ProteinAction.java

package GeDBIT.web;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import com.opensymphony.xwork2.ActionSupport;

@SuppressWarnings("serial")
public class ProteinAction extends ActionSupport {
    private String prostr; // 输入DNA串
    private Map<String, String> result = new LinkedHashMap<String, String>(); // 用于JSP显示
    private String resdna = "";// 返回的总串
    private int pronum = 0; // 结果数量
    private double time = 0.0001; // 搜索时间
    private int allcount = 10000; // 搜索数据库的大小
    private int page = 0; // 显示当前页数
    private int allpage = 0; // 总页数

    private double r = 0;

    public void setR(double r) {
	this.r = r;
    }

    public double getR() {
	return r;
    }

    public void setAllpage(int allpage) {
	this.allpage = allpage;
    }

    public int getAllpage() {
	return allpage;
    }

    public void setPage(int page) {
	this.page = page;
    }

    public int getPage() {
	return page;
    }

    public void setTime(double time) {
	this.time = time;
    }

    public double getTime() {
	return time;
    }

    public void setAllcount(int allcount) {
	this.allcount = allcount;
    }

    public int getAllcount() {
	return allcount;
    }

    public String getResdna() {
	return resdna;
    }

    public void setResdna(String resdna) {
	this.resdna = resdna;
    }

    public int getPronum() {
	return pronum;
    }

    public void setPronum(int pronum) {
	this.pronum = pronum;
    }

    public String getProstr() {
	return prostr;
    }

    public void setProstr(String prostr) {
	this.prostr = prostr;
    }

    public Map<String, String> getResult() {
	return result;
    }

    public void setResult(Map<String, String> result) {
	this.result = result;
    }

    public void setRes() {
	int count = 1;
	int evpg = 10; // 每一页的数量 用于演示可修改
	String res;
	Pattern patt = Pattern.compile("fragment:.+source"); // 这里生成txt文件
	@SuppressWarnings("unused")
	Pattern pattend = Pattern.compile(" source: >([^'])+");
	try // 这里读取txt文件
	{
	    File file = new File("D:/data/protein/presult.txt");
	    if (file.isFile() && file.exists()) {
		InputStreamReader read = new InputStreamReader(
			new FileInputStream(file), "GBK");
		BufferedReader buffreader = new BufferedReader(read);
		String lineTxt = null;
		String tpo;
		buffreader.readLine();
		while ((lineTxt = buffreader.readLine()) != null) {
		    Matcher matcher = patt.matcher(lineTxt);
		    // System.out.println("OPEN OK");
		    while (matcher.find()) {
			res = matcher.group().toString()
				.replaceFirst("fragment: ", "");
			res = res.replaceFirst(" source", "");
			tpo = lineTxt.replace(res,
				"<strong style='color:blue'>" + res
					+ "</strong>");
			tpo = tpo.replace("source:",
				"<strong style='color:red'>source:</strong>");
			tpo = tpo.replace("fragment:",
				"<strong style='color:red'>fragment:</strong>");
			tpo = tpo.replace("offset:",
				"<strong style='color:red'>offset:</strong>");
			if ((count > (page * evpg))
				&& (count <= (page + 1) * evpg)) {
			    result.put(String.valueOf(count), tpo);
			}
			// System.out.println(res);
			++count;
		    }
		}
		allpage = ((count - 1) / evpg) - 1;
		pronum = count - 1;
		read.close();
	    } else
		System.out.println("Open Error");
	} catch (Exception e) {
	    System.out.println("Error");
	}
    }

    public String execute() throws Exception {
	String[] tp = prostr.split(",");
	prostr = tp[0];
	r = Double.valueOf(tp[1]);
	new ProteinQuery().runQuery(r);
	setRes();
	// System.out.println(prostr);
	allcount = 100000;
	time = 0.001;
	prostr = prostr + "," + r;
	return SUCCESS;

    }

}