import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.HMMFile;
import jalview.io.NewickFile;
import jalview.math.Matrix;
import jalview.math.MatrixI;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
-import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.api.ServiceWithParameters;
+import jalview.ws.jws2.PreferredServiceRegistry;
import jalview.ws.jws2.dm.AAConSettings;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
private static final String RNA_PREFIX = "rna_";
+ private static final String HMMER_PREFIX = "hmmer_";
+
private static final String UTF_8 = "UTF-8";
/**
jseq.getFeatures().add(features);
}
+ /*
+ * save PDB entries for sequence
+ */
if (jdatasq.getAllPDBEntries() != null)
{
Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
+ if (jds.hasHMMProfile())
+ {
+ saveHmmerProfile(jout, jseq, jds);
+ }
+
// jms.addJSeq(jseq);
object.getJSeq().add(jseq);
}
}
return object;
}
+ /**
+ * Saves the HMMER profile associated with the sequence as a file in the jar,
+ * in HMMER format, and saves the name of the file as a child element of the
+ * XML sequence element
+ *
+ * @param jout
+ * @param xmlSeq
+ * @param seq
+ */
+ protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+ SequenceI seq)
+ {
+ HiddenMarkovModel profile = seq.getHMM();
+ if (profile == null)
+ {
+ warn("Want to save HMM profile for " + seq.getName()
+ + " but none found");
+ return;
+ }
+ HMMFile hmmFile = new HMMFile(profile);
+ String hmmAsString = hmmFile.print();
+ String jarEntryName = HMMER_PREFIX + nextCounter();
+ try
+ {
+ writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+ xmlSeq.setHmmerProfile(jarEntryName);
+ } catch (IOException e)
+ {
+ warn("Error saving HMM profile: " + e.getMessage());
+ }
+ }
+
/**
* Writes PCA viewer attributes and computed values to an XML model object and
* adds it to the JalviewModel. Any exceptions are reported by logging.
}
else if (!matchedFile.equals(pdbentry.getFile()))
{
- Cache.log.warn(
- "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
+ Cache.log.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
}
// record the
// file so we
if (calcIdParam.getVersion().equals("1.0"))
{
final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getInstance()
+ ServiceWithParameters service = PreferredServiceRegistry.getRegistry()
.getPreferredServiceFor(calcIds);
if (service != null)
{
argList = parmSet.getArguments();
parmSet = null;
}
- AAConSettings settings = new AAConSettings(
+ AutoCalcSetting settings = new AAConSettings(
calcIdParam.isAutoUpdate(), service, parmSet, argList);
av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
calcIdParam.isNeedsUpdate());
}
else
{
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a server in the Web Services preferences tab.");
return false;
}
}
}
}
+ /*
+ * load any HMMER profile
+ */
+ // TODO fix this
+
+ String hmmJarFile = jseqs.get(i).getHmmerProfile();
+ if (hmmJarFile != null && jprovider != null)
+ {
+ loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
+ }
}
} // end !multipleview
}
/**
+ * Loads a HMMER profile from a file stored in the project, and associates it
+ * with the specified sequence
+ *
+ * @param jprovider
+ * @param hmmJarFile
+ * @param seq
+ */
+ protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+ String hmmJarFile, SequenceI seq)
+ {
+ try
+ {
+ String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+ HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+ HiddenMarkovModel hmmModel = parser.getHMM();
+ hmmModel = new HiddenMarkovModel(hmmModel, seq);
+ seq.setHMM(hmmModel);
+ } catch (IOException e)
+ {
+ warn("Error loading HMM profile for " + seq.getName() + ": "
+ + e.getMessage());
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
return true;
}
return false;
jmap.setTo(djs);
incompleteSeqs.put(sqid, djs);
seqRefIds.put(sqid, djs);
-
}
jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
NoValueColour noCol = colourModel.getNoValueColour();
git://source.jalview.org / jalview.git / blobdiff