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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
f4263b1
..
3b84ee3
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-30,6
+30,7
@@
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structure.StructureViewSettings;
import java.awt.Color;
import java.util.List;
import java.awt.Color;
import java.util.List;
@@
-147,6
+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)
{
@@
-188,6
+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))
@@
-385,9
+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
{
@@
-423,11
+435,15
@@
public class PDBChain
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
// System.out.println("PDB Sequence is :\nSequence = " + seq);
// System.out.println("No of residues = " + residues.size());
+
+ if (StructureViewSettings.isShowSeqFeatures())
+ {
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
{
sequence.addSequenceFeature(resFeatures.elementAt(i));
resFeatures.setElementAt(null, i);
}
for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
{
sequence.addSequenceFeature(resFeatures.elementAt(i));
resFeatures.setElementAt(null, i);
}
+ }
if (visibleChainAnnotation)
{
Annotation[] annots = new Annotation[resAnnotation.size()];
if (visibleChainAnnotation)
{
Annotation[] annots = new Annotation[resAnnotation.size()];