Integer overflow bug in AbstractMatrixAligner

[josemduarte]

There seems to be an integer overflow bug in AbstractMatrixAligner, the type used for max and min scores is short. Whenever the score is higher than that, then it overflows and goes to the negative side.

Code to reproduce:

import org.biojava3.alignment.NeedlemanWunsch;
import org.biojava3.alignment.SimpleGapPenalty;
import org.biojava3.alignment.SubstitutionMatrixHelper;
import org.biojava3.alignment.template.SubstitutionMatrix;
import org.biojava3.core.sequence.DNASequence;
import org.biojava3.core.sequence.compound.AmbiguityDNACompoundSet;
import org.biojava3.core.sequence.compound.NucleotideCompound;

public class Test {

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

        SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
        SimpleGapPenalty gap = new SimpleGapPenalty();

        String str1 =
        "AGATATATCTGAAGCTTAAAGGGCAGTGACAATGGCTGGCTCGGTTAACGGGAATCATAGTGCTGTAGGACCTGGTATAAATTATGAGACGGTGTCTCAAGTGGATGAGTTCTGTAAAGCACTTAGAGGGAAAAGGCCGATCCATAGTATTTTGATAGCTAACAATGGAATGGCGGCTGTGAAGTTTATACGTAGTGTCAGAACATGGGCTTATGAAACATTTGGTACGGAAAAAGCCATATTGTTGGTGGGGATGGCAACCCCTGAAGACATGCGGATCAATGCGGAGCATATCAGAATCGCTGATCAGTTTGTTGAGGTTCCCGGAGGAACCAACAATAACAATTATGCTAACGTTCAGCTGATTGTGGAGATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATATTTCTTGGTCCTCCAGCATCTTCAATGGCAGCACTGGGAGATAAGATTGGTTCTTCGTTGATTGCACAAGCTGCTGATGTACCCACTCTGCCATGGAGTGGTTCCCATGTTAAAATACCTCCTAATAGCAACTTGGTAACCATCCCAGAGGAGATCTACCGGCAAGCATGTGTCTACACAACTGAAGAAGCGATTGCTAGCTGTCAAGTTGTCGGTTACCCAGCAATGATCAAAGCATCGTGGGGTGGTGGTGGTAAAGGAATCAGGAAGGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAGAGTCGGCATCTAGAGGTCCAGCTGCTCTGTGACAAGCATGGAAATGTTTCAGCTCTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACATCAAAAGATCATAGAGGAGGGTCCAATTACTGTGGCTCCGCCAGAAACTGTCAAGAAACTTGAACAAGCAGCTAGAAGGTTGGCTAAGAGTGTTAACTATGTTGGAGCTGCTACTGTTGAGTATCTCTACAGTATGGACACTGGGGAGTACTACTTCTTAGAGCTTAACCCTCGCTTACAGGTTGAGCATCCTGTCACTGAGTGGATTGCCGAGATAAATCTTCCTGCTGCCCAAGTTGCTGTGGGGATGGGAATTCCTCTCTGGCAAATCCCTGAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATCTATAAGGCCAAAAGGTCATTGTGTGGCTGTACGTGTGACAAGTGAGGATCCTGATGACGGGTTCAAACCAACCAGCGGTAGAGTTCAGGAGTTGAGTTTTAAGAGCAAGCCAAATGTGTGGGCGTACTTCTCTGTCAAGTCTGGTGGAGGCATCCACGAGTTCTCGGATTCCCAGTTTGGACATGTTTTTGCATTTGGGGAATCCAGAGCCCTGGCGATAGCGAATATGGTTCTTGGGCTAAAAGAAATTCAGATCCGTGGAGAAATTAGGACTAACGTTGACTACACGATCGACCTTTTACATGCTTCTGATTACCGTGATAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATAAAGCATCAGCGACCAGTGCTGCTGTGGTTTCAGATTACGTTGGTTATCTGGAGAAGGGGCAAATCCCTCCAAAGCATATATCTCTTGTACATTCTCAAGTGTCTCTGAATATTGAAGGAAGTAAATATACGATTGATGTAGTCCGGGGTGGATCAGGAACCTACAGGCTAAGAATGAACAAGTCAGAAGTGGTAGCAGAAATACACACTCTACGTGATGGAGGTCTGTTGATGCAGTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAGAATGACCACGATCCATCAAAGTTAATGGCTGAGACACCGTGCAAGTTGATGAGGTATTTGATTTCCGACAACAGCAATATTGACGCTGATACGCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTGCAATATCCGGTAGAGTTCATCAGAGATGTGCCGCAACATTAAATGCTGCACGCATGATTCTTGCTGGCTATGAGCATAAAGTAGATGAGGTTGTTCAAGACTTACTTAATTGCCTTGATAGCCCTGAACTCCCATTTCTTCAGTGGCAAGAGTGCTTTGCAGTTCTGGCGACACGACTACCTAAAAATCTCAGGAACATGCTAGAATCAAAGTATAGGGAATTTGAGAGTATTTCCAGAAACTCTTTGACCACCGATTTCCCTGCCAAACTTTTAAAAGGCATTCTTGAGGCACATTTATCTTCTTGTGATGAGAAAGAGAGAGGTGCCCTTGAAAGGCTCATTGAACCATTGATGAGCCTTGCAAAATCTTATGAAGGTGGTAGAGAAAGTCATGCCCGTGTTATTGTTCATTCTCTCTTTGAAGAATATCTATCAGTAGAAGAATTATTCAATGATAACATGCTGGCTGATGTTATAGAACGCATGCGTCAGCTATACAAGAAAGATCTGTTGAAAATTGTGGATATAGTGCTCTCACACCAGGGCATAAAAAACAAAAACAAACTCGTTCTCCGGCTCATGGAGCAGCTTGTTTACCCTAATCCTGCTGCTTACAGAGATAAACTTATTCGATTCTCAACACTTAACCATACTAACTACTCTGAGTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGGACGGAGAAAATATGGATACTCCCAAGAGGAAAAGTGCCATTAATGAAAGAATAGAAGATCTTGTAAGCGCATCTTTAGCTGTTGAAGACGCTCTCGTGGGACTATTTGACCATAGCGATCACACACTTCAAAGACGGGTTGTTGAGACTTATATTCGCAGATTATACCAGCCCTACGTCGTTAAAGATAGCGTGAGGATGCAGTGGCACCGTTCTGGTCTTCTTGCTTCCTGGGAGTTCCTAGAGGAGCATATGGAAAGAAAAAACATTGGCTTAGACGATCCCGACACATCTGAAAAAGGATTGGTTGAGAAGCGTAGTAAGAGAAAATGGGGGGCTATGGTTATAATCAAATCTTTGCAGTTTCTTCCAAGTATAATAAGTGCAGCATTGAGAGAAACAAAGCACAACGACTATGAAACTGCCGGAGCTCCTTTATCTGGCAATATGATGCACATTGCTATTGTGGGCATCAACAACCAGATGAGTCTGCTTCAGGACAGTGGGGATGAAGACCAAGCTCAGGAAAGAGTAAACAAGTTGGCCAAAATTCTTAAAGAGGAAGAAGTGAGTTCAAGCCTCTGTTCTGCCGGTGTTGGTGTAATCAGCTGTATAATTCAGCGAGATGAAGGACGAACACCCATGAGACATTCTTTCCATTGGTCGTTGGAGAAACAGTATTATGTAGAAGAGCCGTTGCTGCGTCATCTTGAACCTCCTCTGTCCATTTACCTTGAGTTGGATAAGCTGAAAGGATACTCAAATATACAATATACGCCTTCTCGAGATCGTCAATGGCATCTGTATACTGTTACAGACAAGCCAGTGCCAATCAAGAGGATGTTCCTGAGATCTCTTGTTCGACAGGCTACAATGAACGATGGATTTATATTGCAGCAAGGGCAGGATAAGCAGCTTAGCCAAACACTGATCTCCATGGCGTTTACGTCGAAATGTGTTCTGAGGTCTTTGATGGATGCCATGGAGGAACTGGAACTGAATGCCCATAATGCTGCAATGAAACCAGATCACGCACATATGTTTCTTTGCATATTGCGTGAGCAGCAGATAGATGATCTTGTGCCTTTCCCCAGGAGAGTTGAAGTGAATGCGGAGGATGAAGAAACTACAGTTGAAATGATCTTAGAAGAAGCAGCACGAGAGATACATAGATCTGTTGGAGTGAGAATGCATAGGTTGGGCGTGTGCGAGTGGGAAGTGCGGCTGTGGTTGGTGTCCTCTGGACTGGCATGTGGTGCTTGGAGGGTTGTGGTTGCAAACGTGACAGGCCGTACATGCACTGTCCACATATACCGAGAAGTTGAAACTCCTGGAAGAAACAGTTTAATCTACCACTCAATAACCAAGAAGGGACCTTTGCATGAAACACCAATCAGTGATCAATATAAGCCCCTGGGATATCTCGACAGGCAACGTTTAGCAGCAAGGAGGAGTAACACTACTTATTGCTATGACTTCCCGTTGGCATTTGGGACAGCCTTGGAACTGTTGTGGGCATCACAACACCCAGGAGTTAAGAAACCATATAAGGATACTCTGATCAATGTTAAAGAGCTTGTATTCTCAAAACCAGAAGGTTCTTCGGGTACATCTCTAGATCTGGTTGAAAGACCACCCGGTCTCAACGACTTTGGAATGGTTGCCTGGTGCCTAGATATGTCGACCCCAGAGTTTCCTATGGGGCGGAAACTTCTCGTGATTGCGAATGATGTCACCTTCAAAGCTGGTTCTTTTGGTCCTAGAGAGGACGCGTTTTTCCTTGCTGTTACTGAACTCGCTTGTGCCAAGAAGCTTCCCTTGATTTACTTGGCAGCAAATTCTGGTGCCCGACTTGGGGTTGCTGAAGAAGTCAAAGCCTGCTTCAAAGTTGGATGGTCGGATGAAATTTCCCCTGAGAATGGTTTTCAGTATATATACCTAAGCCCTGAAGACCACGAAAGGATTGGATCATCTGTCATTGCCCATGAAGTAAAGCTCTCTAGTGGGGAAACTAGGTGGGTGATTGATACGATCGTTGGCAAAGAAGATGGTATTGGTGTAGAGAACTTAACAGGAAGTGGGGCCATAGCGGGTGCTTACTCAAAGGCATACAATGAAACTTTTACTTTAACCTTTGTTAGTGGAAGAACGGTTGGAATTGGTGCTTATCTTGCCCGCCTAGGTATGCGGTGCATACAGAGACTTGATCAGCCGATCATCTTGACTGGCTTCTCTACACTCAACAAGTTACTTGGGCGTGAGGTCTATAGCTCTCACATGCAACTGGGTGGCCCGAAAATCATGGGCACAAATGGTGTTGTTCATCTTACAGTCTCAGATGATCTTGAAGGCGTATCAGCAATTCTCAACTGGCTCAGCTACATTCCTGCTTACGTGGGTGGTCCTCTTCCTGTTCTTGCCCCTTTAGATCCACCGGAGAGAATTGTGGAGTATGTCCCAGAGAACTCTTGCGACCCACGAGCGGCTATAGCTGGGGTCAAAGACAATACCGGTAAATGGCTTGGAGGTATCTTTGATAAAAATAGTTTCATTGAGACTCTTGAAGGCTGGGCAAGGACGGTAGTGACTGGTAGAGCCAAGCTCGGGGGAATACCCGTTGGAGTTGTTGCAGTTGAGACACAGACTGTCATGCAGATCATCCCAGCCGATCCTGGACAGCTTGACTCTCATGAAAGAGTGGTTCCGCAAGCAGGGCAAGTCTGGTTTCCTGATTCAGCGGCCAAGACTGCTCAAGCGCTTATGGATTTCAACCGGGAAGAGCTTCCATTGTTTATCCTAGCGAACTGGAGAGGGTTTTCAGGTGGGCAGAGAGATCTTTTCGAAGGAATACTTCAGGCAGGTTCAACTATAGTAGAAAATCTGAGAACCTATCGTCAGCCAGTGTTTGTGTACATCCCAATGATGGGAGAGCTGCGCGGTGGAGCGTGGGTTGTTGTTGACAGCCAGATAAATTCGGATTATGTTGAAATGTATGCTGATGAAACAGCTCGTGGAAATGTGCTTGAGCCAGAAGGGACAATAGAGATAAAATTTAGAACAAAAGAGCTATTAGAGTGCATGGGAAGGTTGGACCAGAAGCTAATCAGTCTGAAAGCAAAACTGCAAGATGCCAAGCAAAGCGAGGCCTATGCAAACATCGAGCTTCTCCAGCAACAGATTAAAGCCCGAGAGAAACAGCTTTTACCAGTTTATATCCAAATCGCCACCAAATTTGCAGAACTTCATGACACTTCCATGAGAATGGCTGCAAAGGGAGTGATCAAAAGTGTTGTGGAATGGAGCGGCTCGCGGTCCTTCTTCTACAAAAAGCTCAATAGGAGAATCGCTGAGAGCTCTCTTGTGAAAAACGTAAGAGAAGCATCTGGAGACAACTTAGCATATAAATCTTCAATGCGTCTGATTCAGGATTGGTTCTGCAACTCTGATATTGCAAAGGGGAAAGAAGAAGCTTGGACAGACGACCAAGTGTTCTTTACATGGAAGGACAATGTTAGTAACTACGAGTTGAAGCTGAGCGAGTTGAGAGCGCAGAAACTACTGAACCAACTTGCAGAGATTGGGAATTCCTCAGATTTGCAAGCTCTGCCACAAGGACTTGCTAATCTTCTAAACAAGGTGGAGCCGTCGAAAAGAGAAGAGCTGGTGGCTGCTATTCGAAAGGTCTTGGGTTGACTGA";
        String str2 =
        "TAAAGTCTTCGATATCAGTCAACCCAAGACCTTTCGAATAGCAGCCACCAGCTCTTCTCTTTTCGACGGCTCCACCTTGTTTAGAAGATTAGCAAGTCCTTGTGGCAGAGCTTGCAAATCTGAGGAATTCCCAATCTCTGCAAGTTGGTTCAGTAGTTTCTGCGCTCTCAACTCGCTCAGCTTCAACTCGTAGTTACTAACATTGTCCTTCCATGTAAAGAACACTTGGTCGTCTGTCCAAGCTTCTTCTTTCCCCTTTGCAATATCAGAGTTGCAGAACCAATCCTGAATCAGACGCATTGAAGATTTATATGCTAAGTTGTCTCCAGATGCTTCTCTTACGTTTTTTACAAGAGAGCTCTCAGCGATTCTCCTATTGAGCTTTTTGTAGAAGAAGGACCGCGAGCCGCTCCATTCCACAACACTTTTGATCACTCCCTTTGCAGCCATTCTCATGGAAGTGTCATGAAGTTCTGCAAATTTGGTGGCGATTTGGATATAAACTGGTAAAAGCTGTTTCTCTCGGGCTTTAATCTGTTGCTGGAGAAGCTCGATGTTTGCATAGGCCTCGCTTTGCTTGGCATCTTGCAGTTTTGCTTTCAGACTGATTAGCTTCTGGTCCAACCTTCCCATGCACTCTAATAGCTCTTTTGTTCTAAATTTTATCTCTATTGTCCCTTCTGGCTCGAGCACATTTCCACGAGCTGTTTCATCAGCATACATTTCAACATAATCCGAATTTATCTGGCTGTCAACAACAACCCACGCTCCACCGCGCAGCTCTCCCATCATTGGGATGTACACAAACACTGGCTGACGATAGGTTCTCAGATTTTCTACTATAGTTGAACCTGCCTGAAGTATTCCTTCGAAAAGATCTCTCTGCCCACCTGAAAACCCTCTCCAGTTCGCTAGGATAAACAATGGAAGCTCTTCCCGGTTGAAATCCATAAGTGCTTGAGCAGTCTTGGCCGCTGAATCAGGAAACCAGACTTGCCCTGCTTGCGGAACCACTCTTTCATGAGAGTCAAGCTGTCCAGGATCGGCTGGGATGATCTGCATGACAGTCTGTGTCTCAACTGCAACAACTCCAACGGGTATTCCCCCGAGCTTGGCTCTACCAGTCACTACCGTCCTTGCCCAGCCTTCAAGAGTCTCAATGAAACTATTTTTATCAAAGATACCTCCAAGCCATTTACCGGTATTGTCTTTGACCCCAGCTATAGCCGCTCGTGGGTCGCAAGAGTTCTCTGGGACATACTCCACAATTCTCTCCGGTGGATCTAAAGGGGCAAGAACAGGAAGAGGACCACCCACGTAAGCAGGAATGTAGCTGAGCCAGTTGAGAATTGCTGATACGCCTTCAAGATCATCTGAGACTGTAAGATGAACAACACCATTTGTGCCCATGATTTTCGGGCCACCCAGTTGCATGTGAGAGCTATAGACCTCACGCCCAAGTAACTTGTTGAGTGTAGAGAAGCCAGTCAAGATGATCGGCTGATCAAGTCTCTGTATGCACCGCATACCTAGGCGGGCAAGATAAGCACCAATTCCAACCGTTCTTCCACTAACAAAGGTTAAAGTAAAAGTTTCATTGTATGCCTTTGAGTAAGCACCCGCTATGGCCCCACTTCCTGTTAAGTTCTCTACACCAATACCATCTTCTTTGCCAACGATCGTATCAATCACCCACCTAGTTTCCCCACTAGGGAGCTTTACTTCATGGGCAATGACAGATGATCCAATCCTTTCGTGGTCTTCAGGGCTTAGGTATATATACTGAAAACCATTCTCAGGGGAAATTTCATCCGACCATCCAACTTTGAAGCAGGCTTTGACTTCTTCAGCAACCCCAAGTCGGGCACCAGAATTTGCTGCCAAGTAAATCAAGGGAAGCTTCTTGGCACAAGCGAGTTCAGTAACAGCAAGGAAAAACGCGTCCTCTCTAGGACCAAAAGAACCAGCTTTGAAGGTGACATCATTCGCAATCACGAGAAGTTTCCGCCCCATAGGAAACTCTGGGGTCGACATATCTAGGCACCAGGCAACCATTCCAAAGTCGTTGAGACCGGGTGGTCTTTCAACCAGATCTAGAGATGTACCCGAAGAACCTTCTGGTTTTGAGAATACAAGCTCTTTAACATTGATCAGAGTATCCTTATATGGTTTCTTAACTCCTGGGTGTTGTGATGCCCACAACAGTTCCAAGGCTGTCCCAAATGCCAACGGGAAGTCATAGCAATAAGTAGTGTTACTCCTCCTTGCTGCTAAACGTTGCCTGTCGAGATATCCCAGGGGCTTATATTGATCACTGATTGGGGTTTCATGCAAAGGTCCCTTCTTGGTTATTGAGTGGTAGATTAAACTGTTTCTTCCAGGAGTTTCAACTTCTCGGTATATGTGGACAGTGCATGTACGGCCTGTCACGTTTGCAACCACAACCCTCCAAGCACCACATGCCAGTCCAGAGGACACCAACCACAGCCGCACTTCCCACTCGCACACGCCCAACCTATGCATTCTCACTCCAACAGATCTATGTATCTCTCGTGCTGCTTCTTCTAAGATCATTTCAACTGTAGTTTCTTCATCCTCCGCATTCACTTCAACTCTCCTGGGGAAAGGCACAAGATCATCTATCTGCTGCTCACGCAATATGCAAAGAAACATATGTGCGTGATCTGGTTTCATTGCAGCATTATGGGCATTCAGTTCCAGTTCCTCCATGGCATCCATCAAAGACCTCAGAACACATTTCGACGTAAACGCCATGGAGATCAGTGTTTGGCTAAGCTGCTTATCCTGCCCTTGCTGCAATATAAATCCATCGTTCATTGTAGCCTGTCGAACAAGAGATCTCAGGAACATCCTCTTGATTGGCACTGGCTTGTCTGTAACAGTATACAGATGCCATTGACGATCTCGAGAAGGCGTATATTGTATATTTGAGTATCCTTTCAGCTTATCCAACTCAAGGTAAATGGACAGAGGAGGTTCAAGATGACGCAGCAACGGCTCTTCTACATAATACTGTTTCTCCAACGACCAATGGAAAGAATGTCTCATGGGTGTTCGTCCTTCATCTCGCTGAATTATACAGCTGATTACACCAACACCGGCAGAACAGAGGCTTGAACTCACTTCTTCCTCTTTAAGAATTTTGGCCAACTTGTTTACTCTTTCCTGAGCTTGGTCTTCATCCCCACTGTCCTGAAGCAGACTCATCTGGTTGTTGATGCCCACAATAGCAATGTGCATCATATTGCCAGATAAAGGAGCTCCGGCAGTTTCATAGTCGTTGTGCTTTGTTTCTCTCAATGCTGCACTTATTATACTTGGAAGAAACTGCAAAGATTTGATTATAACCATAGCCCCCCATTTTCTCTTACTACGCTTCTCAACCAATCCTTTTTCAGATGTGTCGTGATCGTCTAAGCCAATGTTTTTTCTTTCCATATGCTCCTCTAGGAAATCCCAGGAAGCAAGAAGACCAGAACGGTGCCACTGCATCCTCACGCTATCTTTAACGACGTAGGGCTGGTATAATCTGCGAATATAAGTCTCAACAACCCGTCTTTGAAGTGTGTGATCGCTATGGTCAAATAGTCCCACGAGAGCGTCTTCAACAGCTAAAGATGCGCTTACAAGATCTTCTATTCTTTCATTAATGGCACTTTTCCTCTTGGGAGTATCCATATTTTCTCCGTCCTCTGTAAACATTTCTAACTCTGAAAGGCTTCTAGCAATGTTTGAACGAAGCTCACTTAGTTTGGTCTGTTCAAGTAATTGACTCGCCTTGAGCGCCAACTCAGAGTAGTTAGTATGGTTAAGTGTTGAGAATCGAATAAGTTTATCTCTGTAAGCAGCAGGATTAGGGTAAACAAGCTGCTCCATGAGCCGGAGAACGAGTTTGTTTTTGTTTTTTATGCCCTGGTGTGAGAGCACTATATCCACAATTTTCAACAGATCTTTCTTGTATAGCTGACGCATGCGTTCTATAACATCAGCCAGCATGTTATCATTGAATAATTCTTCTACTGATAGATATTCTTCAAAGAGAGAATGAACAATAACACGGGCATGACTTTCTCTACCACCTTCATAAGATTTTGCAAGGCTCATCAATGGTTCAATGAGCCTTTCAAGGGCACCTCTCTCTTTCTCATCACAAGAAGATAAATGTGCCTCAAGAATGCCTTTTAAAAGTTTGGCAGGGAAATCGGTGGTCAAAGAGTTTCTGGAAATACTCTCAAATTCCCTATACTTTGATTCTAGCATGTTCCTGAGATTTTTAGGTAGTCGTGTCGCCAGAACTGCAAAGCACTCTTGCCACTGAAGAAATGGGAGTTCAGGGCTATCAAGGCAATTAAGTAAGTCTTGAACAACCTCATCTACTTTATGCTCATAGCCAGCAAGAATCATGCGTGCAGCATTTAATGTTGCGGCACATCTCTGATGAACTCTACCGGATATTGCAGTTGGAAGCCCTAATCTTGGGAAACTTCCATGGAAGGGTTCGGCCTTTCTTACAGCAGAAGGATCATCAAGATCAAGATTGGCGATAAGTTCACCAGCCTGCATGGCTTGTCCTTCAGACATTTTAAAATGGATAACTCCTGAAGCAGGTGAAAGAAGTGGCATGCACATCTTCATGACCTCAACTTCGGCATAAGGCGTATCAGCGTCAATATTGCTGTTGTCAGAAACCAAATACCTCATCAACTTGCACGGTGTCTCAGCCATTAACTTTGATGGATCATGGTCATTCTGTAGCAAACAAGTTCTTCCATCAATGAGAAGACGAGTTCCTGCAGCTTCTTCCTCTGCATATATCACATGGCTTTTGCCATCCAACTGCATCAACAGACCTCCATCACGTAGAGTGTGTATTTCTGCTACCACTTCTGACTTGTTCATTCTTAGCCTGTAGGTTCCTGATCCACCCCGGACTACATCAATCGTATATTTACTTCCTTCAATATTCAGAGACACTTGAGAATGCACAAGAGATATATGCTTTGGGGGAATTTGCCCCTTTTCTAGATAGCCAACGTAATCCGAAACTACAGCAGAACTGGTCGTAGATGCTTTATAAAGAGCCCCACCGACTACAGAGAGATACCATGGAGGTCTCTCTGCTCTGACCCGCATAGCAATCCTACTGTCCAACCAACCAGTGTGTATTTTGTTTTCCCGGTAATCAGAAGCATGTAGAAGGTCGATCGTGTAGTCAACGTTAGTCCTAATTTCTCCACGGATCTGAATTTCTTTTAGCCCAAGAACCATATTCGCTATCGCCAGGGCTCTGGATTCCCCAAATGCAAAAACATGTCCAAACTGGGAATCCGAGAACTCGTGGATGCCTCCACCAGACTTGACAGAGAAGTACGCCCACACATTTGGCTTGCTCTTAAAACTCAACTCCTGAACTCTACCGCTGGTTGGTTTGAACCCGTCATCAGGATCCTCACTTGTCACACGTACAGCCACACAATGACCTTTTGGCCTTATAGATTGAGCTTTATCAAAATCAAAAGGGAAGGCTACAACAGATGTTTTTCGCCAAGAATCATAACCTCCACCATGTTCTATTCCATAGAACCGTCTTATCTCAGGGATTTGCCAGAGAGGAATTCCCATCCCCACAGCAACTTGGGCAGCAGGAAGATTTATCTCGGCAATCCACTCAGTGACAGGATGCTCAACCTGTAAGCGAGGGTTAAGCTCTAAGAAGTAGTACTCCCCAGTGTCCATACTGTAGAGATACTCAACAGTAGCAGCTCCAACATAGTTAACACTCTTAGCCAACCTTCTAGCTGCTTGTTCAAGTTTCTTGACAGTTTCTGGCGGAGCCACAGTAATTGGACCCTCCTCTATGATCTTTTGATGTCTTCTCTGGACGCTACAATCACGGCTATGCAGAGCTGAAACATTTCCATGCTTGTCACAGAGCAGCTGGACCTCTAGATGCCGACTCTGTGACGCAACCTTCATTATGAATATTGGTGAGCCTGGGACCTCACCCTGAACTTGCTTGAATAGAGCCCTAACCTCATCATCATTATGAACCTTCCTGATTCCTTTACCACCACCACCCCACGATGCTTTGATCATTGCTGGGTAACCGACAACTTGACAGCTAGCAATCGCTTCTTCAGTTGTGTAGACACATGCTTGCCGGTAGATCTCCTCTGGGATGGTTACCAAGTTGCTATTAGGAGGTATTTTAACATGGGAACCACTCCATGGCAGAGTGGGTACATCAGCAGCTTGTGCAATCAACGAAGAACCAATCTTATCTCCCAGTGCTGCCATTGAAGATGCTGGAGGACCAAGAAATATGATTCCTTTTGCATCTAGGGCATCAGGTAATTCGGGGTTTTCAGATGCATGACCCCAACCAGGCCAAACTGCATCCACGCGTGTTACTTCAGCCATCTCCACAATCAGCTGAACGTTAGCATAATTGTTATTGTTAGTTCCTCCGGGAACCTCAACAAACTGATCAGCGATTCTGATATGCTCCGCATTGATCCGCATGTCTTCAGGGGTTGCCATCCCCACCAACAATATGGCTTTTTCCGTACCAAATGTTTCATAAGCCCATGTTCTGACACTACGTATAAACTTCACAGCCGCCATTCCATTGTTAGCTATCAAAATACTATGGATCGGCCTTTTCCCTCTAAGTGCTTTA";
        System.out.println("Lengths: "+str1.length()+" "+str2.length());


        DNASequence target = new DNASequence(str1,
                AmbiguityDNACompoundSet.getDNACompoundSet());

        DNASequence query = new DNASequence(str2,
                AmbiguityDNACompoundSet.getDNACompoundSet());

        NeedlemanWunsch aligner = new NeedlemanWunsch(query, target, gap, matrix);

        System.out.println("getScore: " + aligner.getScore());
        System.out.println("getMaxScore: " + aligner.getMaxScore());
        System.out.println("getMinScore: " + aligner.getMinScore());
        System.out.println("getSimilarity: " + aligner.getSimilarity());
    }            
}

The output for that is:

Lengths: 6800 6700
getScore: 3440.0
getMaxScore: -31536.0
getMinScore: -13520.0
getSimilarity: -0.9413854351687388

Where it is clear that the max score is overflowing and the similarity value is then wrong.