本文整理汇总了Java中org.biojava3.core.sequence.compound.NucleotideCompound类的典型用法代码示例。如果您正苦于以下问题：Java NucleotideCompound类的具体用法？Java NucleotideCompound怎么用？Java NucleotideCompound使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
NucleotideCompound类属于org.biojava3.core.sequence.compound包，在下文中一共展示了NucleotideCompound类的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: filterFastaByLength
import org.biojava3.core.sequence.compound.NucleotideCompound; //导入依赖的package包/类
/**
* Filters a fasta file by length
*
* @param fastaIn the fasta file to filter
* @param fastaOut the filtered fasta file
* @param minLength the minimum contig length to keep
* @throws IOException
* @throws BioException
*/
public void filterFastaByLength(File fastaIn, File fastaOut, int minLength) throws IOException, BioException
{
FileWriter fw = new FileWriter(fastaOut.getAbsoluteFile());
String newLine = System.getProperty("line.separator");
FileInputStream inStream = new FileInputStream(fastaIn);
FastaReader<DNASequence, NucleotideCompound> fastaReader = new FastaReader<>(inStream,
new GenericFastaHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String, DNASequence> b = fastaReader.process();
for (Entry<String, DNASequence> entry : b.entrySet())
{
//System.out.println(entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString());
if (entry.getValue().getSequenceAsString().length() >= minLength)
{
fw.write(">" + entry.getValue().getOriginalHeader() + newLine + entry.getValue().getSequenceAsString() + newLine);
}
}
fw.close();
}
示例2: compareTwoFastaSequences
import org.biojava3.core.sequence.compound.NucleotideCompound; //导入依赖的package包/类
public Map<String, String[]> compareTwoFastaSequences(File seq1, File seq2) throws Exception
{
HashMap<String, String[]> snps = new HashMap<>();
LinkedHashMap<String, DNASequence> dna1 = FastaReaderHelper.readFastaDNASequence(seq1);
LinkedHashMap<String, DNASequence> dna2 = FastaReaderHelper.readFastaDNASequence(seq2);
for (Entry<String, DNASequence> entry : dna1.entrySet())
{
DNASequence dna1seq = entry.getValue();
//System.out.println(entry.getValue().getOriginalHeader() + "=" + entry.getValue().getSequenceAsString());
if (dna2.containsKey(entry.getValue().getOriginalHeader()))
{
DNASequence dna2seq = dna2.get(dna1seq.getOriginalHeader());
if (dna1seq.getLength() != dna2seq.getLength())
{
System.err.println("Can't compare " + entry.getValue().getOriginalHeader() + " as they are different sizes: " + dna1seq.getLength() + " and " + dna2seq.getLength());
}
else
{
Iterator it1 = dna1seq.iterator();
Iterator it2 = dna2seq.iterator();
int position = 1;
while (it1.hasNext())
{
NucleotideCompound nt1 = (NucleotideCompound) it1.next();
NucleotideCompound nt2 = (NucleotideCompound) it2.next();
//System.out.println("Comparing " +nt1.toString()+ " to "+nt2.toString());
if (!nt1.equalsIgnoreCase(nt2))
{
String loci = dna1seq.getOriginalHeader().concat(":").concat(Integer.toString(position));
System.out.println("Found " + loci + " " + nt1 + " in File 1 and " + nt2 + " in File 2");
String[] snpArray = new String[2];
snpArray[0] = nt1.toString();
snpArray[1] = nt2.toString();
//Arrays.sort(snpArray);
snps.put(loci, snpArray);
}
position++;
}
}
}
}
return snps;
}