JAL-1517 source formatting

[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 c5fbf49..34969d1 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -50,6 +50,7 @@ public class AADisorderClient extends JabawsCalcWorker implements
 {
 
   private static final String THRESHOLD = "THRESHOLD";
+
   private static final String RANGE = "RANGE";
 
   String typeName;
@@ -123,7 +124,7 @@ public class AADisorderClient extends JabawsCalcWorker implements
     amap.get("Dydx").put(THRESHOLD, new double[]
     { 1, 0 });
     amap.get("Dydx").put(RANGE, new float[]
-            { -1, +1 });
+    { -1, +1 });
 
     amap.put("SmoothedScore", new HashMap<String, Object>());
     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
@@ -137,17 +138,16 @@ public class AADisorderClient extends JabawsCalcWorker implements
     amap.get("COILS").put(THRESHOLD, new double[]
     { 1, 0.516 });
     amap.get("COILS").put(RANGE, new float[]
-            { 0, 1 });
+    { 0, 1 });
 
     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
     { 1, 0.6 });
     amap.get("HOTLOOPS").put(RANGE, new float[]
-            { 0, 1 });
+    { 0, 1 });
     amap.get("REM465").put(THRESHOLD, new double[]
     { 1, 0.1204 });
     amap.get("REM465").put(RANGE, new float[]
-            { 0, 1 });
-
+    { 0, 1 });
 
     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
             amap = new HashMap<String, Map<String, Object>>());
@@ -156,18 +156,18 @@ public class AADisorderClient extends JabawsCalcWorker implements
     amap.get("Long").put(THRESHOLD, new double[]
     { 1, 0.5 });
     amap.get("Long").put(RANGE, new float[]
-            { 0, 1 });
+    { 0, 1 });
     amap.get("Short").put(THRESHOLD, new double[]
     { 1, 0.5 });
     amap.get("Short").put(RANGE, new float[]
-            { 0, 1 });
+    { 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(RANGE, new float[]
-            { 0, 1 });
+    { 0, 1 });
   }
 
   @Override
@@ -203,14 +203,15 @@ public class AADisorderClient extends JabawsCalcWorker implements
       {
         boolean sameGroup = false;
         SequenceI dseq, aseq, seq = seqNames.get(seqId);
-        int base = seq.findPosition(start)-1;
+        int base = seq.findPosition(start) - 1;
         aseq = seq;
         while ((dseq = seq).getDatasetSequence() != null)
         {
           seq = seq.getDatasetSequence();
         }
         ScoreHolder scores = null;
-        try {
+        try
+        {
           scores = scoremanager.getAnnotationForSequence(seqId);
         } catch (Exception q)
         {
@@ -218,12 +219,14 @@ public class AADisorderClient extends JabawsCalcWorker implements
                   .info("Couldn't recover disorder prediction for sequence "
                           + seq.getName()
                           + "(Prediction name was "
-                          + seqId+")"
+                          + 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();
-        if (scores!=null && scores.scores!=null) {
+        if (scores != null && scores.scores != null)
+        {
           for (Score scr : scores.scores)
           {
 
@@ -275,21 +278,21 @@ public class AADisorderClient extends JabawsCalcWorker implements
                       service.getServiceTypeURI() + "/" + scr.getMethod(),
                       aseq, base + 1, scr);
               annot.graph = AlignmentAnnotation.LINE_GRAPH;
-              
-              Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
-              
+
+              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)
+              double[] thrsh = (styleMap == null) ? null
+                      : (double[]) styleMap.get(THRESHOLD);
+              float[] range = (styleMap == null) ? null
+                      : (float[]) styleMap.get(RANGE);
+              if (range != null)
               {
                 annot.graphMin = range[0];
                 annot.graphMax = range[1];
               }
-              if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
+              if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
               {
                 {
                   if (!sameGroup)