JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / io / SequenceAnnotationReport.java

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 9ffdf21..c5bc902 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -59,7 +59,7 @@ public class SequenceAnnotationReport
 
   private static String linkImageURL;
 
- // public static final String[][] PRIMARY_SOURCES  moved to DBRefSource.java
+  // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
 
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
@@ -91,32 +91,32 @@ public class SequenceAnnotationReport
       {
         return 1;
       }
-      int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
-              .compareToIgnoreCase(s2));
+      int comp = s1 == null ? -1
+              : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
       if (comp == 0)
       {
         String a1 = ref1.getAccessionId();
         String a2 = ref2.getAccessionId();
-        comp = a1 == null ? -1 : (a2 == null ? 1 : a1
-                .compareToIgnoreCase(a2));
+        comp = a1 == null ? -1
+                : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
       }
       return comp;
     }
 
-//    private boolean isPrimarySource(String source)
-//    {
-//      for (String[] primary : DBRefSource.PRIMARY_SOURCES)
-//      {
-//        for (String s : primary)
-//        {
-//          if (source.equals(s))
-//          {
-//            return true;
-//          }
-//        }
-//      }
-//      return false;
-//    }
+    // private boolean isPrimarySource(String source)
+    // {
+    // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+    // {
+    // for (String s : primary)
+    // {
+    // if (source.equals(s))
+    // {
+    // return true;
+    // }
+    // }
+    // }
+    // return false;
+    // }
   };
 
   private boolean forTooltip;
@@ -150,9 +150,9 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param maxlength
    */
-  public int appendFeatures(final StringBuilder sb,
-          int residuePos, List<SequenceFeature> features,
-          FeatureRendererModel fr, int maxlength)
+  public int appendFeatures(final StringBuilder sb, int residuePos,
+          List<SequenceFeature> features, FeatureRendererModel fr,
+          int maxlength)
   {
     for (int i = 0; i < features.size(); i++)
     {
@@ -412,21 +412,19 @@ public class SequenceAnnotationReport
           {
             for (List<String> urllink : createLinksFrom(null, urlstring))
             {
-              sb.append("<br/> <a href=\""
-                      + urllink.get(3)
-                      + "\" target=\""
-                      + urllink.get(0)
-                      + "\">"
-                      + (urllink.get(0).toLowerCase(Locale.ROOT)
-                              .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
-                              .get(0) : (urllink.get(0) + ":" + urllink
-                                              .get(1)))
+              sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+                      + urllink.get(0) + "\">"
+                      + (urllink.get(0).toLowerCase(Locale.ROOT).equals(
+                              urllink.get(1).toLowerCase(Locale.ROOT))
+                                      ? urllink.get(0)
+                                      : (urllink.get(0) + ":"
+                                              + urllink.get(1)))
                       + "</a><br/>");
             }
           } catch (Exception x)
           {
-            System.err.println("problem when creating links from "
-                    + urlstring);
+            System.err.println(
+                    "problem when creating links from " + urlstring);
             x.printStackTrace();
           }
         }
@@ -620,8 +618,8 @@ public class SequenceAnnotationReport
           SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
           FeatureRendererModel fr)
   {
-    int maxWidth = createSequenceAnnotationReport(tip, sequence,
-            showDbRefs, showNpFeats, fr, true);
+    int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+            showNpFeats, fr, true);
 
     if (maxWidth > 60)
     {