Examples of nextEntry()

Examples of com.orientechnologies.orient.core.index.OIndexCursor.nextEntry()

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    long lastTs = 0;
    long minLostTs = Long.MAX_VALUE;

    long restoredRecords = 0;

    Map.Entry<Object, OIdentifiable> entry = cursor.nextEntry();
    while (entry != null) {
      ODatabaseRecordThreadLocal.INSTANCE.set(baseDocumentTx);
      Integer key = (Integer) entry.getKey();

      OIdentifiable identifiable = entry.getValue();
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Examples of com.zwl.util.zip.impl.ZipFileEntryInputStream.nextEntry()

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      UnsupportedEncodingException {
    ZipFileEntryInputStream zfe = new ZipFileEntryInputStream(inFile);
    Enumeration<? extends ZipEntry> en = inFile.entries();
    while (en.hasMoreElements()) {
      ZipEntry ze = en.nextElement();
      zfe.nextEntry(ze);
      add(ze, zfe, password);
    }
    zfe.close();
  }
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Examples of fork.lib.base.file.io.txt.MarkReader.nextEntry()

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    MarkReader mr= new MarkReader(f, "variableStep");
    MarkEntry en;
    LandscapeBuilder lb= new LandscapeBuilder();
    while((en=mr.nextEntry())!=null){
        String chr= en.tit.split("chrom=")[1].split("\t")[0];
       
        if(!chr.equals("chrM")){
            ArrayList<String> rs= en.chunk;
            int ps= 1;
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Examples of fork.lib.base.file.io.txt.MarkReader.nextEntry()

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protected void init() throws Exception{
    MarkReader mr= new MarkReader(file,">");
    MarkEntry en;
    while((en=mr.nextEntry())!=null){
        sets.add( new GeneSet(en.getChunk(), en.getTitle()) );
    }
    mr.close();
}
   
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Examples of fork.lib.base.file.io.txt.MarkReader.nextEntry()

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    MarkReader ff= new MarkReader(f,">");
    MarkEntry en;
   
    while( (en=ff.nextEntry())!=null ){
        String nm= en.getTitle().split("_TRH1")[0];
        NamedTable<Character,Integer,Double> tab= new NamedTable<>();
        ArrayList<String> ch= en.getChunk();
        for(int i=1; i<ch.size() ; i++){
            String[] ss= ch.get(i).split("\t");
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Examples of fork.lib.bio.seq.FastaReader.nextEntry()

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    FrequencyCount<String> fcg= new FrequencyCount();
    FastaReader frg= new FastaReader(genomef);
    FastaEntry eng;
    while( (eng=frg.nextEntry())!=null ){
        String s= eng.getSequence();
        for( int i=0; i<s.length()-size; i++ ){
            String ss= s.substring(i, i+size);
            fcg.add(ss);
        }
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Examples of fork.lib.bio.seq.FastaReader.nextEntry()

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            FastaReader fr= new FastaReader(f);
            FastaEntry en;
            FrequencyCount<String> fc= new FrequencyCount<>();


            while( (en=fr.nextEntry())!=null ){
                String s= en.getSequence();
                for( int i=0; i<s.length()-size; i++ ){
                    String ss= s.substring(i, i+size);
                    fc.add(ss);
                }
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Examples of fork.lib.bio.seq.FastaReader.nextEntry()

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    File gen= new File(dir+"/anno/genomes/sacCer1/sacCer1.fa");
    FastaReader fr= new FastaReader(gen);
    BufferedWriter bw= new BufferedWriter(new FileWriter(new File(dir+"/anno/sacCer1_chr.bed")));
    FastaEntry en;
    while( (en=fr.nextEntry())!=null ){
        String chr= en.getTitle();
        int l= en.getSequence().length();
        bw.write(chr+"\t0\t"+l+"\t"+chr+"\t0\t+\n");
    }
    bw.close();
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Examples of fork.lib.bio.seq.FastaSequenceExtractor.nextEntry()

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    BufferedWriter bw= new BufferedWriter(new FileWriter(out));
    BedGraphExporter.writeTitle(bw, tit);
   
    FastaSequenceExtractor se= new FastaSequenceExtractor(gen, gbout);
    SequenceExtractorEntry en;
    while( (en= se.nextEntry())!=null ){
        GenomicRegion gr= en.getGenomicRegion();
        NucleotideSequence seq= NucleotideSequenceParser.parseSequence(en.getSequence());
        double at= seq.atContent();
        bw.write( gr.toBedFormat()+"\t"+ ((double)Math.round(at*100)/100)+"\n" );
    }
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Examples of fork.lib.bio.seq.FastaSequenceExtractor.nextEntry()

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protected void init() throws Exception{
    GenomicRegionsBuilder gb= new BedReader(f).getGenomicRegionsBuilder();
    FastaSequenceExtractor se= new FastaSequenceExtractor(sf, gb);
    SequenceExtractorEntry en;
    while((en=se.nextEntry())!=null){
        GenomicRegion reg= en.getGenomicRegion();
        String seq= en.getSequence();
        String id= reg.getID();
        idseq.put(id , seq);
        tab.appendEmptyRow(id);
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