Examples of param()

Examples of fork.lib.bio.anno.genomic.BedExporter.param()

114
115
116
117
118
119
120
121
122
123
124
        protected String column6On(GenomicRegion gr){
            Object[] os= (Object[])gr.attr;
            return (Double)os[1]+"\t"+ (Double)os[2];
        }
    };
    be.param().ifExpanded= true;
    be.writeToFile(out);
}


View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

61
62
63
64
65
66
67
68
69
70
71
        }
    }
   
   
    BedGraphExporter be =new BedGraphExporter(lb);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
   
   
}
View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

33
34
35
36
37
38
39
40
41
42
43
   
    Distribution dnz= lb.getDistributionNonZero();
    double nf= dnz.sum()/ 100000000;
    new LandscapeTransformer(lb).divideBy(nf);
    BedGraphExporter be= new BedGraphExporter(lb);
    be.param().tit= tit;
    be.writeToFile(f);
}
   
   
   
View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

40
41
42
43
44
45
46
47
48
49
50
}

protected void write(ArrayList<String> ids, ArrayList<Double> vs, File f,String std, String tag)throws Exception{
    ProbeMapperStrand pp= new ProbeMapperStrand(anno, probe, std);
    BedGraphExporter be= new BedGraphExporter(pp.toLandscapeBuilder(ids, vs));
    be.param().tit= tag+"_"+std;
    be.writeToFile(f);
}


View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

64
65
66
67
68
69
70
71
72
73
74
        }
    }
   
   
    BedGraphExporter be =new BedGraphExporter(lb);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
   
   
}
View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

54
55
56
57
58
59
60
61
62
63
64
            }
        }
    }
   
    BedGraphExporter be= new BedGraphExporter(lbout);
    be.param().tit= FileName.getBaseName(out);
    be.writeToFile(out);
}
   
   
View Full Code Here

Examples of fork.lib.bio.anno.genomic.BedGraphExporter.param()

105
106
107
108
109
110
111
112
113
114
115
                    }
                }
            }
        }
    };
    be.param().tit= tit;
    be.writeToFile(of);
}
   

public static void toRatio(File f, File ref, File out) throws Exception{
View Full Code Here

Examples of fork.lib.bio.anno.genomic.PeakIdentifier.param()

29
30
31
32
33
34
35
36
37
38
39
    }
   
   
public void writeToFile(File out)throws Exception {
    PeakIdentifier pi= new PeakIdentifier(lb, null);
    pi.param().joinGap=150;
    GenomicRegionsBuilder gb= pi.getPeaks();
    new BedExporter(gb).writeToFile(out);
}
   
   
View Full Code Here

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsMerger.param()

33
34
35
36
37
38
39
40
41
42
43
    File d= new File(dir+"/data/human_magnus/h2az/macs");
    File od= new File(d+"/merge");
    File out= new File(od+"/merge.bed");
   
    GenomicRegionsMerger mer= new GenomicRegionsMerger();
    mer.param().gap= 1000;
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
View Full Code Here

Examples of fork.lib.bio.anno.genomic.region.GenomicRegionsMerger.param()

27
28
29
30
31
32
33
34
35
36
37
    File dir= Dirs.getFile("dir");
    File d= new File(dir+"/data/human_magnus/h2az/norm/peak/novel");
    File out= new File(d+"/merge.bed");
   
    GenomicRegionsMerger mer= new GenomicRegionsMerger();
    mer.param().gap= 1000;
    File[] fs= d.listFiles();
    for( int i=0; i<fs.length; i++ ){
        File f= fs[i];
        if(FileName.getExt(f).equals("bed") && !f.getName().equals(out.getName()) ){
            System.out.println(f);
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. 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.