From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 21 Nov 2014 08:59:49 +0000 (+0000)
Subject: JAL-1569 formatting
X-Git-Tag: Jalview_2_9~148^2~13
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d9f963f9290e699cd00304461ebdc85c5bc4c53a;p=jalview.git

JAL-1569 formatting
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 0a18be0..1c84f00 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -23,7 +23,6 @@
  */
 package jalview.io;
 
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -842,7 +841,9 @@ public class StockholmFile extends AlignFile
     {
       annot = (AlignmentAnnotation) e.nextElement();
       if (annot.label.equals(type))
+      {
         break;
+      }
       annot = null;
     }
     if (annot == null)
@@ -887,7 +888,9 @@ public class StockholmFile extends AlignFile
         for (int idb = 0; idb < s[in].getDBRef().length; idb++)
         {
           if (dataRef == null)
+          {
             dataRef = new Hashtable();
+          }
 
           String datAs1 = s[in].getDBRef()[idb].getSource().toString()
                   + " ; "
@@ -960,7 +963,9 @@ public class StockholmFile extends AlignFile
             String key = type2id(feature);
 
             if (key == null)
+            {
               continue;
+            }
 
             // out.append("#=GR ");
             out.append(new Format("%-" + maxid + "s").form("#=GR "
@@ -1021,12 +1026,18 @@ public class StockholmFile extends AlignFile
         String label;
 
         if (aa.label.equals("seq"))
+        {
           label = "seq_cons";
+        }
         else
+        {
           label = type2id(aa.label.toLowerCase()) + "_cons";
+        }
 
         if (label == null)
+        {
           label = aa.label;
+        }
 
         out.append(new Format("%-" + maxid + "s").form("#=GC " + label
                 + " "));
@@ -1038,9 +1049,13 @@ public class StockholmFile extends AlignFile
           {
             char ll = aa.annotations[j].secondaryStructure;
             if (Character.toString(ll).equals(" "))
+            {
               seq += "C";
+            }
             else
+            {
               seq += ll;
+            }
           }
           else if (ch.length() == 1)
           {
@@ -1121,7 +1136,7 @@ public class StockholmFile extends AlignFile
     }
     if (key != null)
     {
-      return (String) key;
+      return key;
     }
     System.err.println("Warning : Unknown Stockholm annotation type: "
             + type);