- 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;
+ *
+ * }