formatting

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index ed21f60..693291f 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -92,12 +92,12 @@ public class SequenceGroup implements AnnotatedCollectionI
    * consensus calculation property
    */
   private boolean showSequenceLogo = false;
+
   /**
    * flag indicating if logo should be rendered normalised
    */
   private boolean normaliseSequenceLogo;
 
-
   /**
    * @return the includeAllConsSymbols
    */
@@ -285,11 +285,14 @@ public class SequenceGroup implements AnnotatedCollectionI
 
     return eres;
   }
+
   public List<SequenceI> getSequences()
   {
     return sequences;
   }
-  public List<SequenceI> getSequences(Map<SequenceI, SequenceCollectionI> hiddenReps)
+
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     if (hiddenReps == null)
     {
@@ -306,7 +309,7 @@ public class SequenceGroup implements AnnotatedCollectionI
         if (hiddenReps.containsKey(seq))
         {
           SequenceCollectionI hsg = hiddenReps.get(seq);
-          for (SequenceI seq2:hsg.getSequences())
+          for (SequenceI seq2 : hsg.getSequences())
           {
             if (seq2 != seq && !allSequences.contains(seq2))
             {
@@ -320,10 +323,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
-  public SequenceI[] getSequencesAsArray(Map<SequenceI, SequenceCollectionI> map)
+  public SequenceI[] getSequencesAsArray(
+          Map<SequenceI, SequenceCollectionI> map)
   {
     List<SequenceI> tmp = getSequences(map);
-    if (tmp==null)
+    if (tmp == null)
     {
       return null;
     }
@@ -479,9 +483,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       return;
     }
-    if (cs!=null)
+    if (cs != null)
     {
-      cs.alignmentChanged(this,null);
+      cs.alignmentChanged(this, null);
     }
     try
     {
@@ -494,7 +498,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (cs != null)
       {
         cs.setConsensus(cnsns);
-        cs.alignmentChanged(this,null);
+        cs.alignmentChanged(this, null);
       }
 
       if ((conservation != null)
@@ -514,7 +518,7 @@ public class SequenceGroup implements AnnotatedCollectionI
           if (cs.conservationApplied())
           {
             cs.setConservation(c);
-            cs.alignmentChanged(this,null);
+            cs.alignmentChanged(this, null);
           }
         }
       }
@@ -948,7 +952,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    *          (may be null)
    * @return new group containing sequences common to this group and alignment
    */
-  public SequenceGroup intersect(AlignmentI alignment, Map<SequenceI, SequenceCollectionI> map)
+  public SequenceGroup intersect(AlignmentI alignment,
+          Map<SequenceI, SequenceCollectionI> map)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
@@ -1166,51 +1171,56 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * set flag indicating if logo should be normalised when rendered
+   * 
    * @param norm
    */
   public void setNormaliseSequenceLogo(boolean norm)
   {
-    normaliseSequenceLogo=norm;
+    normaliseSequenceLogo = norm;
   }
+
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
+
   @Override
   /**
    * returns a new array with all annotation involving this group
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
-    // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
+    // TODO add in other methods like 'getAlignmentAnnotation(String label),
+    // etc'
     ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
-    for (SequenceI seq:(Vector<SequenceI>)sequences)
+    for (SequenceI seq : (Vector<SequenceI>) sequences)
     {
-      for (AlignmentAnnotation al: seq.getAnnotation())
+      for (AlignmentAnnotation al : seq.getAnnotation())
       {
-        if (al.groupRef==this)
+        if (al.groupRef == this)
         {
           annot.add(al);
         }
       }
     }
-    if (consensus!=null)
+    if (consensus != null)
     {
       annot.add(consensus);
     }
-    if (conservation!=null)
+    if (conservation != null)
     {
       annot.add(conservation);
     }
     return annot.toArray(new AlignmentAnnotation[0]);
   }
+
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a:getAlignmentAnnotation())
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId()==calcId)
+      if (a.getCalcId() == calcId)
       {
         aa.add(a);
       }