ratio = Math.max(ratio, minRatio); setRelativeDividerLocation(ratio); } /** * Add a listener to tidy up when the frame is closed. */ protected void addCloseFrameListener() { addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameClosed(InternalFrameEvent evt) { close(); }; }); } /** * 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. *
* 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();
}
break;
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()
{
overrideFind();
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,
jalview.util.ShortcutKeyMaskExWrapper
.getMenuShortcutKeyMaskEx(),
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,
jalview.util.ShortcutKeyMaskExWrapper
.getMenuShortcutKeyMaskEx(),
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
* 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.
*
* 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();
final boolean scaleProteinAsCdna = topFrame.viewport
.isScaleProteinAsCdna();
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.setViewName(newTopPanel.av.getViewName());
newTopPanel.av.setCodingComplement(newBottomPanel.av);
/*
* These lines can be removed once scaleProteinAsCdna is added to element
* Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
* care of it
*/
newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
/*
* Line up id labels etc
*/
adjustLayout();
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;
}
/**
* Set the 'other half' to hidden / revealed.
*/
@Override
public void setComplementVisible(Object alignFrame, boolean show)
{
/*
* Hiding the AlignPanel suppresses unnecessary repaints
*/
if (alignFrame == getTopFrame())
{
((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
}
else if (alignFrame == getBottomFrame())
{
((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
}
super.setComplementVisible(alignFrame, show);
}
/**
* return the AlignFrames held by this container
*
* @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
* Protein)}
*/
public List