+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.controller.FeatureSettingsControllerGuiI;
+import jalview.datamodel.AlignmentI;
+import jalview.jbgui.GAlignFrame;
+import jalview.jbgui.GSplitFrame;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+
import java.awt.Component;
-import java.awt.Toolkit;
+import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.beans.PropertyVetoException;
+import java.util.Arrays;
+import java.util.List;
import java.util.Map.Entry;
import javax.swing.AbstractAction;
import javax.swing.InputMap;
import javax.swing.JComponent;
+import javax.swing.JDesktopPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JTabbedPane;
import javax.swing.KeyStroke;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-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;
-
/**
* 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
*/
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);
((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
((AlignFrame) getBottomFrame()).getViewport());
- int width = ((AlignFrame) getTopFrame()).getWidth();
- // about 50 pixels for the SplitFrame's title bar etc
+ /*
+ * estimate width and height of SplitFrame; this.getInsets() doesn't seem to
+ * give the full additional size (a few pixels short)
+ */
+ int widthFudge = Platform.isAMac() ? MAC_INSETS_WIDTH
+ : WINDOWS_INSETS_WIDTH;
+ int heightFudge = Platform.isAMac() ? MAC_INSETS_HEIGHT
+ : WINDOWS_INSETS_HEIGHT;
+ int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
int height = ((AlignFrame) getTopFrame()).getHeight()
- + ((AlignFrame) getBottomFrame()).getHeight() + 50;
- height = Math.min(height, Desktop.instance.getHeight() - 20);
- // setSize(AlignFrame.DEFAULT_WIDTH, Desktop.instance.getHeight() - 20);
+ + ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
+ + heightFudge;
+ height = fitHeightToDesktop(height);
setSize(width, height);
adjustLayout();
addCloseFrameListener();
-
+
addKeyListener();
addKeyBindings();
}
/**
+ * 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).
*/
public void adjustLayout()
{
/*
- * Ensure sequence ids are the same width for good alignment.
+ * Ensure sequence ids are the same width so sequences line up
*/
int w1 = ((AlignFrame) getTopFrame()).getViewport().getIdWidth();
int w2 = ((AlignFrame) getBottomFrame()).getViewport().getIdWidth();
}
/*
- * Set the character width for protein to 3 times that for dna.
+ * Scale protein to either 1 or 3 times character width of dna
*/
- boolean scaleThreeToOne = true; // TODO a new Preference option?
- if (scaleThreeToOne)
- {
- 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();
- ViewStyleI vs2 = protein.getViewStyle();
- vs2.setCharWidth(3 * vs.getCharWidth());
- protein.setViewStyle(vs2);
- }
+ 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)
+ {
+ 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.
+ * <p>
+ * 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.isAMac() ? 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()
@Override
public void internalFrameClosed(InternalFrameEvent evt)
{
- if (getTopFrame() instanceof AlignFrame)
- {
- ((AlignFrame) getTopFrame())
- .closeMenuItem_actionPerformed(true);
- }
- if (getBottomFrame() instanceof AlignFrame)
- {
- ((AlignFrame) getBottomFrame())
- .closeMenuItem_actionPerformed(true);
- }
+ close();
};
});
}
*/
protected void addKeyListener()
{
- addKeyListener(new KeyAdapter() {
+ addKeyListener(new KeyAdapter()
+ {
@Override
public void keyPressed(KeyEvent e)
}
}
}
-
+
});
}
actioned = true;
e.consume();
}
+ break;
default:
}
return actioned;
/*
* Ctrl-W / Cmd-W - close view or window
*/
- KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
action = new AbstractAction()
{
@Override
/*
* Ctrl-T / Cmd-T open new view
*/
- KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
AbstractAction action = new AbstractAction()
{
@Override
Component c = getFrameAtMouse();
if (c != null && c instanceof AlignFrame)
{
- for (ActionListener a : ((AlignFrame) c).getAccelerators()
- .get(ks).getActionListeners())
+ for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
+ .getActionListeners())
{
a.actionPerformed(null);
}
{
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);
topFrame.setDisplayedView(newTopPanel);
}
- newBottomPanel.av.viewName = newTopPanel.av.viewName;
+ 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);
}
/**
+ * return the AlignFrames held by this container
+ *
+ * @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
+ * Protein)}
+ */
+ public List<AlignFrame> getAlignFrames()
+ {
+ return Arrays
+ .asList(new AlignFrame[]
+ { (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
+ }
+
+ @Override
+ public AlignFrame getComplementAlignFrame(
+ AlignViewControllerGuiI alignFrame)
+ {
+ if (getTopFrame() == alignFrame)
+ {
+ return (AlignFrame) getBottomFrame();
+ }
+ if (getBottomFrame() == alignFrame)
+ {
+ return (AlignFrame) getTopFrame();
+ }
+ // we didn't know anything about this frame...
+ return null;
+ }
+
+ /**
* Replace Cmd-F Find action with our version. This is necessary because the
* 'default' Finder searches in the first AlignFrame it finds. We need it to
* search in the half of the SplitFrame that has the mouse.
/*
* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
*/
- KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
- .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
AbstractAction action = new AbstractAction()
{
@Override
};
overrideKeyBinding(key_cmdF, action);
}
-}
+ /**
+ * Override to do nothing if triggered from one of the child frames
+ */
+ @Override
+ public void setSelected(boolean selected) throws PropertyVetoException
+ {
+ JDesktopPane desktopPane = getDesktopPane();
+ JInternalFrame fr = desktopPane == null ? null
+ : desktopPane.getSelectedFrame();
+ if (fr == getTopFrame() || fr == getBottomFrame())
+ {
+ /*
+ * patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
+ * it may be possible to remove this method in future
+ * if the underlying Java behaviour changes
+ */
+ if (selected)
+ {
+ moveToFront();
+ }
+ return;
+ }
+ super.setSelected(selected);
+ }
+
+ /**
+ * holds the frame for feature settings, so Protein and DNA tabs can be managed
+ */
+ JInternalFrame featureSettingsUI;
+
+ JTabbedPane featureSettingsPanels;
+
+ @Override
+ public void addFeatureSettingsUI(
+ FeatureSettingsControllerGuiI featureSettings)
+ {
+ boolean showInternalFrame = false;
+ if (featureSettingsUI == null || featureSettingsPanels == null)
+ {
+ showInternalFrame = true;
+ featureSettingsPanels = new JTabbedPane();
+ featureSettingsUI = new JInternalFrame(
+ "Feature Settings for CDS and Protein Views");
+ featureSettingsPanels.setOpaque(true);
+ featureSettingsUI.setContentPane(featureSettingsPanels);
+ createDummyTabs();
+ }
+ if (featureSettingsPanels
+ .indexOfTabComponent((Component) featureSettings) > -1)
+ {
+ // just show the feature settings !
+ featureSettingsPanels
+ .setSelectedComponent((Component) featureSettings);
+ return;
+ }
+ // otherwise replace the dummy tab with the given feature settings
+ int pos = getAlignFrames().indexOf(featureSettings.getAlignframe());
+ // if pos==-1 then alignFrame isn't managed by this splitframe
+ if (pos == 0)
+ {
+ featureSettingsPanels.removeTabAt(0);
+ featureSettingsPanels.insertTab("CDS", null,
+ (Component) featureSettings, "Feature Settings for DNA CDS",
+ 0);
+ }
+ if (pos == 1)
+ {
+ featureSettingsPanels.removeTabAt(1);
+ featureSettingsPanels.insertTab("Protein", null,
+ (Component) featureSettings, "Feature Settings for Protein",
+ 1);
+ }
+ featureSettingsPanels.setSelectedComponent((Component) featureSettings);
+ if (showInternalFrame)
+ {
+ if (Platform.isAMac())
+ {
+ Desktop.addInternalFrame(featureSettingsUI,
+ MessageManager.getString(
+ "Feature Settings for CDS and Protein Views"),
+ 600, 480);
+ }
+ else
+ {
+ Desktop.addInternalFrame(featureSettingsUI,
+ MessageManager.getString(
+ "Feature Settings for CDS and Protein Views"),
+ 600, 450);
+ }
+ featureSettingsUI
+ .setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT));
+
+ featureSettingsUI.addInternalFrameListener(
+ new javax.swing.event.InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ for (int tab = 0; tab < featureSettingsPanels
+ .getTabCount();)
+ {
+ FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels
+ .getTabComponentAt(tab);
+ if (fsettings != null)
+ {
+ featureSettingsPanels.removeTabAt(tab);
+ fsettings.featureSettings_isClosed();
+ }
+ else
+ {
+ tab++;
+ }
+ }
+ featureSettingsPanels = null;
+ };
+ });
+ featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ }
+
+ /*
+ * for materialising feature settings for a tab when clicked on
+ */
+ private FocusListener fl1 = new FocusListener()
+ {
+
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ int tab = featureSettingsPanels.getSelectedIndex();
+ getAlignFrames().get(tab).showFeatureSettingsUI();
+ }
+ };
+
+ /**
+ * tab names for feature settings
+ */
+ private String[] tabName = new String[] {
+ MessageManager.getString("label.CDS"),
+ MessageManager.getString("label.Protein") };
+
+ /**
+ * create placeholder tabs which materialise the feature settings for a given
+ * view. Also reinitialises any tabs containing stale feature settings
+ */
+ private void createDummyTabs()
+ {
+ for (int tabIndex = 0; tabIndex < 2; tabIndex++)
+ {
+ JPanel dummyTab = new JPanel();
+ dummyTab.addFocusListener(fl1);
+ featureSettingsPanels.addTab(tabName[tabIndex], dummyTab);
+ }
+ }
+
+ private void replaceWithDummyTab(FeatureSettingsControllerI toClose)
+ {
+ Component dummyTab = null;
+ for (int tabIndex = 0; tabIndex < 2; tabIndex++)
+ {
+ if (featureSettingsPanels.getTabCount() > tabIndex)
+ {
+ dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex);
+ if (dummyTab instanceof FeatureSettingsControllerGuiI
+ && !dummyTab.isVisible())
+ {
+ featureSettingsPanels.removeTabAt(tabIndex);
+ // close the feature Settings tab
+ ((FeatureSettingsControllerGuiI) dummyTab)
+ .featureSettings_isClosed();
+ // create a dummy tab in its place
+ dummyTab = new JPanel();
+ dummyTab.addFocusListener(fl1);
+ featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab,
+ MessageManager.formatMessage(
+ "label.sequence_feature_settings_for",
+ tabName[tabIndex]),
+ tabIndex);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void closeFeatureSettings(
+ FeatureSettingsControllerI featureSettings,
+ boolean closeContainingFrame)
+ {
+ if (featureSettingsUI != null)
+ {
+ if (closeContainingFrame)
+ {
+ try
+ {
+ featureSettingsUI.setClosed(true);
+ } catch (Exception x)
+ {
+ }
+ featureSettingsUI = null;
+ }
+ else
+ {
+ replaceWithDummyTab(featureSettings);
+ }
+ }
+ }
+
+ @Override
+ public boolean isFeatureSettingsOpen()
+ {
+ return featureSettingsUI != null && !featureSettingsUI.isClosed();
+ }
+}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff