JAL-2349 allow PAE or other contact matrices to hold a coordinate mapping allowing...

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

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 9a7f138..ba2ee48 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -1,8 +1,73 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
 public interface ContactMatrixI
 {
 
   ContactListI getContactList(int column);
 
+  float getMin();
+
+  float getMax();
+
+  String getAnnotDescr();
+
+  String getAnnotLabel();
+
+  /**
+   * string indicating how the contactMatrix should be rendered - stored in calcId
+   * @return 
+   */
+  String getType();
+
+  int getWidth();
+  int getHeight();
+  
+  default boolean hasGroups() {
+    return false;
+  }
+  default BitSet getGroupsFor(int column) {
+    BitSet colbitset  = new BitSet();
+    colbitset.set(column);
+    return colbitset;
+  }
+
+  default List<BitSet> getGroups() {
+    return Arrays.asList();
+  }
+
+  default boolean hasTree() {
+    return false;
+  }
+
+  /**
+   * Newick representation of clustered matrix
+   * @return null unless hasTree is true
+   */
+  default String getNewick() {
+    return null;
+  }
+
+  default String getTreeMethod() {
+    return null;
+  }
+
+  default boolean hasCutHeight() {
+    return false;
+  }
+
+  default double getCutHeight() {
+    return 0;
+  }
+
+  void updateGroups(List<BitSet> colGroups);
+
+  void setColorForGroup(BitSet bs, Color color);
+
+  default Color getColourForGroup(BitSet bs) { return Color.white;}
+
 }