formatting

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 21b877d..f14b5a5 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -54,9 +54,9 @@ public class Sequence implements SequenceI
    * to the residues of this sequence
    */
   Vector annotation;
-  
+
   /**
-   * The index of the sequence in a MSA 
+   * The index of the sequence in a MSA
    */
   int index = -1;
 
@@ -122,7 +122,8 @@ public class Sequence implements SequenceI
 
   void checkValidRange()
   {
-    // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
+    // Note: JAL-774 :
+    // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
@@ -137,7 +138,8 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      if (end<endRes) { 
+      if (end < endRes)
+      {
         end = endRes;
       }
     }
@@ -577,8 +579,9 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
@@ -1177,16 +1180,24 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * @return The index (zero-based) on this sequence in the MSA. 
-   * It returns {@code -1} if this information is not available.
+   * @return The index (zero-based) on this sequence in the MSA. It returns
+   *         {@code -1} if this information is not available.
    */
-  public int getIndex() { return index; }
-  
+  public int getIndex()
+  {
+    return index;
+  }
+
   /**
-   * Defines the position of this sequence in the MSA. 
-   * Use the value {@code -1} if this information is undefined.
+   * Defines the position of this sequence in the MSA. Use the value {@code -1}
+   * if this information is undefined.
    * 
-   * @param The position for this sequence. This value is zero-based (zero for this first sequence)
+   * @param The
+   *          position for this sequence. This value is zero-based (zero for
+   *          this first sequence)
    */
-  public void setIndex(int value) { index = value; }
+  public void setIndex(int value)
+  {
+    index = value;
+  }
 }