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 32fa5b1..b8593d8 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -6,7 +26,8 @@ import java.util.StringTokenizer;
 
 import jalview.bin.Console;
 
-public abstract class ContactMatrix extends GroupSetHolder implements ContactMatrixI
+public abstract class ContactMatrix extends GroupSetHolder
+        implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?
@@ -112,9 +133,10 @@ public abstract class ContactMatrix extends GroupSetHolder implements ContactMat
       }
     });
   }
+
   private Float getFloatElementAt(int column, int p)
   {
-    
+
     List<Float> clist;
     Float cl = null;
     if (symmetric)
@@ -137,16 +159,18 @@ public abstract class ContactMatrix extends GroupSetHolder implements ContactMat
     }
     return cl;
   }
+
   @Override
   public double getElementAt(int column, int row)
   {
     Float cl = getFloatElementAt(column, row);
-    if (cl!=null)
+    if (cl != null)
     {
       return cl;
     }
-    throw(new RuntimeException("Out of Bounds "+column+","+row));
+    throw (new RuntimeException("Out of Bounds " + column + "," + row));
   }
+
   @Override
   public float getMin()
   {
@@ -170,19 +194,30 @@ public abstract class ContactMatrix extends GroupSetHolder implements ContactMat
   {
     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)
           {
-            sb.append('\t');
+            if (sb.length() - lastsb > 320)
+            {
+              // newline
+              sb.append('\n');
+              lastsb = sb.length();
+            }
+            else
+            {
+              sb.append('\t');
+            }
           }
           sb.append(cl.getContactAt(h));
         }
@@ -195,7 +230,7 @@ public abstract class ContactMatrix extends GroupSetHolder implements ContactMat
           int rows)
   {
     float[][] vals = new float[cols][rows];
-    StringTokenizer tabsep = new StringTokenizer(values, "" + '\t');
+    StringTokenizer tabsep = new StringTokenizer(values, "" + '\t' + '\n');
     int c = 0, r = 0;
     while (tabsep.hasMoreTokens())
     {