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JAL-1551 formatting
author
Jim Procter
<j.procter@dundee.ac.uk>
Mon, 20 Oct 2014 08:25:08 +0000
(09:25 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 21 Oct 2014 10:33:17 +0000
(11:33 +0100)
src/MCview/PDBChain.java
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diff --git
a/src/MCview/PDBChain.java
b/src/MCview/PDBChain.java
index
c9301e8
..
6055a5b
100755
(executable)
--- a/
src/MCview/PDBChain.java
+++ b/
src/MCview/PDBChain.java
@@
-20,15
+20,20
@@
*/
package MCview;
*/
package MCview;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
public class PDBChain
{
/**
@@
-187,7
+192,9
@@
public class PDBChain
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
if (tx.begin != 0 && tx.end != 0)
+ {
sq.addSequenceFeature(tx);
sq.addSequenceFeature(tx);
+ }
}
}
return features;
}
}
return features;
@@
-275,7
+282,7
@@
public class PDBChain
// remains the same as the first atom's resNumber (res)
while ((resNumber == res) && (i < atoms.size()))
{
// remains the same as the first atom's resNumber (res)
while ((resNumber == res) && (i < atoms.size()))
{
- resAtoms.addElement((Atom) atoms.elementAt(i));
+ resAtoms.addElement(atoms.elementAt(i));
i++;
if (i < atoms.size())
i++;
if (i < atoms.size())
@@
-364,7
+371,9
@@
public class PDBChain
{
annots[i] = (Annotation) resAnnotation.elementAt(i);
if (annots[i].value > max)
{
annots[i] = (Annotation) resAnnotation.elementAt(i);
if (annots[i].value > max)
+ {
max = annots[i].value;
max = annots[i].value;
+ }
resAnnotation.setElementAt(null, i);
}
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
resAnnotation.setElementAt(null, i);
}
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
@@
-496,7
+505,7
@@
public class PDBChain
{
int prn = mapping.getPDBResNum(k + 1);
{
int prn = mapping.getPDBResNum(k + 1);
- an[k] = new Annotation((float) prn);
+ an[k] = new Annotation(prn);
if (min == -1)
{
min = k;
if (min == -1)
{
min = k;
@@
-516,7
+525,8
@@
public class PDBChain
}
sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
"PDB Residue Numbering for " + this.pdbid + ":" + this.id,
}
sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
"PDB Residue Numbering for " + this.pdbid + ":" + this.id,
- an, (float) min, (float) max, AlignmentAnnotation.LINE_GRAPH));
+ an, min, max, AlignmentAnnotation.LINE_GRAPH));
+
}
}
}
}
}
}