X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=887a5d93e20f049a5177edf76e4be5da74b79f1b;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=e97174676a8491d9c35b704b516889fe5f1b9dd7;hpb=968bc59842cfb502e5e9cc4503efe27b4b4412b2;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index e971746..887a5d9 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,15 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2;
 
-import jalview.api.AlignCalcWorkerI;
+import jalview.api.FeatureColourI;
 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.schemes.FeatureColour;
+import jalview.util.ColorUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 
@@ -20,18 +39,20 @@ import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+
+import compbio.data.sequence.FastaSequence;
 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
+public class AADisorderClient extends JabawsCalcWorker
 {
 
   private static final String THRESHOLD = "THRESHOLD";
 
+  private static final String RANGE = "RANGE";
+
   String typeName;
 
   String methodName;
@@ -41,9 +62,9 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
   AlignFrame af;
 
   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
-          WsParamSetI preset, List<Argument> paramset)
+          WsParamSetI thePreset, List<Argument> paramset)
   {
-    super(sh, alignFrame, preset, paramset);
+    super(sh, alignFrame, thePreset, paramset);
     af = alignFrame;
     typeName = sh.action;
     methodName = sh.serviceType;
@@ -61,67 +82,84 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     return "Submitting amino acid sequences for disorder prediction.";
   }
 
+  @Override
+  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+  {
+    return (seqs.size() > 0);
+  }
+
   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[]>>();
+    // TODO: turn this into some kind of configuration file that's a bit easier
+    // to edit
+    featureMap = new HashMap<>();
     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" });
+            fmap = new HashMap<>());
+    fmap.put("Glob",
+            new String[]
+            { "Globular Domain", "Predicted globular domain" });
     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
-            fmap = new HashMap<String, String[]>());
+            fmap = new HashMap<>());
     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" });
+            fmap = new HashMap<>());
+    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" });
+            fmap = new HashMap<>());
+    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 = new HashMap<>();
     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
-            amap = new HashMap<String, Map<String, Object>>());
+            amap = new HashMap<>());
     amap.put("Dydx", new HashMap<String, Object>());
     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
-    amap.get("Dydx").put(THRESHOLD, new double[] {1, 0});
+    amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
+    amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
+
     amap.put("SmoothedScore", new HashMap<String, Object>());
-    amap.get("SmoothedScore").put(INVISIBLE,INVISIBLE);
+    amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
     amap.put("RawScore", new HashMap<String, Object>());
-    amap.get("RawScore").put(INVISIBLE,INVISIBLE);
+    amap.get("RawScore").put(INVISIBLE, INVISIBLE);
     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
-            amap = new HashMap<String, Map<String, Object>>());
+            amap = new HashMap<>());
     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});
-    
+    amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
+    amap.get("COILS").put(RANGE, new float[] { 0, 1 });
+
+    amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
+    amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
+    amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
+    amap.get("REM465").put(RANGE, new float[] { 0, 1 });
+
     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
-            amap = new HashMap<String, Map<String, Object>>());
+            amap = new HashMap<>());
     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});
+    amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("Long").put(RANGE, new float[] { 0, 1 });
+    amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("Short").put(RANGE, new float[] { 0, 1 });
     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
-            amap = new HashMap<String, Map<String, Object>>());
+            amap = new HashMap<>());
     amap.put("JRonn", new HashMap<String, Object>());
-    amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5});
+    amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+    amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
   }
 
   @Override
@@ -135,8 +173,8 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
       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>();
+      Map<String, Object> fc = new Hashtable<>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
       /**
        * grouping for any annotation rows created
        */
@@ -157,99 +195,134 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
       {
         boolean sameGroup = false;
         SequenceI dseq, aseq, seq = seqNames.get(seqId);
-        int base = seq.getStart() - 1;
+        int base = seq.findPosition(start) - 1;
         aseq = seq;
         while ((dseq = seq).getDatasetSequence() != null)
         {
           seq = seq.getDatasetSequence();
         }
-        ;
-        ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
+        ScoreHolder scores = null;
+        try
+        {
+          scores = scoremanager.getAnnotationForSequence(seqId);
+        } catch (Exception q)
+        {
+          Cache.info("Couldn't recover disorder prediction for sequence "
+                          + seq.getName() + "(Prediction name was " + seqId
+                          + ")"
+                          + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+        }
         float last = Float.NaN, val = Float.NaN;
         int lastAnnot = ourAnnot.size();
-        for (Score scr : scores.scores)
+        if (scores != null && scores.scores != null)
         {
-
-          if (scr.getRanges() != null && scr.getRanges().size() > 0)
+          for (Score scr : scores.scores)
           {
-            Iterator<Float> vals = scr.getScores().iterator();
-            // make features on sequence
-            for (Range rn : scr.getRanges())
-            {
 
-              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())
+            if (scr.getRanges() != null && scr.getRanges().size() > 0)
+            {
+              Iterator<Float> vals = scr.getScores().iterator();
+              // make features on sequence
+              for (Range rn : scr.getRanges())
               {
-                sf = new SequenceFeature(type[0], type[1], base + rn.from,
-                        base + rn.to, val = vals.next().floatValue(),
-                        methodName);
+
+                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())
+                {
+                  val = vals.next().floatValue();
+                  sf = new SequenceFeature(type[0], type[1],
+                          base + rn.from, base + rn.to, val, methodName);
+                }
+                else
+                {
+                  sf = new SequenceFeature(type[0], type[1],
+                          base + rn.from, base + rn.to, methodName);
+                }
+                dseq.addSequenceFeature(sf);
+                if (last != val && !Float.isNaN(last))
+                {
+                  fc.put(sf.getType(), sf);
+                }
+                last = val;
+                dispFeatures = true;
               }
-              else
+            }
+            else
+            {
+              if (scr.getScores().size() == 0)
               {
-                sf = new SequenceFeature(type[0], type[1], null, base
-                        + rn.from, base + rn.to, methodName);
+                continue;
               }
-              dseq.addSequenceFeature(sf);
-              if (last != val && last != Float.NaN)
+              String typename, calcName;
+              AlignmentAnnotation annot = createAnnotationRowsForScores(
+                      ourAnnot,
+                      typename = service.serviceType + " ("
+                              + scr.getMethod() + ")",
+                      calcName = service.getServiceTypeURI() + "/"
+                              + scr.getMethod(),
+                      aseq, base + 1, scr);
+              annot.graph = AlignmentAnnotation.LINE_GRAPH;
+
+              Map<String, Object> styleMap = (annotTypeMap == null) ? null
+                      : annotTypeMap.get(scr.getMethod());
+
+              annot.visible = (styleMap == null
+                      || styleMap.get(INVISIBLE) == null);
+              double[] thrsh = (styleMap == null) ? null
+                      : (double[]) styleMap.get(THRESHOLD);
+              float[] range = (styleMap == null) ? null
+                      : (float[]) styleMap.get(RANGE);
+              if (range != null)
               {
-                fc.put(sf.getType(), sf);
+                annot.graphMin = range[0];
+                annot.graphMax = range[1];
               }
-              last = val;
-              dispFeatures = true;
-            }
-          }
-          else
-          {
-            if (scr.getScores().size()==0)
-            {
-              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 (styleMap == null || styleMap.get(DONTCOMBINE) == null)
               {
-                if (!sameGroup)
                 {
-                  graphGroup++;
-                  sameGroup = true;
+                  if (!sameGroup)
+                  {
+                    graphGroup++;
+                    sameGroup = true;
+                  }
+
+                  annot.graphGroup = graphGroup;
                 }
+              }
 
-                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>"+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.description += "</html>";
+              Color col = ColorUtils
+                      .createColourFromName(typeName + scr.getMethod());
+              for (int p = 0, ps = annot.annotations.length; p < ps; p++)
               {
-                annot.annotations[p].colour = col;
+                if (annot.annotations[p] != null)
+                {
+                  annot.annotations[p].colour = col;
+                }
               }
+              annot._linecolour = col;
+              // finally, update any dataset annotation
+              replaceAnnotationOnAlignmentWith(annot, typename, calcName,
+                      aseq);
             }
-            annot._linecolour=col;
           }
         }
         if (lastAnnot + 1 == ourAnnot.size())
@@ -261,29 +334,30 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
       {
         if (dispFeatures)
         {
-          jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+          jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
                   .cloneFeatureRenderer();
           for (String ft : fc.keySet())
           {
-            Object gc = fr.getFeatureStyle(ft);
-            if (gc instanceof Color)
+            FeatureColourI gc = fr.getFeatureStyle(ft);
+            if (gc.isSimpleColour())
             {
               // 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);
+              FeatureColourI ggc = new FeatureColour(gc.getColour(),
+                      Color.white, gc.getColour(), Color.white,
+                      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
+          // 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)
+          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)
         {
@@ -291,9 +365,17 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
           // new alignment annotation rows created.
           updateOurAnnots(ourAnnot);
           ap.adjustAnnotationHeight();
+          ap.paintAlignment(true, true);
         }
       }
     }
   }
 
+  @Override
+  public String getCalcId()
+  {
+    // Disorder predictions are not dynamically updated so we return null
+    return null;
+  }
+
 }