/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
* 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.
+ * 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.
*
- * 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.appletgui;
import jalview.datamodel.AlignmentI;
-
-import java.awt.*;
-import java.awt.event.*;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+
+import java.awt.Color;
+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;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
sr.renderGaps = false;
sr.forOverview = true;
fr = new FeatureRenderer(av);
- fr.overview = true;
// scale the initial size of overviewpanel to shape of alignment
float initialScale = (float) av.getAlignment().getWidth()
return;
}
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
- fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+ fr.transferSettings(ap.seqPanel.seqCanvas.fr);
}
resizing = true;
{
miniMe = null;
int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
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();
+
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
for (row = 0; row <= sequencesHeight; row++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
if ((int) (row * sampleRow) == lastrow)
{
sameRow++;
}
hiddenRow = false;
- if (av.hasHiddenRows())
+ if (hasHiddenRows)
{
seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
if (seq == null)
if (seq.getLength() > lastcol)
{
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.showSequenceFeatures)
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
+ color = sr.getResidueColour(seq, lastcol, finder);
}
else
{
- color = Color.white; // White
+ color = Color.white;
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = color.darker().darker();
}
{
for (col = 0; col < width; col++)
{
+ if (resizeAgain)
+ {
+ break;
+ }
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);