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JAL-1632 remove unused check for sequences aligned
[jalview.git]
/
src
/
MCview
/
PDBChain.java
diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
34f09c8
..
ba93046
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-39,6
+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
*/
@@
-147,7
+149,7
@@
public class PDBChain
pdbpos++;
}
pdbpos++;
}
- boolean sameResidue = Comparison.compareChars(as.astr1.charAt(i),
+ boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i),
as.astr2.charAt(i), false);
if (sameResidue)
{
as.astr2.charAt(i), false);
if (sameResidue)
{
@@
-367,7
+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);
@@
-516,10
+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)
{