--- /dev/null
+package jalview.gui;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
++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 javax.swing.JComponent;
+
+public class OverviewCanvas extends JComponent
+{
+ private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
+
+ private BufferedImage miniMe;
+
+ private BufferedImage lastMiniMe = null;
+
+ public boolean updating = false;
+
+ // This is set true if the user resizes whilst
+ // the overview is being calculated
+ public volatile boolean updateAgain = false;
+
+ // Can set different properties in this seqCanvas than
+ // main visible SeqCanvas
+ private SequenceRenderer sr;
+
+ private jalview.renderer.seqfeatures.FeatureRenderer fr;
+
+ private final AnnotationRenderer renderer = new AnnotationRenderer();
+
+ OverviewDimensions od;
+
+ OverviewPanel op;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ public OverviewCanvas(OverviewDimensions overviewDims,
+ AlignViewportI alignvp, AlignmentPanel alignp, OverviewPanel overp)
+ {
+ od = overviewDims;
+ av = alignp.av;
+ ap = alignp;
+ op = overp;
+
+ sr = new SequenceRenderer(av);
+ sr.renderGaps = false;
+ sr.forOverview = true;
+ fr = new FeatureRenderer(ap);
+ }
+
+ public void draw(boolean showSequenceFeatures, boolean showAnnotation)
+ {
+ miniMe = null;
+
+ if (showSequenceFeatures)
+ {
+ 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 (showAnnotation)
+ {
+ renderer.updateFromAlignViewport(av);
+ for (int col = 0; col < od.getWidth() && !updateAgain; 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();
+
+ updating = false;
+
+ if (updateAgain)
+ {
+ updateAgain = false;
+ op.updateOverviewImage();
+ }
+ else
+ {
+ lastMiniMe = miniMe;
+ }
+ }
+
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ if (updating || updateAgain)
+ {
+ 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);
+ }
+
+ /*
+ * Build the overview panel image
+ */
+ private void buildImage(float sampleRow, float sampleCol)
+ {
+ int lastcol = -1;
+ int lastrow = -1;
- int color = Color.white.getRGB();
++ 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() && !updateAgain; row++)
+ {
+ 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() && !updateAgain; col++)
+ {
+ if (doCopy)
+ {
- color = miniMe.getRGB(col, row - 1);
++ rgbcolor = 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);
++ 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, color);
++ miniMe.setRGB(col, row, rgbcolor);
+ }
+ }
+ }
+
+ /*
+ * Find the colour of a sequence at a specified column position
+ */
+ private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol)
++ boolean hiddenRow, boolean hasHiddenCols, int lastcol,
++ FeatureColourFinder finder)
+ {
- int color;
++ Color color = Color.white;
+
- if (seq == null)
++ if ((seq != null) && (seq.getLength() > lastcol))
+ {
- color = Color.white.getRGB();
- }
- else if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white.getRGB();
++ color = sr.getResidueColour(seq, lastcol, finder);
+ }
+
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection()
+ .isVisible(lastcol)))
+ {
- color = new Color(color).darker().darker().getRGB();
++ color = color.darker().darker();
+ }
+
- return color;
++ return color.getRGB();
+ }
+
+}
{
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(), av.isShowAnnotation());
+ od = new OverviewDimensions(av.getRanges(),
+ (av.isShowAnnotation() && av
+ .getAlignmentConservationAnnotation() != null));
+ oviewCanvas = new OverviewCanvas(od, av, ap, this);
+ setLayout(new BorderLayout());
+ add(oviewCanvas, BorderLayout.CENTER);
+
addComponentListener(new ComponentAdapter()
{
@Override
@Override
public void run()
{
- oviewCanvas.draw(av.isShowSequenceFeatures(), av.isShowAnnotation());
- 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))
- {
- 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));
setBoxPosition();
}
git://source.jalview.org / jalview.git / commitdiff