float getMax();
- boolean hasReferenceSeq();
-
- SequenceI getReferenceSeq();
-
String getAnnotDescr();
String getAnnotLabel();
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;
+ }
default boolean hasGroups()
{
- return false;
+ return hasGroupSet() && getGroupSet().hasGroups();
}
default BitSet getGroupsFor(int column)
{
- BitSet colbitset = new BitSet();
- colbitset.set(column);
- return colbitset;
+ if (!hasGroupSet())
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+ return getGroupSet().getGroupsFor(column);
}
default List<BitSet> getGroups()
{
- return Arrays.asList();
+ if (!hasGroupSet())
+ {
+ return Arrays.asList();
+ }
+ return getGroupSet().getGroups();
}
default boolean hasTree()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasTree() : false;
}
/**
*/
default String getNewick()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
}
default String getTreeMethod()
{
- return null;
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
}
default boolean hasCutHeight()
{
- return false;
+ return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
}
default double getCutHeight()
{
- return 0;
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
}
- void updateGroups(List<BitSet> colGroups);
+ default void updateGroups(List<BitSet> colGroups)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().updateGroups(colGroups);
+ }
+ }
- void setColorForGroup(BitSet bs, Color color);
+ default void setColorForGroup(BitSet bs, Color color)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().setColorForGroup(bs, color);
+ }
+ }
default Color getColourForGroup(BitSet bs)
{
- return Color.white;
- };
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
}