git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2388 New iterators and tests
[jalview.git]
/
src
/
MCview
/
PDBChain.java
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
b74f101
..
ba93046
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-31,6
+31,7
@@
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
import java.awt.Color;
import java.util.List;
import java.awt.Color;
import java.util.List;
@@
-38,6
+39,8
@@
import java.util.Vector;
public class PDBChain
{
public class PDBChain
{
+ public static final String RESNUM_FEATURE = "RESNUM";
+
/**
* SequenceFeature group for PDB File features added to sequences
*/
/**
* SequenceFeature group for PDB File features added to sequences
*/
@@
-146,7
+149,9
@@
public class PDBChain
pdbpos++;
}
pdbpos++;
}
- if (as.astr1.charAt(i) == as.astr2.charAt(i))
+ boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
+ as.astr2.charAt(i), false);
+ if (sameResidue)
{
if (pdbpos >= residues.size())
{
{
if (pdbpos >= residues.size())
{
@@
-199,7
+204,8
@@
public class PDBChain
}
for (int i = 0; i < features.length; i++)
{
}
for (int i = 0; i < features.length; i++)
{
- if (features[i].getFeatureGroup().equals(pdbid))
+ if (features[i].getFeatureGroup() != null
+ && features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
{
SequenceFeature tx = new SequenceFeature(features[i]);
tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
@@
-363,7
+369,7
@@
public class PDBChain
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
- SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+ SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ count, offset + count, pdbid);
resFeatures.addElement(sf);
+ ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
+ count, offset + count, pdbid);
resFeatures.addElement(sf);
@@
-512,10
+518,12
@@
public class PDBChain
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
try
{
index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
- b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0),
+ 0, null, null, 0f);
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
- b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
+ b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0,
+ null, null, 0f);
} catch (Exception e)
{
} catch (Exception e)
{