blast java_如何利用BioJava设置一个BLAST解析器解析BLAST结果

import java.io.*;

import java.util.*;

import org.biojava.bio.program.sax.*;

import org.biojava.bio.program.ssbind.*;

import org.biojava.bio.search.*;

import org.biojava.bio.seq.db.*;

import org.xml.sax.*;

import org.biojava.bio.*;

public class BlastParser {

// args[0] 为Blast输出文件

public static void main(String[] args){

try{

// 以流的方式得到Blast输出

InputStream is = new FileInputStream(args[0]);

// 创建一个Blast类型的SAX解析器

BlastLikeSAXParser parser = new BlastLikeSAXParser();

// 创建一个可以将事件传送给句柄的SAX事件适配器

SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

// 给parser设置SAX事件适配器

parser.setContentHandler(adapter);

// 保存序列相似性搜索结果(SeqSimilaritySearchResults)的链表

List results = new ArrayList();

// 创建在结果链表(Results List)中生成序列相似性搜索结果对象的搜索内容句柄(SearchContentHandler)

SearchContentHandler builder = new BlastLikeSearchBuilder(results,

new DummySequenceDB("queries"), new DummySequenceDBInstallation());

// 解析文件，序列相似性搜索结果填充到结果链表

parser.parse(new InputSource(is));

// 输出一些Blast细节

for (Iterator i = results.iterator(); i.hasNext(); ){

SeqSimilaritySearchResult result = (SeqSimilaritySearchResult)i.next();

Annotation anno = result.getAnnotation();

for(Iterator j = anno.keys().iterator(); j.hasNext(); ){

Object key = j.next();

Object property = anno.getProperty(key);

System.out.println(key+" : "+property);

}

System.out.println("Hits: ");

// 列出匹配

for (Iterator k = result.getHits().iterator(); k.hasNext(); ){

SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next();

System.out.println("\tmatch: "+hit.getSubjectID());

System.out.println("\te score: "+hit.getEValue());

}

System.out.println("\n");

}

}

catch (SAXException ex) {

//XML 出问题

ex.printStackTrace();

}catch (IOException ex) {

//IO 出问题，例如文件找不到

ex.printStackTrace();

}

}

}