-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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, MouseMotionListener, MouseListener\r
-{\r
- Image miniMe;\r
- Image offscreen;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- float scalew = 1f;\r
- float scaleh = 1f;\r
-\r
- public int width, sequencesHeight;\r
- int graphHeight = 20;\r
- int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;\r
-\r
- boolean resizing = false;\r
-\r
- // Can set different properties in this seqCanvas than\r
- // main visible SeqCanvas\r
- SequenceRenderer sr;\r
- FeatureRenderer fr;\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
- sr = new SequenceRenderer(av);\r
- sr.graphics = nullFrame.getGraphics();\r
- sr.renderGaps = false;\r
- sr.forOverview = true;\r
- fr = new FeatureRenderer(av);\r
- fr.overview = true;\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
-\r
- if (av.hconsensus == null)\r
- {\r
- graphHeight = 0;\r
- }\r
-\r
- if (av.alignment.getWidth() > av.alignment.getHeight())\r
- {\r
- // wider\r
- width = 400;\r
- sequencesHeight = (int) (400f / initialScale);\r
- if (sequencesHeight < 40)\r
- {\r
- sequencesHeight = 40;\r
- }\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(this);\r
-\r
- addMouseListener(this);\r
-\r
- updateOverviewImage();\r
-\r
- }\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {}\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- boxX = evt.getX();\r
- boxY = evt.getY();\r
- checkValid();\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
- if (av.hasHiddenColumns)\r
- {\r
- //Try smallest possible box\r
- boxWidth = (int) ( (av.endRes - av.startRes + 1) *\r
- av.getCharWidth() * scalew);\r
- }\r
- boxX = width - boxWidth;\r
- }\r
-\r
- int col = (int) (boxX / scalew / av.getCharWidth());\r
- int row = (int) (boxY / scaleh / av.getCharHeight());\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- if (!av.getColumnSelection().isVisible(col))\r
- {\r
- return;\r
- }\r
-\r
- col = av.getColumnSelection().findColumnPosition(col);\r
- }\r
-\r
- if (av.hasHiddenRows)\r
- {\r
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row);\r
- }\r
-\r
- ap.setScrollValues(col, row);\r
- ap.paintAlignment(false);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateOverviewImage()\r
- {\r
- if (resizing)\r
- {\r
- resizeAgain = true;\r
- return;\r
- }\r
-\r
- if (av.showSequenceFeatures)\r
- {\r
- fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
- featureGroups;\r
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().\r
- featureColours;\r
- }\r
-\r
- resizing = true;\r
-\r
- if ( (getSize().width > 0) && (getSize().height > 0))\r
- {\r
- width = getSize().width;\r
- sequencesHeight = getSize().height - graphHeight;\r
- }\r
- setSize(new Dimension(width, sequencesHeight + graphHeight));\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 (av.showSequenceFeatures)\r
- {\r
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());\r
- }\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
- offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);\r
-\r
- Graphics mg = miniMe.getGraphics();\r
- float sampleCol = (float) alwidth / (float) width;\r
- float sampleRow = (float) alheight / (float) sequencesHeight;\r
-\r
- int lastcol = 0, lastrow = 0;\r
- int xstart = 0, ystart = 0;\r
- Color color = Color.yellow;\r
- int row, col, sameRow = 0, sameCol = 0;\r
- jalview.datamodel.SequenceI seq;\r
- boolean hiddenRow = false;\r
- for (row = 0; row <= sequencesHeight; row++)\r
- {\r
- if ( (int) (row * sampleRow) == lastrow)\r
- {\r
- sameRow++;\r
- continue;\r
- }\r
-\r
- hiddenRow = false;\r
- if (av.hasHiddenRows)\r
- {\r
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);\r
- if (seq == null)\r
- {\r
- int index =\r
- av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(\r
- lastrow);\r
-\r
- seq = av.alignment.getSequenceAt(index);\r
- }\r
- else\r
- {\r
- hiddenRow = true;\r
- }\r
- }\r
- else\r
- {\r
- seq = av.alignment.getSequenceAt(lastrow);\r
- }\r
-\r
- for (col = 0; col < width; col++)\r
- {\r
- if ( (int) (col * sampleCol) == lastcol &&\r
- (int) (row * sampleRow) == lastrow)\r
- {\r
- sameCol++;\r
- continue;\r
- }\r
-\r
- lastcol = (int) (col * sampleCol);\r
-\r
- if (seq.getLength() > lastcol)\r
- {\r
- color = sr.getResidueBoxColour(\r
- seq, lastcol);\r
-\r
- if (av.showSequenceFeatures)\r
- {\r
- color = fr.findFeatureColour(color, seq, lastcol);\r
- }\r
- }\r
- else\r
- {\r
- color = Color.white; //White\r
- }\r
-\r
- if (hiddenRow ||\r
- (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol)))\r
- {\r
- color = color.darker().darker();\r
- }\r
-\r
- mg.setColor(color);\r
- if (sameCol == 1 && sameRow == 1)\r
- {\r
- mg.drawLine(xstart, ystart, xstart, ystart);\r
- }\r
- else\r
- {\r
- mg.fillRect(xstart, ystart, sameCol, sameRow);\r
- }\r
-\r
- xstart = col;\r
- sameCol = 1;\r
- }\r
- lastrow = (int) (row * sampleRow);\r
- ystart = row;\r
- sameRow = 1;\r
- }\r
-\r
- if (av.conservation != null)\r
- {\r
- for (col = 0; col < width; col++)\r
- {\r
- lastcol = (int) (col * sampleCol);\r
- {\r
- mg.translate(col, sequencesHeight);\r
- ap.annotationPanel.drawGraph(mg, av.conservation,\r
- (int) (sampleCol) + 1,\r
- graphHeight,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol) + 1);\r
- mg.translate( -col, -sequencesHeight);\r
- }\r
- }\r
- }\r
- System.gc();\r
-\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()\r
- + av.alignment.getHiddenSequences().getSize()) *\r
- av.getCharHeight();\r
-\r
- int startRes = av.getStartRes();\r
- int endRes = av.getEndRes();\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);\r
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);\r
- }\r
-\r
- int startSeq = av.startSeq;\r
- int endSeq = av.endSeq;\r
-\r
- if (av.hasHiddenRows)\r
- {\r
- startSeq =\r
- av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq);\r
-\r
- endSeq =\r
- av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq);\r
-\r
- }\r
-\r
- scalew = (float) width / (float) fullsizeWidth;\r
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;\r
-\r
- boxX = (int) (startRes * av.getCharWidth() * scalew);\r
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
- }\r
- else\r
- {\r
- boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew);\r
- }\r
-\r
- boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh);\r
-\r
- repaint();\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- Graphics og = offscreen.getGraphics();\r
- if (miniMe != null)\r
- {\r
- og.drawImage(miniMe, 0, 0, this);\r
- og.setColor(Color.red);\r
- og.drawRect(boxX, boxY, boxWidth, boxHeight);\r
- og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);\r
- g.drawImage(offscreen, 0, 0, this);\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;
+
+import javax.swing.SwingUtilities;
+
+@SuppressWarnings("serial")
+public class OverviewPanel extends Panel implements Runnable,
+ MouseMotionListener, MouseListener, ViewportListenerI
+{
+ OverviewDimensions od;
+
+ OverviewCanvas canvas;
+
+ private AlignViewport av;
+
+ 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));
+
+ canvas = new OverviewCanvas(this, od, av);
+ setLayout(new BorderLayout());
+ add(canvas, 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()))
+ {
+ this.getParent()
+ .setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ this.getParent()
+ .setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if ((evt.getModifiers()
+ & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_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)
+ {
+ draggingBox = false;
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (Platform.isWinRightButton(evt))
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
+ }
+
+ 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 (canvas == 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)
+ {
+ canvas.restartDraw();
+ return;
+ }
+
+ updateRunning = true;
+ }
+ Thread thread = new Thread(this);
+ thread.start();
+ repaint();
+ updateRunning = false;
+ }
+
+ @Override
+ public void run()
+ {
+ canvas.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));
+ }
+ canvas.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 (canvas != null)
+ {
+ canvas.dispose();
+ }
+ canvas = null;
+ ap = null;
+ od = null;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff