线程"main“java.lang.ArrayIndexOutOfBoundsException中的生化异常：

Question

我对多序列比对有问题。我有两个序列，如下所示，我试图使用生物have方法对齐它们，得到这样的错误。我不知道是怎么回事。我知道序列不是相同的长度，但这不重要。

线程"main“中的异常:1在org.forester.evoinference.distance.NeighborJoining.getValueFromD(NeighborJoining.java:150) at org.forester.evoinference.distance.NeighborJoining.execute(NeighborJoining.java:123) at org.biojava3.alignment.GuideTree.(GuideTree.java:88) at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:183) at Fasta.main(Fasta.java:41)

public class Fasta {

    public static void main(String[] args) throws Exception{


        ArrayList<String> fileName = new ArrayList<String> ();
        fileName.add("2M3T.fasta.txt");
        fileName.add("3LWK.fasta.txt");
        ArrayList<ProteinSequence> al = new ArrayList<ProteinSequence>();
        //ArrayList<ProteinSequence> all =  new ArrayList<ProteinSequence>();
        for (String fn : fileName)
        {
        al = getProteinSequenceFromFasta(fn);
        //all.add(al.get(0));
        for  (ProteinSequence s : al)
        {
            System.out.println(s);
        }
        }
        Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(al);
        System.out.printf("Clustalw:%n%s%n", profile);
        ConcurrencyTools.shutdown();
        }
        //for (int i=0;i<sequence.size();i++)
        //  System.out.println(sequence);


    public static ArrayList<ProteinSequence> getProteinSequenceFromFasta(String file) throws Exception{

        LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(file));
        //sztuczne
        ArrayList<ProteinSequence> sequence =  new ArrayList<ProteinSequence>(a.values());


        return sequence;
    }
}

Answer 1

我猜问题就在这条线上：

for (String fn : fileName)
{
    al = getProteinSequenceFromFasta(fn);
...
 }

您正在覆盖每个文件的a1内容。(我假设您希望将所有fasta记录添加到a1中。如果您的fasta文件每个只有一个记录，那么它不能对单个记录进行多次对齐。

你可能想

for (String fn : fileName)
{
    al.addAll(getProteinSequenceFromFasta(fn) );
...
 }

当然，您所使用的库应该首先检查以确保有超过一个序列.