X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=3fa674e60f8d6f1661dc57df07fc601e101ed171;hb=fe654aee9b43fb9c9307830c277f1e63576826ae;hp=fc3cc4b3e5287d5548db28c89e5572807422b05d;hpb=aa6643d51133a8541dcbe30191b344aa09907a5f;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index fc3cc4b..3fa674e 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,74 +20,73 @@ */ package jalview.gui; -import jalview.renderer.AnnotationRenderer; +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.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 javax.swing.JCheckBoxMenuItem; 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 { - 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; - - // This is set true if the user resizes whilst - // the overview is being calculated - private boolean resizeAgain = false; - - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; + private JCheckBoxMenuItem displayToggle; - private jalview.renderer.seqfeatures.FeatureRenderer fr; + private boolean showHidden = true; /** * Creates a new OverviewPanel object. * - * @param ap + * @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); + this.av = alPanel.av; + this.ap = alPanel; - sr = new SequenceRenderer(av); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(ap); + od = new OverviewDimensionsShowHidden(av.getRanges(), + (av.isShowAnnotation() && av + .getAlignmentConservationAnnotation() != null)); - od = new OverviewDimensions(av); + setSize(od.getWidth(), od.getHeight()); + + oviewCanvas = new OverviewCanvas(od, av); + setLayout(new BorderLayout()); + add(oviewCanvas, BorderLayout.CENTER); + + av.getRanges().addPropertyChangeListener(this); addComponentListener(new ComponentAdapter() { @@ -98,6 +97,7 @@ public class OverviewPanel extends JPanel implements Runnable || (getHeight() != (od.getHeight()))) { updateOverviewImage(); + setBoxPosition(); } } }); @@ -107,13 +107,13 @@ public class OverviewPanel extends JPanel implements Runnable @Override public void mouseDragged(MouseEvent evt) { - if (!av.getWrapAlignment()) + if (!SwingUtilities.isRightMouseButton(evt) + && !av.getWrapAlignment()) { - // TODO: feature: jv2.5 detect shift drag and update selection from - // it. - od.setBoxX(evt.getX()); - od.setBoxY(evt.getY()); - checkValid(); + od.updateViewportFromMouse(evt.getX(), evt.getY(), av + .getAlignment().getHiddenSequences(), av.getAlignment() + .getHiddenColumns()); + } } }); @@ -123,26 +123,82 @@ public class OverviewPanel extends JPanel implements Runnable @Override public void mousePressed(MouseEvent evt) { - if (!av.getWrapAlignment()) + if (SwingUtilities.isRightMouseButton(evt)) { - od.setBoxX(evt.getX()); - od.setBoxY(evt.getY()); - checkValid(); + if (!Platform.isAMac()) + { + showPopupMenu(evt); + } + } + else if (!av.getWrapAlignment()) + { + od.updateViewportFromMouse(evt.getX(), evt.getY(), av + .getAlignment().getHiddenSequences(), av.getAlignment() + .getHiddenColumns()); + } + } + + @Override + public void mouseClicked(MouseEvent evt) + { + if (SwingUtilities.isRightMouseButton(evt)) + { + showPopupMenu(evt); } } }); + updateOverviewImage(); } - /** - * Check box dimensions and scroll positions and correct if necessary + /* + * Displays the popup menu and acts on user input */ - private void checkValid() + private void showPopupMenu(MouseEvent e) { - od.checkValid(); - ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); + 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(); } /** @@ -150,250 +206,50 @@ public class OverviewPanel extends JPanel implements Runnable */ public void updateOverviewImage() { - if (resizing) + if ((getWidth() > 0) && (getHeight() > 0)) { - resizeAgain = true; - return; + od.setWidth(getWidth()); + od.setHeight(getHeight()); } + + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - resizing = true; - - if ((getWidth() > 0) && (getHeight() > 0)) + if (oviewCanvas.restartDraw()) { - od.setWidth(getWidth()); // width = getWidth(); - od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight; + return; } - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - 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 scale based on current alignment width and height - od.updateScales(); - - // 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().getHeight() - + av.getAlignment().getHiddenSequences().getSize(); - - // 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) - { - 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()); - - } - } - 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(); } - private void buildImage(float sampleRow, float sampleCol) - { - int lastcol = -1; - int lastrow = -1; - int color = Color.white.getRGB(); - - jalview.datamodel.SequenceI seq = null; - final boolean hasHiddenRows = av.hasHiddenRows(); - 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++) - { - boolean doCopy = true; - int currentrow = (int) (row * sampleRow); - if (currentrow != lastrow) - { - doCopy = false; - - lastrow = currentrow; - - hiddenRow = false; - // should be method(s) in Alignment - 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); - } - // end of Alignment method(s) - } - - 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); - } - } - } - - /* - * Find the colour of a sequence at a specified column position - */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) - { - int color; - - if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - 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() + private void setBoxPosition() { - od.setBoxPosition(); + od.setBoxPosition(av.getAlignment().getHiddenSequences(), av + .getAlignment().getHiddenColumns()); repaint(); } - @Override - public void paintComponent(Graphics g) + public void propertyChange(PropertyChangeEvent evt) { - if (resizing || resizeAgain) - { - if (lastMiniMe == null) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else - { - g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); - } - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - else if (lastMiniMe != null) - { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) - { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); - } - } - // TODO: render selected regions - g.setColor(Color.red); - g.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(), - od.getBoxHeight()); - g.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2, - od.getBoxHeight() - 2); + setBoxPosition(); } }