X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=e8555f74711978bb2579297be19ae44d83dc1122;hb=61a4ffb7cfd54b95c16bd78c14f4e86d2a7b037e;hp=475f0c711d1e4e54fc73547e24ea39f807eed634;hpb=3f734555193e56f46b07d5bc12df77d26e180ec0;p=jalview.git
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 475f0c7..e8555f7 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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;
@@ -26,7 +29,7 @@ import javax.swing.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
@@ -39,6 +42,7 @@ public class OverviewPanel extends JPanel implements Runnable
AlignmentPanel ap;
final AnnotationRenderer renderer = new AnnotationRenderer();
+
float scalew = 1f;
float scaleh = 1f;
@@ -67,7 +71,7 @@ public class OverviewPanel extends JPanel implements Runnable
/**
* Creates a new OverviewPanel object.
- *
+ *
* @param ap
* DOCUMENT ME!
*/
@@ -86,7 +90,7 @@ 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;
}
@@ -204,8 +208,8 @@ 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);
@@ -300,7 +304,8 @@ public class OverviewPanel extends JPanel implements Runnable
hiddenRow = false;
if (av.hasHiddenRows())
{
- seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
+ seq = av.getAlignment().getHiddenSequences()
+ .getHiddenSequence(lastrow);
if (seq == null)
{
int index = av.getAlignment().getHiddenSequences()
@@ -361,7 +366,7 @@ 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 +374,8 @@ 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 +402,8 @@ 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 +419,8 @@ 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 +449,7 @@ public class OverviewPanel extends JPanel implements Runnable
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/