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/* JamView
*
* created: 2009
*
* This file is part of Artemis
*
* Copyright(C) 2009 Genome Research Limited
*
* 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 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.
*
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
import java.awt.AlphaComposite;
import java.awt.BasicStroke;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Composite;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
import java.awt.event.FocusEvent;
import java.awt.event.FocusListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.awt.event.WindowEvent;
import java.awt.event.WindowFocusListener;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import javax.swing.ButtonGroup;
import javax.swing.JMenu;
import javax.swing.JSeparator;
import javax.swing.border.Border;
import javax.swing.border.EmptyBorder;
import net.sf.samtools.AlignmentBlock;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.util.CloseableIterator;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.SelectionChangeEvent;
import uk.ac.sanger.artemis.SelectionChangeListener;
import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
import uk.ac.sanger.artemis.components.FeatureDisplay;
import uk.ac.sanger.artemis.editor.MultiLineToolTipUI;
import uk.ac.sanger.artemis.sequence.MarkerRange;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.Document;
import uk.ac.sanger.artemis.util.DocumentFactory;
import uk.ac.sanger.artemis.util.OutOfRangeException;
public class BamView extends JPanel
implements DisplayAdjustmentListener, SelectionChangeListener
private Hashtable<String, Integer> seqLengths = new Hashtable<String, Integer>();
private Vector<String> seqNames = new Vector<String>();
private String bam;
private boolean isSingle = false;
private boolean isSNPs = false;
private boolean isStackView = false;
private boolean isPairedStackView = false;
private FeatureDisplay feature_display;
private Selection selection;
private JPanel mainPanel;
private int startBase = -1;
private int endBase = -1;
private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
private boolean showBaseAlignment = false;
tjc
committed
private AlphaComposite translucent =
AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.6f);
tjc
committed
private Color lightGrey = new Color(200, 200, 200);
private Color darkGreen = new Color(0, 150, 0);
private Color darkOrange = new Color(255,140,0);
private Point lastMousePoint = null;
private SAMRecord mouseOverSAMRecord = null;
// record of where a mouse drag starts
private int dragStart = -1;
private int maxHeight = 800;
tjc
committed
public BamView(String bam,
String reference,
int nbasesInView)
{
super();
setBackground(Color.white);
this.bam = bam;
this.nbasesInView = nbasesInView;
if(reference != null)
{
try
{
getEntry(reference,entryGroup);
}
catch (NoSequenceException e)
{
e.printStackTrace();
}
}
//Options.getOptions().getFontUIResource();
//final javax.swing.plaf.FontUIResource font_ui_resource =
// new javax.swing.plaf.FontUIResource(getFont());
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