X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=9397cebbeaae42116937602076ff815fb8e382d4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=475f0c711d1e4e54fc73547e24ea39f807eed634;hpb=3f734555193e56f46b07d5bc12df77d26e180ec0;p=jalview.git
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 475f0c7..9397ceb 100755
--- 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 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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!
- *
+ *
* @author $author$
* @version $Revision$
*/
@@ -39,6 +49,7 @@ public class OverviewPanel extends JPanel implements Runnable
AlignmentPanel ap;
final AnnotationRenderer renderer = new AnnotationRenderer();
+
float scalew = 1f;
float scaleh = 1f;
@@ -63,11 +74,11 @@ public class OverviewPanel extends JPanel implements Runnable
// main visible SeqCanvas
SequenceRenderer sr;
- FeatureRenderer fr;
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
/**
* Creates a new OverviewPanel object.
- *
+ *
* @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();
- if (av.getAlignmentConservationAnnotation()== null)
+ if (av.getAlignmentConservationAnnotation() == null)
{
graphHeight = 0;
}
@@ -131,7 +142,7 @@ public class OverviewPanel extends JPanel implements Runnable
@Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
// 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)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
boxX = evt.getX();
boxY = evt.getY();
@@ -204,8 +215,8 @@ public class OverviewPanel extends JPanel implements Runnable
if (av.hasHiddenRows())
{
- row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
@@ -250,9 +261,9 @@ public class OverviewPanel extends JPanel implements Runnable
{
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();
@@ -281,6 +292,8 @@ public class OverviewPanel extends JPanel implements Runnable
int color = Color.white.getRGB();
int row, col;
jalview.datamodel.SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
for (row = 0; row < sequencesHeight; row++)
{
@@ -298,9 +311,10 @@ public class OverviewPanel extends JPanel implements Runnable
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()
@@ -339,7 +353,7 @@ public class OverviewPanel extends JPanel implements Runnable
{
color = sr.getResidueBoxColour(seq, lastcol).getRGB();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
color = fr.findFeatureColour(color, seq, lastcol);
}
@@ -350,8 +364,8 @@ public class OverviewPanel extends JPanel implements Runnable
}
if (hiddenRow
- || (av.hasHiddenColumns() && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = new Color(color).darker().darker().getRGB();
}
@@ -361,7 +375,7 @@ public class OverviewPanel extends JPanel implements Runnable
}
}
- if (av.getAlignmentConservationAnnotation()!= null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
@@ -369,7 +383,8 @@ public class OverviewPanel extends JPanel implements Runnable
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);
@@ -396,7 +411,8 @@ public class OverviewPanel extends JPanel implements Runnable
{
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();
@@ -412,8 +428,8 @@ public class OverviewPanel extends JPanel implements Runnable
if (av.hasHiddenRows())
{
- startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
@@ -442,7 +458,7 @@ public class OverviewPanel extends JPanel implements Runnable
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/