X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=887a5d93e20f049a5177edf76e4be5da74b79f1b;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=b877d206a33eca95a5241e359f52cdd6861e98a5;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index b877d20..887a5d9 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -62,9 +62,9 @@ public class AADisorderClient extends JabawsCalcWorker
   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;
@@ -99,29 +99,32 @@ public class AADisorderClient extends JabawsCalcWorker
   {
     // TODO: turn this into some kind of configuration file that's a bit easier
     // to edit
-    featureMap = new HashMap<String, Map<String, String[]>>();
+    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 = 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 });
@@ -132,7 +135,7 @@ public class AADisorderClient extends JabawsCalcWorker
     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 = new HashMap<>());
     amap.put("COILS", new HashMap<String, Object>());
     amap.put("HOTLOOPS", new HashMap<String, Object>());
     amap.put("REM465", new HashMap<String, Object>());
@@ -145,7 +148,7 @@ public class AADisorderClient extends JabawsCalcWorker
     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 });
@@ -153,7 +156,7 @@ public class AADisorderClient extends JabawsCalcWorker
     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(RANGE, new float[] { 0, 1 });
@@ -170,8 +173,8 @@ public class AADisorderClient extends JabawsCalcWorker
       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
        */
@@ -204,11 +207,8 @@ public class AADisorderClient extends JabawsCalcWorker
           scores = scoremanager.getAnnotationForSequence(seqId);
         } catch (Exception q)
         {
-          Cache.log
-                  .info("Couldn't recover disorder prediction for sequence "
-                          + seq.getName()
-                          + "(Prediction name was "
-                          + seqId
+          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.");
         }
@@ -267,13 +267,15 @@ public class AADisorderClient extends JabawsCalcWorker
                       typename = service.serviceType + " ("
                               + scr.getMethod() + ")",
                       calcName = service.getServiceTypeURI() + "/"
-                              + scr.getMethod(), aseq, base + 1, scr);
+                              + 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);
+              annot.visible = (styleMap == null
+                      || styleMap.get(INVISIBLE) == null);
               double[] thrsh = (styleMap == null) ? null
                       : (double[]) styleMap.get(THRESHOLD);
               float[] range = (styleMap == null) ? null
@@ -307,8 +309,8 @@ public class AADisorderClient extends JabawsCalcWorker
                 annot.description += "<br/>" + threshNote;
               }
               annot.description += "</html>";
-              Color col = ColorUtils.createColourFromName(typeName
-                      + scr.getMethod());
+              Color col = ColorUtils
+                      .createColourFromName(typeName + scr.getMethod());
               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
               {
                 if (annot.annotations[p] != null)
@@ -341,8 +343,9 @@ public class AADisorderClient extends JabawsCalcWorker
             {
               // set graduated color as fading to white for minimum, and
               // autoscaling to values on alignment
-              FeatureColourI ggc = new FeatureColour(Color.white,
-                      gc.getColour(), 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);
             }
@@ -355,7 +358,6 @@ public class AADisorderClient extends JabawsCalcWorker
             // only do this if the alignFrame is currently showing this view.
             af.setShowSeqFeatures(true);
           }
-          ap.paintAlignment(true);
         }
         if (ourAnnot.size() > 0)
         {
@@ -363,6 +365,7 @@ public class AADisorderClient extends JabawsCalcWorker
           // new alignment annotation rows created.
           updateOurAnnots(ourAnnot);
           ap.adjustAnnotationHeight();
+          ap.paintAlignment(true, true);
         }
       }
     }