Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 35ec87b..b8593d8 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,9 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.StringTokenizer;
 
-public class ContactMatrix implements ContactMatrixI
+import jalview.bin.Console;
+
+public abstract class ContactMatrix extends GroupSetHolder
+        implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?
@@ -99,26 +123,7 @@ public class ContactMatrix implements ContactMatrixI
       @Override
       public double getContactAt(int column)
       {
-        List<Float> clist;
-        Float cl = null;
-        if (symmetric)
-        {
-          if (p < column)
-          {
-            clist = contacts.get(p);
-            cl = clist.get(column);
-          }
-          else
-          {
-            clist = contacts.get(column);
-            cl = clist.get(p);
-          }
-        }
-        else
-        {
-          clist = contacts.get(p);
-          cl = clist.get(column);
-        }
+        Float cl = getFloatElementAt(column, p);
         if (cl == null)
         {
           // return 0 not NaN ?
@@ -129,30 +134,53 @@ public class ContactMatrix implements ContactMatrixI
     });
   }
 
-  @Override
-  public float getMin()
+  private Float getFloatElementAt(int column, int p)
   {
-    return min;
+
+    List<Float> clist;
+    Float cl = null;
+    if (symmetric)
+    {
+      if (p < column)
+      {
+        clist = contacts.get(p);
+        cl = clist.get(column);
+      }
+      else
+      {
+        clist = contacts.get(column);
+        cl = clist.get(p);
+      }
+    }
+    else
+    {
+      clist = contacts.get(p);
+      cl = clist.get(column);
+    }
+    return cl;
   }
 
   @Override
-  public float getMax()
+  public double getElementAt(int column, int row)
   {
-    return max;
+    Float cl = getFloatElementAt(column, row);
+    if (cl != null)
+    {
+      return cl;
+    }
+    throw (new RuntimeException("Out of Bounds " + column + "," + row));
   }
 
   @Override
-  public boolean hasReferenceSeq()
+  public float getMin()
   {
-    // TODO Auto-generated method stub
-    return false;
+    return min;
   }
 
   @Override
-  public SequenceI getReferenceSeq()
+  public float getMax()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return max;
   }
 
   @Override
@@ -166,4 +194,63 @@ public class ContactMatrix implements ContactMatrixI
   {
     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);
+      long lastsb = -1;
+      if (cl != null)
+      {
+        for (int h = 0; h <= cl.getContactHeight(); h++)
+        {
+          if (sb.length() > 0)
+          {
+            if (sb.length() - lastsb > 320)
+            {
+              // newline
+              sb.append('\n');
+              lastsb = sb.length();
+            }
+            else
+            {
+              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' + '\n');
+    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;
+  }
 }