动态规划 序列对比 Needleman-Wunsch Smith-Waterman algorthm（java）

可以使用需要重新加载biojava.jar jar包代码是全的，不会可以问我。jar包在lib目录下面 输出结果： Global alignment with Needleman-Wunsch: Time (ms): 3 Length: 9 Score: 0 Query: query, Length: 9 Target: target, Length: 8 Query: 1 gccctagcg 9 || | | | Target: 1 gcgc-aatg 8 Local alignment with Smith-Waterman: Time (ms): 0 Length: 3 Score: 3 Query: query, Length: 9 Target: target, Length: 8 Query: 7 gcg 9 ||| Target: 1 gcg 3

/**
 * Author: Paul Reiners
 */
package com.ibm.biojava.sample;

import org.biojava.bio.alignment.NeedlemanWunsch;
import org.biojava.bio.alignment.SequenceAlignment;
import org.biojava.bio.alignment.SmithWaterman;
import org.biojava.bio.alignment.SubstitutionMatrix;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.FiniteAlphabet;

/**
 * @author Paul Reiners
 * 
 * based closely on code by Andreas Dräger
 */
public class BioJavaSample {

   /**
    * @param args
    * @throws Exception
    */
   public static void main（String[] args） throws Exception {
      // The alphabet of the sequences. For this example DNA is chosen.
      FiniteAlphabet alphabet = （FiniteAlphabet） AlphabetManager
            .alphabetForName（“DNA“）;
      // Use a substitution matrix with equal scores for every match and every
      // replace.
      short match = 1;
      short replace = -1;
      SubstitutionMatrix matrix = new SubstitutionMatrix（alphabet match
            replace）;
      // Firstly define the expenses （penalties） for every single operation.
      short insert = 2;
      short delete = 2;
      short gapExtend = 2;
      // Global alignment.
      SequenceAlignment aligner = new NeedlemanWunsch（match replace insert
            delete gapExtend matrix）;
      Sequence query = DNATools.createDNASequence（“GCCCTAGCG“ “query“）;
      Sequence target = DNATools.createDNASequence（“GCGCAATG“ “target“）;
      // Perform an alignment and save the results.
      aligner.pairwiseAlignment（query // first sequence
            target // second one
            ）;
      // Print the alignment to the screen
      System.out.println（“Global alignment with Needleman-Wunsch:\n“
            + aligner.getAlignmentString（））;

      // Perform a local alignment from the sequences with Smith-Waterman.
      aligner = new SmithWaterman（match replace insert delete gapExtend
            matrix）;
      // Perform the local alignment.
      aligner.pairwiseAlignment（query target）;
      System.out.println（“\nLocal alignment with Smith-Waterman:\n“
            + aligner.getAlignmentString（））;
   }
}

 属性            大小     日期    时间   名称
----------- ---------  ---------- -----  ----

     文件        481  2016-08-10 13:58  SequenceAlignment\.classpath

    .......       393  2008-02-28 12:58  SequenceAlignment\.project

    .......     21864  2008-02-28 12:58  SequenceAlignment\.settings\org.eclipse.jdt.core.prefs

    .......       228  2008-02-28 12:58  SequenceAlignment\.settings\org.eclipse.jdt.ui.prefs

     文件       2299  2016-08-10 14:32  SequenceAlignment\bin\com\ibm\biojava\sample\BioJavaSample.class

     文件       1414  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\Cell.class

     文件       4041  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\DynamicProgramming.class

     文件       2426  2016-08-10 14:37  SequenceAlignment\bin\com\ibm\compbio\misc\DNAGenerator.class

     文件       1391  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\misc\Fibonacci.class

     文件       2611  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\seqalign\NeedlemanWunsch.class

     文件       2239  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\seqalign\SequenceAlignment.class

     文件       2653  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\seqalign\SmithWaterman.class

     文件       2532  2016-08-10 13:58  SequenceAlignment\bin\com\ibm\compbio\sequence\LongestCommonSubsequence.class

     文件    3607968  2016-08-10 13:38  SequenceAlignment\lib\biojava.jar

     文件     102896  2016-08-10 13:54  SequenceAlignment\lib\biojava3-alignment-3.0.1.jar

     文件     163026  2016-08-10 13:54  SequenceAlignment\lib\biojava3-alignment-3.0.5-sources.jar

     文件     183516  2016-08-10 13:54  SequenceAlignment\lib\biojava3-alignment-3.0.5.jar

     文件     190116  2016-08-10 13:54  SequenceAlignment\lib\biojava3-core-3.0-sources.jar

     文件     255177  2016-08-10 13:54  SequenceAlignment\lib\biojava3-core-3.0.1.jar

     文件     315410  2016-08-10 13:54  SequenceAlignment\lib\biojava3-structure-gui-3.0.5.jar

     文件     391834  2016-08-10 13:49  SequenceAlignment\lib\log4j-1.2.15.jar

     文件       2283  2016-08-10 13:57  SequenceAlignment\src\com\ibm\biojava\sample\BioJavaSample.java

    .......      1252  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\Cell.java

    .......      4489  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\DynamicProgramming.java

     文件       3875  2016-08-10 14:37  SequenceAlignment\src\com\ibm\compbio\misc\DNAGenerator.java

    .......      1130  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\misc\Fibonacci.java

    .......      2713  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\seqalign\NeedlemanWunsch.java

    .......      2431  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\seqalign\SequenceAlignment.java

    .......      2835  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\seqalign\SmithWaterman.java

    .......      3225  2008-02-28 12:58  SequenceAlignment\src\com\ibm\compbio\sequence\LongestCommonSubsequence.java

............此处省略25个文件信息