X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=d955db544b2edd037a158ea084eebd518a195657;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d64a9564034aec46c92b87048fa638194d2c729a;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index d64a956..d955db5 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,25 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
-
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -36,17 +39,21 @@ 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;
 
-public class AADisorderClient extends JabawsAlignCalcWorker implements
+public class AADisorderClient extends JabawsCalcWorker implements
         AlignCalcWorkerI
 {
 
   private static final String THRESHOLD = "THRESHOLD";
 
+  private static final String RANGE = "RANGE";
+
   String typeName;
 
   String methodName;
@@ -76,6 +83,12 @@ 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;
@@ -91,32 +104,30 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     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.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" });
+    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.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.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.put("RawScore", new HashMap<String, Object>());
@@ -126,26 +137,27 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     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.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.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
@@ -181,109 +193,135 @@ 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.log
+                  .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())
+                {
+                  sf = new SequenceFeature(type[0], type[1],
+                          base + rn.from, base + rn.to, val = vals.next()
+                                  .floatValue(), methodName);
+                }
+                else
+                {
+                  sf = new SequenceFeature(type[0], type[1], null, 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>";
-            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>" + 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++)
               {
-                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())
@@ -295,7 +333,7 @@ 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())
           {
@@ -331,4 +369,11 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
     }
   }
 
+  @Override
+  public String getCalcId()
+  {
+    // Disorder predictions are not dynamically updated so we return null
+    return null;
+  }
+
 }