import java.awt.Color;
import java.util.List;
+import java.util.Locale;
import java.util.Vector;
public class PDBChain
String tfacName = "Temperature Factor";
-
- public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
+ public PDBChain(String thePdbid, String theId,
+ String tempFactorColumnName)
{
- this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+ this.pdbid = thePdbid == null ? thePdbid
+ : thePdbid.toLowerCase(Locale.ROOT);
this.id = theId;
- if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+ if (tempFactorColumnName != null && tempFactorColumnName.length() > 0)
{
tfacName = tempFactorColumnName;
}
}
/**
- * import chain data assuming Temperature Factor is in the Temperature Factor column
+ * import chain data assuming Temperature Factor is in the Temperature Factor
+ * column
+ *
* @param thePdbid
* @param theId
*/
public PDBChain(String thePdbid, String theId)
{
- this(thePdbid,theId, null);
+ this(thePdbid, theId, null);
}
/**
}
char seqchar = ds.getCharAt(seqpos - ds.getStart());
- boolean sameResidue = Comparison.isSameResidue(
- seqchar, strchar, false);
+ boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
+ false);
if (sameResidue)
{
for (Atom atom : res.atoms)
* @param status
* The Status of the transferred annotation
*
- * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
+ * @param altPDBID
+ * the group id for the features on the destination sequence (e.g.
+ * the official accession ID)
*/
- public void transferRESNUMFeatures(SequenceI seq,
- String status, String altPDBID)
+ public void transferRESNUMFeatures(SequenceI seq, String status,
+ String altPDBID)
{
- if (altPDBID==null)
+ if (altPDBID == null)
{
altPDBID = pdbid;
}
if (feature.getFeatureGroup() != null
&& feature.getFeatureGroup().equals(pdbid))
{
- int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
- .elementAt(0).alignmentMapping;
+ int newBegin = 1
+ + residues.elementAt(feature.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping;
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
{
String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ pdbid + id;
- SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
- + count - 1, offset + count - 1, "PDB_INS");
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc,
+ offset + count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
- String desc = tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id;
+ String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid
+ + id;
SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- tfacName, tfacName + " for " + pdbid + id,
- annots, min, max, AlignmentAnnotation.LINE_GRAPH);
-
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(tfacName,
+ tfacName + " for " + pdbid + id, annots, min, max,
+ AlignmentAnnotation.LINE_GRAPH);
+
tfactorann.setCalcId(getClass().getName());
tfactorann.setSequenceRef(sequence);
}
}
-
/**
* Colour start/end of bonds by charge
* <ul>