X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Febi%2FHmmerJSONProcessor.java;h=428c4983406df1ed0bd12b129b6bf161413c1d98;hb=79d76d41dc80b2c5a71201f26f832af337b7809f;hp=731df912cd3041b770edb4b354e3e3161ad66a04;hpb=8137e3257cb7c28bf46b2194ccbf98d1ea35335a;p=jalview.git

diff --git a/src/jalview/ws/ebi/HmmerJSONProcessor.java b/src/jalview/ws/ebi/HmmerJSONProcessor.java
index 731df91..428c498 100644
--- a/src/jalview/ws/ebi/HmmerJSONProcessor.java
+++ b/src/jalview/ws/ebi/HmmerJSONProcessor.java
@@ -3,10 +3,17 @@ package jalview.ws.ebi;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
@@ -14,8 +21,16 @@ import org.json.simple.parser.JSONParser;
 
 public class HmmerJSONProcessor
 {
+  /**
+   * result to be annotated. may not be null
+   */
   AlignmentI resultAl;
 
+  /**
+   * viewport on the alignment. may be null at construction time
+   */
+  AlignmentViewport viewAl = null;
+
   public HmmerJSONProcessor(AlignmentI searchResult)
   {
     resultAl = searchResult;
@@ -137,15 +152,20 @@ public class HmmerJSONProcessor
       // alippline
       String aliaseq = (String) dhit.get("aliaseq"), alimodel = (String) dhit
               .get("alimodel"), ppline = (String) dhit.get("alippline");
-      AlignmentAnnotation alipp = parsePosteriorProb(ppline);
       //
       int found = 0;
+      SequenceI firsthit = null;
       for (SequenceI hitseq : hits)
       {
         // match alisqfrom,alisqto,seq
         if (hitseq.getStart() == alisqfrom && hitseq.getEnd() == alisqto)
         {
+          if (found == 0)
+          {
+            firsthit = hitseq;
+          }
           found++; // annotated a sequence
+          AlignmentAnnotation alipp = parsePosteriorProb(ppline);
           AlignmentAnnotation pval = new AlignmentAnnotation("p-value",
                   "hmmer3 pvalue", pvalue);
           AlignmentAnnotation eval = new AlignmentAnnotation("e-value",
@@ -157,6 +177,16 @@ public class HmmerJSONProcessor
           hitseq.addAlignmentAnnotation(eval);
           alipp.createSequenceMapping(hitseq, hitseq.getStart(), false);
           hitseq.addAlignmentAnnotation(alipp);
+          String arch;
+          hitseq.addSequenceFeature(new SequenceFeature(
+                  "Pfam Domain Architecture", (hmmrhit.get("archindex"))
+                          + " " + (arch = (String) hmmrhit.get("arch")), 0,
+                  0,
+                  (hmmrhit.get("archScore") != null ? Integer
+                          .valueOf((String) hmmrhit.get("archScore")) : 0f),
+                  "HMMER3"));
+          addArchGroup(hitseq, arch);
+          alipp.setScore(Double.valueOf("" + dhit.get("bitscore")));
           alipp.adjustForAlignment();
           resultAl.addAnnotation(pval);
           resultAl.addAnnotation(eval);
@@ -164,19 +194,114 @@ public class HmmerJSONProcessor
           alipp.validateRangeAndDisplay();
         }
       }
-      if (found == 0)
+      // look for other sequences represented by this hit and create rep groups
+      // could be in "pdbs", or ..
+      addRedundantSeqGroup(firsthit, alisqfrom, alisqto,
+              (JSONArray) hmmrhit.get("seqs"), true);
+    }
+  }
+
+  /**
+   * series of operations to perform for the viewpanel associated with the
+   * alignment
+   */
+  private List<Runnable> viewOps = new ArrayList<Runnable>();
+
+  public void updateView(AlignmentViewport view)
+  {
+    viewAl = view;
+    for (Runnable op : viewOps)
+    {
+      op.run();
+    }
+  }
+
+  private void addRedundantSeqGroup(final SequenceI firsthit,
+          long alisqfrom, long alisqto, JSONArray others, boolean justDelete)
+  {
+    if (others != null)
+    {
+      final SequenceGroup repgroup = new SequenceGroup();
+      repgroup.setSeqrep(firsthit);
+      repgroup.addOrRemove(firsthit, false);
+      repgroup.setStartRes(0);
+      repgroup.setEndRes(resultAl.getWidth() - 1);
+      for (Object otherseq : others.toArray(new JSONObject[0]))
       {
-        System.err.println("Warn - no match for json hit " + sname + "/"
-                + alisqfrom + "-" + alisqto);
+        String repseq = (String) ((JSONObject) otherseq).get("dn");
+        SequenceI[] other = resultAl.findSequenceMatch(repseq);
+        if (other != null && other.length > 0)
+        {
+          if (justDelete)
+          {
+            for (SequenceI oth : other)
+            {
+              resultAl.deleteSequence(oth);
+            }
+            ;
+          }
+          else
+          {
+            int ofound = 0;
+            for (SequenceI oth : other)
+            {
+              if (oth.getStart() == alisqfrom && oth.getEnd() == alisqto)
+              {
+                ofound++;
+                repgroup.addSequence(oth, false);
+              }
+            }
+            if (ofound == 0)
+            {
+              System.err.println("Warn - no match for redundant hit "
+                      + repseq + "/" + alisqfrom + "-" + alisqto);
+            }
+            if (ofound > 1)
+            {
+              System.err
+                      .println("Warn - multiple matches for redundant hit "
+                              + repseq + "/" + alisqfrom + "-" + alisqto);
+            }
+          }
+        }
       }
-      if (found > 1)
+      if (repgroup.getSequences().size() > 1)
       {
-        System.err.println("Warn - multiple matches for json hit " + sname
-                + "/" + alisqfrom + "-" + alisqto);
+        // queue a hide operation
+        final HmmerJSONProcessor me = this;
+        viewOps.add(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            me.viewAl.hideRepSequences(firsthit, repgroup);
+          }
+        });
       }
     }
   }
 
+  Map<String, SequenceGroup> groups = new HashMap<String, SequenceGroup>();
+
+  private void addArchGroup(SequenceI seqToAdd, String groupNam)
+  {
+    SequenceGroup sg = groups.get(groupNam);
+    if (sg == null)
+    {
+      sg = new SequenceGroup();
+      sg.setName(groupNam);
+      sg.addSequence(seqToAdd, false);
+      sg.setStartRes(0);
+      sg.setEndRes(resultAl.getWidth() - 1);
+      groups.put(groupNam, sg);
+      resultAl.addGroup(sg);
+    }
+    else
+    {
+      sg.addSequence(seqToAdd, false);
+    }
+  }
+
   private AlignmentAnnotation parsePosteriorProb(String ppline)
   {
     Annotation[] ae = new Annotation[ppline.length()];
@@ -199,7 +324,7 @@ public class HmmerJSONProcessor
     AlignmentAnnotation pprob = new AlignmentAnnotation(
             "Posterior Probability",
             "Likelihood of HMM fit at each hit position.", ae);
-    pprob.graph = pprob.BAR_GRAPH;
+    pprob.graph = AlignmentAnnotation.BAR_GRAPH;
     pprob.visible = false;
     return pprob;
   }