* @param viewer
* JmolViewer instance
* @param sequenceIds
- * - sequence Ids to search for associations
- * This method doesn't work. See http://issues.jalview.org/browse/JAL-621
+ * - sequence Ids to search for associations This method doesn't
+ * work. See http://issues.jalview.org/browse/JAL-621
*
- public SequenceStructureBinding addStructureViewInstance(Object jmolviewer, String[] sequenceIds)
- {
- org.jmol.api.JmolViewer viewer=null;
- try {
- viewer = (org.jmol.api.JmolViewer) jmolviewer;
- }
- catch (ClassCastException ex) {
- System.err.println("Unsupported viewer object :"+jmolviewer.getClass());
- }
- if (viewer==null)
- {
- System.err.println("Can't use this object as a structure viewer:"+jmolviewer.getClass());
- return null;
- }
- SequenceI[] seqs=null;
- if (sequenceIds==null || sequenceIds.length==0)
- {
- seqs = viewport.getAlignment().getSequencesArray();
- } else {
- Vector sqi=new Vector();
- AlignmentI al = viewport.getAlignment();
- for (int sid=0;sid<sequenceIds.length;sid++) {
- SequenceI sq = al.findName(sequenceIds[sid]);
- if (sq!=null) {
- sqi.addElement(sq);
- }
- }
- if (sqi.size()>0) {
- seqs = new SequenceI[sqi.size()];
- for (int sid=0,sSize=sqi.size();sid<sSize;sid++)
- {
- seqs[sid] = (SequenceI) sqi.elementAt(sid);
- }
- } else {
- return null;
- }
- }
- ExtJmol jmv=null;
- // TODO: search for a jmv that involves viewer
- if (jmv==null){
- // create a new viewer/jalview binding.
- jmv = new ExtJmol(viewer, alignPanel, seqs);
- }
- return jmv;
-
- }
+ * public SequenceStructureBinding addStructureViewInstance(Object
+ * jmolviewer, String[] sequenceIds) { org.jmol.api.JmolViewer
+ * viewer=null; try { viewer = (org.jmol.api.JmolViewer) jmolviewer;
+ * } catch (ClassCastException ex) {
+ * System.err.println("Unsupported viewer object :"
+ * +jmolviewer.getClass()); } if (viewer==null) {
+ * System.err.println("Can't use this object as a structure viewer:"
+ * +jmolviewer.getClass()); return null; } SequenceI[] seqs=null; if
+ * (sequenceIds==null || sequenceIds.length==0) { seqs =
+ * viewport.getAlignment().getSequencesArray(); } else { Vector
+ * sqi=new Vector(); AlignmentI al = viewport.getAlignment(); for
+ * (int sid=0;sid<sequenceIds.length;sid++) { SequenceI sq =
+ * al.findName(sequenceIds[sid]); if (sq!=null) { sqi.addElement(sq);
+ * } } if (sqi.size()>0) { seqs = new SequenceI[sqi.size()]; for (int
+ * sid=0,sSize=sqi.size();sid<sSize;sid++) { seqs[sid] = (SequenceI)
+ * sqi.elementAt(sid); } } else { return null; } } ExtJmol jmv=null;
+ * // TODO: search for a jmv that involves viewer if (jmv==null){ //
+ * create a new viewer/jalview binding. jmv = new ExtJmol(viewer,
+ * alignPanel, seqs); } return jmv;
+ *
+ * }
**/
public boolean addPdbFile(String sequenceId, String pdbEntryString,
String pdbFile)
if (needtoadd)
{
// make a note of the access mode and add
- if (pdbentry.getProperty()==null)
- {pdbentry.setProperty(new Hashtable());}
+ if (pdbentry.getProperty() == null)
+ {
+ pdbentry.setProperty(new Hashtable());
+ }
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
}
}
return true;
}
+
private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
{
if (seqs != null)
{
if (seqs[i] != null)
{
- sequences.addElement(new Object[] { seqs[i], (chains!=null) ? chains[i] : null});
+ sequences.addElement(new Object[]
+ { seqs[i], (chains != null) ? chains[i] : null });
}
}
seqs = new SequenceI[sequences.size()];
chains[i] = (String) oj[1];
}
}
- return new Object[] { seqs, chains};
+ return new Object[]
+ { seqs, chains };
}
+
public void newStructureView(JalviewLite applet, PDBEntry pdb,
SequenceI[] seqs, String[] chains, String protocol)
{
break;
}
}
- if (ajm!=null)
+ if (ajm != null)
{
- System.err.println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
+ System.err
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
// try and add the pdb structure
// ajm.addS
ajm = null;