import jalview.datamodel.SequenceI;
import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.sifts.SiftsClient;
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public PDBfile setMapping(SequenceI[] sequence,
+ synchronized public StructureFile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
+
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public PDBfile setMapping(boolean forStructureView,
+ synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
String pdbFile,
String protocol)
}
}
}
- PDBfile pdb = null;
+ StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
+
+ if (pdbFile != null && isCIFFile(pdbFile))
+ {
+ pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
+ }
+ else
+ {
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
+ }
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
return pdb;
}
+ private boolean isCIFFile(String filename)
+ {
+ String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
+ filename.length());
+ return "cif".equalsIgnoreCase(fileExt);
+ }
+
private StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String targetChainId, PDBfile pdb,
+ String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
AlignSeq maxAlignseq)
{
private StructureMapping getNWMappings(SequenceI seq,
String pdbFile,
- String maxChainId, PDBChain maxChain, PDBfile pdb,
+ String maxChainId, PDBChain maxChain, StructureFile pdb,
AlignSeq maxAlignseq)
{
final StringBuilder mappingDetails = new StringBuilder(128);
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+ if (sm.sequence == seq
+ || sm.sequence == seq.getDatasetSequence()
+ || (sm.sequence.getDatasetSequence() != null && sm.sequence
+ .getDatasetSequence() == seq.getDatasetSequence()))
{
for (int index : positions)
{
public void setProgressBar(String message)
{
+ if (progressIndicator == null)
+ {
+ return;
+ }
progressIndicator.setProgressBar(message, progressSessionId);
}