基因数据处理119之java调用SSW在linux下运行

更多代码请见：https://github.com/xubo245

基因数据处理系列

1.解释

测试自带Example：

xubo@xubo:~/xubo/tools/Complete-Striped-Smith-Waterman-Library/src$ scala  -Djava.library.path=. -cp SparkSW.jar ssw.Example
Aligning nucleotides
score1=21 score2=8 ref_begin1=8 ref_end1=21 read_begin1=0 read_end1=14 ref_end2=4 cigar=9M1I5M 

但是有时候需要自己写或者调用

2.代码：

自己写java调用

package ssw;

/**
 * Created by xubo on 2016/11/24.
 */
public class SSWRun {
    public static void main(String[] args) {
        try {
            System.loadLibrary("sswjni");
        } catch (UnsatisfiedLinkError e) {
            System.out.println(String.format("Cannot find libsswjni.so. Has the library been built and LD_LIBRARY_PATH or -Djava.library.path set appropriately?\n%s", e));
            throw e;
        }

        int[][] score = new int[128][128];
        for (int i = 0; i < 128; i++) {
            for (int j = 0; j < 128; j++) {
                if (i == j) score[i][j] = 2;
                else score[i][j] = -2;
            }
        }
        System.out.println("Aligning nucleotides");
        Alignment aln = Aligner.align(args[0].getBytes(), args[1].getBytes(), score, 3, 1, true);
//        Alignment aln = Aligner.align("CTGAGCCGGTAAATC".getBytes(), "CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA".getBytes(), score, 3, 1, true);
        if (aln == null) {
            throw new RuntimeException();
        }
        System.out.print(String.format("score1=%d ", aln.score1));
        System.out.print(String.format("score2=%d ", aln.score2));
        System.out.print(String.format("ref_begin1=%d ", aln.ref_begin1));
        System.out.print(String.format("ref_end1=%d ", aln.ref_end1));
        System.out.print(String.format("read_begin1=%d ", aln.read_begin1));
        System.out.print(String.format("read_end1=%d ", aln.read_end1));
        System.out.print(String.format("ref_end2=%d ", aln.ref_end2));
        System.out.print(String.format("cigar=%s ", aln.cigar));
        System.out.println();

    }
}

3.结果：

xubo@xubo:~/xubo/tools/Complete-Striped-Smith-Waterman-Library/src$ scala  -Djava.library.path=. -cp SparkSW.jar ssw.SSWRun A A
Aligning nucleotides
score1=2 score2=0 ref_begin1=0 ref_end1=0 read_begin1=0 read_end1=0 ref_end2=0 cigar=1M 
xubo@xubo:~/xubo/tools/Complete-Striped-Smith-Waterman-Library/src$ scala  -Djava.library.path=. -cp SparkSW.jar ssw.SSWRun AB A
Aligning nucleotides
score1=2 score2=0 ref_begin1=0 ref_end1=0 read_begin1=0 read_end1=0 ref_end2=0 cigar=1M 
xubo@xubo:~/xubo/tools/Complete-Striped-Smith-Waterman-Library/src$ scala  -Djava.library.path=. -cp SparkSW.jar ssw.SSWRun AB AB
Aligning nucleotides
score1=4 score2=0 ref_begin1=0 ref_end1=1 read_begin1=0 read_end1=1 ref_end2=0 cigar=2M 
xubo@xubo:~/xubo/tools/Complete-Striped-Smith-Waterman-Library/src$ scala  -Djava.library.path=. -cp SparkSW.jar ssw.SSWRun AGCT ACT
Aligning nucleotides
score1=4 score2=0 ref_begin1=1 ref_end1=2 read_begin1=2 read_end1=3 ref_end2=0 cigar=2M 

参考

【1】https://github.com/xubo245
【2】http://blog.csdn.net/xubo245/