From 6fc163433164d93374330fa0a603eea1e1fd42b3 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Dec 2016 10:45:41 +0000
Subject: [PATCH] =?utf8?q?JAL-2349=20interfaces=20and=20logic=20for=20adding?=
 =?utf8?q?=20contact=20matrices=20as=20an=20alignment=E2=80=99s=20annotation?=
 =?utf8?q?=20row?=
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---
 src/jalview/api/AlignViewportI.java          |    3 +++
 src/jalview/datamodel/Alignment.java         |   31 ++++++++++++++++++++++++++
 src/jalview/datamodel/AlignmentI.java        |   12 ++++++++++
 src/jalview/datamodel/ContactListI.java      |   14 ++++++++++++
 src/jalview/datamodel/ContactMatrixI.java    |    8 +++++++
 src/jalview/viewmodel/AlignmentViewport.java |    7 ++++++
 6 files changed, 75 insertions(+)
 create mode 100644 src/jalview/datamodel/ContactListI.java
 create mode 100644 src/jalview/datamodel/ContactMatrixI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 72542b3..cb11886 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceCollectionI;
@@ -445,4 +446,6 @@ public interface AlignViewportI extends ViewStyleI
    * @return search results or null
    */
   SearchResultsI getSearchResults();
+
+  ContactListI getContactList(AlignmentAnnotation _aa, int column);
 }
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d651c1d..758e1cb 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,6 +30,7 @@ import jalview.util.MessageManager;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
@@ -1946,4 +1947,34 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  Map<Object, ContactMatrixI> contactmaps = new HashMap<Object, ContactMatrixI>();
+  @Override
+  public
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+    if (cm == null)
+    {
+      return null;
+    }
+    return cm.getContactList(column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    Annotation _aa[] = new Annotation[getWidth()];
+    Annotation dummy = new Annotation(0.0f);
+    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    {
+      ;
+    }
+    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
+            "Contact Matrix", _aa);
+    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+    contactmaps.put(aa.annotationId, cm);
+    addAnnotation(aa);
+    return aa;
+  }
 }
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7274e5f..8ddba6c 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -556,4 +556,16 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+  /**
+   * resolve a contact list instance (if any) associated with the annotation row
+   * and column position
+   * 
+   * @param _aa
+   * @param column
+   * @return
+   */
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column);
+
+  AlignmentAnnotation addContactList(ContactMatrixI cm);
 }
diff --git a/src/jalview/datamodel/ContactListI.java b/src/jalview/datamodel/ContactListI.java
new file mode 100644
index 0000000..c08c07b
--- /dev/null
+++ b/src/jalview/datamodel/ContactListI.java
@@ -0,0 +1,14 @@
+package jalview.datamodel;
+
+import java.awt.Color;
+
+public interface ContactListI
+{
+
+  int getColumnWidth();
+
+  int getContactHeight();
+
+  Color getColorForScore(int column);
+
+}
diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
new file mode 100644
index 0000000..9a7f138
--- /dev/null
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -0,0 +1,8 @@
+package jalview.datamodel;
+
+public interface ContactMatrixI
+{
+
+  ContactListI getContactList(int column);
+
+}
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fecccb0..cb9dd67 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -35,6 +35,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -2872,4 +2873,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     return searchResults;
   }
+
+  @Override
+  public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+  {
+    return alignment.getContactListFor(_aa, column);
+  }
 }
-- 
1.7.10.2