There will be better ways of doing this in the future, for now we'll use
the tried and tested MCview pdb mapping
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
- String pdbFile,
- String protocol)
+ synchronized public MCview.PDBfile setMapping(
+ SequenceI[] sequence,
+ String[] targetChains,
+ String pdbFile,
+ String protocol)
{
MCview.PDBfile pdb = null;
try
return null;
}
+ String targetChain;
for (int s = 0; s < sequence.length; s++)
{
- String targetChain = "";
-
- if (sequence[s].getName().indexOf("|") > -1)
+ if(targetChains!=null && targetChains[s]!=null)
+ targetChain = targetChains[s];
+ else if (sequence[s].getName().indexOf("|") > -1)
{
targetChain = sequence[s].getName().substring(
sequence[s].getName().lastIndexOf("|") + 1);
}
+ else
+ targetChain = "";
+
int max = -10;
AlignSeq maxAlignseq = null;
mappings[mappings.length - 1]
= new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,
mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(mappings[mappings.length-1]);
}
/////////
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
SequenceListener sl;
+ SearchResults results = new SearchResults();
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof SequenceListener)
{
- sl = (SequenceListener) listeners.elementAt(i);
for (int j = 0; j < mappings.length; j++)
{
if (mappings[j].pdbfile.equals(pdbfile) &&
mappings[j].pdbchain.equals(chain))
{
- sl.highlightSequence(mappings[j].sequence,
- mappings[j].getSeqPos(pdbResNum));
+ results.addResult(mappings[j].sequence,
+ mappings[j].getSeqPos(pdbResNum),
+ mappings[j].getSeqPos(pdbResNum)
+ );
}
}
- sl.highlightSequence(null, pdbResNum);
+ if(results.getSize()>0)
+ {
+ ( (SequenceListener) listeners.elementAt(i))
+ .highlightSequence(results);
+ }
+
}
}
}
public Annotation[] colourSequenceFromStructure(SequenceI seq, String pdbid)
{
- Annotation [] annotations = new Annotation[seq.getLength()];
+ return null;
+ //THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
+ //UNTIL THE COLOUR BY ANNOTATION IS REWORKED
+ /* Annotation [] annotations = new Annotation[seq.getLength()];
StructureListener sl;
int atomNo = 0;
mappings[j].getPDBResNum(index),
mappings[j].pdbchain,
mappings[j].pdbfile);
-
- // System.out.println(atomNo+" "+mappings[j].getPDBResNum(index)
- // +" "+index+" "+col);
}
annotations[index] = new Annotation("X",null,' ',0,col);
}
}
- return annotations;
+ return annotations;*/
}
public void structureSelectionChanged()
- {
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
- {
- svl = (StructureListener) listeners.elementAt(i);
- }
- }
+ { }
public void sequenceSelectionChanged()
- {
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
- {
- svl = (StructureListener) listeners.elementAt(i);
- }
- }
+ { }
public void sequenceColoursChanged(Object source)
{