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JAL-2136 merged develop into branch to fix build failure
[jalview.git]
/
src
/
MCview
/
PDBCanvas.java
diff --git
a/src/MCview/PDBCanvas.java
b/src/MCview/PDBCanvas.java
index
dfe7c8f
..
3b12ee9
100644
(file)
--- a/
src/MCview/PDBCanvas.java
+++ b/
src/MCview/PDBCanvas.java
@@
-26,6
+26,9
@@
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
import jalview.gui.AlignmentPanel;
import jalview.gui.FeatureRenderer;
import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.AtomSpec;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
@@
-65,7
+68,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
int my = 0;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBEntry pdbentry;
@@
-140,7
+143,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
String errorMessage;
void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap, String protocol)
+ AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
this.pdbentry = pdbentry;
{
this.ap = ap;
this.pdbentry = pdbentry;
@@
-150,9
+153,10
@@
public class PDBCanvas extends JPanel implements MouseListener,
try
{
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+ ap.alignFrame);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
pdbentry.setFile("INLINE" + pdb.getId());
}
{
pdbentry.setFile("INLINE" + pdb.getId());
}
@@
-187,8
+191,10
@@
public class PDBCanvas extends JPanel 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");
@@
-201,11
+207,13
@@
public class PDBCanvas extends JPanel implements MouseListener,
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
{
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");
@@
-245,6
+253,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
addKeyListener(new KeyAdapter()
{
addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent evt)
{
keyPressed(evt);
public void keyPressed(KeyEvent evt)
{
keyPressed(evt);
@@
-452,6
+461,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
centre[2] = ztot / (2 * (float) bsize);
}
centre[2] = ztot / (2 * (float) bsize);
}
+ @Override
public void paintComponent(Graphics g)
{
super.paintComponent(g);
public void paintComponent(Graphics g)
{
super.paintComponent(g);
@@
-538,6
+548,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
showFeatures = true;
}
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
PDBChain chain;
if (bysequence && pdb != null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
@@
-565,23
+576,15
@@
public class PDBCanvas extends JPanel implements MouseListener,
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.startCol = fr.findFeatureColour(tmp.startCol,
- sequence[s], pos);
- }
+ tmp.startCol = sr.getResidueColour(sequence[s], pos,
+ finder);
}
pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
}
pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
if (pos > 0)
{
pos = sequence[s].findIndex(pos);
- tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
- if (showFeatures)
- {
- tmp.endCol = fr.findFeatureColour(tmp.endCol,
- sequence[s], pos);
- }
+ tmp.endCol = sr
+ .getResidueColour(sequence[s], pos, finder);
}
}
}
}
@@
-745,6
+748,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
public void mousePressed(MouseEvent e)
{
pdbAction = true;
@@
-789,6
+793,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
dragging = false;
}
dragging = false;
}
+ @Override
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
public void mouseMoved(MouseEvent e)
{
pdbAction = true;
@@
-824,18
+829,22
@@
public class PDBCanvas extends JPanel 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();
@@
-885,6
+894,7
@@
public class PDBCanvas extends JPanel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
dragging = false;
public void mouseReleased(MouseEvent evt)
{
dragging = false;
@@
-1065,7
+1075,8
@@
public class PDBCanvas extends JPanel implements MouseListener,
// ////////////////////////////////
// /StructureListener
// ////////////////////////////////
// /StructureListener
- public String[] getPdbFile()
+ @Override
+ public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}
{
return new String[] { pdbentry.getFile() };
}
@@
-1169,6
+1180,7
@@
public class PDBCanvas extends JPanel 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();