import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
import java.io.PrintStream;
import java.util.ArrayList;
private boolean addTempFacAnnot = false;
+ private IProgressIndicator progressIndicator;
+
+ private long progressSessionId;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
}
}
PDBfile pdb = null;
- boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
- "MAP_WITH_SIFTS", "false"));
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
SiftsClient siftsClient = null;
try
{
ArrayList<StructureMapping> seqToStrucMapping = null;
if (isMapUsingSIFTs)
{
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with SIFTS");
try
{
jalview.datamodel.Mapping sqmpping = maxAlignseq
e.printStackTrace();
System.err
.println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
+ setProgressBar(null);
+ setProgressBar("SIFTs mapping could not be obtained... Now mapping with NW alignment");
seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
maxChain, pdb, maxAlignseq);
}
}
else
{
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with NW alignment");
seqToStrucMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb,
maxAlignseq);
}
return null;
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
}