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copy only the sequence associated alignment annotation displayed in the current view
[jalview.git]
/
src
/
MCview
/
PDBCanvas.java
diff --git
a/src/MCview/PDBCanvas.java
b/src/MCview/PDBCanvas.java
index
bd90b19
..
a5c0e70
100755
(executable)
--- a/
src/MCview/PDBCanvas.java
+++ b/
src/MCview/PDBCanvas.java
@@
-77,7
+77,6
@@
public class PDBCanvas
{
this.seqcanvas = seqcanvas;
this.sequence = seq;
{
this.seqcanvas = seqcanvas;
this.sequence = seq;
- seqcanvas.setPDBCanvas(this);
}
public void setPDBFile(PDBfile pdb)
}
public void setPDBFile(PDBfile pdb)
@@
-146,7
+145,7
@@
public class PDBCanvas
mainchain.seqend = seqend;
mainchain.isVisible = true;
mainchain.makeExactMapping(maxAlignseq, sequence);
mainchain.seqend = seqend;
mainchain.isVisible = true;
mainchain.makeExactMapping(maxAlignseq, sequence);
- mainchain.transferRESNUMFeatures(sequence.getDatasetSequence(), null);
+ mainchain.transferRESNUMFeatures(sequence, null);
seqcanvas.getFeatureRenderer().featuresAdded();
this.pdb = pdb;
this.prefsize = new Dimension(getWidth(), getHeight());
seqcanvas.getFeatureRenderer().featuresAdded();
this.pdb = pdb;
this.prefsize = new Dimension(getWidth(), getHeight());
@@
-513,12
+512,15
@@
public class PDBCanvas
{
// System.out.println("colour by seq");
boolean showFeatures = false;
{
// System.out.println("colour by seq");
boolean showFeatures = false;
- if (seqcanvas.getViewport().getShowSequenceFeatures())
+
+ //NO LONGER USED SINCE APPJMOL
+// if (seqcanvas.getViewport().getShowSequenceFeatures())
{
showFeatures = true;
if (fr == null)
{
{
showFeatures = true;
if (fr == null)
{
- fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
+ //NO LONGER USED SINCE APPJMOL
+// fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
}
fr.transferSettings(seqcanvas.getFeatureRenderer());
}
fr.transferSettings(seqcanvas.getFeatureRenderer());
@@
-539,7
+541,7
@@
public class PDBCanvas
{
int index = findTrueIndex(tmp.at1.alignmentMapping);
//sequence.findIndex(tmp.at1.alignmentMapping);
{
int index = findTrueIndex(tmp.at1.alignmentMapping);
//sequence.findIndex(tmp.at1.alignmentMapping);
- if (index > 0)
+ if (index != -1)
{
tmp.startCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);
{
tmp.startCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);
@@
-562,7
+564,7
@@
public class PDBCanvas
int index = findTrueIndex(tmp.at2.alignmentMapping);
//sequence.findIndex( tmp.at2.alignmentMapping );
int index = findTrueIndex(tmp.at2.alignmentMapping);
//sequence.findIndex( tmp.at2.alignmentMapping );
- if (index > 0)
+ if (index != -1)
{
tmp.endCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);
{
tmp.endCol = seqcanvas.getSequenceRenderer().
getResidueBoxColour(sequence, index);