Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3

[jalview.git] / src / jalview / ws2 / actions / alignment / AlignmentJob.java

diff --git a/src/jalview/ws2/actions/alignment/AlignmentJob.java b/src/jalview/ws2/actions/alignment/AlignmentJob.java
new file mode 100644 (file)
index 0000000..5ddb64a
--- /dev/null
+++ b/src/jalview/ws2/actions/alignment/AlignmentJob.java
@@ -0,0 +1,114 @@
+package jalview.ws2.actions.alignment;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.ws2.actions.BaseJob;
+import jalview.ws2.api.WebServiceJobHandle;
+
+/**
+ * A wrapper class that extends basic job container with data specific to
+ * alignment services. It stores input and empty sequences (with uniquified
+ * names) along the original sequence information. {@link AlignmentJob} objects
+ * are created by {@link AlignmentTask} during a preparation stage.
+ * 
+ * @author mmwarowny
+ *
+ */
+class AlignmentJob extends BaseJob
+{
+  private final List<SequenceI> emptySeqs;
+
+  private final Map<String, SequenceInfo> names;
+
+  private AlignmentI alignmentResult;
+
+  AlignmentJob(List<SequenceI> inputSeqs, List<SequenceI> emptySeqs,
+      Map<String, SequenceInfo> names)
+  {
+    super(Collections.unmodifiableList(inputSeqs));
+    this.emptySeqs = Collections.unmodifiableList(emptySeqs);
+    this.names = Collections.unmodifiableMap(names);
+  }
+
+  public static AlignmentJob create(SequenceI[] seqs, int minlen, boolean keepGaps)
+  {
+    int nseqs = 0;
+    for (int i = 0; i < seqs.length; i++)
+    {
+      if (seqs[i].getEnd() - seqs[i].getStart() >= minlen)
+        nseqs++;
+    }
+    boolean valid = nseqs > 1; // need at least two sequences
+    Map<String, SequenceInfo> names = new LinkedHashMap<>();
+    List<SequenceI> inputSeqs = new ArrayList<>();
+    List<SequenceI> emptySeqs = new ArrayList<>();
+    for (int i = 0; i < seqs.length; i++)
+    {
+      SequenceI seq = seqs[i];
+      String newName = SeqsetUtils.unique_name(i);
+      names.put(newName, SeqsetUtils.SeqCharacterHash(seq));
+      if (valid && seq.getEnd() - seq.getStart() >= minlen)
+      {
+        // make new input sequence
+        String seqString = seq.getSequenceAsString();
+        if (!keepGaps)
+          seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
+        inputSeqs.add(new Sequence(newName, seqString));
+      }
+      else
+      {
+        String seqString = "";
+        if (seq.getEnd() >= seq.getStart()) // true if gaps only
+        {
+          seqString = seq.getSequenceAsString();
+          if (!keepGaps)
+            seqString = AlignSeq.extractGaps(Comparison.GapChars, seqString);
+        }
+        emptySeqs.add(new Sequence(newName, seqString));
+      }
+    }
+    return new AlignmentJob(inputSeqs, emptySeqs, names);
+  }
+
+  @Override
+  public boolean isInputValid()
+  {
+    return inputSeqs.size() >= 2;
+  }
+
+  List<SequenceI> getEmptySequences()
+  {
+    return emptySeqs;
+  }
+
+  Map<String, SequenceInfo> getNames()
+  {
+    return names;
+  }
+
+  boolean hasResult()
+  {
+    return alignmentResult != null;
+  }
+
+  AlignmentI getAlignmentResult()
+  {
+    return alignmentResult;
+  }
+
+  void setAlignmentResult(AlignmentI alignment)
+  {
+    this.alignmentResult = alignment;
+  }
+}