X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=7750374290dd3f65b96a238999cc365d64d4c394;hb=d4c27a996e22436dd4c4d8f64f6341d5315ff621;hp=e42d25f8b8daadea591b2661cc97f8222e0cad3d;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index e42d25f..7750374 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,22 +20,26 @@ */ package jalview.gui; -import jalview.datamodel.SequenceI; -import jalview.renderer.AnnotationRenderer; -import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.OverviewDimensionsHideHidden; +import jalview.viewmodel.OverviewDimensionsShowHidden; -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 javax.swing.JMenuItem; import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; /** * Panel displaying an overview of the full alignment, with an interactive box @@ -46,32 +50,15 @@ import javax.swing.JPanel; */ public class OverviewPanel extends JPanel implements Runnable { - 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; - - jalview.renderer.seqfeatures.FeatureRenderer fr; + private boolean showHidden = true; /** * Creates a new OverviewPanel object. @@ -83,17 +70,15 @@ 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(ap); - - od = new OverviewDimensions(av.getRanges(), + od = new OverviewDimensionsShowHidden(av.getRanges(), (av.isShowAnnotation() && av .getAlignmentConservationAnnotation() != null)); + oviewCanvas = new OverviewCanvas(od, av); + setLayout(new BorderLayout()); + add(oviewCanvas, BorderLayout.CENTER); + addComponentListener(new ComponentAdapter() { @Override @@ -112,11 +97,12 @@ public class OverviewPanel extends JPanel implements Runnable @Override public void mouseDragged(MouseEvent evt) { - if (!av.getWrapAlignment()) + if (!SwingUtilities.isRightMouseButton(evt) + && !av.getWrapAlignment()) { od.updateViewportFromMouse(evt.getX(), evt.getY(), av .getAlignment().getHiddenSequences(), av.getAlignment() - .getHiddenColumns(), av.getRanges()); + .getHiddenColumns()); ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); } } @@ -127,191 +113,113 @@ 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 if (!av.getWrapAlignment()) { od.updateViewportFromMouse(evt.getX(), evt.getY(), av .getAlignment().getHiddenSequences(), av.getAlignment() - .getHiddenColumns(), av.getRanges()); + .getHiddenColumns()); ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); } } + + @Override + public void mouseClicked(MouseEvent evt) + { + if (SwingUtilities.isRightMouseButton(evt)) + { + showPopupMenu(evt); + } + } }); + updateOverviewImage(); } - /** - * Updates the overview image when the related alignment panel is updated + /* + * Displays the popup menu and acts on user input */ - public void updateOverviewImage() - { - if (resizing) - { - resizeAgain = true; - return; - } - - resizing = true; - - if ((getWidth() > 0) && (getHeight() > 0)) - { - od.setWidth(getWidth()); - od.setHeight(getHeight()); - } - - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - - Thread thread = new Thread(this); - thread.start(); - repaint(); - } - - @Override - public void run() + private void showPopupMenu(MouseEvent e) { - 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); - - // check for conservation annotation to make sure overview works for DNA too - if (av.isShowAnnotation() - && (av.getAlignmentConservationAnnotation() != null)) + JPopupMenu popup = new JPopupMenu(); + ActionListener menuListener = new ActionListener() { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) + @Override + public void actionPerformed(ActionEvent event) { - 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()); - + // switch on/off the hidden columns view + toggleHiddenColumns(); } - } - System.gc(); - - resizing = false; - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - else - { - lastMiniMe = miniMe; - } - - setBoxPosition(); + }; + JMenuItem item = new JMenuItem( + MessageManager.getString("label.togglehidden")); + popup.add(item); + item.addActionListener(menuListener); + popup.show(this, e.getX(), e.getY()); } /* - * Build the overview panel image + * Toggle overview display between showing hidden columns and hiding hidden columns */ - private void buildImage(float sampleRow, float sampleCol) + private void toggleHiddenColumns() { - int lastcol = -1; - int lastrow = -1; - int rgbColour = Color.white.getRGB(); - - SequenceI seq = null; - FeatureColourFinder finder = new FeatureColourFinder(fr); - - 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 (showHidden) { - 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 - // rows were hidden, and determine whether it is hidden or not - hiddenRow = av.getAlignment().isHidden(lastrow); - seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); - } - - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - if (doCopy) - { - rgbColour = miniMe.getRGB(col, row - 1); - } - else if ((int) (col * sampleCol) != lastcol - || (int) (row * sampleRow) != lastrow) - { - lastcol = (int) (col * sampleCol); - rgbColour = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol, finder); - } - // else we just use the color we already have , so don't need to set it - - miniMe.setRGB(col, row, rgbColour); - } + 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(); } - /* - * Find the colour of a sequence at a specified column position + /** + * Updates the overview image when the related alignment panel is updated */ - private int getColumnColourFromSequence( - jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol, - FeatureColourFinder finder) + public void updateOverviewImage() { - Color color = Color.white; - - if ((seq != null) && (seq.getLength() > lastcol)) + if ((getWidth() > 0) && (getHeight() > 0)) { - color = sr.getResidueColour(seq, lastcol, finder); + od.setWidth(getWidth()); + od.setHeight(getHeight()); } + + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - if (hiddenRow - || (hasHiddenCols && !av.getAlignment().getHiddenColumns() - .isVisible(lastcol))) + if (oviewCanvas.restartDraw()) { - color = color.darker().darker(); + return; } - return color.getRGB(); + Thread thread = new Thread(this); + thread.start(); + repaint(); + + } + + @Override + public void run() + { + oviewCanvas.draw(av.isShowSequenceFeatures(), + (av.isShowAnnotation() && av + .getAlignmentConservationAnnotation() != null), ap + .getSeqPanel().seqCanvas.getFeatureRenderer()); + setBoxPosition(); } /** @@ -321,41 +229,8 @@ public class OverviewPanel extends JPanel implements Runnable */ public void setBoxPosition() { - od.setBoxPosition(av.getAlignment() -.getHiddenSequences(), av - .getAlignment().getHiddenColumns(), av.getRanges()); + od.setBoxPosition(av.getAlignment().getHiddenSequences(), av + .getAlignment().getHiddenColumns()); repaint(); } - - - @Override - public void paintComponent(Graphics g) - { - 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()); - } - } - - g.setColor(Color.red); - od.drawBox(g); - } }