Package fork.lib.base.file.io.txt

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

47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
        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];
View Full Code Here
31
32
33
34
35
36
37
38
39
40
41
    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")){
View Full Code Here
25
26
27
28
29
30
31
32
33
34
35
   
   
   
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();
}
View Full Code Here
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
    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++){
View Full Code Here
TOP

Related Classes of fork.lib.base.file.io.txt.MarkEntry

  • common.inspect.ClassifierList
  • data.cerevisiae.histmod.cai2011.ToWig
  • data.cerevisiae.tfpwm.BadisToLandscape
  • data.cerevisiae.tfpwm.ZhuToLandscape
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.