*/
package jalview.appletgui;
-import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.OverviewDimensions;
import java.awt.Color;
import java.awt.Dimension;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
{
- Image miniMe;
+ private OverviewDimensions od;
- Image offscreen;
+ private Image miniMe;
- AlignViewport av;
+ private Image offscreen;
- AlignmentPanel ap;
+ private AlignViewport av;
- float scalew = 1f;
+ private AlignmentPanel ap;
- float scaleh = 1f;
+ private boolean resizing = false;
- public int width, sequencesHeight;
-
- int graphHeight = 20;
-
- int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
- 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;
- FeatureRenderer fr;
+ private FeatureRenderer fr;
- Frame nullFrame;
+ private Frame nullFrame;
- 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.forOverview = true;
fr = new FeatureRenderer(av);
- // scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.getAlignment().getWidth()
- / (float) av.getAlignment().getHeight();
+ od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
- if (av.getSequenceConsensusHash() == null)
- {
- graphHeight = 0;
- }
-
- 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;
- }
- }
-
- setSize(new Dimension(width, sequencesHeight + graphHeight));
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
addComponentListener(new ComponentAdapter()
{
@Override
public void componentResized(ComponentEvent evt)
{
- if (getSize().width != width
- || getSize().height != sequencesHeight + graphHeight)
+ if ((getWidth() != od.getWidth())
+ || (getHeight() != (od.getHeight())))
{
updateOverviewImage();
}
@Override
public void mousePressed(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ mouseAction(evt);
}
@Override
public void mouseReleased(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ mouseAction(evt);
}
@Override
public void mouseDragged(MouseEvent evt)
{
- boxX = evt.getX();
- boxY = evt.getY();
- checkValid();
+ mouseAction(evt);
}
- void checkValid()
+ private void mouseAction(MouseEvent evt)
{
- 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);
+ 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 ((getSize().width > 0) && (getSize().height > 0))
{
- width = getSize().width;
- sequencesHeight = getSize().height - graphHeight;
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
}
- setSize(new Dimension(width, sequencesHeight + graphHeight));
+ setSize(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;
-
@Override
public void run()
{
miniMe = null;
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight()
- + av.getAlignment().getHiddenSequences().getSize();
if (av.isShowSequenceFeatures())
{
if (getSize().width > 0 && getSize().height > 0)
{
- width = getSize().width;
- sequencesHeight = getSize().height - graphHeight;
+ od.setWidth(getSize().width);
+ od.setHeight(getSize().height);
}
- setSize(new Dimension(width, sequencesHeight + graphHeight));
+ setSize(new Dimension(od.getWidth(), od.getHeight()));
- int fullsizeWidth = alwidth * av.getCharWidth();
- int fullsizeHeight = alheight * av.getCharHeight();
-
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
- offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+ miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
+ offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
Graphics mg = miniMe.getGraphics();
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = 0, lastrow = 0;
- int xstart = 0, ystart = 0;
- Color color = Color.yellow;
- int row, col, sameRow = 0, sameCol = 0;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
- .hasHiddenColumns();
- boolean hiddenRow = false;
- AlignmentI alignment = av.getAlignment();
- for (row = 0; row <= sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- continue;
- }
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = alignment.getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = alignment.getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = alignment.getSequenceAt(lastrow);
- }
- for (col = 0; col < width; col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- 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();
- }
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getAbsoluteHeight();
+ float sampleCol = alwidth / (float) od.getWidth();
+ float sampleRow = alheight / (float) od.getSequencesHeight();
- xstart = col;
- sameCol = 1;
- }
- lastrow = (int) (row * sampleRow);
- ystart = row;
- sameRow = 1;
- }
+ buildImage(sampleRow, sampleCol, mg);
- if (av.getAlignmentConservationAnnotation() != null)
+ if (av.isShowAnnotation())
{
- 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);
- ap.annotationPanel.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());
+ 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();
}
}
- public void setBoxPosition()
+ /*
+ * Build the overview panel image
+ */
+ private void buildImage(float sampleRow, float sampleCol, Graphics mg)
{
- int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize())
- * av.getCharHeight();
-
- int startRes = av.getStartRes();
- int endRes = av.getEndRes();
+ int lastcol = 0;
+ int lastrow = 0;
+ int xstart = 0;
+ int ystart = 0;
+ Color color = Color.yellow;
+ int sameRow = 0;
+ int sameCol = 0;
- if (av.hasHiddenColumns())
- {
- startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
- endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
- }
+ SequenceI seq = null;
- int startSeq = av.startSeq;
- int endSeq = av.endSeq;
+ final boolean hasHiddenCols = av.hasHiddenColumns();
+ boolean hiddenRow = false;
- if (av.hasHiddenRows())
+ for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
{
- startSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(startSeq);
-
- endSeq = av.getAlignment().getHiddenSequences()
- .adjustForHiddenSeqs(endSeq);
+ if ((int) (row * sampleRow) == lastrow)
+ {
+ sameRow++;
+ }
+ else
+ {
+ // get the sequence which would be at alignment index 'lastrow' if no
+ // columns 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(); 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;
+ }
}
+ }
- scalew = (float) width / (float) fullsizeWidth;
- scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
- boxX = (int) (startRes * av.getCharWidth() * scalew);
- boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
- if (av.hasHiddenColumns())
+ /*
+ * 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)
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ color = sr.getResidueBoxColour(seq, lastcol);
+
+ if (av.isShowSequenceFeatures())
+ {
+ color = fr.findFeatureColour(color, seq, lastcol);
+ }
}
else
{
- boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+ color = Color.white;
}
- boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+ if (hiddenRow
+ || (hasHiddenCols && !av.getColumnSelection()
+ .isVisible(lastcol)))
+ {
+ color = color.darker().darker();
+ }
+ return color;
+ }
+ /**
+ * Update the overview panel box when the associated alignment panel is
+ * changed
+ *
+ */
+ public void setBoxPosition()
+ {
+ od.setBoxPosition(av.getAlignment()
+ .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
repaint();
}
{
og.drawImage(miniMe, 0, 0, this);
og.setColor(Color.red);
- og.drawRect(boxX, boxY, boxWidth, boxHeight);
- og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+ od.drawBox(og);
g.drawImage(offscreen, 0, 0, this);
}
}
git://source.jalview.org / jalview.git / blobdiff