JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset...

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

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 07934a1..f2e207c 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,11 +1,14 @@
 package jalview.datamodel;
 
-import jalview.ws.params.InvalidArgumentException;
-
+import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Spliterator;
+import java.util.StringTokenizer;
+
+import jalview.bin.Console;
 
-public class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?
@@ -27,7 +30,7 @@ public class ContactMatrix implements ContactMatrixI
   {
     if (left < 0 || right < 0)
     {
-      throw new Error(new InvalidArgumentException(
+      throw new Error(new RuntimeException(
               "Cannot have negative indices for contact left=" + left
                       + " right=" + right + " strength=" + strength));
     }
@@ -73,7 +76,6 @@ public class ContactMatrix implements ContactMatrixI
     }
   }
 
-
   @Override
   public ContactListI getContactList(final int column)
   {
@@ -87,6 +89,12 @@ public class ContactMatrix implements ContactMatrixI
       int p = column;
 
       @Override
+      public int getPosition()
+      {
+        return p;
+      }
+
+      @Override
       public int getContactHeight()
       {
         return width;
@@ -151,4 +159,65 @@ public class ContactMatrix implements ContactMatrixI
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "Contact Matrix";
+  }
+
+  @Override
+  public String getAnnotDescr()
+  {
+    return "Contact Matrix";
+  }
+
+  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)
+  {
+    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;
+  }
 }