JAL-1517 source formatting

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 3b9e26a..b4cb3b1 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -6,14 +6,16 @@
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
@@ -470,7 +472,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * Max Gaps Threshold (percent) for performing a conservation calculation 
+   * Max Gaps Threshold (percent) for performing a conservation calculation
    */
   private int consPercGaps = 25;
 
@@ -484,7 +486,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * set Max Gaps Threshold (percent) for performing a conservation calculation
-   * @param consPercGaps 
+   * 
+   * @param consPercGaps
    */
   public void setConsPercGaps(int consPercGaps)
   {
@@ -535,7 +538,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       }
       if (cs != null)
       {
-        cs.alignmentChanged(context!=null ? context : this, null);
+        cs.alignmentChanged(context != null ? context : this, null);
       }
     } catch (java.lang.OutOfMemoryError err)
     {
@@ -584,9 +587,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
 
     AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
-            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
-                                                      // for
-                                                      // ignoreGapsInConsensusCalculation);
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+                                                            // container
+    // for
+    // ignoreGapsInConsensusCalculation);
   }
 
   /**
@@ -1250,16 +1254,22 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     sequences.clear();
   }
+
   private AnnotatedCollectionI context;
+
   /**
    * set the alignment or group context for this group
+   * 
    * @param context
    */
   public void setContext(AnnotatedCollectionI context)
   {
-    this.context = context; 
+    this.context = context;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.AnnotatedCollectionI#getContext()
    */
   @Override