/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * 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.appletgui;
-import java.awt.*;
-import java.awt.event.*;
+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.CheckboxMenuItem;
+import java.awt.Cursor;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
+
+import javax.swing.SwingUtilities;
public class OverviewPanel extends Panel implements Runnable,
- MouseMotionListener, MouseListener
+ MouseMotionListener, MouseListener, ViewportListenerI
{
- Image miniMe;
-
- Image offscreen;
-
- AlignViewport av;
-
- AlignmentPanel ap;
-
- float scalew = 1f;
-
- float scaleh = 1f;
+ private OverviewDimensions od;
- public int width, sequencesHeight;
+ private OverviewCanvas oviewCanvas;
- int graphHeight = 20;
+ private AlignViewport av;
- int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
+ private AlignmentPanel ap;
- boolean resizing = false;
+ private boolean showHidden = true;
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- SequenceRenderer sr;
+ private boolean updateRunning = false;
- FeatureRenderer fr;
+ private boolean draggingBox = false;
- Frame nullFrame;
-
- public OverviewPanel(AlignmentPanel ap)
+ public OverviewPanel(AlignmentPanel alPanel)
{
- this.av = ap.av;
- this.ap = ap;
+ this.av = alPanel.av;
+ this.ap = alPanel;
setLayout(null);
- nullFrame = new Frame();
- nullFrame.addNotify();
- sr = new SequenceRenderer(av);
- sr.graphics = nullFrame.getGraphics();
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(av);
- fr.overview = true;
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getSequenceConsensusHash() != null));
- // scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.alignment.getWidth()
- / (float) av.alignment.getHeight();
+ oviewCanvas = new OverviewCanvas(od, av);
+ setLayout(new BorderLayout());
+ add(oviewCanvas, BorderLayout.CENTER);
- if (av.hconsensus == null)
- {
- graphHeight = 0;
- }
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
- if (av.alignment.getWidth() > av.alignment.getHeight())
- {
- // wider
- width = 400;
- sequencesHeight = (int) (400f / initialScale);
- if (sequencesHeight < 40)
- {
- sequencesHeight = 40;
- }
- }
- else
- {
- // taller
- width = (int) (400f * initialScale);
- sequencesHeight = 300;
- if (width < 120)
- {
- width = 120;
- }
- }
+ av.getRanges().addPropertyChangeListener(this);
- setSize(new Dimension(width, sequencesHeight + graphHeight));
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
- if (getSize().width != width
- || getSize().height != sequencesHeight + graphHeight)
+ if ((getWidth() != od.getWidth())
+ || (getHeight() != (od.getHeight())))
{
updateOverviewImage();
}
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ {
+ showPopupMenu(evt);
+ }
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ this.getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ this.getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
+ }
}
+ @Override
public void mousePressed(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
+ {
+ if (!Platform.isMac()) // BH was excluding JavaScript
+ {
+ showPopupMenu(evt);
+ }
+ }
+ 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;
+
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
+ 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());
+ }
+ }
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ draggingBox = false;
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
- }
-
- void checkValid()
- {
- if (boxY < 0)
- {
- boxY = 0;
- }
-
- if (boxY > (sequencesHeight - boxHeight))
- {
- boxY = sequencesHeight - boxHeight + 1;
- }
-
- if (boxX < 0)
+ if (Platform.isWinRightButton(evt))
{
- boxX = 0;
+ showPopupMenu(evt);
+ return;
}
- if (boxX > (width - boxWidth))
+ if (SwingUtilities.isRightMouseButton(evt))
{
- if (av.hasHiddenColumns)
- {
- // Try smallest possible box
- boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
- }
- boxX = width - boxWidth;
+ return;
}
- int col = (int) (boxX / scalew / av.getCharWidth());
- int row = (int) (boxY / scaleh / av.getCharHeight());
-
- if (av.hasHiddenColumns)
+ if (draggingBox)
{
- if (!av.getColumnSelection().isVisible(col))
- {
- return;
- }
-
- col = av.getColumnSelection().findColumnPosition(col);
+ // 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());
}
-
- if (av.hasHiddenRows)
+ else
{
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
}
-
- ap.setScrollValues(col, row);
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
/**
- * 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;
}
- if (av.showSequenceFeatures)
+ if ((getSize().width > 0) && (getSize().height > 0))
{
- fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
}
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
- resizing = true;
-
- if ((getSize().width > 0) && (getSize().height > 0))
+ synchronized (this)
{
- width = getSize().width;
- sequencesHeight = getSize().height - graphHeight;
- }
- setSize(new Dimension(width, sequencesHeight + graphHeight));
+ if (updateRunning)
+ {
+ oviewCanvas.restartDraw();
+ return;
+ }
- Thread thread = new Thread(this);
+ updateRunning = true;
+ }
+ Thread thread = new Thread(this, "OverviewUpdate");
thread.start();
repaint();
+ updateRunning = false;
}
- // This is set true if the user resizes whilst
- // the overview is being calculated
- boolean resizeAgain = false;
-
+ @Override
public void run()
{
- miniMe = null;
- int alwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
-
- if (av.showSequenceFeatures)
- {
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- if (getSize().width > 0 && getSize().height > 0)
- {
- width = getSize().width;
- sequencesHeight = getSize().height - graphHeight;
- }
-
- setSize(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 = nullFrame.createImage(width, sequencesHeight + graphHeight);
- offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
-
- Graphics mg = miniMe.getGraphics();
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = 0, lastrow = 0;
- int xstart = 0, ystart = 0;
- Color color = Color.yellow;
- int row, col, sameRow = 0, sameCol = 0;
- jalview.datamodel.SequenceI seq;
- boolean hiddenRow = false;
- for (row = 0; row <= sequencesHeight; row++)
- {
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- continue;
- }
-
- hiddenRow = false;
- if (av.hasHiddenRows)
- {
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.alignment.getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.alignment.getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.alignment.getSequenceAt(lastrow);
- }
-
- for (col = 0; col < width; col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.showSequenceFeatures)
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white; // White
- }
-
- if (hiddenRow
- || (av.hasHiddenColumns && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
+ oviewCanvas.draw(av.isShowSequenceFeatures(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
+ ap.seqPanel.seqCanvas.getFeatureRenderer());
+ setBoxPosition();
+ }
- xstart = col;
- sameCol = 1;
- }
- lastrow = (int) (row * sampleRow);
- ystart = row;
- sameRow = 1;
- }
+ /**
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
+ */
+ private void setBoxPosition()
+ {
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ repaint();
+ }
- if (av.conservation != null)
+ /*
+ * Displays the popup menu and acts on user input
+ */
+ private void showPopupMenu(MouseEvent e)
+ {
+ PopupMenu popup = new PopupMenu();
+ ItemListener menuListener = new ItemListener()
{
- for (col = 0; col < width; col++)
+ @Override
+ public void itemStateChanged(ItemEvent e)
{
- lastcol = (int) (col * sampleCol);
- {
- mg.translate(col, sequencesHeight);
- ap.annotationPanel.drawGraph(mg, av.conservation,
- (int) (sampleCol) + 1, graphHeight,
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -sequencesHeight);
- }
+ toggleHiddenColumns();
}
- }
- System.gc();
-
- resizing = false;
+ };
+ CheckboxMenuItem item = new CheckboxMenuItem(
+ MessageManager.getString("label.togglehidden"));
+ item.setState(showHidden);
+ popup.add(item);
+ item.addItemListener(menuListener);
+ this.add(popup);
+ popup.show(this, e.getX(), e.getY());
+ }
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
setBoxPosition();
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
}
- public void setBoxPosition()
+ /*
+ * Toggle overview display between showing hidden columns and hiding hidden columns
+ */
+ private void toggleHiddenColumns()
{
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.alignment.getHeight() + av.alignment
- .getHiddenSequences().getSize()) * av.getCharHeight();
-
- int startRes = av.getStartRes();
- int endRes = av.getEndRes();
-
- if (av.hasHiddenColumns)
- {
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
- }
-
- int startSeq = av.startSeq;
- int endSeq = av.endSeq;
-
- if (av.hasHiddenRows)
+ if (showHidden)
{
- startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
-
- endSeq = av.alignment.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);
+ showHidden = false;
+ od = new OverviewDimensionsHideHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
else
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ showHidden = true;
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
-
- boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-
- repaint();
- }
-
- public void update(Graphics g)
- {
- paint(g);
+ oviewCanvas.resetOviewDims(od);
+ updateOverviewImage();
}
- public void paint(Graphics g)
+ /**
+ * Removes this object as a property change listener, and nulls references
+ */
+ protected void dispose()
{
- Graphics og = offscreen.getGraphics();
- if (miniMe != null)
+ try
+ {
+ av.getRanges().removePropertyChangeListener(this);
+ Frame parent = (Frame) getParent();
+ parent.dispose();
+ parent.setVisible(false);
+ } finally
{
- og.drawImage(miniMe, 0, 0, this);
- og.setColor(Color.red);
- og.drawRect(boxX, boxY, boxWidth, boxHeight);
- og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
- g.drawImage(offscreen, 0, 0, this);
+ av = null;
+ if (oviewCanvas != null)
+ {
+ oviewCanvas.dispose();
+ }
+ oviewCanvas = null;
+ ap = null;
+ od = null;
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff