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)