import jalview.datamodel.Annotation;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol)
+ String[] targetChains, String pdbFile, DataSourceType protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
* (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
- * @param protocol
+ * @param sourceType
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, String protocol)
+ String pdbFile, DataSourceType sourceType)
{
/*
* There will be better ways of doing this in the future, for now we'll use
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
- pdb = new JmolParser(pdbFile, protocol);
+ pdb = new JmolParser(pdbFile, sourceType);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
+ && DataSourceType.FILE == sourceType)
{
registerPDBFile(pdb.getId().trim(), pdbFile);
}
+ // if PDBId is unavailable then skip SIFTS mapping execution path
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+
} catch (Exception ex)
{
ex.printStackTrace();
continue;
}
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ if (sourceType == DataSourceType.PASTE)
{
pdbFile = "INLINE" + pdb.getId();
}
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
}
else
{
- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
for (PDBChain chain : pdb.getChains())
{
try
return;
}
- SearchResults results = new SearchResults();
+ SearchResultsI results = new SearchResults();
for (AtomSpec atom : atoms)
{
SequenceI lastseq = null;
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
- SearchResults results = null;
+ SearchResultsI results = null;
if (seqPos == -1)
{
seqPos = seq.findPosition(indexpos);