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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
7fdf11b
..
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;
@@
-192,6
+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))
@@
-339,6
+344,7
@@
public class PDBChain
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
if (currAtom.insCode != ' '
// Add inserted residues as features to the base residue
Atom currAtom = resAtoms.get(0);
if (currAtom.insCode != ' '
+ && !residues.isEmpty()
&& residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
{
SequenceFeature sf = new SequenceFeature("INSERTION",
&& residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber)
{
SequenceFeature sf = new SequenceFeature("INSERTION",
@@
-351,6
+357,18
@@
public class PDBChain
else
{
else
{
+ // boolean baseDetected = false;
+ // for (Atom resAtom : resAtoms)
+ // {
+ // if (resAtom.insCode == ' ')
+ // {
+ // baseDetected = true;
+ // }
+ // }
+ // if (!baseDetected)
+ // {
+ // continue;
+ // }
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
// Make a new Residue object with the new atoms vector
residues.addElement(new Residue(resAtoms, resNumber - 1, count));
@@
-364,6
+382,7
@@
public class PDBChain
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
resFeatures.addElement(sf);
resAnnotation.addElement(new Annotation(tmpat.tfactor));
// Keep totting up the sequence
+
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null)
{
String nucname = tmpat.resName.trim();
@@
-375,9
+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
{
@@
-413,11
+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()];