/*
- * 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 <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;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
AlignmentPanel ap;
final AnnotationRenderer renderer = new AnnotationRenderer();
+
float scalew = 1f;
float scaleh = 1f;
/**
* Creates a new OverviewPanel object.
- *
+ *
* @param ap
* DOCUMENT ME!
*/
float initialScale = (float) av.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
- if (av.getAlignmentConservationAnnotation()== null)
+ if (av.getAlignmentConservationAnnotation() == null)
{
graphHeight = 0;
}
if (av.hasHiddenRows())
{
- row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
if (av.showSequenceFeatures)
{
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
}
int alwidth = av.getAlignment().getWidth();
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()
}
}
- if (av.getAlignmentConservationAnnotation()!= null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
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 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();
if (av.hasHiddenRows())
{
- startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
*/