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JAL-2446 FeatureStore with NCList - work in progress
[jalview.git]
/
src
/
jalview
/
gui
/
OverviewPanel.java
diff --git
a/src/jalview/gui/OverviewPanel.java
b/src/jalview/gui/OverviewPanel.java
index
95d194b
..
36a4575
100755
(executable)
--- a/
src/jalview/gui/OverviewPanel.java
+++ b/
src/jalview/gui/OverviewPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
*
@@
-22,10
+22,17
@@
package jalview.gui;
import jalview.renderer.AnnotationRenderer;
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!
@@
-85,7
+92,7
@@
public class OverviewPanel extends JPanel implements Runnable
sr.renderGaps = false;
sr.forOverview = true;
fr = new FeatureRenderer(ap);
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();
// scale the initial size of overviewpanel to shape of alignment
float initialScale = (float) av.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
@@
-135,7
+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.
@@
-151,7
+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();
@@
-285,15
+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;
@@
-302,7
+322,7
@@
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);
@@
-329,8
+349,13
@@
public class OverviewPanel extends JPanel implements Runnable
continue;
}
continue;
}
+ // long start = System.currentTimeMillis();
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)
{
@@
-355,8
+380,8
@@
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();
}
@@
-364,6
+389,8
@@
public class OverviewPanel extends JPanel implements Runnable
miniMe.setRGB(col, row, color);
}
miniMe.setRGB(col, row, color);
}
+ // System.out.println(String.format("Row %d with width %d took %dms",
+ // row, width, System.currentTimeMillis() - start));
}
if (av.getAlignmentConservationAnnotation() != null)
}
if (av.getAlignmentConservationAnnotation() != null)
@@
-371,6
+398,10
@@
public class OverviewPanel extends JPanel implements Runnable
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);
@@
-386,13
+417,17
@@
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();
}
/**
}
/**
@@
-447,6
+482,8
@@
public class OverviewPanel extends JPanel implements Runnable
repaint();
}
repaint();
}
+ private BufferedImage lastMiniMe = null;
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-456,19
+493,32
@@
public class OverviewPanel extends JPanel implements Runnable
@Override
public void paintComponent(Graphics g)
{
@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);
-
}
}
}
}