JAL-974 create mixture of sequence features marking disordered regions and sequence...

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index c5c7a13..7bf2045 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -2,23 +2,28 @@ package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
 import java.awt.Color;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
-
 import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
 import compbio.data.sequence.ScoreManager.ScoreHolder;
 import compbio.metadata.Argument;
+import compbio.ws.client.Services;
 
 public class AADisorderClient extends JabawsAlignCalcWorker implements
         AlignCalcWorkerI
@@ -53,25 +58,89 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     return "Submitting amino acid sequences for disorder prediction.";
   }
 
+  private static Map<String, Map<String, String[]>> featureMap;
+
+  private static Map<String, Map<String, Map<String, Object>>> annotMap;
+
+  private static String DONTCOMBINE = "DONTCOMBINE";
+  static
+  {
+    featureMap = new HashMap<String, Map<String, String[]>>();
+    Map<String, String[]> fmap;
+    featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+            fmap = new HashMap<String, String[]>());
+    fmap.put("Glob", new String[]
+    { "Globular Domain", "Predicted globular domain" });
+    featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
+            fmap = new HashMap<String, String[]>());
+    featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+            fmap = new HashMap<String, String[]>());
+    fmap.put("REM465", new String[]
+    { "REM465", "Missing density" });
+    fmap.put("HOTLOOPS", new String[]
+    { "HOTLOOPS", "Flexible loops" });
+    fmap.put("COILS", new String[]
+    { "COILS", "Random coil" });
+    featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+            fmap = new HashMap<String, String[]>());
+    fmap.put("GlobDoms", new String[]
+    { "Globular Domain", "Predicted globular domain" });
+    fmap.put("Disorder", new String[]
+    { "Protein Disorder", "Probable unstructured peptide region" });
+    Map<String, Map<String, Object>> amap;
+    annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
+    annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    amap.put("Dydx", new HashMap<String, Object>());
+    amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
+    annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    
+  }
+
   @Override
   public void updateResultAnnotation(boolean immediate)
   {
 
     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
     {
+      Map<String, String[]> featureTypeMap = featureMap
+              .get(service.serviceType);
+      Map<String, Map<String, Object>> annotTypeMap = annotMap
+              .get(service.serviceType);
       boolean dispFeatures = false;
-      Map<String,Object> fc=new Hashtable<String, Object>();
+      Map<String, Object> fc = new Hashtable<String, Object>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      /**
+       * grouping for any annotation rows created
+       */
+      int graphGroup = 1, iGraphGroup = 1;
+      if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
+      {
+        for (AlignmentAnnotation ala : alignViewport.getAlignment()
+                .getAlignmentAnnotation())
+        {
+          if (ala.graphGroup > graphGroup)
+          {
+            graphGroup = ala.graphGroup;
+          }
+        }
+      }
+
       for (String seqId : seqNames.keySet())
       {
-        SequenceI dseq, seq = seqNames.get(seqId);
+        boolean sameGroup = false;
+        SequenceI dseq, aseq, seq = seqNames.get(seqId);
         int base = seq.getStart() - 1;
+        aseq = seq;
         while ((dseq = seq).getDatasetSequence() != null)
         {
           seq = seq.getDatasetSequence();
         }
         ;
         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
-        float last=Float.NaN,val=Float.NaN;
+        float last = Float.NaN, val = Float.NaN;
+        int lastAnnot = ourAnnot.size();
         for (Score scr : scores.scores)
         {
 
@@ -83,67 +152,106 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
             {
 
               SequenceFeature sf;
+              String[] type = featureTypeMap.get(scr.getMethod());
+              if (type == null)
+              {
+                // create a default type for this feature
+                type = new String[]
+                { typeName + " (" + scr.getMethod() + ")",
+                    service.getActionText() };
+              }
               if (vals.hasNext())
               {
-                sf = new SequenceFeature(typeName + "(" + scr.getMethod()
-                        + ")", "Disordered Region", base + rn.from, base
-                        + rn.to, val=vals.next().floatValue(), methodName);
+                sf = new SequenceFeature(type[0], type[1], base + rn.from,
+                        base + rn.to, val = vals.next().floatValue(),
+                        methodName);
               }
               else
               {
-                sf = new SequenceFeature(typeName + "(" + scr.getMethod()
-                        + ")", "Disordered Region", null, base + rn.from,
-                        base + rn.to, methodName);
+                sf = new SequenceFeature(type[0], type[1], null, base
+                        + rn.from, base + rn.to, methodName);
               }
               dseq.addSequenceFeature(sf);
-              if (last!=val && last!=Float.NaN)
+              if (last != val && last != Float.NaN)
               {
-                fc.put(sf.getType(),sf);
+                fc.put(sf.getType(), sf);
               }
-              last=val;
+              last = val;
               dispFeatures = true;
             }
           }
           else
           {
-            Iterator<Float> vals = scr.getScores().iterator();
-            for (int start = base + 1; vals.hasNext(); start++)
+
+            AlignmentAnnotation annot = createAnnotationRowsForScores(
+                    ourAnnot, service.serviceType + " (" + scr.getMethod()
+                            + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
+                    base, scr);
+            annot.graph = AlignmentAnnotation.LINE_GRAPH;
+            if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
             {
-              SequenceFeature sf = new SequenceFeature(typeName + "("
-                      + scr.getMethod() + ")", "Disordered Region", start,
-                      start, val=vals.next().floatValue(), methodName);
-              if (last!=val && last!=Float.NaN)
               {
-                fc.put(sf.getType(),sf);
+                if (!sameGroup)
+                {
+                  graphGroup++;
+                  sameGroup = true;
+                }
+
+                annot.graphGroup = graphGroup;
+              }
+            }
+            annot.description = service.getActionText() + " - raw scores";
+            Color col = new UserColourScheme(typeName)
+                    .createColourFromName(typeName + scr.getMethod());
+            for (int p = 0, ps = annot.annotations.length; p < ps; p++)
+            {
+              if (annot.annotations[p] != null)
+              {
+                annot.annotations[p].colour = col;
               }
-              last=val;
-              dseq.addSequenceFeature(sf);
-              dispFeatures = true;
             }
           }
         }
+        if (lastAnnot + 1 == ourAnnot.size())
+        {
+          // remove singleton alignment annotation row
+          ourAnnot.get(lastAnnot).graphGroup = -1;
+        }
       }
       {
         if (dispFeatures)
         {
-          jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer();
-          // TODO: configure feature display settings for added types if they don't already exist
-          for (String ft:fc.keySet())
+          jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+                  .cloneFeatureRenderer();
+          for (String ft : fc.keySet())
           {
-            Cache.log.debug("Set graduated feature for new type:"+ft);
-            Object gc=fr.getFeatureStyle(ft);
+            Object gc = fr.getFeatureStyle(ft);
             if (gc instanceof Color)
             {
-              // set graduated color as fading to white for minimum, and autoscaling to values on alignment
-              GraduatedColor ggc=new GraduatedColor(Color.white, (Color)gc,Float.MIN_VALUE, Float.MAX_VALUE);
+              // set graduated color as fading to white for minimum, and
+              // autoscaling to values on alignment
+              GraduatedColor ggc = new GraduatedColor(Color.white,
+                      (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
               ggc.setAutoScaled(true);
               fr.setColour(ft, ggc);
             }
           }
-          af.alignPanel.updateFeatureRendererFrom(fr);
-          af.alignPanel.av.setShowSequenceFeatures(true);
+          // TODO: JAL-1150 - create sequence feature settings API for defining styles and enabling/disabling feature overlay on alignment panel
+          ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
+          if (af.alignPanel==ap)
+          {
+            // only do this if the alignFrame is currently showing this view.
+            af.setShowSeqFeatures(true);
+          } 
           ap.paintAlignment(true);
         }
+        if (ourAnnot.size() > 0)
+        {
+          // Modify the visible annotation on the alignment viewport with the
+          // new alignment annotation rows created.
+          updateOurAnnots(ourAnnot);
+          ap.adjustAnnotationHeight();
+        }
       }
     }
   }