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2.3 updates
[jalview.git]
/
src
/
MCview
/
AppletPDBCanvas.java
diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
a61ecb2
..
e11e558
100755
(executable)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-83,6
+83,7
@@
public class AppletPDBCanvas
public AppletPDBCanvas(PDBEntry pdbentry,
SequenceI[] seq,
public AppletPDBCanvas(PDBEntry pdbentry,
SequenceI[] seq,
+ String [] chains,
AlignmentPanel ap,
String protocol)
AlignmentPanel ap,
String protocol)
@@
-94,12
+95,11
@@
public class AppletPDBCanvas
ssm = StructureSelectionManager.getStructureSelectionManager();
try{
ssm = StructureSelectionManager.getStructureSelectionManager();
try{
- pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
pdbentry.setFile("INLINE"+pdb.id);
if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
pdbentry.setFile("INLINE"+pdb.id);
- //if (fr!=null)
- // fr.featuresAdded();
+
}catch(Exception ex)
{
ex.printStackTrace();
}catch(Exception ex)
{
ex.printStackTrace();
@@
-110,9
+110,7
@@
public class AppletPDBCanvas
ssm.addStructureViewerListener(this);
ssm.addStructureViewerListener(this);
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- fr : null);
+ colourBySequence();
int max = -10;
int maxchain = -1;
int max = -10;
int maxchain = -1;
@@
-120,7
+118,6
@@
public class AppletPDBCanvas
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
int pdbend = 0;
int seqstart = 0;
int seqend = 0;
- AlignSeq maxAlignseq = null;
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
//JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
@@
-167,8
+164,7
@@
public class AppletPDBCanvas
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
pdbend = as.seq2end;
seqstart = as.seq1start + sequence.getStart() - 1;
seqend = as.seq1end + sequence.getEnd() - 1;
- maxAlignseq = as;
- }
+ }
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
@@
-243,9
+239,7
@@
public class AppletPDBCanvas
}
}
seqColoursReady = true;
}
}
seqColoursReady = true;
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- fr : null);
+ colourBySequence();
redrawneeded = true;
repaint();
}
redrawneeded = true;
repaint();
}
@@
-500,19
+494,21
@@
public class AppletPDBCanvas
// This method has been taken out of PDBChain to allow
// Applet and Application specific sequence renderers to be used
// This method has been taken out of PDBChain to allow
// Applet and Application specific sequence renderers to be used
- void colourBySequence(SequenceRenderer sr, FeatureRenderer seqcanvasfr)
+ void colourBySequence()
{
{
+ SequenceRenderer sr = new SequenceRenderer(ap.av);
+
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
boolean showFeatures = false;
- if (seqcanvasfr!=null)
+ if (ap.av.getShowSequenceFeatures())
{
if (fr == null)
{
fr = new jalview.appletgui.FeatureRenderer(ap.av);
}
{
if (fr == null)
{
fr = new jalview.appletgui.FeatureRenderer(ap.av);
}
- fr.transferSettings(seqcanvasfr);
+ fr.transferSettings(ap.getFeatureRenderer());
showFeatures = true;
}
showFeatures = true;
}
@@
-1080,7
+1076,7
@@
public class AppletPDBCanvas
///StructureListener
public String getPdbFile()
{
///StructureListener
public String getPdbFile()
{
- return "???";
+ return pdbentry.getFile();
}
}
@@
-1161,10
+1157,7
@@
public class AppletPDBCanvas
public void updateColours(Object source)
{
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.getSequenceRenderer(),
- ap.av.getShowSequenceFeatures() ?
- fr : null);
+ colourBySequence();
redrawneeded = true;
repaint();
}
redrawneeded = true;
repaint();
}