X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=9d0a55da93a501d6bc1eee4ecdd6632d8ab2baf2;hb=5010b95e8e250e744eefc5a1c976d70c044be32f;hp=d15ec40aefe67fd7da4915c1dfcf60ce4530029b;hpb=2a1ff16b273585d8cefe5d799a8c1e1cee20404f;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index d15ec40..9d0a55d 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,20 +20,33 @@ */ package jalview.gui; -import jalview.renderer.AnnotationRenderer; +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 @@ -42,34 +55,24 @@ import javax.swing.JPanel; * @author $author$ * @version $Revision$ */ -public class OverviewPanel extends JPanel implements Runnable +public class OverviewPanel extends JPanel + implements Runnable, ViewportListenerI { - private static final Color TRANS_GREY = new Color(100, 100, 100, 25); - - private final AnnotationRenderer renderer = new AnnotationRenderer(); - private OverviewDimensions od; - private BufferedImage miniMe; - - private BufferedImage lastMiniMe = null; + private OverviewCanvas oviewCanvas; private AlignViewport av; private AlignmentPanel ap; - // - private boolean resizing = false; + private JCheckBoxMenuItem displayToggle; - // This is set true if the user resizes whilst - // the overview is being calculated - private boolean resizeAgain = false; + private boolean showHidden = true; - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; + private boolean draggingBox = false; - private jalview.renderer.seqfeatures.FeatureRenderer fr; + private ProgressPanel progressPanel; /** * Creates a new OverviewPanel object. @@ -81,33 +84,63 @@ public class OverviewPanel extends JPanel implements Runnable { this.av = alPanel.av; this.ap = alPanel; - setLayout(null); - sr = new SequenceRenderer(av); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(alPanel); - - boolean showAnnotation = false; - // TODO: in applet this was getSequenceConsensusHash() - // check if it makes any functional difference: hconsensus or conservation - if (av.getAlignmentConservationAnnotation() == null) + showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, + false); + if (showHidden) { - showAnnotation = true; + od = new OverviewDimensionsShowHidden(av.getRanges(), + (av.isShowAnnotation() + && av.getAlignmentConservationAnnotation() != null)); } - od = new OverviewDimensions(av, showAnnotation); + else + { + 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() != od.getWidth()) - || (getHeight() != (od.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() + + 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() @@ -115,14 +148,45 @@ public class OverviewPanel extends JPanel implements Runnable @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())) + { + /* + * using HAND_CURSOR rather than DRAG_CURSOR + * as the latter is not supported on Mac + */ + getParent().setCursor( + Cursor.getPredefinedCursor(Cursor.HAND_CURSOR)); + } + else { - // TODO: feature: jv2.5 detect shift drag and update selection from - // it. - od.updateViewportFromMouse(evt.getX(), evt.getY()); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); + // reset cursor + getParent().setCursor( + Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR)); } } + }); addMouseListener(new MouseAdapter() @@ -130,15 +194,106 @@ public class OverviewPanel extends JPanel implements Runnable @Override public void mousePressed(MouseEvent evt) { - if (!av.getWrapAlignment()) + if (SwingUtilities.isRightMouseButton(evt)) + { + if (!Platform.isAMac()) + { + showPopupMenu(evt); + } + } + else { - od.updateViewportFromMouse(evt.getX(), evt.getY()); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); + // 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 mouseClicked(MouseEvent evt) + { + if (SwingUtilities.isRightMouseButton(evt)) + { + showPopupMenu(evt); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + draggingBox = false; + } + }); + } + /* + * Displays the popup menu and acts on user input + */ + private void showPopupMenu(MouseEvent e) + { + JPopupMenu popup = new JPopupMenu(); + ActionListener menuListener = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent event) + { + // 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()); + } + + /* + * 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(); + setBoxPosition(); } /** @@ -146,224 +301,115 @@ public class OverviewPanel extends JPanel implements Runnable */ public void updateOverviewImage() { - if (resizing) + if (oviewCanvas == null) { - resizeAgain = true; + /* + * panel has been disposed + */ return; } - resizing = true; - if ((getWidth() > 0) && (getHeight() > 0)) { - od.setWidth(getWidth()); // width = getWidth(); - od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight; + od.setWidth(getWidth()); + od.setHeight(getHeight() - progressPanel.getHeight()); } + + setPreferredSize(new Dimension(od.getWidth(), + od.getHeight() + progressPanel.getHeight())); - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + if (oviewCanvas.restartDraw()) + { + return; + } Thread thread = new Thread(this); thread.start(); repaint(); + + } @Override public void run() { - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); - } - - // 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); - - if (av.getAlignmentConservationAnnotation() != null) + if (oviewCanvas != null) { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - 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()); - - } + oviewCanvas.draw(av.isShowSequenceFeatures(), + (av.isShowAnnotation() + && av.getAlignmentConservationAnnotation() != null), + ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + setBoxPosition(); } - System.gc(); - - resizing = false; - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - else - { - lastMiniMe = miniMe; - } - - setBoxPosition(); } - private void buildImage(float sampleRow, float sampleCol) + /** + * Update the overview panel box when the associated alignment panel is + * changed + * + */ + private void setBoxPositionOnly() { - int lastcol = -1; - int lastrow = -1; - int color = Color.white.getRGB(); - - jalview.datamodel.SequenceI seq = null; - - 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++) + if (od != null) { - boolean doCopy = true; - int currentrow = (int) (row * sampleRow); - if (currentrow != lastrow) - { - doCopy = false; - - lastrow = currentrow; - - // get the sequence which would be at alignment index 'lastrow' if no - // columns were hidden, and determine whether it is hidden or not - hiddenRow = av.getAlignment().isHidden(lastrow); - seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); - } - - if (seq == null) - { - System.out.println(lastrow + " null"); - continue; - } - - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - if (doCopy) - { - color = miniMe.getRGB(col, row - 1); - } - else if ((int) (col * sampleCol) != lastcol - || (int) (row * sampleRow) != lastrow) - { - lastcol = (int) (col * sampleCol); - color = getColumnColourFromSequence(seq, hiddenRow, hasHiddenCols, - lastcol); - } - // else if ((int) (col * sampleCol) == lastcol && (int) (row * - // sampleRow) == lastrow)) - // we just use the color we already have , so don't need to set it - - miniMe.setRGB(col, row, color); - } + 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()); } } - /* - * Find the colour of a sequence at a specified column position - */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) + private void setBoxPosition() { - int color; - - if (seq.getLength() > lastcol) + if (od != null) { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } + od.setBoxPosition(av.getAlignment().getHiddenSequences(), + av.getAlignment().getHiddenColumns()); + repaint(); } - else - { - color = Color.white.getRGB(); // White - } - - if (hiddenRow - || (hasHiddenCols && !av.getColumnSelection() - .isVisible(lastcol))) - { - color = new Color(color).darker().darker().getRGB(); - } - - return color; } - /** - * Update the overview panel box when the associated alignment panel is - * changed - * - */ - public void setBoxPosition() + @Override + public void propertyChange(PropertyChangeEvent evt) { - od.setBoxPosition(); - repaint(); + setBoxPositionOnly(); } - - @Override - public void paintComponent(Graphics g) + /** + * Removes this object as a property change listener, and nulls references + */ + protected void dispose() { - if (resizing || resizeAgain) + try { - if (lastMiniMe == null) + if (av != null) { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); + av.getRanges().removePropertyChangeListener(this); } - else - { - g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); - } - g.setColor(TRANS_GREY); - 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(TRANS_GREY); - 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); - od.drawBox(g); } }