- updateOverviewImage();
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- resizing = true;
-
- if ((getWidth() > 0) && (getHeight() > 0))
- {
- od.setWidth(getWidth()); // width = getWidth();
- od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
- }
-
- 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;
- }
-
- 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++)