/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
+import jalview.renderer.AnnotationRenderer;
+
+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!
AlignmentPanel ap;
+ final AnnotationRenderer renderer = new AnnotationRenderer();
+
float scalew = 1f;
float scaleh = 1f;
// main visible SeqCanvas
SequenceRenderer sr;
- FeatureRenderer fr;
+ jalview.renderer.seqfeatures.FeatureRenderer fr;
/**
* Creates a new OverviewPanel object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public OverviewPanel(AlignmentPanel ap)
{
fr = new FeatureRenderer(ap);
// scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.alignment.getWidth()
- / (float) av.alignment.getHeight();
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
- if (av.conservation == null)
+ if (av.getAlignmentConservationAnnotation() == null)
{
graphHeight = 0;
}
- if (av.alignment.getWidth() > av.alignment.getHeight())
+ if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
{
// wider
width = 400;
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
if ((getWidth() != width)
addMouseMotionListener(new MouseMotionAdapter()
{
+ @Override
public void mouseDragged(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
+ // TODO: feature: jv2.5 detect shift drag and update selection from
+ // it.
boxX = evt.getX();
boxY = evt.getY();
checkValid();
addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent evt)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
boxX = evt.getX();
boxY = evt.getY();
if (boxX > (width - boxWidth))
{
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
// Try smallest possible box
boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
int col = (int) (boxX / scalew / av.getCharWidth());
int row = (int) (boxY / scaleh / av.getCharHeight());
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
if (!av.getColumnSelection().isVisible(col))
{
col = av.getColumnSelection().findColumnPosition(col);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
miniMe = null;
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
- fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
+ fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
}
- int alwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight()
- + av.alignment.getHiddenSequences().getSize();
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
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++)
{
lastrow = (int) (row * sampleRow);
hiddenRow = false;
- if (av.hasHiddenRows)
+ if (hasHiddenRows)
{
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+ seq = av.getAlignment().getHiddenSequences()
+ .getHiddenSequence(lastrow);
if (seq == null)
{
- int index = av.alignment.getHiddenSequences()
+ int index = av.getAlignment().getHiddenSequences()
.findIndexWithoutHiddenSeqs(lastrow);
- seq = av.alignment.getSequenceAt(index);
+ seq = av.getAlignment().getSequenceAt(index);
}
else
{
}
else
{
- seq = av.alignment.getSequenceAt(lastrow);
+ seq = av.getAlignment().getSequenceAt(lastrow);
}
if (seq == null)
{
color = sr.getResidueBoxColour(seq, lastcol).getRGB();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
color = fr.findFeatureColour(color, seq, lastcol);
}
}
if (hiddenRow
- || (av.hasHiddenColumns && !av.getColumnSelection()
- .isVisible(lastcol)))
+ || (hasHiddenCols && !av.getColumnSelection().isVisible(
+ lastcol)))
{
color = new Color(color).darker().darker().getRGB();
}
}
}
- if (av.conservation != null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
+ renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
{
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- ap.annotationPanel.drawGraph(mg, av.conservation,
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
*/
public void setBoxPosition()
{
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+ int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
+ int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
.getHiddenSequences().getSize())
* av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
int startSeq = av.startSeq;
int endSeq = av.endSeq;
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
- endSeq = av.alignment.getHiddenSequences()
+ endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
}
boxX = (int) (startRes * av.getCharWidth() * scalew);
boxY = (int) (startSeq * av.getCharHeight() * scaleh);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
}
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
if (resizing)
git://source.jalview.org / jalview.git / blobdiff