*/
package jalview.gui;
+import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
+import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.JPanel;
/**
- * DOCUMENT ME!
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
*
* @author $author$
* @version $Revision$
*/
public class OverviewPanel extends JPanel implements Runnable
{
- BufferedImage miniMe;
+ private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
- AlignViewport av;
+ private final AnnotationRenderer renderer = new AnnotationRenderer();
- AlignmentPanel ap;
+ private OverviewDimensions od;
- final AnnotationRenderer renderer = new AnnotationRenderer();
+ private BufferedImage miniMe;
- float scalew = 1f;
-
- float scaleh = 1f;
-
- int width;
-
- int sequencesHeight;
-
- int graphHeight = 20;
-
- int boxX = -1;
+ private BufferedImage lastMiniMe = null;
- int boxY = -1;
+ private AlignViewport av;
- int boxWidth = -1;
+ private AlignmentPanel ap;
- int boxHeight = -1;
+ //
+ private boolean resizing = false;
- 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
- SequenceRenderer sr;
+ private SequenceRenderer sr;
- jalview.renderer.seqfeatures.FeatureRenderer fr;
+ private jalview.renderer.seqfeatures.FeatureRenderer fr;
/**
* Creates a new OverviewPanel object.
*
- * @param ap
- * DOCUMENT ME!
+ * @param alPanel
+ * The alignment panel which is shown in the overview panel
*/
- public OverviewPanel(AlignmentPanel ap)
+ public OverviewPanel(AlignmentPanel alPanel)
{
- this.av = ap.av;
- this.ap = ap;
+ this.av = alPanel.av;
+ this.ap = alPanel;
setLayout(null);
sr = new SequenceRenderer(av);
sr.renderGaps = false;
sr.forOverview = true;
- fr = new FeatureRenderer(ap);
-
- // scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.getAlignment().getWidth()
- / (float) av.getAlignment().getHeight();
-
- if (av.getAlignmentConservationAnnotation() == null)
- {
- graphHeight = 0;
- }
+ fr = new FeatureRenderer(alPanel);
- if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
- {
- // wider
- width = 400;
- sequencesHeight = (int) (400f / initialScale);
- if (sequencesHeight < 40)
- {
- sequencesHeight = 40;
- }
- }
- else
- {
- // taller
- width = (int) (400f * initialScale);
- sequencesHeight = 300;
-
- if (width < 120)
- {
- width = 120;
- }
- }
+ od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
addComponentListener(new ComponentAdapter()
{
@Override
public void componentResized(ComponentEvent evt)
{
- if ((getWidth() != width)
- || (getHeight() != (sequencesHeight + graphHeight)))
+ if ((getWidth() != od.getWidth())
+ || (getHeight() != (od.getHeight())))
{
updateOverviewImage();
}
{
if (!av.getWrapAlignment())
{
- // TODO: feature: jv2.5 detect shift drag and update selection from
- // it.
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+ .getAlignment().getHiddenSequences(), av
+ .getColumnSelection(), av.getRanges());
+ ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
}
}
});
{
if (!av.getWrapAlignment())
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+ .getAlignment().getHiddenSequences(), av
+ .getColumnSelection(), av.getRanges());
+ ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
}
}
});
}
/**
- * 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!
+ * Updates the overview image when the related alignment panel is updated
*/
public void updateOverviewImage()
{
if ((getWidth() > 0) && (getHeight() > 0))
{
- width = getWidth();
- sequencesHeight = getHeight() - graphHeight;
+ od.setWidth(getWidth());
+ od.setHeight(getHeight());
}
- setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
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()
{
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;
+ // why do we need to set preferred size again? was set in
+ // updateOverviewImage
+ setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
- miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+ miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
BufferedImage.TYPE_INT_RGB);
Graphics mg = miniMe.getGraphics();
mg.setColor(Color.orange);
- mg.fillRect(0, 0, width, miniMe.getHeight());
+ mg.fillRect(0, 0, od.getWidth(), 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++)
- {
- if (resizeAgain)
- {
- break;
- }
- miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
- }
- continue;
- }
-
- lastrow = (int) (row * sampleRow);
-
- 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);
- }
-
- if (seq == null)
- {
- System.out.println(lastrow + " null");
- continue;
- }
-
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- miniMe.setRGB(col, row, color);
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = -1; // White
- }
+ // 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();
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection().isVisible(
- lastcol)))
- {
- color = new Color(color).darker().darker().getRGB();
- }
+ // 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();
- miniMe.setRGB(col, row, color);
+ buildImage(sampleRow, sampleCol);
- }
- }
-
- if (av.getAlignmentConservationAnnotation() != null)
+ if (av.isShowAnnotation())
{
renderer.updateFromAlignViewport(av);
- for (col = 0; col < width; col++)
+ for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
{
- if (resizeAgain)
- {
- break;
- }
- lastcol = (int) (col * sampleCol);
- {
- mg.translate(col, sequencesHeight);
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
- av.getAlignmentConservationAnnotation().annotations,
- (int) (sampleCol) + 1, graphHeight,
- (int) (col * sampleCol), (int) (col * sampleCol) + 1);
- mg.translate(-col, -sequencesHeight);
- }
+ 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();
setBoxPosition();
}
- /**
- * DOCUMENT ME!
+ /*
+ * Build the overview panel image
*/
- public void setBoxPosition()
+ private void buildImage(float sampleRow, float sampleCol)
{
- int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize())
- * av.getCharHeight();
+ int lastcol = -1;
+ int lastrow = -1;
+ int color = Color.white.getRGB();
- int startRes = av.getStartRes();
- int endRes = av.getEndRes();
+ SequenceI seq = null;
- if (av.hasHiddenColumns())
+ 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++)
{
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
- }
+ boolean doCopy = true;
+ int currentrow = (int) (row * sampleRow);
+ if (currentrow != lastrow)
+ {
+ doCopy = false;
- int startSeq = av.startSeq;
- int endSeq = av.endSeq;
+ lastrow = currentrow;
- if (av.hasHiddenRows())
- {
- startSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(startSeq);
+ // 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);
+ }
- endSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(endSeq);
+ for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+ {
+ if (doCopy)
+ {
+ color = 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);
+ }
+ // else we just use the color we already have , so don't need to set it
+ miniMe.setRGB(col, row, color);
+ }
}
+ }
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- boxX = (int) (startRes * av.getCharWidth() * scalew);
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+ /*
+ * Find the colour of a sequence at a specified column position
+ */
+ private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
+ boolean hiddenRow, boolean hasHiddenCols, int lastcol)
+ {
+ int color;
- if (av.hasHiddenColumns())
+ if (seq == null)
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ 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
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ color = Color.white.getRGB();
}
- boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection()
+ .isVisible(lastcol)))
+ {
+ color = new Color(color).darker().darker().getRGB();
+ }
- repaint();
+ return color;
}
- private BufferedImage lastMiniMe = null;
-
/**
- * DOCUMENT ME!
+ * Update the overview panel box when the associated alignment panel is
+ * changed
*
- * @param g
- * DOCUMENT ME!
*/
+ public void setBoxPosition()
+ {
+ od.setBoxPosition(av.getAlignment()
+ .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
+ repaint();
+ }
+
+
@Override
public void paintComponent(Graphics g)
{
{
g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
}
- g.setColor(new Color(100, 100, 100, 25));
+ 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(new Color(100, 100, 100, 25));
+ g.setColor(TRANS_GREY);
g.fillRect(0, 0, getWidth(), getHeight());
}
}
- // TODO: render selected regions
+
g.setColor(Color.red);
- g.drawRect(boxX, boxY, boxWidth, boxHeight);
- g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+ od.drawBox(g);
}
}
git://source.jalview.org / jalview.git / blobdiff