JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[jalview.git] / src / jalview / ws / jws2 / AADisorderClient.java

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index fb6ffc4..315e69f 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -20,9 +20,8 @@
  */
 package jalview.ws.jws2;
 
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceFeature;
@@ -63,9 +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;
@@ -100,22 +99,22 @@ 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 = 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 = new HashMap<>());
     fmap.put("GlobDoms",
             new String[]
             { "Globular Domain", "Predicted globular domain" });
@@ -123,9 +122,9 @@ public class AADisorderClient extends JabawsCalcWorker
             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 });
@@ -136,7 +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>());
@@ -149,7 +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 });
@@ -157,7 +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 });
@@ -174,8 +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
        */
@@ -208,8 +207,7 @@ public class AADisorderClient extends JabawsCalcWorker
           scores = scoremanager.getAnnotationForSequence(seqId);
         } catch (Exception q)
         {
-          Cache.log
-                  .info("Couldn't recover disorder prediction for sequence "
+          Console.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.");
@@ -239,13 +237,13 @@ public class AADisorderClient extends JabawsCalcWorker
                 }
                 if (vals.hasNext())
                 {
-                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
-                          base + rn.to, val = vals.next().floatValue(),
-                          methodName);
+                  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], null,
+                  sf = new SequenceFeature(type[0], type[1],
                           base + rn.from, base + rn.to, methodName);
                 }
                 dseq.addSequenceFeature(sf);
@@ -345,8 +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);
             }
@@ -359,7 +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)
         {
@@ -367,6 +365,7 @@ public class AADisorderClient extends JabawsCalcWorker
           // new alignment annotation rows created.
           updateOurAnnots(ourAnnot);
           ap.adjustAnnotationHeight();
+          ap.paintAlignment(true, true);
         }
       }
     }