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JAL-2089 Merge branch releases/Release_2_10_Branch to master
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
74bec63
..
61ac94c
100644
(file)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-26,6
+26,7
@@
import jalview.appletgui.FeatureRenderer;
import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.appletgui.SequenceRenderer;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.io.StructureFile;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
@@
-67,7
+68,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
int my = 0;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBEntry pdbentry;
@@
-188,8
+189,10
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
for (int i = 0; i < pdb.getChains().size(); i++)
{
for (int i = 0; i < pdb.getChains().size(); i++)
{
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+ mappingDetails
+ .append("\n\nPDB Sequence is :\nSequence = "
+ + pdb.getChains().elementAt(i).sequence
+ .getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
mappingDetails.append("\nNo of residues = "
+ pdb.getChains().elementAt(i).residues.size() + "\n\n");
@@
-198,17
+201,19
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
// Align the sequence to the pdb
// TODO: DNa/Pep switch
AlignSeq as = new AlignSeq(sequence,
- pdb.getChains().elementAt(i).sequence,
- pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+ pdb.getChains().elementAt(i).sequence, pdb.getChains()
+ .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
public void println()
{
mappingDetails.append("\n");
@@
-267,6
+272,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
addKeyListener(new KeyAdapter()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
public void keyPressed(KeyEvent evt)
{
doKeyPressed(evt);
@@
-470,6
+476,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
centre[2] = ztot / (2 * (float) bsize);
}
centre[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paint(Graphics g)
{
public void paint(Graphics g)
{
@@
-774,6
+781,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
public void mousePressed(MouseEvent e)
{
pdbAction = true;
@@
-818,6
+826,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
dragging = false;
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
@@
-860,18
+869,22
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mouseClicked(MouseEvent e)
{
}
public void mouseClicked(MouseEvent e)
{
}
+ @Override
public void mouseEntered(MouseEvent e)
{
}
public void mouseEntered(MouseEvent e)
{
}
+ @Override
public void mouseExited(MouseEvent e)
{
}
public void mouseExited(MouseEvent e)
{
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
public void mouseDragged(MouseEvent evt)
{
int x = evt.getX();
@@
-921,6
+934,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
public void mouseReleased(MouseEvent evt)
{
dragging = false;
@@
-1037,6
+1051,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
return fatom;
}
return fatom;
}
+ @Override
public void update(Graphics g)
{
paint(g);
public void update(Graphics g)
{
paint(g);
@@
-1108,6
+1123,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// ////////////////////////////////
// /StructureListener
// ////////////////////////////////
// /StructureListener
+ @Override
public String[] getPdbFile()
{
return new String[] { pdbentry.getFile() };
public String[] getPdbFile()
{
return new String[] { pdbentry.getFile() };
@@
-1210,6
+1226,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// return new Color(viewer.getAtomArgb(atomIndex));
}
// return new Color(viewer.getAtomArgb(atomIndex));
}
+ @Override
public void updateColours(Object source)
{
colourBySequence();
public void updateColours(Object source)
{
colourBySequence();