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Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'
[jalview.git] / src / jalview / io / JnetAnnotationMaker.java
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 3feae5d..55138e7 100755 (executable)
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -64,17 +64,14 @@ public class JnetAnnotationMaker
     if ((delMap != null && delMap.length > width)
             || (delMap == null && gapmap.length != width))
     {
-      throw (new Exception(
-              MessageManager
-                      .formatMessage(
-                              "exception.number_of_residues_in_query_sequence_differ_from_prediction",
-                              new String[] {
-                                  (delMap == null ? "" : MessageManager
-                                          .getString("label.mapped")),
-                                  al.getSequenceAt(firstSeq).getName(),
-                                  al.getSequenceAt(firstSeq)
-                                          .getSequenceAsString(),
-                                  Integer.valueOf(width).toString() })));
+      throw (new Exception(MessageManager.formatMessage(
+              "exception.number_of_residues_in_query_sequence_differ_from_prediction",
+              new String[]
+              { (delMap == null ? ""
+                      : MessageManager.getString("label.mapped")),
+                  al.getSequenceAt(firstSeq).getName(),
+                  al.getSequenceAt(firstSeq).getSequenceAsString(),
+                  Integer.valueOf(width).toString() })));
     }
 
     AlignmentAnnotation annot;
@@ -98,7 +95,8 @@ public class JnetAnnotationMaker
       {
         if (id.startsWith("JNETSOL"))
         {
-          float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+          float amnt = (id.endsWith("25") ? 3f
+                  : id.endsWith("5") ? 6f : 9f);
           for (int spos = 0; spos < width; spos++)
           {
             int sposw = (delMap == null) ? gapmap[spos]
@@ -222,8 +220,7 @@ public class JnetAnnotationMaker
     if (!firstsol)
     {
       // add the solvent accessibility
-      annot = new AlignmentAnnotation(
-              "Jnet Burial",
+      annot = new AlignmentAnnotation("Jnet Burial",
               "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
               sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
 
@@ -234,8 +231,8 @@ public class JnetAnnotationMaker
         seqRef.addAlignmentAnnotation(annot);
       }
       al.addAnnotation(annot);
-      al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
-              - existingAnnotations - 1);
+      al.setAnnotationIndex(annot,
+              al.getAlignmentAnnotation().length - existingAnnotations - 1);
     }
     // Hashtable scores = prediction.getScores();