/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package MCview;
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
+
public class PDBChain
{
/**
if (features[i].getFeatureGroup().equals(pdbid))
{
SequenceFeature tx = new SequenceFeature(features[i]);
- tx.setBegin(1 + residues.elementAt(tx.getBegin()
- - offset).atoms.elementAt(0).alignmentMapping);
- tx.setEnd(1 + residues.elementAt(tx.getEnd()
- - offset).atoms.elementAt(0).alignmentMapping);
+ tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping);
+ tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+ .elementAt(0).alignmentMapping);
tx.setStatus(status
+ ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
: ":" + tx.getStatus()));
AlignmentAnnotation tfactorann = new AlignmentAnnotation(
"Temperature Factor", "Temperature Factor for " + pdbid + id,
- annots, 0, max,
- AlignmentAnnotation.LINE_GRAPH);
+ annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
tfactorann.setSequenceRef(sequence);
sequence.addAlignmentAnnotation(tfactorann);
}
{
try
{
- index = ResidueProperties.aa3Hash.get(b.at1.resName)
- .intValue();
+ index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
- 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));
} catch (Exception e)
* @param sqmpping
* - mapping between destination sequence and local chain
*/
- public void transferResidueAnnotation(
- StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
+ public void transferResidueAnnotation(StructureMapping mapping,
+ jalview.datamodel.Mapping sqmpping)
{
SequenceI sq = mapping.getSequence();
SequenceI dsq = sq;