Merge branch 'develop' into patch/JAL-4281_idwidthandannotHeight_in_project

[jalview.git] / src / jalview / ws / datamodel / alphafold / MappableContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
index d545741..5f27a2c 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
@@ -7,6 +7,7 @@ import java.util.BitSet;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactListImpl;
 import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.GroupSet;
 import jalview.datamodel.GroupSetI;
 import jalview.datamodel.Mapping;
@@ -17,42 +18,77 @@ import jalview.ws.datamodel.MappableContactMatrixI;
 public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
         implements MappableContactMatrixI
 {
-  SequenceI refSeq = null;
-
-  MapList toSeq = null;
-
   /**
-   * the length that refSeq is expected to be (excluding gaps, of course)
+   * the matrix that is being mapped to
    */
-  int length;
+  protected ContactMatrixI mappedMatrix=null;
+  
+  public ContactListI getContactList(int column)
+  {
+    return mappedMatrix.getContactList(column);
+  }
+
+  public float getMin()
+  {
+    return mappedMatrix.getMin();
+  }
+
+  public float getMax()
+  {
+    return mappedMatrix.getMax();
+  }
+
+  public int getWidth()
+  {
+    return mappedMatrix.getWidth();
+  }
+
+  public int getHeight()
+  {
+    return mappedMatrix.getHeight();
+  }
 
   @Override
-  public boolean hasReferenceSeq()
+  public ContactMatrixI getMappedMatrix()
   {
-    return (refSeq != null);
+    return mappedMatrix;
   }
+  
+  @Override
+  public GroupSetI getGroupSet()
+  {
+    return mappedMatrix.getGroupSet();
+  };
 
   @Override
-  public SequenceI getReferenceSeq()
+  public void setGroupSet(GroupSet makeGroups)
   {
-    return refSeq;
+    mappedMatrix.setGroupSet(makeGroups);
   }
+  
+  /**
+   * the sequence and how it is mapped to the matrix
+   */
+
+  SequenceI refSeq = null;
+
+  MapList toSeq = null;
 
   /**
-   * container for groups - defined on matrix columns
+   * the length that refSeq is expected to be (excluding gaps, of course)
    */
-  GroupSet grps = new GroupSet();
+  int length;
 
   @Override
-  public GroupSetI getGroupSet()
+  public boolean hasReferenceSeq()
   {
-    return grps;
-  };
+    return (refSeq != null);
+  }
 
   @Override
-  public void setGroupSet(GroupSet makeGroups)
+  public SequenceI getReferenceSeq()
   {
-    grps = makeGroups;
+    return refSeq;
   }
 
   @Override
@@ -439,7 +475,7 @@ public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
   }
 
   /**
-   * get a specific element of the contact matrix in its data-local coordinates
+   * get a specific element of the underlying contact matrix in its data-local coordinates
    * rather than the mapped frame. Implementations are allowed to throw
    * RunTimeExceptions if _column/i are out of bounds
    * 
@@ -447,6 +483,29 @@ public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
    * @param i
    * @return
    */
-  protected abstract double getElementAt(int _column, int i);
+  public double getElementAt(int _column, int i) {
+    return mappedMatrix.getElementAt(_column, i);
+  }
+
+  @Override
+  public int hashCode()
+  {
+    return 7 * (refSeq != null ? refSeq.hashCode() : 0)
+            + 11 * (toSeq != null ? toSeq.hashCode() : 0)
+            + 13 * (mappedMatrix != null ? mappedMatrix.hashCode() : 0)
+            + length * 3;
+  }
 
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj == null || !(obj.getClass().equals(getClass())))
+    {
+      return false;
+    }
+    T them = (T) obj;
+    return mappedMatrix == them.mappedMatrix && length == them.length
+            && refSeq == them.refSeq && toSeq.equals(them.toSeq);
+
+  }
 }