X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=546e9791da1bf75860813b662a2de04e920c58b9;hb=80b889f0cca49103e1b20ed806755a0719789906;hp=256d43d347eab1a828220723bbe0452c8a5bea7e;hpb=8288438dd58cfc2d1fe18a060afda0d647b85c32;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 256d43d..546e979 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -19,69 +19,80 @@ public interface ContactMatrixI
   String getAnnotLabel();
 
   /**
-   * string indicating how the contactMatrix should be rendered - stored in calcId
-   * @return 
+   * string indicating how the contactMatrix should be rendered - stored in
+   * calcId
+   * 
+   * @return
    */
   String getType();
 
   int getWidth();
+
   int getHeight();
-  
+
   public GroupSetI getGroupSet();
-  
+
   /// proxy methods to simplify use of the interface
   /// Mappable contact matrices can override these to perform mapping
-  
+
   default public boolean hasGroupSet()
   {
-    return getGroupSet()!=null;
+    return getGroupSet() != null;
   }
 
-  default boolean hasGroups() {
+  default boolean hasGroups()
+  {
     return hasGroupSet() && getGroupSet().hasGroups();
   }
 
-
-  default BitSet getGroupsFor(int column) {
+  default BitSet getGroupsFor(int column)
+  {
     if (!hasGroupSet())
     {
-    BitSet colbitset  = new BitSet();
-    colbitset.set(column);
-    return colbitset;
+      BitSet colbitset = new BitSet();
+      colbitset.set(column);
+      return colbitset;
     }
     return getGroupSet().getGroupsFor(column);
   }
 
-  default List<BitSet> getGroups() {
+  default List<BitSet> getGroups()
+  {
     if (!hasGroupSet())
     {
-    return Arrays.asList();
-    } 
+      return Arrays.asList();
+    }
     return getGroupSet().getGroups();
   }
 
-  default boolean hasTree() {
+  default boolean hasTree()
+  {
     return hasGroupSet() ? getGroupSet().hasTree() : false;
   }
 
   /**
    * Newick representation of clustered matrix
+   * 
    * @return null unless hasTree is true
    */
-  default String getNewick() {
-    return hasGroupSet() ? getGroupSet().getNewick(): null;
+  default String getNewick()
+  {
+    return hasGroupSet() ? getGroupSet().getNewick() : null;
   }
 
-  default String getTreeMethod() {
-    return hasGroupSet() ? getGroupSet().getTreeMethod() :null;
+  default String getTreeMethod()
+  {
+    return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
   }
 
-  default boolean hasCutHeight() {
+  default boolean hasCutHeight()
+  {
     return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
   }
 
-  default double getCutHeight() {
-    return hasGroupSet() ? getGroupSet().getCutHeight():0;
+  default double getCutHeight()
+  {
+    return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
   }
 
   default void updateGroups(List<BitSet> colGroups)