biojava Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException：

Question

我有多个序列对齐的问题。我有两个序列如下，我试图对齐他们使用生物java方法，我得到这样的错误。我不知道怎么了。我知道序列的长度不一样，但这应该无关紧要。

GSKTGTKITFYEDKNFQGRRYDCDCDCADFHTYLSRCNSIKVEGGTWAVYERPNFAGYMYILPQGEYPEYQRWMGLNDRLSSCRAVHLPSGGQYKIQIFEKGDFSGQMYETTEDCPSIMEQFHMREIHSCKVLEGVWIFYELPNYRGRQYLLDKKEYRKPIDWGAASPAVQSFRRIVESMSAGPWKMVVWDEDGFQGRRHEFTAECPSVLELGFETVRSLKVLSGAWVGFEHAGFQGQQYILERGEYPSWDAWGGNTAYPAERLTSFRPAACANHRDSRLTIFEQENFLGKKGELSDDYPSLQAMGWEGNEVGSFHVHSGAWVCSQFPGYRGFQYVLECDHHSGDYKHFREWGSHAPTFQVQSIRRIQQ

线程"main"异常java.lang.ArrayIndexOutOfBoundsException: 1在org.forester.evoinference.distance.NeighborJoining.getValueFromD (NeighborJoining.java: 150)在org.forester.evoinference.distance.NeighborJoining.execute (NeighborJoining.java: 123)(GuideTree.java:88org.biojava3.alignment.Alignments.getMultipleSequenceAlignment (Alignments.java: 183)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

我猜问题在这一行:

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

您正在为每个文件覆盖a1的内容。(我假设您想将所有fasta记录添加到a1中。如果你的fasta文件只有1条记录，那么它不能对单个记录进行多次对齐。

你可能想要

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

当然，您正在使用的库可能应该首先检查以确保有超过1个序列....