Examples of MarkEntry

Examples of fork.lib.base.file.io.txt.MarkEntry

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        this.pwm=pwm;
    }
}

public PWMEntry nextEntry() throws Exception{
    MarkEntry en= mr.nextEntry();
    if(en==null){
        return null;
    }
    String tit= en.getTitle().split("-primary")[0].toUpperCase();
    NamedTable<Character,Integer,Double> tab= new NamedTable<>();
    ArrayList<String> ch= en.getChunk();
    char[] rs= new char[]{'A','C','G','T'};

    for(int i=0; i<ch.size() ; i++){
        String[] ss= ch.get(i).split("\t");
        Character row= rs[i];
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Examples of fork.lib.base.file.io.txt.MarkEntry

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    File f= new File(d+"/GSM711896.wig"), out=new File(d+"/h3k9ac_cai2011.wig");
   
   
   
    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")){
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Examples of fork.lib.base.file.io.txt.MarkEntry

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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.MarkEntry

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    File f= new File(dir+"/data/tf/badis_2008_tf.txt");
    File od= new File(dir+"/data/tf/"+FileName.getBaseName(f));
   
   
    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");
            Character row = ss[0].charAt(0);
            tab.appendEmptyRow(row);
            for(int j=1; j<ss.length ; j++){
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