Package edu.msu.cme.rdp.unifrac.UnifracTreeBuilder

Examples of edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample

107
108
109
110
111
112
113
114
115
116
117
            }


            if (leaves.contains(t.getTaxon().getTaxid())) {
                for (MCSample sample : t.getTaxon().getSamples()) {
                    UnifracSample unifracSample = new UnifracSample();
                    unifracSample.count = t.getTaxon().getCount(sample);
                    unifracSample.sample = sample;

                    if (!allSamplesMap.containsKey(sample)) {
                        allSamplesMap.put(sample, new ArrayList());
View Full Code Here
76
77
78
79
80
81
82
83
84
85
86
                    }
                });


        for (String seqName : sampleMap.keySet()) {
            UnifracSample sample = sampleMap.get(seqName);
            Integer taxid = builder.getTaxidByName(seqName);
            if (taxid == null) {
                System.err.println("Couldn't find " + seqName + " in the tree");
                continue;
            }
View Full Code Here
140
141
142
143
144
145
146
147
148
149
150
            }

            if(!sampleMap.containsKey(sampleName))
                sampleMap.put(sampleName, new MCSample(sampleName));

            UnifracSample unifracSample = new UnifracSample();
            unifracSample.sample = sampleMap.get(sampleName);
            unifracSample.count = sampleCount;

            ret.put(seqName, unifracSample);
View Full Code Here
78
79
80
81
82
83
84
85
86
        int sampleCount = sampleCountMap.size();

        this.resetSamples();

        for(int index = 0;index < sampleCount;index++) {
            UnifracSample sample = samplePool.remove(0);
            this.addSampleCount(sample.sample, sample.count);
        }
    }
View Full Code Here
TOP

Related Classes of edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample

  • edu.msu.cme.rdp.taxatree.UnifracTree
  • edu.msu.cme.rdp.unifrac.Unifrac
  • edu.msu.cme.rdp.unifrac.UnifracTaxon
    • 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.