X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=d64a9564034aec46c92b87048fa638194d2c729a;hb=e1476d3c4ebb1c8f6b3ec7d46bb824b23987960e;hp=8a6e9ccd4fac41eee43ac5ed673713e191485059;hpb=378db7e2823248bd4c97af6683006cabec8b390e;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 8a6e9cc..d64a956 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -1,9 +1,26 @@
+/*
+ * 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
+ * 
+ * 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/>.
+ */
 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;
@@ -23,12 +40,13 @@ 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;
@@ -63,9 +81,12 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
   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(),
@@ -94,13 +115,37 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
             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.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.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
@@ -119,7 +164,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
       /**
        * grouping for any annotation rows created
        */
-      int graphGroup = 1, iGraphGroup = 1;
+      int graphGroup = 1;
       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
       {
         for (AlignmentAnnotation ala : alignViewport.getAlignment()
@@ -187,18 +232,25 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
           }
           else
           {
-            if (scr.getScores().size()==0)
+            if (scr.getScores().size() == 0)
             {
               continue;
             }
             AlignmentAnnotation annot = createAnnotationRowsForScores(
                     ourAnnot, service.serviceType + " (" + scr.getMethod()
-                            + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
-                    base, scr);
+                            + ")",
+                    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);
-
-            if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
+            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)
@@ -210,8 +262,18 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
                 annot.graphGroup = graphGroup;
               }
             }
-            
-            annot.description = service.getActionText() + " - raw scores";
+
+            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++)
@@ -221,7 +283,7 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
                 annot.annotations[p].colour = col;
               }
             }
-            annot._linecolour=col;
+            annot._linecolour = col;
           }
         }
         if (lastAnnot + 1 == ourAnnot.size())
@@ -248,13 +310,14 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements
               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)