X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactMatrix.java;h=b8593d842fd8474487f96ae14e3fe4b6dea82e26;hb=b028e684c807365decd0c6e6111aa4bf368a6fa8;hp=fac1deee73cdda802f7259315e9e0d67e7904e8c;hpb=326540793e46af73aed8c7e69bd77a957eec86c1;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index fac1dee..b8593d8 100644
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,12 +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 jalview.ws.params.InvalidArgumentException;
-
-import java.awt.Color;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.StringTokenizer;
+
+import jalview.bin.Console;
 
-public class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix extends GroupSetHolder
+        implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?
@@ -28,7 +49,7 @@ 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));
     }
@@ -74,13 +95,6 @@ public class ContactMatrix implements ContactMatrixI
     }
   }
 
-  Color minColor = Color.white, maxColor = Color.magenta;
-
-  Color shadeFor(float value)
-  {
-    return jalview.util.ColorUtils.getGraduatedColour(value, 0,
-            Color.white, max, Color.magenta);
-  }
   @Override
   public ContactListI getContactList(final int column)
   {
@@ -88,78 +102,155 @@ public class ContactMatrix implements ContactMatrixI
     {
       return null;
     }
-    return new ContactListI()
+
+    return new ContactListImpl(new ContactListProviderI()
     {
       int p = column;
 
       @Override
-      public Color getColorForScore(int column)
+      public int getPosition()
       {
+        return p;
+      }
+
+      @Override
+      public int getContactHeight()
+      {
+        return width;
 
-        return shadeFor((float) getContactAt(column));
       }
 
       @Override
-      public Color getColorForRange(int i, int j)
+      public double getContactAt(int column)
       {
-        double contc;
-        double v = 0;
-        for (int r=i;r<j;r++)
+        Float cl = getFloatElementAt(column, p);
+        if (cl == null)
         {
-          contc = getContactAt(r);
-          if (contc != contc)
-          {
-            v += contc;
-          }
+          // return 0 not NaN ?
+          return Double.NaN;
         }
-        // average for moment - probably more interested in maxIntProj though
-        return shadeFor(((float) v) / (j - i + 1));
+        return cl.doubleValue();
       }
+    });
+  }
 
-      @Override
-      public int getColumnWidth()
+  private Float getFloatElementAt(int column, int p)
+  {
+
+    List<Float> clist;
+    Float cl = null;
+    if (symmetric)
+    {
+      if (p < column)
       {
-        return 1;
+        clist = contacts.get(p);
+        cl = clist.get(column);
       }
-
-      @Override
-      public int getContactHeight()
+      else
       {
-        return width;
-
+        clist = contacts.get(column);
+        cl = clist.get(p);
       }
+    }
+    else
+    {
+      clist = contacts.get(p);
+      cl = clist.get(column);
+    }
+    return cl;
+  }
 
-      @Override
-      public double getContactAt(int column)
+  @Override
+  public double getElementAt(int column, int row)
+  {
+    Float cl = getFloatElementAt(column, row);
+    if (cl != null)
+    {
+      return cl;
+    }
+    throw (new RuntimeException("Out of Bounds " + column + "," + row));
+  }
+
+  @Override
+  public float getMin()
+  {
+    return min;
+  }
+
+  @Override
+  public float getMax()
+  {
+    return max;
+  }
+
+  @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);
+      long lastsb = -1;
+      if (cl != null)
       {
-        List<Float> clist;
-        Float cl = null;
-        if (symmetric)
+        for (int h = 0; h <= cl.getContactHeight(); h++)
         {
-          if (p < column)
-          {
-            clist = contacts.get(p);
-            cl = clist.get(column);
-          }
-          else
+          if (sb.length() > 0)
           {
-            clist = contacts.get(column);
-            cl = clist.get(p);
+            if (sb.length() - lastsb > 320)
+            {
+              // newline
+              sb.append('\n');
+              lastsb = sb.length();
+            }
+            else
+            {
+              sb.append('\t');
+            }
           }
+          sb.append(cl.getContactAt(h));
         }
-        else
-        {
-          clist = contacts.get(p);
-          cl = clist.get(column);
-        }
-        if (cl == null)
-        {
-          // return 0 not NaN ?
-          return Double.NaN;
-        }
-        return cl.doubleValue();
       }
-    };
+    }
+    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;
+  }
 }