package jalview.gui;
import jalview.api.AlignViewportI;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.renderer.OverviewRenderer;
+import jalview.renderer.OverviewResColourFinder;
import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.image.BufferedImage;
-import javax.swing.JComponent;
+import javax.swing.JPanel;
-
-public class OverviewCanvas extends JComponent
+@SuppressWarnings("serial")
+public class OverviewCanvas extends JPanel
{
private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
// the overview is being calculated
private volatile boolean restart = false;
- private BufferedImage miniMe;
-
- private BufferedImage lastMiniMe = null;
+ private volatile boolean updaterunning = false;
+ private boolean disposed = false;
+ BufferedImage lastMiniMe = null;
// Can set different properties in this seqCanvas than
// main visible SeqCanvas
- private SequenceRenderer sr;
+ private final SequenceRenderer sr;
+
+ private final jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ private OverviewDimensions od;
+
+ private OverviewRenderer or = null;
- private jalview.renderer.seqfeatures.FeatureRenderer fr;
+ private final AlignViewportI av;
- private final AnnotationRenderer renderer = new AnnotationRenderer();
+ private final OverviewResColourFinder cf;
- OverviewDimensions od;
+ private final ProgressPanel progressPanel;
- AlignViewport av;
+ private boolean showSequenceFeatures;
- AlignmentPanel ap;
+ private boolean showAnnotation;
- public OverviewCanvas(OverviewDimensions overviewDims,
- AlignViewportI alignvp, AlignmentPanel alignp)
+ private jalview.api.FeatureRenderer featureRenderer;
+
+ private final OverviewPanel panel;
+
+ private final boolean showProgress;
+
+ public OverviewCanvas(OverviewPanel panel,
+ OverviewDimensions overviewDims,
+ AlignViewportI alignvp, ProgressPanel pp)
{
+ this.panel = panel;
od = overviewDims;
- av = alignp.av;
- ap = alignp;
-
+ lastMiniMe = null;
+ av = alignvp;
+ progressPanel = pp;
+ showProgress = (pp != null);
sr = new SequenceRenderer(av);
sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(ap);
+ fr = new jalview.renderer.seqfeatures.FeatureRenderer(av);
+
+ boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false);
+ Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+ cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol);
+
+ setSize(od.getWidth(), od.getHeight());
+ setPreferredSize(getSize()); // BH 2019.07.29 added
}
- /*
- * Signals to drawing code that the associated alignment viewport
- * has changed and a redraw will be required
+ /**
+ * 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 restartDraw()
+ public void resetOviewDims(OverviewDimensions overviewDims)
{
- restart = true;
+ od = overviewDims;
+ lastMiniMe = null;
}
- public void draw(boolean showSequenceFeatures, boolean showAnnotation)
+ /**
+ * Signals to drawing code that the associated alignment viewport has changed
+ * and a redraw will be required
+ */
+ public boolean restartDraw()
{
- miniMe = null;
+ synchronized (this)
+ {
+ if (updaterunning)
+ {
+ setRestart("restartDraw");
+ }
+ else
+ {
+ updaterunning = true;
+ restart = false;
+ }
+ return restart;
+ }
+ }
- if (showSequenceFeatures)
+ private void setRestart(String why)
+ {
+ // System.out.println("OC restart true " + why);
+ restart = true;
+ if (or != null)
{
- fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
+ or.setRedraw(true);
}
+ }
- // why do we need to set preferred size again? was set in
- // updateOverviewImage
+ /**
+ * 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 featureRenderer
+ * the renderer to transfer feature colouring from
+ */
+ public void draw(boolean showSequenceFeatures, boolean showAnnotation,
+ jalview.api.FeatureRenderer featureRenderer)
+ {
+ this.showSequenceFeatures = showSequenceFeatures;
+ this.showAnnotation = showAnnotation;
+ this.featureRenderer = featureRenderer;
+ if (showSequenceFeatures)
+ {
+ fr.transferSettings(featureRenderer);
+ }
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 (showAnnotation)
+ AlignmentI al = av.getAlignment();
+ or = new OverviewRenderer(panel.ap, fr, od, al, av.getResidueShading(),
+ cf, showProgress);
+ if (showProgress)
{
- renderer.updateFromAlignViewport(av);
- for (int col = 0; col < od.getWidth() && !restart; 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());
-
- }
+ or.addPropertyChangeListener(progressPanel);
}
- System.gc();
+ or.drawMiniMe();
+ }
+ synchronized void finalizeDraw(BufferedImage miniMe)
+ {
+ if (showProgress && or != null)
+ {
+ or.removePropertyChangeListener(progressPanel);
+ }
if (restart)
{
+ or = null;
restart = false;
- draw(showSequenceFeatures, showAnnotation);
+ if (!disposed)
+ {
+ draw(showSequenceFeatures, showAnnotation, featureRenderer);
+ }
}
else
{
+ if (showAnnotation && or != null)
+ {
+ or.drawGraph(av.getAlignmentConservationAnnotation());
+ }
+ or = null;
+ updaterunning = false;
lastMiniMe = miniMe;
+ repaint();
}
}
@Override
public void paintComponent(Graphics g)
{
+
+ int w = getWidth();
+ int h = getHeight();
+ if (w == 0 || od.getBoxWidth() <= 0)
+ {
+ // BH 2019.07.27 removes two unnecessary paints, since boxwidth can be -1
+ // or 0 during early-stage painting
+ return;
+ }
+
+ boolean drawMe = (lastMiniMe != null);
if (restart)
{
- if (lastMiniMe == null)
+ if (drawMe)
{
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ g.drawImage(lastMiniMe, 0, 0, w, h, this);
}
else
{
- g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+ g.setColor(Color.white);
+ g.fillRect(0, 0, w, h);
}
g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
+ g.fillRect(0, 0, w, h);
+ drawMe = false;
}
- else if (lastMiniMe != null)
+ else if (drawMe)
{
- g.drawImage(lastMiniMe, 0, 0, this);
- if (lastMiniMe != miniMe)
+ // is this a resize?
+ if (w != od.getWidth() || h != od.getHeight())
{
- g.setColor(TRANS_GREY);
- g.fillRect(0, 0, getWidth(), getHeight());
+
+ lastMiniMe = null;
+ return;
+ // // if there is annotation, scale the alignment and annotation
+ // // separately
+ // if (od.getGraphHeight() <= 0 && od.getSequencesHeight() <= 0)
+ // {
+ // od.setWidth(w);
+ // od.setHeight(h);
+ // return;
+ // }
+ // 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(w);
+ // od.setHeight(h);
+ //
+ // // stick the images back together so lastMiniMe is consistent in the
+ // // event of a repaint - BUT probably not thread safe
+ //
+ // // right -- this fails with fast user action.
+ //
+ // lastMiniMe = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
+ // Graphics lg = lastMiniMe.getGraphics();
+ // lg.drawImage(topImage, 0, 0, w, od.getSequencesHeight(), null);
+ // lg.drawImage(bottomImage, 0, od.getSequencesHeight(), w,
+ // od.getGraphHeight(), this);
+ // lg.dispose();
+ //
+ // } catch (RasterFormatException e)
+ // {
+ // System.out.println("OC Raster Exception " + lastMiniMe.getWidth()
+ // + "/" + w + "," + lastMiniMe.getHeight() + "/" + h + " "
+ // + od.getSequencesHeight() + " " + od.getGraphHeight());
+ // }
+ // BH 2019: removed -- this is now taken care of using vpbox in
+ // OverviewDimension
+ // // make sure the box is in the right place
+ // od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+ // av.getAlignment().getHiddenColumns());
}
}
+ if (drawMe)
+ {
+ g.drawImage(lastMiniMe, 0, 0, w, h, this);
+ }
+ // draw the box
g.setColor(Color.red);
+ // System.out.println("OC paintComponent nd=" + ndraw + " nr=" + nrepaint
+ // + " np=" + ++npaint);
od.drawBox(g);
}
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol)
- {
- int lastcol = -1;
- int lastrow = -1;
- int rgbcolor = 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() && !restart; row++)
- {
- boolean doCopy = true;
- int currentrow = (int) (row * sampleRow);
- if (currentrow != lastrow)
- {
- doCopy = false;
+ // private int ndraw, npaint, nrepaint;
- 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() && !restart; col++)
- {
- if (doCopy)
- {
- rgbcolor = miniMe.getRGB(col, row - 1);
- }
- else if ((int) (col * sampleCol) != lastcol
- || (int) (row * sampleRow) != lastrow)
- {
- lastcol = (int) (col * sampleCol);
- rgbcolor = 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, rgbcolor);
- }
- }
- }
+ // @Override
+ // public void repaint()
+ // {
+ // System.out.println("OC repaint " + (++nrepaint));
+ // super.repaint();
+ // }
- /*
- * Find the colour of a sequence at a specified column position
- */
- private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol,
- FeatureColourFinder finder)
+ public void dispose()
{
- Color color = Color.white;
-
- if ((seq != null) && (seq.getLength() > lastcol))
+ disposed = true;
+ od = null;
+ lastMiniMe = null;
+ synchronized (this)
{
- color = sr.getResidueColour(seq, lastcol, finder);
+ setRestart("dispose");
}
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
-
- return color.getRGB();
}
}
git://source.jalview.org / jalview.git / blobdiff