formatting
[jalview.git] / src / jalview / ws / jws2 / AADisorderClient.java
index baec458..ea225d4 100644 (file)
@@ -1,24 +1,37 @@
 package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+
+import jalview.datamodel.GraphLine;
 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
 {
 
+  private static final String THRESHOLD = "THRESHOLD";
+
   String typeName;
 
   String methodName;
@@ -48,24 +61,121 @@ 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";
+
+  private static String INVISIBLE = "INVISIBLE";
+  static
+  {
+    // TODO: turn this into some kind of configuration file that's a bit easier
+    // to edit
+    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);
+    amap.get("Dydx").put(THRESHOLD, new double[]
+    { 1, 0 });
+    amap.put("SmoothedScore", new HashMap<String, Object>());
+    amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
+    amap.put("RawScore", new HashMap<String, Object>());
+    amap.get("RawScore").put(INVISIBLE, INVISIBLE);
+    annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    amap.put("COILS", new HashMap<String, Object>());
+    amap.put("HOTLOOPS", new HashMap<String, Object>());
+    amap.put("REM465", new HashMap<String, Object>());
+    amap.get("COILS").put(THRESHOLD, new double[]
+    { 1, 0.516 });
+    amap.get("HOTLOOPS").put(THRESHOLD, new double[]
+    { 1, 0.6 });
+    amap.get("REM465").put(THRESHOLD, new double[]
+    { 1, 0.1204 });
+
+    annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    amap.put("Long", new HashMap<String, Object>());
+    amap.put("Short", new HashMap<String, Object>());
+    amap.get("Long").put(THRESHOLD, new double[]
+    { 1, 0.5 });
+    amap.get("Short").put(THRESHOLD, new double[]
+    { 1, 0.5 });
+    annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
+            amap = new HashMap<String, Map<String, Object>>());
+    amap.put("JRonn", new HashMap<String, Object>());
+    amap.get("JRonn").put(THRESHOLD, new double[]
+    { 1, 0.5 });
+  }
+
   @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>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      /**
+       * grouping for any annotation rows created
+       */
+      int graphGroup = 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;
+        int lastAnnot = ourAnnot.size();
         for (Score scr : scores.scores)
         {
 
@@ -77,48 +187,132 @@ 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, 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)
+              {
+                fc.put(sf.getType(), sf);
+              }
+              last = val;
               dispFeatures = true;
             }
           }
           else
           {
-            Iterator<Float> vals = scr.getScores().iterator();
-            for (int start = base + 1; vals.hasNext(); start++)
+            if (scr.getScores().size() == 0)
             {
-              SequenceFeature sf = new SequenceFeature(typeName + "("
-                      + scr.getMethod() + ")", "Disordered Region", start,
-                      start, vals.next().floatValue(), methodName);
-              dseq.addSequenceFeature(sf);
-              dispFeatures = true;
+              continue;
+            }
+            AlignmentAnnotation annot = createAnnotationRowsForScores(
+                    ourAnnot, service.serviceType + " (" + scr.getMethod()
+                            + ")",
+                    service.getServiceTypeURI() + "/" + scr.getMethod(),
+                    aseq, base + 1, scr);
+            annot.graph = AlignmentAnnotation.LINE_GRAPH;
+            annot.visible = (annotTypeMap == null
+                    || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
+                    .get(scr.getMethod()).get(INVISIBLE) == null);
+            double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
+                    .getMethod()) == null) ? null : (double[]) annotTypeMap
+                    .get(scr.getMethod()).get(THRESHOLD);
+            if (annotTypeMap == null
+                    || annotTypeMap.get(scr.getMethod()) == null
+                    || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
+            {
+              {
+                if (!sameGroup)
+                {
+                  graphGroup++;
+                  sameGroup = true;
+                }
+
+                annot.graphGroup = graphGroup;
+              }
+            }
+
+            annot.description = "<html>" + service.getActionText()
+                    + " - raw scores";
+            if (thrsh != null)
+            {
+              String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
+                      + thrsh[1] + " indicates disorder";
+              annot.threshold = new GraphLine((float) thrsh[1], threshNote,
+                      Color.red);
+              annot.description += "<br/>" + threshNote;
+            }
+            annot.description += "</html>";
+            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;
+              }
             }
+            annot._linecolour = col;
           }
         }
+        if (lastAnnot + 1 == ourAnnot.size())
+        {
+          // remove singleton alignment annotation row
+          ourAnnot.get(lastAnnot).graphGroup = -1;
+        }
       }
       {
         if (dispFeatures)
         {
-          // TODO: configure feature display settings for added types if they don't already exist
-          
-          af.alignPanel.av.setShowSequenceFeatures(true);
+          jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+                  .cloneFeatureRenderer();
+          for (String ft : fc.keySet())
+          {
+            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);
+              ggc.setAutoScaled(true);
+              fr.setColour(ft, ggc);
+            }
+          }
+          // 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();
+        }
       }
-      /*
-       * else { ap.paintAlignment(true); }
-       */
     }
   }