Merge branch 'develop' into features/JAL-2446NCList

[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 b877d20..c24ea05 100644 (file)
--- 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;
@@ -103,8 +103,9 @@ public class AADisorderClient extends JabawsCalcWorker
     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(),
@@ -114,10 +115,12 @@ public class AADisorderClient extends JabawsCalcWorker
     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(),
@@ -206,9 +209,7 @@ public class AADisorderClient extends JabawsCalcWorker
         {
           Cache.log
                   .info("Couldn't recover disorder prediction for sequence "
-                          + seq.getName()
-                          + "(Prediction name was "
-                          + seqId
+                          + 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 +268,15 @@ 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 +310,8 @@ 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)