/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on Mar 1, 2010
 * Author: Andreas Prlic 
 *
 */

package org.biojava.bio.structure.align;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;

import org.biojava.bio.structure.Atom;
import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.StructureTools;
import org.biojava.bio.structure.align.ce.CeMain;
import org.biojava.bio.structure.align.util.AtomCache;

import junit.framework.TestCase;

public class TestAlignDBSearchPairs extends TestCase
{

   public void testParsePairs(){

      String tmpDir = System.getProperty("java.io.tmpdir");
      
      AtomCache cache = new AtomCache(tmpDir,true);

      InputStream inStream = this.getClass().getResourceAsStream("/db_search.pairs");
      assertNotNull(inStream);

      BufferedReader is = new BufferedReader (new InputStreamReader(inStream)) ;
      try {
         StructureAlignment algorithm =  StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
         String line = null;
         while ( (line = is.readLine()) != null){
            if ( line.startsWith("#"))
               continue;
            System.out.println("aligning: " + line);
            String[] spl = line.split(" ");
            String pdb1 = spl[0];
            String pdb2 = spl[1];


            Structure structure1 = cache.getStructure(pdb1);
            Structure structure2 = cache.getStructure(pdb2);

            Atom[] ca1;
            Atom[] ca2;


            ca1 = StructureTools.getAtomCAArray(structure1);
            ca2 = StructureTools.getAtomCAArray(structure2);

            algorithm.align(ca1,ca2);

         }
      } catch (Exception e){
         e.printStackTrace();
         fail(e.getMessage());
      }
   }
}

@@ -1734,16 +1734,18 @@
         
+//
  System.

less verbose