*/
package jalview.gui;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-
-import java.awt.Color;
+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.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;
/**
- * DOCUMENT ME!
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
*
* @author $author$
* @version $Revision$
*/
-public class OverviewPanel extends JPanel implements Runnable
+public class OverviewPanel extends JPanel
+ implements Runnable, ViewportListenerI
{
- BufferedImage miniMe;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- final AnnotationRenderer renderer = new AnnotationRenderer();
-
- float scalew = 1f;
-
- float scaleh = 1f;
-
- int width;
+ private OverviewDimensions od;
- int sequencesHeight;
+ private OverviewCanvas oviewCanvas;
- int graphHeight = 20;
+ private AlignViewport av;
- int boxX = -1;
+ private AlignmentPanel ap;
- int boxY = -1;
+ private JCheckBoxMenuItem displayToggle;
- int boxWidth = -1;
+ private boolean showHidden = true;
- int boxHeight = -1;
+ private boolean draggingBox = false;
- boolean resizing = false;
-
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- SequenceRenderer sr;
-
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ private ProgressPanel progressPanel;
/**
* Creates a new OverviewPanel object.
*
- * @param ap
- * DOCUMENT ME!
+ * @param alPanel
+ * The alignment panel which is shown in the overview panel
*/
- public OverviewPanel(AlignmentPanel ap)
+ public OverviewPanel(AlignmentPanel alPanel)
{
- this.av = ap.av;
- this.ap = ap;
- setLayout(null);
-
- sr = new SequenceRenderer(av);
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(ap);
-
- // scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.getAlignment().getWidth()
- / (float) av.getAlignment().getHeight();
-
- if (av.getAlignmentConservationAnnotation() == null)
- {
- graphHeight = 0;
- }
+ this.av = alPanel.av;
+ this.ap = alPanel;
- if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
+ showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ if (showHidden)
{
- // wider
- width = 400;
- sequencesHeight = (int) (400f / initialScale);
- if (sequencesHeight < 40)
- {
- sequencesHeight = 40;
- }
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
else
{
- // taller
- width = (int) (400f * initialScale);
- sequencesHeight = 300;
-
- if (width < 120)
- {
- width = 120;
- }
+ od = new OverviewDimensionsHideHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
+ setLayout(new BorderLayout());
+ progressPanel = new ProgressPanel(OverviewRenderer.UPDATE,
+ MessageManager.getString("label.oview_calc"), getWidth());
+ this.add(progressPanel, BorderLayout.SOUTH);
+ oviewCanvas = new OverviewCanvas(od, av, progressPanel);
+
+ add(oviewCanvas, BorderLayout.CENTER);
+
+ av.getRanges().addPropertyChangeListener(this);
+
+ // without this the overview window does not size to fit the overview canvas
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
+
addComponentListener(new ComponentAdapter()
{
@Override
public void componentResized(ComponentEvent evt)
{
- if ((getWidth() != width)
- || (getHeight() != (sequencesHeight + graphHeight)))
+ // 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()
+ + progressPanel.getHeight())
{
updateOverviewImage();
}
+ else
+ {
+ if ((getWidth() > 0) && (getHeight() > 0))
+ {
+ od.setWidth(getWidth());
+ od.setHeight(getHeight() - progressPanel.getHeight());
+ }
+
+ setPreferredSize(new Dimension(od.getWidth(),
+ od.getHeight() + progressPanel.getHeight()));
+ }
}
+
});
addMouseMotionListener(new MouseMotionAdapter()
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (!SwingUtilities.isRightMouseButton(evt))
+ {
+ 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());
+ }
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
{
- // TODO: feature: jv2.5 detect shift drag and update selection from
- // it.
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ /*
+ * using HAND_CURSOR rather than DRAG_CURSOR
+ * as the latter is not supported on Mac
+ */
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
+
});
addMouseListener(new MouseAdapter()
@Override
public void mousePressed(MouseEvent evt)
{
- if (!av.getWrapAlignment())
+ if (SwingUtilities.isRightMouseButton(evt))
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ if (!Platform.isAMac())
+ {
+ showPopupMenu(evt);
+ }
}
- }
- });
-
- updateOverviewImage();
- }
+ else
+ {
+ // 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;
- /**
- * DOCUMENT ME!
- */
- void checkValid()
- {
- if (boxY < 0)
- {
- boxY = 0;
- }
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- if (boxY > (sequencesHeight - boxHeight))
- {
- boxY = sequencesHeight - boxHeight + 1;
- }
+ 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());
+ }
+ }
+ }
- if (boxX < 0)
- {
- boxX = 0;
- }
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ showPopupMenu(evt);
+ }
+ }
- if (boxX > (width - boxWidth))
- {
- if (av.hasHiddenColumns())
+ @Override
+ public void mouseReleased(MouseEvent evt)
{
- // Try smallest possible box
- boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
+ draggingBox = false;
}
- boxX = width - boxWidth;
- }
- int col = (int) (boxX / scalew / av.getCharWidth());
- int row = (int) (boxY / scaleh / av.getCharHeight());
+ });
+ }
- if (av.hasHiddenColumns())
+ /*
+ * Displays the popup menu and acts on user input
+ */
+ private void showPopupMenu(MouseEvent e)
+ {
+ JPopupMenu popup = new JPopupMenu();
+ ActionListener menuListener = new ActionListener()
{
- if (!av.getColumnSelection().isVisible(col))
+ @Override
+ public void actionPerformed(ActionEvent event)
{
- return;
+ // 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());
+ }
- col = av.getColumnSelection().findColumnPosition(col);
+ /*
+ * Toggle overview display between showing hidden columns and hiding hidden columns
+ */
+ private void toggleHiddenColumns()
+ {
+ if (showHidden)
+ {
+ showHidden = false;
+ od = new OverviewDimensionsHideHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
-
- if (av.hasHiddenRows())
+ else
{
- row = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(row);
+ showHidden = true;
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
-
- ap.setScrollValues(col, row);
-
+ oviewCanvas.resetOviewDims(od);
+ updateOverviewImage();
+ setBoxPosition();
}
/**
- * DOCUMENT ME!
+ * Updates the overview image when the related alignment panel is updated
*/
public void updateOverviewImage()
{
- if (resizing)
+ if (oviewCanvas == null)
{
- resizeAgain = true;
+ /*
+ * panel has been disposed
+ */
return;
}
- resizing = true;
-
if ((getWidth() > 0) && (getHeight() > 0))
{
- width = getWidth();
- sequencesHeight = getHeight() - graphHeight;
+ od.setWidth(getWidth());
+ od.setHeight(getHeight() - progressPanel.getHeight());
}
+
+ setPreferredSize(new Dimension(od.getWidth(),
+ od.getHeight() + progressPanel.getHeight()));
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+ if (oviewCanvas.restartDraw())
+ {
+ return;
+ }
Thread thread = new Thread(this);
thread.start();
repaint();
- }
- // This is set true if the user resizes whilst
- // the overview is being calculated
- boolean resizeAgain = false;
+
+ }
- /**
- * DOCUMENT ME!
- */
@Override
public void run()
{
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
- }
-
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
-
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
- int fullsizeWidth = alwidth * av.getCharWidth();
- int fullsizeHeight = alheight * av.getCharHeight();
-
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
- BufferedImage.TYPE_INT_RGB);
-
- Graphics mg = miniMe.getGraphics();
- mg.setColor(Color.orange);
- mg.fillRect(0, 0, width, miniMe.getHeight());
-
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = -1, lastrow = -1;
- Color color = Color.white;
- int row, col;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), 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
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- for (row = 0; row < sequencesHeight; row++)
+ if (oviewCanvas != null)
{
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- // No need to recalculate the colours,
- // Just copy from the row above
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
- }
- continue;
- }
-
- lastrow = (int) (row * sampleRow);
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
-
- if (seq == null)
- {
- System.out.println(lastrow + " null");
- continue;
- }
-
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- miniMe.setRGB(col, row, color.getRGB());
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = finder.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.WHITE;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection().isVisible(
- lastcol)))
- {
- color = color.darker().darker();
- }
-
- miniMe.setRGB(col, row, color.getRGB());
-
- }
- }
-
- if (av.getAlignmentConservationAnnotation() != null)
- {
- renderer.updateFromAlignViewport(av);
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- lastcol = (int) (col * sampleCol);
- {
- mg.translate(col, sequencesHeight);
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, graphHeight,
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -sequencesHeight);
- }
- }
- }
- System.gc();
-
- resizing = false;
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
- else
- {
- lastMiniMe = miniMe;
+ oviewCanvas.draw(av.isShowSequenceFeatures(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
+ ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ setBoxPosition();
}
-
- setBoxPosition();
}
/**
- * DOCUMENT ME!
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
*/
- public void setBoxPosition()
+ private void setBoxPositionOnly()
{
- int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize())
- * av.getCharHeight();
-
- int startRes = av.getStartRes();
- int endRes = av.getEndRes();
-
- if (av.hasHiddenColumns())
+ if (od != null)
{
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
+ 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());
}
+ }
- int startSeq = av.startSeq;
- int endSeq = av.endSeq;
-
- if (av.hasHiddenRows())
- {
- startSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(startSeq);
-
- endSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(endSeq);
-
- }
-
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- boxX = (int) (startRes * av.getCharWidth() * scalew);
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
- if (av.hasHiddenColumns())
- {
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
- }
- else
+ private void setBoxPosition()
+ {
+ if (od != null)
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ repaint();
}
-
- boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-
- repaint();
}
- private BufferedImage lastMiniMe = null;
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ setBoxPositionOnly();
+ }
/**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
+ * Removes this object as a property change listener, and nulls references
*/
- @Override
- public void paintComponent(Graphics g)
+ protected void dispose()
{
- if (resizing || resizeAgain)
+ try
{
- if (lastMiniMe == null)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else
+ if (av != null)
{
- g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+ av.getRanges().removePropertyChangeListener(this);
}
- g.setColor(new Color(100, 100, 100, 25));
- g.fillRect(0, 0, getWidth(), getHeight());
- }
- else if (lastMiniMe != null)
+
+ oviewCanvas.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)
{
- g.drawImage(lastMiniMe, 0, 0, this);
- if (lastMiniMe != miniMe)
- {
- g.setColor(new Color(100, 100, 100, 25));
- g.fillRect(0, 0, getWidth(), getHeight());
- }
+ // ignore
+ } finally
+ {
+ progressPanel = null;
+ av = null;
+ oviewCanvas = null;
+ ap = null;
+ od = null;
}
- // TODO: render selected regions
- g.setColor(Color.red);
- g.drawRect(boxX, boxY, boxWidth, boxHeight);
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
}
}
git://source.jalview.org / jalview.git / blobdiff