import jalview.viewmodel.OverviewDimensions;
-import java.awt.Color;
+import java.awt.BorderLayout;
import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Image;
import java.awt.Panel;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
{
private OverviewDimensions od;
- private Image miniMe;
-
- private Image offscreen;
+ private OverviewCanvas oviewCanvas;
private AlignViewport av;
private AlignmentPanel ap;
- private boolean resizing = false;
-
- // This is set true if the user resizes whilst
- // the overview is being calculated
- private boolean resizeAgain = false;
-
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
- private FeatureRenderer fr;
-
- private Frame nullFrame;
+ private boolean updateRunning = false;
- public OverviewPanel(AlignmentPanel ap)
+ public OverviewPanel(AlignmentPanel alPanel)
{
- this.av = ap.av;
- this.ap = ap;
+ this.av = alPanel.av;
+ this.ap = alPanel;
setLayout(null);
- nullFrame = new Frame();
- nullFrame.addNotify();
- sr = new SequenceRenderer(av);
- sr.graphics = nullFrame.getGraphics();
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(av);
+ od = new OverviewDimensions(av.getRanges(),
+ (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
- od = new OverviewDimensions(av);
+ oviewCanvas = new OverviewCanvas(od, av, ap);
+ setLayout(new BorderLayout());
+ add(oviewCanvas, BorderLayout.CENTER);
setSize(new Dimension(od.getWidth(), od.getHeight()));
addComponentListener(new ComponentAdapter()
@Override
public void mousePressed(MouseEvent evt)
{
- od.setBoxX(evt.getX());
- od.setBoxY(evt.getY());
- checkValid();
+ mouseAction(evt);
}
@Override
public void mouseReleased(MouseEvent evt)
{
- od.setBoxX(evt.getX());
- od.setBoxY(evt.getY());
- checkValid();
+ mouseAction(evt);
}
@Override
public void mouseDragged(MouseEvent evt)
{
- od.setBoxX(evt.getX());
- od.setBoxY(evt.getY());
- checkValid();
+ mouseAction(evt);
}
- /**
- * Check box dimensions and scroll positions and correct if necessary
- */
- private void checkValid()
+ private void mouseAction(MouseEvent evt)
{
- od.checkValid();
+ od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
+ .getHiddenSequences(), av.getColumnSelection(), av
+ .getRanges());
ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
ap.paintAlignment(false);
}
/**
- * DOCUMENT ME!
+ * Updates the overview image when the related alignment panel is updated
*/
public void updateOverviewImage()
{
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- if (av.isShowSequenceFeatures())
+ if ((getSize().width > 0) && (getSize().height > 0))
{
- fr.transferSettings(ap.seqPanel.seqCanvas.fr);
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
}
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
- resizing = true;
-
- if ((getWidth() > 0) && (getHeight() > 0))
+ if (updateRunning)
{
- od.setWidth(getWidth()); // width = getWidth();
- od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+ oviewCanvas.restartDraw();
+ return;
}
- setSize(new Dimension(od.getWidth(), od.getHeight()));
+ updateRunning = true;
Thread thread = new Thread(this);
thread.start();
repaint();
+ updateRunning = false;
}
@Override
public void run()
{
- miniMe = null;
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- if (getSize().width > 0 && getSize().height > 0)
- {
- od.setWidth(getSize().width);
- od.setHeight(getSize().height - od.getGraphHeight());
- }
-
- setSize(new Dimension(od.getWidth(), od.getHeight()));
-
- miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
- offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
-
- Graphics mg = miniMe.getGraphics();
-
- od.updateScales();
-
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-
- buildImage(sampleRow, sampleCol, mg);
-
- if (av.getAlignmentConservationAnnotation() != null)
- {
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- mg.translate(col, od.getSequencesHeight());
- ap.annotationPanel.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;
-
+ oviewCanvas.draw(av.isShowSequenceFeatures(),
+ (av.isShowAnnotation() && av
+ .getAlignmentConservationAnnotation() != null));
setBoxPosition();
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
- }
-
- private void buildImage(float sampleRow, float sampleCol, Graphics mg)
- {
- int lastcol = 0;
- int lastrow = 0;
- int xstart = 0;
- int ystart = 0;
- Color color = Color.yellow;
- int sameRow = 0;
- int sameCol = 0;
-
- jalview.datamodel.SequenceI seq = null;
- final boolean hasHiddenRows = av.hasHiddenRows();
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
-
- for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
- {
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- continue;
- }
- else
- {
- // this should largely be a method in Alignment
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
- // end of Alignment method
-
- for (int col = 0; col < od.getWidth(); col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- }
- else
- {
- lastcol = (int) (col * sampleCol);
-
- color = getColumnColourFromSequence(seq, hiddenRow,
- hasHiddenCols, lastcol);
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
-
- xstart = col;
- sameCol = 1;
- }
- }
- lastrow = (int) (row * sampleRow);
- ystart = row;
- sameRow = 1;
- }
- }
-
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private Color getColumnColourFromSequence(
- jalview.datamodel.SequenceI seq, boolean hiddenRow,
- boolean hasHiddenCols, int lastcol)
- {
- Color color;
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white; // White
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
- return color;
}
/**
*/
public void setBoxPosition()
{
- od.setBoxPosition();
+ od.setBoxPosition(av.getAlignment()
+ .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
repaint();
}
- @Override
- public void update(Graphics g)
- {
- paint(g);
- }
- @Override
- public void paint(Graphics g)
- {
- Graphics og = offscreen.getGraphics();
- if (miniMe != null)
- {
- og.drawImage(miniMe, 0, 0, this);
- og.setColor(Color.red);
- og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
- od.getBoxHeight());
- og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
- od.getBoxHeight() - 2);
- g.drawImage(offscreen, 0, 0, this);
- }
- }
+
}
git://source.jalview.org / jalview.git / blobdiff