- if (!av.getWrapAlignment())
- {
- // TODO: feature: jv2.5 detect shift drag and update selection from
- // it.
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
- }
- }
- });
-
- addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (!av.getWrapAlignment())
- {
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
- }
- }
- });
-
- updateOverviewImage();
- }
-
- /**
- * DOCUMENT ME!
- */
- void checkValid()
- {
- if (boxY < 0)
- {
- boxY = 0;
- }
-
- if (boxY > (sequencesHeight - boxHeight))
- {
- boxY = sequencesHeight - boxHeight + 1;
- }
-
- if (boxX < 0)
- {
- boxX = 0;
- }
-
- if (boxX > (width - boxWidth))
- {
- if (av.hasHiddenColumns())
- {
- // Try smallest possible box
- boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
- }
- boxX = width - boxWidth;
- }
-
- int col = (int) (boxX / scalew / av.getCharWidth());
- int row = (int) (boxY / scaleh / av.getCharHeight());
-
- if (av.hasHiddenColumns())
- {
- if (!av.getColumnSelection().isVisible(col))
- {
- return;
- }
-
- col = av.getColumnSelection().findColumnPosition(col);
- }
-
- if (av.hasHiddenRows())
- {
- row = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(row);
- }
-
- ap.setScrollValues(col, row);
-
- }
-
- /**
- * DOCUMENT ME!
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- resizing = true;
-
- if ((getWidth() > 0) && (getHeight() > 0))
- {
- width = getWidth();
- sequencesHeight = getHeight() - graphHeight;
- }
-
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
- Thread thread = new Thread(this);
- thread.start();
- repaint();
- }
-
- // This is set true if the user resizes whilst
- // the overview is being calculated
- boolean resizeAgain = false;
-
- /**
- * DOCUMENT ME!
- */
- @Override
- public void run()
- {
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
- }
-
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
-
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
- int fullsizeWidth = alwidth * av.getCharWidth();
- int fullsizeHeight = alheight * av.getCharHeight();
-
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
- BufferedImage.TYPE_INT_RGB);
-
- Graphics mg = miniMe.getGraphics();
- mg.setColor(Color.orange);
- mg.fillRect(0, 0, width, miniMe.getHeight());
-
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = -1, lastrow = -1;
- int color = Color.white.getRGB();
- int row, col;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), 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 (row = 0; row < sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- // No need to recalculate the colours,
- // Just copy from the row above
- for (col = 0; col < width; col++)