X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrix.java;h=48b6e6b45b3476fc97548fbd3ad4bf47ada00b9d;hb=2f36a546ff554e3db3d7cb6bcc899dcd01dd242c;hp=de7cba4a1b11df6ea8833fe1cc3df7c5ca9b500b;hpb=eb7a26d5a2a6168aabe6a35d434aa6546159e977;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index de7cba4..48b6e6b 100644
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,9 +1,17 @@
 package jalview.datamodel;
 
+import java.awt.Color;
+import java.math.BigInteger;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Spliterator;
+import java.util.StringTokenizer;
 
-public class ContactMatrix implements ContactMatrixI
+import jalview.bin.Console;
+
+public abstract class ContactMatrix implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?
@@ -142,16 +150,73 @@ public class ContactMatrix implements ContactMatrixI
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public String getAnnotLabel()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return "Contact Matrix";
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public String getAnnotDescr()
+  {
+    return "Contact Matrix";
+  }
+  GroupSet grps = new GroupSet();
+  @Override
+  public GroupSetI getGroupSet()
+  {
+    return grps;
+  }
+  @Override
+  public void setGroupSet(GroupSet makeGroups)
+  {
+    grps = makeGroups;
+  }
+  public static String contactToFloatString(ContactMatrixI cm)
+  {
+    StringBuilder sb = new StringBuilder();
+    for (int c = 0; c < cm.getWidth(); c++)
+    {
+      ContactListI cl = cm.getContactList(c);
+      if (cl != null)
+      {
+        for (int h = 0; h <= cl.getContactHeight(); h++)
+        {
+          if (sb.length() > 0)
+          {
+            sb.append('\t');
+          }
+          sb.append(cl.getContactAt(h));
+        }
+      }
+    }
+    return sb.toString();
+  }
+
+  public static float[][] fromFloatStringToContacts(String values, int cols,
+          int rows)
   {
-    // TODO Auto-generated method stub
-    return null;
+    float[][] vals = new float[cols][rows];
+    StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+    int c = 0, r = 0;
+    while (tabsep.hasMoreTokens())
+    {
+      double elem = Double.valueOf(tabsep.nextToken());
+      vals[c][r++] = (float) elem;
+      if (r >= vals[c].length)
+      {
+        r = 0;
+        c++;
+      }
+      if (c >= vals.length)
+      {
+        break;
+      }
+    }
+    if (tabsep.hasMoreElements())
+    {
+      Console.warn(
+              "Ignoring additional elements for Float string to contact matrix parsing.");
+    }
+    return vals;
   }
 }