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Merge remote-tracking branch 'origin/develop' into features/JAL-2316
[jalview.git]
/
src
/
jalview
/
gui
/
OverviewPanel.java
diff --git
a/src/jalview/gui/OverviewPanel.java
b/src/jalview/gui/OverviewPanel.java
index
475f0c7
..
1c48690
100755
(executable)
--- a/
src/jalview/gui/OverviewPanel.java
+++ b/
src/jalview/gui/OverviewPanel.java
@@
-1,32
+1,42
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
* PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.renderer.AnnotationRenderer;
*/
package jalview.gui;
import jalview.renderer.AnnotationRenderer;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseMotionAdapter;
+import java.awt.image.BufferedImage;
+
+import javax.swing.JPanel;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
@@
-39,6
+49,7
@@
public class OverviewPanel extends JPanel implements Runnable
AlignmentPanel ap;
final AnnotationRenderer renderer = new AnnotationRenderer();
AlignmentPanel ap;
final AnnotationRenderer renderer = new AnnotationRenderer();
+
float scalew = 1f;
float scaleh = 1f;
float scalew = 1f;
float scaleh = 1f;
@@
-63,11
+74,11
@@
public class OverviewPanel extends JPanel implements Runnable
// main visible SeqCanvas
SequenceRenderer sr;
// main visible SeqCanvas
SequenceRenderer sr;
- FeatureRenderer fr;
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
/**
* Creates a new OverviewPanel object.
/**
* Creates a new OverviewPanel object.
- *
+ *
* @param ap
* DOCUMENT ME!
*/
* @param ap
* DOCUMENT ME!
*/
@@
-86,7
+97,7
@@
public class OverviewPanel extends JPanel implements Runnable
float initialScale = (float) av.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
float initialScale = (float) av.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
- if (av.getAlignmentConservationAnnotation()== null)
+ if (av.getAlignmentConservationAnnotation() == null)
{
graphHeight = 0;
}
{
graphHeight = 0;
}
@@
-131,7
+142,7
@@
public class OverviewPanel extends JPanel implements Runnable
@Override
public void mouseDragged(MouseEvent evt)
{
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
// TODO: feature: jv2.5 detect shift drag and update selection from
// it.
{
// TODO: feature: jv2.5 detect shift drag and update selection from
// it.
@@
-147,7
+158,7
@@
public class OverviewPanel extends JPanel implements Runnable
@Override
public void mousePressed(MouseEvent evt)
{
@Override
public void mousePressed(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
boxX = evt.getX();
boxY = evt.getY();
{
boxX = evt.getX();
boxY = evt.getY();
@@
-204,8
+215,8
@@
public class OverviewPanel extends JPanel implements Runnable
if (av.hasHiddenRows())
{
if (av.hasHiddenRows())
{
- row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
}
ap.setScrollValues(col, row);
@@
-250,9
+261,9
@@
public class OverviewPanel extends JPanel implements Runnable
{
miniMe = null;
{
miniMe = null;
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
{
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
}
int alwidth = av.getAlignment().getWidth();
}
int alwidth = av.getAlignment().getWidth();
@@
-281,15
+292,28
@@
public class OverviewPanel extends JPanel implements Runnable
int color = Color.white.getRGB();
int row, col;
jalview.datamodel.SequenceI seq;
int color = Color.white.getRGB();
int row, col;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
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++)
{
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 ((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;
miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
}
continue;
@@
-298,9
+322,10
@@
public class OverviewPanel extends JPanel implements Runnable
lastrow = (int) (row * sampleRow);
hiddenRow = false;
lastrow = (int) (row * sampleRow);
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
{
- seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
+ seq = av.getAlignment().getHiddenSequences()
+ .getHiddenSequence(lastrow);
if (seq == null)
{
int index = av.getAlignment().getHiddenSequences()
if (seq == null)
{
int index = av.getAlignment().getHiddenSequences()
@@
-326,6
+351,10
@@
public class OverviewPanel extends JPanel implements Runnable
for (col = 0; col < width; col++)
{
for (col = 0; col < width; col++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
if ((int) (col * sampleCol) == lastcol
&& (int) (row * sampleRow) == lastrow)
{
if ((int) (col * sampleCol) == lastcol
&& (int) (row * sampleRow) == lastrow)
{
@@
-339,7
+368,7
@@
public class OverviewPanel extends JPanel implements Runnable
{
color = sr.getResidueBoxColour(seq, lastcol).getRGB();
{
color = sr.getResidueBoxColour(seq, lastcol).getRGB();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
color = fr.findFeatureColour(color, seq, lastcol);
}
{
color = fr.findFeatureColour(color, seq, lastcol);
}
@@
-350,8
+379,8
@@
public class OverviewPanel extends JPanel implements Runnable
}
if (hiddenRow
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = new Color(color).darker().darker().getRGB();
}
{
color = new Color(color).darker().darker().getRGB();
}
@@
-361,15
+390,20
@@
public class OverviewPanel extends JPanel implements Runnable
}
}
}
}
- if (av.getAlignmentConservationAnnotation()!= null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
{
{
renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
@@
-380,13
+414,17
@@
public class OverviewPanel extends JPanel implements Runnable
resizing = false;
resizing = false;
- setBoxPosition();
-
if (resizeAgain)
{
resizeAgain = false;
updateOverviewImage();
}
if (resizeAgain)
{
resizeAgain = false;
updateOverviewImage();
}
+ else
+ {
+ lastMiniMe = miniMe;
+ }
+
+ setBoxPosition();
}
/**
}
/**
@@
-396,7
+434,8
@@
public class OverviewPanel extends JPanel implements Runnable
{
int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
{
int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize()) * av.getCharHeight();
+ .getHiddenSequences().getSize())
+ * av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
@@
-412,8
+451,8
@@
public class OverviewPanel extends JPanel implements Runnable
if (av.hasHiddenRows())
{
if (av.hasHiddenRows())
{
- startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
@@
-440,28
+479,43
@@
public class OverviewPanel extends JPanel implements Runnable
repaint();
}
repaint();
}
+ private BufferedImage lastMiniMe = null;
+
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/
@Override
public void paintComponent(Graphics g)
{
* @param g
* DOCUMENT ME!
*/
@Override
public void paintComponent(Graphics g)
{
- if (resizing)
+ if (resizing || resizeAgain)
{
{
- g.setColor(Color.white);
+ if (lastMiniMe == null)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ else
+ {
+ g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+ }
+ g.setColor(new Color(100, 100, 100, 25));
g.fillRect(0, 0, getWidth(), getHeight());
}
g.fillRect(0, 0, getWidth(), getHeight());
}
- else if (miniMe != null)
+ else if (lastMiniMe != null)
{
{
- g.drawImage(miniMe, 0, 0, this);
+ g.drawImage(lastMiniMe, 0, 0, this);
+ if (lastMiniMe != miniMe)
+ {
+ g.setColor(new Color(100, 100, 100, 25));
+ 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);
g.setColor(Color.red);
g.drawRect(boxX, boxY, boxWidth, boxHeight);
g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
-
}
}
}
}