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JAL-2074 corrected classpathentry for Groovy 2.4.6
[jalview.git]
/
src
/
MCview
/
PDBChain.java
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
91526e1
..
3b84ee3
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-148,6
+148,10
@@
public class PDBChain
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
if (as.astr1.charAt(i) == as.astr2.charAt(i))
{
+ if (pdbpos >= residues.size())
+ {
+ continue;
+ }
Residue res = residues.elementAt(pdbpos);
for (Atom atom : res.atoms)
{
Residue res = residues.elementAt(pdbpos);
for (Atom atom : res.atoms)
{
@@
-189,6
+193,10
@@
public class PDBChain
status = PDBChain.IEASTATUS;
}
SequenceFeature[] features = sequence.getSequenceFeatures();
status = PDBChain.IEASTATUS;
}
SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features == null)
+ {
+ return null;
+ }
for (int i = 0; i < features.length; i++)
{
if (features[i].getFeatureGroup().equals(pdbid))
for (int i = 0; i < features.length; i++)
{
if (features[i].getFeatureGroup().equals(pdbid))
@@
-386,9
+394,12
@@
public class PDBChain
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
|| ResidueProperties.nucleotideIndex[nucname
.charAt((deoxyn ? 1 : 0))] == -1)
{
- seq.append("X");
- // System.err.println("PDBReader:Null aa3Hash for " +
- // tmpat.resName);
+ char r = ResidueProperties
+ .getSingleCharacterCode(ResidueProperties
+ .getCanonicalAminoAcid(tmpat.resName));
+ seq.append(r == '0' ? 'X' : r);
+ // System.err.println("PDBReader:Null aa3Hash for " +
+ // tmpat.resName);
}
else
{
}
else
{