/**
?*?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（））;
???}
}

?屬性????????????大小?????日期????時(shí)間???名稱
-----------?---------??----------?-----??----

?????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

............此處省略25個(gè)文件信息