-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class OverviewPanel\r
- extends Panel implements Runnable\r
-{\r
- Image miniMe;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- float scalew = 1f;\r
- float scaleh = 1f;\r
-\r
- public int width, sequencesHeight;\r
- int graphHeight = 30;\r
- int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;\r
-\r
- boolean resizing = false;\r
-\r
- Frame nullFrame;\r
-\r
- public OverviewPanel(AlignmentPanel ap)\r
- {\r
- this.av = ap.av;\r
- this.ap = ap;\r
- setLayout(null);\r
- nullFrame = new Frame();\r
- nullFrame.addNotify();\r
-\r
- // scale the initial size of overviewpanel to shape of alignment\r
- float initialScale = (float) av.alignment.getWidth() /\r
- (float) av.alignment.getHeight();\r
- if (av.alignment.getWidth() > av.alignment.getHeight())\r
- {\r
- // wider\r
- width = 400;\r
- sequencesHeight = (int) (400f / initialScale);\r
- }\r
- else\r
- {\r
- // taller\r
- width = (int) (400f * initialScale);\r
- sequencesHeight = 300;\r
- if (width < 120)\r
- {\r
- width = 120;\r
- }\r
- }\r
-\r
- setSize(new Dimension(width, sequencesHeight + graphHeight));\r
- addComponentListener(new ComponentAdapter()\r
- {\r
-\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- if (getSize().width != width ||\r
- getSize().height != sequencesHeight + graphHeight)\r
- {\r
- updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- doMouseDragged(evt);\r
- }\r
- });\r
-\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- doMousePressed(evt);\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- });\r
-\r
- updateOverviewImage();\r
-\r
- }\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
-\r
- checkValid();\r
- repaint();\r
- }\r
-\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- if (!resizing)\r
- {\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- if (!resizing)\r
- {\r
- ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()),\r
- (int) (boxY / scaleh / av.getCharHeight()));\r
- }\r
- repaint();\r
- ap.repaint();\r
- }\r
-\r
- void checkValid()\r
- {\r
- if (boxY < 0)\r
- {\r
- boxY = 0;\r
- }\r
-\r
- if (boxY > sequencesHeight - boxHeight)\r
- {\r
- boxY = sequencesHeight - boxHeight + 1;\r
- }\r
-\r
- if (boxX < 0)\r
- {\r
- boxX = 0;\r
- }\r
-\r
- if (boxX > width - boxWidth)\r
- {\r
- boxX = width - boxWidth;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateOverviewImage()\r
- {\r
- if (resizing)\r
- {\r
- resizeAgain = true;\r
- return;\r
- }\r
-\r
- resizing = true;\r
-\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- repaint();\r
- }\r
-\r
- // This is set true if the user resizes whilst\r
- // the overview is being calculated\r
- boolean resizeAgain = false;\r
-\r
- public void run()\r
- {\r
- miniMe = null;\r
- int alwidth = av.alignment.getWidth();\r
- int alheight = av.alignment.getHeight();\r
-\r
- if (getSize().width > 0 && getSize().height > 0)\r
- {\r
- width = getSize().width;\r
- sequencesHeight = getSize().height - graphHeight;\r
- }\r
-\r
- setSize(new Dimension(width, sequencesHeight + graphHeight));\r
-\r
- int fullsizeWidth = alwidth * av.getCharWidth();\r
- int fullsizeHeight = alheight * av.getCharHeight();\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);\r
-\r
- Graphics mg = miniMe.getGraphics();\r
- Image consensus = nullFrame.createImage(fullsizeWidth, 60);\r
- Graphics g = consensus.getGraphics();\r
- ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60);\r
- mg.drawImage(consensus, 0, sequencesHeight, width,\r
- sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this);\r
-\r
- boolean oldRenderGaps = av.renderGaps;\r
- try\r
- {\r
- // We'll have to draw the full size alignment in chunks, as an image of the\r
- // whole alignment requires too much memory\r
-\r
- // Max size depends on the font size, the following is a\r
- // guess at a size which works\r
- int maxSize = 2000 / av.getFont().getSize();\r
- Image block;\r
- int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0;\r
-\r
- av.setRenderGaps(false);\r
- for (int sRes = 0, chunkx = 0; sRes < alwidth; sRes += maxSize, chunkx++)\r
- {\r
- eSeq = 0;\r
- eRes += maxSize;\r
- if (eRes > alwidth)\r
- {\r
- eRes = alwidth;\r
- }\r
-\r
- for (int sSeq = 0, chunky = 0; sSeq < alheight; sSeq += maxSize, chunky++)\r
- {\r
- if(resizeAgain)\r
- break;\r
-\r
- eSeq += maxSize;\r
- if (eSeq > alheight)\r
- {\r
- eSeq = alheight;\r
- }\r
-\r
- blocky = 0;\r
- blockx = (int) ( (float) sRes / (float) alwidth * width);\r
-\r
- block = nullFrame.createImage( (eRes - sRes) * av.charWidth,\r
- (eSeq - sSeq) * av.charHeight);\r
- g = block.getGraphics();\r
-\r
- ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, sRes, sSeq,\r
- 0);\r
-\r
- blockh = (int) ( (float) (eSeq - sSeq) / (float) alheight *\r
- sequencesHeight) + 1;\r
- blockw = (int) ( (float) (eRes - sRes) / (float) alwidth * width) + 1;\r
-\r
- blocky += (int) ( (float) sSeq / (float) alheight * sequencesHeight);\r
-\r
- mg.drawImage(block, blockx,\r
- blocky,\r
- blockx + blockw,\r
- blocky + blockh,\r
-\r
- 0, 0, block.getWidth(null), block.getHeight(null), this);\r
-\r
- block = null;\r
- }\r
-\r
- }\r
-\r
- }\r
- catch (OutOfMemoryError error)\r
- {\r
- System.err.println(\r
- "Out of memory when trying to calculate the overview window image!");\r
- }\r
-\r
- System.gc();\r
-\r
- av.setRenderGaps(oldRenderGaps);\r
- resizing = false;\r
-\r
- setBoxPosition();\r
-\r
- if(resizeAgain)\r
- {\r
- resizeAgain = false;\r
- updateOverviewImage();\r
- }\r
- }\r
-\r
- public void setBoxPosition()\r
- {\r
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();\r
- int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight();\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew);\r
- boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh);\r
- boxWidth = (int) ( (av.getEndRes() - av.getStartRes() + 1) *\r
- av.getCharWidth() * scalew);\r
- boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY;\r
- repaint();\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- if (resizing)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\r
-\r
- g.setFont(new Font("Verdana", Font.BOLD, 15));\r
- g.drawString("Recalculating", 5, sequencesHeight / 2);\r
- g.drawString("Overview.....", 5, sequencesHeight / 2 + 20);\r
- }\r
- else\r
- {\r
- if (miniMe != null)\r
- {\r
- g.drawImage(miniMe, 0, 0, this);\r
- }\r
-\r
- g.setColor(Color.red);\r
- g.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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.appletgui;
+
+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;
+
+public class OverviewPanel extends Panel implements Runnable,
+ MouseMotionListener, MouseListener, ViewportListenerI
+{
+ private OverviewDimensions od;
+
+ private OverviewCanvas oviewCanvas;
+
+ private AlignViewport av;
+
+ private AlignmentPanel ap;
+
+ private boolean showHidden = true;
+
+ private boolean updateRunning = false;
+
+ private boolean draggingBox = false;
+
+ public OverviewPanel(AlignmentPanel alPanel)
+ {
+ this.av = alPanel.av;
+ this.ap = alPanel;
+ setLayout(null);
+
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getSequenceConsensusHash() != null));
+
+ oviewCanvas = new OverviewCanvas(od, av);
+ setLayout(new BorderLayout());
+ add(oviewCanvas, BorderLayout.CENTER);
+
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+ av.getRanges().addPropertyChangeListener(this);
+
+ addComponentListener(new ComponentAdapter()
+ {
+
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ if ((getWidth() != od.getWidth())
+ || (getHeight() != (od.getHeight())))
+ {
+ updateOverviewImage();
+ }
+ }
+ });
+
+ addMouseMotionListener(this);
+
+ addMouseListener(this);
+
+ updateOverviewImage();
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ showPopupMenu(evt);
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ }
+ else
+ {
+ // reset cursor
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ if (!Platform.isAMac())
+ {
+ 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());
+ }
+ else
+ {
+ draggingBox = true;
+ od.setDragPoint(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ draggingBox = false;
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ if (!Platform.isAMac())
+ {
+ showPopupMenu(evt);
+ }
+ }
+ else
+ {
+ 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());
+ }
+ ap.paintAlignment(false, false);
+ }
+ }
+
+ /**
+ * Updates the overview image when the related alignment panel is updated
+ */
+ public void updateOverviewImage()
+ {
+ if (oviewCanvas == null)
+ {
+ /*
+ * panel has been disposed
+ */
+ return;
+ }
+
+ if ((getSize().width > 0) && (getSize().height > 0))
+ {
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
+ }
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
+
+ synchronized (this)
+ {
+ if (updateRunning)
+ {
+ oviewCanvas.restartDraw();
+ return;
+ }
+
+ updateRunning = true;
+ }
+ Thread thread = new Thread(this);
+ thread.start();
+ repaint();
+ updateRunning = false;
+ }
+
+ @Override
+ public void run()
+ {
+ oviewCanvas.draw(av.isShowSequenceFeatures(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null),
+ ap.seqPanel.seqCanvas.getFeatureRenderer());
+ setBoxPosition();
+ }
+
+ /**
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
+ */
+ private void setBoxPosition()
+ {
+ od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ repaint();
+ }
+
+ /*
+ * Displays the popup menu and acts on user input
+ */
+ private void showPopupMenu(MouseEvent e)
+ {
+ PopupMenu popup = new PopupMenu();
+ ItemListener menuListener = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ toggleHiddenColumns();
+ }
+ };
+ 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();
+ }
+
+ /*
+ * 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));
+ }
+ else
+ {
+ showHidden = true;
+ od = new OverviewDimensionsShowHidden(av.getRanges(),
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
+ }
+ oviewCanvas.resetOviewDims(od);
+ updateOverviewImage();
+ }
+
+ /**
+ * Removes this object as a property change listener, and nulls references
+ */
+ protected void dispose()
+ {
+ try
+ {
+ av.getRanges().removePropertyChangeListener(this);
+ Frame parent = (Frame) getParent();
+ parent.dispose();
+ parent.setVisible(false);
+ } finally
+ {
+ av = null;
+ if (oviewCanvas != null)
+ {
+ oviewCanvas.dispose();
+ }
+ oviewCanvas = null;
+ ap = null;
+ od = null;
+ }
+ }
+}