X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewCanvas.java;h=99dba3d97e39ce7b32c741d0895439dc3092eb2c;hb=f3d6a13271e3f34dfb4e40d6a2a7df1d392f8014;hp=e4c2056200d522761ba4a19754cac6f9a02f8c45;hpb=2feac6dabe64b144783f8538fab352e987eadcb6;p=jalview.git diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index e4c2056..99dba3d 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -20,20 +20,35 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.renderer.seqfeatures.FeatureColourFinder; -import jalview.viewmodel.OverviewDimensions; - import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics; import java.awt.image.BufferedImage; +import java.awt.image.RasterFormatException; -import javax.swing.JComponent; +import javax.swing.JPanel; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +import jalview.bin.Console; +import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; +import jalview.viewmodel.OverviewDimensions; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; -public class OverviewCanvas extends JComponent +public class OverviewCanvas extends JPanel { + public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white; + + public static final Color OVERVIEW_DEFAULT_RESIDUE = Color.white; + + public static final Color OVERVIEW_DEFAULT_LEGACY_RESIDUE = Color.lightGray; + + public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray + .darker(); + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); // This is set true if the alignment view changes whilst @@ -42,6 +57,8 @@ public class OverviewCanvas extends JComponent private volatile boolean updaterunning = false; + private boolean dispose = false; + private BufferedImage miniMe; private BufferedImage lastMiniMe = null; @@ -52,30 +69,53 @@ public class OverviewCanvas extends JComponent private jalview.renderer.seqfeatures.FeatureRenderer fr; - OverviewDimensions od; + private OverviewDimensions od; + + private OverviewRenderer or = null; + + private AlignViewportI av; - AlignViewportI av; + private OverviewResColourFinder cf; + + private ProgressPanel progressPanel; public OverviewCanvas(OverviewDimensions overviewDims, - AlignViewportI alignvp) + AlignViewportI alignvp, ProgressPanel pp) { od = overviewDims; av = alignvp; + progressPanel = pp; sr = new SequenceRenderer(av); sr.renderGaps = false; - sr.forOverview = true; fr = new jalview.renderer.seqfeatures.FeatureRenderer(av); + + boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false); + Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR, + OVERVIEW_DEFAULT_GAP); + Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR, + OVERVIEW_DEFAULT_HIDDEN); + Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE; + + cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol); + + setSize(od.getWidth(), od.getHeight()); } + /** + * Update the overview dimensions object used by the canvas (e.g. if we change + * from showing hidden columns to hiding them or vice versa) + * + * @param overviewDims + */ public void resetOviewDims(OverviewDimensions overviewDims) { od = overviewDims; } - /* - * Signals to drawing code that the associated alignment viewport - * has changed and a redraw will be required + /** + * Signals to drawing code that the associated alignment viewport has changed + * and a redraw will be required */ public boolean restartDraw() { @@ -84,6 +124,10 @@ public class OverviewCanvas extends JComponent if (updaterunning) { restart = true; + if (or != null) + { + or.setRedraw(true); + } } else { @@ -93,8 +137,18 @@ public class OverviewCanvas extends JComponent } } + /** + * Draw the overview sequences + * + * @param showSequenceFeatures + * true if sequence features are to be shown + * @param showAnnotation + * true if the annotation is to be shown + * @param transferRenderer + * the renderer to transfer feature colouring from + */ public void draw(boolean showSequenceFeatures, boolean showAnnotation, - FeatureRenderer transferRenderer) + FeatureRendererModel transferRenderer) { miniMe = null; @@ -102,15 +156,16 @@ public class OverviewCanvas extends JComponent { fr.transferSettings(transferRenderer); } - FeatureColourFinder finder = new FeatureColourFinder(fr); - // why do we need to set preferred size again? was set in - // updateOverviewImage setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - OverviewRenderer or = new OverviewRenderer(sr, finder, od); - miniMe = or.draw(od.getRows(av.getRanges(), av.getAlignment()), - od.getColumns(av.getRanges(), av.getColumnSelection())); + or = new OverviewRenderer(fr, od, av.getAlignment(), + av.getResidueShading(), cf); + + or.addPropertyChangeListener(progressPanel); + + miniMe = or.draw(od.getRows(av.getAlignment()), + od.getColumns(av.getAlignment())); Graphics mg = miniMe.getGraphics(); @@ -118,16 +173,19 @@ public class OverviewCanvas extends JComponent { mg.translate(0, od.getSequencesHeight()); or.drawGraph(mg, av.getAlignmentConservationAnnotation(), - av.getCharWidth(), od.getGraphHeight(), - od.getColumns(av.getRanges(), av.getColumnSelection())); + od.getGraphHeight(), od.getColumns(av.getAlignment())); mg.translate(0, -od.getSequencesHeight()); } - System.gc(); + or.removePropertyChangeListener(progressPanel); + or = null; if (restart) { restart = false; - draw(showSequenceFeatures, showAnnotation, transferRenderer); + if (!dispose) + { + draw(showSequenceFeatures, showAnnotation, transferRenderer); + } } else { @@ -139,6 +197,8 @@ public class OverviewCanvas extends JComponent @Override public void paintComponent(Graphics g) { + // super.paintComponent(g); + if (restart) { if (lastMiniMe == null) @@ -155,16 +215,108 @@ public class OverviewCanvas extends JComponent } else if (lastMiniMe != null) { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) + // is this a resize? + if ((getWidth() > 0) && (getHeight() > 0) + && ((getWidth() != od.getWidth()) + || (getHeight() != od.getHeight()))) { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); + // if there is annotation, scale the alignment and annotation + // separately + if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019 + ) + { + try + { + BufferedImage topImage = lastMiniMe.getSubimage(0, 0, + od.getWidth(), od.getSequencesHeight()); + BufferedImage bottomImage = lastMiniMe.getSubimage(0, + od.getSequencesHeight(), od.getWidth(), + od.getGraphHeight()); + + // must be done at this point as we rely on using old width/height + // above, and new width/height below + od.setWidth(getWidth()); + od.setHeight(getHeight()); + + // stick the images back together so lastMiniMe is consistent in the + // event of a repaint - BUT probably not thread safe + lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(), + BufferedImage.TYPE_INT_RGB); + Graphics lg = lastMiniMe.getGraphics(); + lg.drawImage(topImage, 0, 0, od.getWidth(), + od.getSequencesHeight(), null); + lg.drawImage(bottomImage, 0, od.getSequencesHeight(), + od.getWidth(), od.getGraphHeight(), this); + lg.dispose(); + } catch (RasterFormatException e) + { + Console.debug( + "Scaling miscalculation resizing Overview window"); + od.setWidth(getWidth()); + od.setHeight(getHeight()); + } + } + else + { + od.setWidth(getWidth()); + od.setHeight(getHeight()); + } + + // make sure the box is in the right place + od.setBoxPosition(av.getAlignment().getHiddenSequences(), + av.getAlignment().getHiddenColumns()); } + // fall back to normal behaviour + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + } + else + { + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); } + // draw the box g.setColor(Color.red); od.drawBox(g); } + public void dispose() + { + dispose = true; + od = null; + synchronized (this) + { + restart = true; + if (or != null) + { + or.setRedraw(true); + } + } + } + + public Color getGapColour() + { + return cf.getGapColour(); + } + + public Color getHiddenColour() + { + return cf.getHiddenColour(); + } + + public Color getResidueColour() + { + return cf.getResidueColour(); + } + + /** + * Sets the colours to use for gaps, residues and hidden regions + * + * @param gaps + * @param residues + * @param hidden + */ + public void setColours(Color gaps, Color residues, Color hidden) + { + cf = new OverviewResColourFinder(gaps, residues, hidden); + } }