Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / ws / jws2 / jabaws2 / JabawsMsaInstance.java

diff --git a/src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java b/src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java
new file mode 100644 (file)
index 0000000..cbb4b05
--- /dev/null
+++ b/src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java
@@ -0,0 +1,105 @@
+package jalview.ws.jws2.jabaws2;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.ws.api.CancellableI;
+import jalview.ws.api.JobId;
+import jalview.ws.api.MultipleSequenceAlignmentI;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.WsParamSetI;
+
+import java.io.IOError;
+import java.rmi.ServerError;
+import java.util.ArrayList;
+import java.util.List;
+
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.FastaSequence;
+import compbio.metadata.ResultNotAvailableException;
+
+public class JabawsMsaInstance
+        extends JabawsServiceInstance<compbio.data.msa.MsaWS>
+        implements MultipleSequenceAlignmentI, CancellableI
+{
+  @Override
+  public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
+          List<ArgumentI> arguments) throws Throwable
+  {
+    List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
+    for (SequenceI seq : toalign)
+    {
+      seqs.add(new FastaSequence(seq.getName(), seq.getSequenceAsString()));
+    }
+    String jobid = null;
+    if (parameters != null)
+    {
+      if (parameters instanceof JabaPreset)
+      {
+        jobid = service.presetAlign(seqs,
+                ((JabaPreset) parameters).getJabaPreset());
+      }
+      else
+      {
+        jobid = service.customAlign(seqs, JabaParamStore
+                .getJabafromJwsArgs(parameters.getArguments()));
+      }
+    }
+    else if (arguments != null && arguments.size() > 0)
+    {
+      jobid = service.customAlign(seqs,
+              JabaParamStore.getJabafromJwsArgs(arguments));
+    }
+    else
+    {
+      jobid = service.align(seqs);
+    }
+
+    if (jobid == null)
+    {
+      return null;
+    }
+    return new JobId(our.getServiceType(), our.getName(), jobid);
+  }
+
+  @Override
+  public AlignmentI getAlignmentFor(JobId jobId)
+          throws InvalidArgumentException, ServerError, IOError
+  {
+    Alignment alignment = null;
+    try
+    {
+      alignment = service.getResult(jobId.getJobId());
+    } catch (ResultNotAvailableException rnotav)
+    {
+
+      // TODO - migrate JABA exception
+      // throw new ServerError("Couldn't get result for job",rnotav);
+    }
+    SequenceI[] alseqs;
+    int alseq_l = 0;
+    if (alignment.getSequences().size() == 0)
+    {
+      return null;
+    }
+
+    alseqs = new SequenceI[alignment.getSequences().size()];
+    for (compbio.data.sequence.FastaSequence seq : alignment.getSequences())
+    {
+      alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
+    }
+    AlignmentI jv_al = new jalview.datamodel.Alignment(alseqs);
+    jv_al.setGapCharacter(alignment.getMetadata().getGapchar());
+    return jv_al;
+
+  }
+
+  public JabawsMsaInstance(Jws2Instance handle)
+  {
+    super(handle);
+  }
+
+}