*/
package jalview.gui;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.renderer.OverviewRenderer;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsHideHidden;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
import jalview.viewmodel.ViewportListenerI;
-import java.awt.Color;
+import java.awt.BorderLayout;
+import java.awt.Cursor;
import java.awt.Dimension;
-import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
-import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
+import java.beans.PropertyVetoException;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
/**
* Panel displaying an overview of the full alignment, with an interactive box
* @author $author$
* @version $Revision$
*/
-public class OverviewPanel extends JPanel implements Runnable,
- ViewportListenerI
+@SuppressWarnings("serial")
+public class OverviewPanel extends JPanel
+ implements Runnable, ViewportListenerI
{
- private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
+ protected OverviewDimensions od;
- private final AnnotationRenderer renderer = new AnnotationRenderer();
+ OverviewCanvas canvas;
- private OverviewDimensions od;
+ protected AlignViewportI av;
- private BufferedImage miniMe;
+ AlignmentViewPanel ap;
- private BufferedImage lastMiniMe = null;
+ protected JCheckBoxMenuItem displayToggle;
- private AlignViewport av;
+ protected boolean showHidden = true;
- private AlignmentPanel ap;
+ protected boolean draggingBox = false;
- //
- private boolean resizing = false;
+ protected ProgressPanel progressPanel;
- // This is set true if the user resizes whilst
- // the overview is being calculated
- private boolean resizeAgain = false;
+ private Dimension dim;
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ private boolean showProgress = !Platform.isJS(); // Jalview.getInstance().getShowStatus()
/**
* Creates a new OverviewPanel object.
* @param alPanel
* The alignment panel which is shown in the overview panel
*/
- public OverviewPanel(AlignmentPanel alPanel)
+ public OverviewPanel(AlignmentViewPanel alPanel, Dimension dim)
{
- this.av = alPanel.av;
+ this.av = alPanel.getAlignViewport();
this.ap = alPanel;
- setLayout(null);
-
- sr = new SequenceRenderer(av);
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(ap);
-
- od = new OverviewDimensions(av.getRanges(),
- (av.isShowAnnotation() && av
- .getAlignmentConservationAnnotation() != null));
+ this.dim = dim;
+
+ showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ createOverviewDimensions();
+ setLayout(new BorderLayout());
+ progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
+ MessageManager.getString("label.oview_calc"), getWidth());
+ if (showProgress) // BH 2019
+ {
+ add(progressPanel, BorderLayout.SOUTH);
+ }
+ canvas = new OverviewCanvas(this, od, av,
+ showProgress ? progressPanel : null);
+ canvas.setPreferredSize(canvas.getSize());
+ add(canvas, BorderLayout.CENTER);
av.getRanges().addPropertyChangeListener(this);
@Override
public void componentResized(ComponentEvent evt)
{
- if ((getWidth() != od.getWidth())
- || (getHeight() != (od.getHeight())))
- {
- updateOverviewImage();
- setBoxPosition();
- }
+ resizePanel();
}
});
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (!SwingUtilities.isRightMouseButton(evt))
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
- // merged
+ if (draggingBox)
+ {
+ // set the mouse position as a fixed point in the box
+ // and drag relative to that position
+ od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
}
}
- });
- addMouseListener(new MouseAdapter()
- {
@Override
- public void mousePressed(MouseEvent evt)
+ public void mouseMoved(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ /*
+ * using HAND_CURSOR rather than DRAG_CURSOR
+ * as the latter is not supported on Mac
+ */
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
{
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
- // merged
+ // reset cursor
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
});
- updateOverviewImage();
- setBoxPosition();
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
+ addMouseListener(new MouseAdapter()
{
- resizeAgain = true;
- return;
- }
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (Platform.isWinRightButton(evt))
+ {
+ showPopupMenu(evt);
+ return;
+ }
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
+ }
+ // don't do anything if the mouse press is in the overview's box
+ // (wait to see if it's a drag instead)
+ // otherwise update the viewport
+ if (!od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ draggingBox = false;
- resizing = true;
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- if ((getWidth() > 0) && (getHeight() > 0))
- {
- od.setWidth(getWidth());
- od.setHeight(getHeight());
- }
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ draggingBox = true;
+ od.setDragPoint(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ }
- setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ showPopupMenu(evt);
+ }
+ }
- Thread thread = new Thread(this);
- thread.start();
- repaint();
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ draggingBox = false;
+ }
+ });
}
- @Override
- public void run()
+ protected void resizePanel()
{
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
+ int ph = (progressPanel.getParent() == null ? 0
+ : progressPanel.getHeight());
+ // Resize is called on the initial display of the overview.
+ // This code adjusts sizes to account for the progress bar if it has not
+ // already been accounted for, which triggers another resize call for
+ // the correct sizing, at which point the overview image is updated.
+ // (This avoids a double recalculation of the image.)
+ if (getWidth() == od.getWidth() && getHeight() == od.getHeight() + ph)
{
- fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ if (canvas.lastMiniMe == null)
+ {
+ updateOverviewImage();
+ }
}
-
- // why do we need to set preferred size again? was set in
- // updateOverviewImage
- setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
- miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
- BufferedImage.TYPE_INT_RGB);
-
- Graphics mg = miniMe.getGraphics();
- mg.setColor(Color.orange);
- mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
-
- // calculate sampleCol and sampleRow
- // alignment width is max number of residues/bases
- // alignment height is number of sequences
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getAbsoluteHeight();
-
- // sampleCol or sampleRow is the width/height allocated to each residue
- // in particular, sometimes we may need more than one row/col of the
- // BufferedImage allocated
- // sampleCol is how much of a residue to assign to each pixel
- // sampleRow is how many sequences to assign to each pixel
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-
- buildImage(sampleRow, sampleCol);
-
- // check for conservation annotation to make sure overview works for DNA too
- if (av.isShowAnnotation()
- && (av.getAlignmentConservationAnnotation() != null))
+ else
{
- renderer.updateFromAlignViewport(av);
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+ int w = getWidth();
+ int h = getHeight();
+ if ((w > 0) && (h > 0))
{
- mg.translate(col, od.getSequencesHeight());
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, od.getGraphHeight(),
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -od.getSequencesHeight());
-
+ if (dim != null)
+ {
+ dim.setSize(w, h - ph);
+ }
+ od.setWidth(w);
+ od.setHeight(h - ph);
+ updateOverviewImage();
}
}
- System.gc();
-
- resizing = false;
+ }
- if (resizeAgain)
+ /**
+ * Create the appropriate type of OverViewDimensions, with the desired size.
+ */
+ private void createOverviewDimensions()
+ {
+ boolean showAnnotation = (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null);
+ if (showHidden)
{
- resizeAgain = false;
- updateOverviewImage();
+ od = new OverviewDimensionsShowHidden(av.getRanges(), showAnnotation,
+ dim);
}
else
{
- lastMiniMe = miniMe;
+ od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation,
+ dim);
}
- // setBoxPosition();
}
- /*
- * Build the overview panel image
+ /**
+ * Displays the popup menu and acts on user input
*/
- private void buildImage(float sampleRow, float sampleCol)
+ protected void showPopupMenu(MouseEvent e)
{
- int lastcol = -1;
- int lastrow = -1;
- int rgbColour = Color.white.getRGB();
-
- SequenceI seq = null;
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
- // get hidden row and hidden column map once at beginning.
- // clone featureRenderer settings to avoid race conditions... if state is
- // updated just need to refresh again
- for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
+ JPopupMenu popup = new JPopupMenu();
+ ActionListener menuListener = new ActionListener()
{
- boolean doCopy = true;
- int currentrow = (int) (row * sampleRow);
- if (currentrow != lastrow)
+ @Override
+ public void actionPerformed(ActionEvent event)
{
- doCopy = false;
-
- lastrow = currentrow;
-
- // get the sequence which would be at alignment index 'lastrow' if no
- // rows were hidden, and determine whether it is hidden or not
- hiddenRow = av.getAlignment().isHidden(lastrow);
- seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
+ // switch on/off the hidden columns view
+ toggleHiddenColumns();
+ displayToggle.setSelected(showHidden);
}
+ };
+ displayToggle = new JCheckBoxMenuItem(
+ MessageManager.getString("label.togglehidden"));
+ displayToggle.setEnabled(true);
+ displayToggle.setSelected(showHidden);
+ popup.add(displayToggle);
+ displayToggle.addActionListener(menuListener);
+ popup.show(this, e.getX(), e.getY());
+ }
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- if (doCopy)
- {
- rgbColour = miniMe.getRGB(col, row - 1);
- }
- else if ((int) (col * sampleCol) != lastcol
- || (int) (row * sampleRow) != lastrow)
- {
- lastcol = (int) (col * sampleCol);
- rgbColour = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol, finder);
- }
- // else we just use the color we already have , so don't need to set it
-
- miniMe.setRGB(col, row, rgbColour);
- }
- }
+ /**
+ * Toggle overview display between showing hidden columns and hiding hidden
+ * columns
+ */
+ protected void toggleHiddenColumns()
+ {
+ showHidden = !showHidden;
+ createOverviewDimensions();
+ canvas.resetOviewDims(od);
+ updateOverviewImage();
+ setBoxPosition();
}
- /*
- * Find the colour of a sequence at a specified column position
+ /**
+ * Updates the overview image when the related alignment panel is updated.
+ *
+ * Cases:
+ *
+ * AlignFrame.setFeatureGroupState
+ *
+ * AlignmentPanel.paintAlignment(true,...) (117 references)
+ *
+ * OverviewPanel..componentResized() OverviewPanel.toggleHiddenColumns()
+ *
+ * PopupMenu for action.reveal_sequences, action.reveal_all
+ *
+ * SliderPanel.mouseReleased()
+ *
*/
- private int getColumnColourFromSequence(
- jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol,
- FeatureColourFinder finder)
+ public void updateOverviewImage()
{
- Color color = Color.white;
+ if (canvas == null)
+ {
+ /*
+ * panel has been disposed
+ */
+ return;
+ }
+
+ int ph = (progressPanel.getParent() == null ? 0
+ : progressPanel.getHeight());
- if ((seq != null) && (seq.getLength() > lastcol))
+ if ((getWidth() > 0) && (getHeight() > 0))
{
- color = sr.getResidueColour(seq, lastcol, finder);
+ od.setWidth(getWidth());
+ od.setHeight(getHeight() - ph);
}
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight() + ph));
+
+ if (canvas.restartDraw())
{
- color = color.darker().darker();
+ return;
}
- return color.getRGB();
+ Thread thread = new Thread(this);
+ thread.start();
+ }
+
+ @Override
+ public void run()
+ {
+ if (canvas != null)
+ {
+ setBoxPosition();
+ canvas.draw(av.isShowSequenceFeatures(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
+ ap.getFeatureRenderer());
+ }
}
/**
* changed
*
*/
- private void setBoxPosition()
+ private void setBoxPositionOnly()
{
- od.setBoxPosition(av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
- repaint();
+ if (od != null)
+ {
+ od.updateBox();
+ int oldX = od.getBoxX();
+ int oldY = od.getBoxY();
+ int oldWidth = od.getBoxWidth();
+ int oldHeight = od.getBoxHeight();
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ repaint(oldX - 1, oldY - 1, oldWidth + 2, oldHeight + 2);
+ repaint(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
+ od.getBoxHeight());
+ }
}
-
- @Override
- public void paintComponent(Graphics g)
+ private void setBoxPosition()
{
- if (resizing || resizeAgain)
- {
- if (lastMiniMe == null)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else
- {
- g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
- }
- g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else if (lastMiniMe != null)
+ if (od != null)
{
- g.drawImage(lastMiniMe, 0, 0, this);
- if (lastMiniMe != miniMe)
- {
- g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ repaint();
}
-
- g.setColor(Color.red);
- od.drawBox(g);
}
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- setBoxPosition();
+ setBoxPositionOnly();
+ }
+
+ /**
+ * Removes this object as a property change listener, and nulls references
+ */
+ protected void dispose()
+ {
+ try
+ {
+ if (av != null)
+ {
+ av.getRanges().removePropertyChangeListener(this);
+ }
+
+ canvas.dispose();
+
+ /*
+ * close the parent frame (which also removes it from the
+ * Desktop Windows menu)
+ */
+ ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, (this)))
+ .setClosed(true);
+ } catch (PropertyVetoException e)
+ {
+ // ignore
+ } finally
+ {
+ progressPanel = null;
+ av = null;
+ canvas = null;
+ ap = null;
+ od = null;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff