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Modified to compile applet with Jmol jar present
[jalview.git]
/
src
/
MCview
/
PDBChain.java
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
dc3743e
..
76a0cde
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-65,7
+65,7
@@
public class PDBChain
return tmp;
}
return tmp;
}
- void makeExactMapping(AlignSeq as, Sequence s1)
+ public void makeExactMapping(AlignSeq as, SequenceI s1)
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
{
int pdbpos = as.getSeq2Start() - 2;
int alignpos = s1.getStart() + as.getSeq1Start() - 3;
@@
-104,13
+104,13
@@
public class PDBChain
public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
{
SequenceI sq = seq;
public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
{
SequenceI sq = seq;
- while (sq != null)
+ while (sq!=null && sq.getDatasetSequence()!=null)
{
{
+ sq = sq.getDatasetSequence();
if (sq == sequence)
{
return null;
}
if (sq == sequence)
{
return null;
}
- sq = sq.getDatasetSequence();
}
/**
* Remove any existing features for this chain if they exist ?
}
/**
* Remove any existing features for this chain if they exist ?
@@
-138,7
+138,8
@@
public class PDBChain
tx.setStatus(status +
( (tx.getStatus() == null || tx.getStatus().length() == 0) ?
"" : ":" + tx.getStatus()));
tx.setStatus(status +
( (tx.getStatus() == null || tx.getStatus().length() == 0) ?
"" : ":" + tx.getStatus()));
- seq.addSequenceFeature(tx);
+ if (tx.begin!=0 && tx.end!=0)
+ sq.addSequenceFeature(tx);
}
}
return features;
}
}
return features;
@@
-252,9
+253,9
@@
public class PDBChain
count++;
}
count++;
}
- if (id.length() < 1 || id.equals(" "))
+ if (id.length() < 1)
{
{
- id = "_";
+ id = " ";
}
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()
}
sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()