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JAL-2512 Fix to show non-gap positions in None colour scheme
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
74bec63
..
c454203
100644
(file)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-26,6
+26,9
@@
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.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;
@@
-67,7
+70,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
int my = 0;
int my = 0;
- public PDBfile pdb;
+ public StructureFile pdb;
PDBEntry pdbentry;
PDBEntry pdbentry;
@@
-144,7
+147,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
StructureSelectionManager ssm;
public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, AlignmentPanel ap, String protocol)
+ String[] chains, AlignmentPanel ap, DataSourceType protocol)
{
this.ap = ap;
{
this.ap = ap;
@@
-158,7
+161,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
{
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
{
pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
pdbentry.setFile("INLINE" + pdb.getId());
}
{
pdbentry.setFile("INLINE" + pdb.getId());
}
@@
-175,7
+178,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
colourBySequence();
colourBySequence();
- int max = -10;
+ float max = -10;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
int maxchain = -1;
int pdbstart = 0;
int pdbend = 0;
@@
-188,8
+191,10
@@
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
+203,19
@@
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
+274,7
@@
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
+478,7
@@
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)
{
@@
-569,6
+578,8
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
showFeatures = true;
}
showFeatures = true;
}
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+
PDBChain chain;
if (bysequence && pdb != null)
{
PDBChain chain;
if (bysequence && pdb != null)
{
@@
-596,25
+607,16
@@
public class AppletPDBCanvas extends Panel 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);
}
}
-
}
}
}
}
}
}
@@
-774,6
+776,7
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public void mousePressed(MouseEvent e)
{
pdbAction = true;
public void mousePressed(MouseEvent e)
{
pdbAction = true;
@@
-818,6
+821,7
@@
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
+864,22
@@
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
+929,7
@@
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
+1046,7
@@
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
+1118,7
@@
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
+1221,7
@@
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();