Examples of UnifracSample

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

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            }


            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());
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Examples of edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample

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                    }
                });


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

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            }

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

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        int sampleCount = sampleCountMap.size();

        this.resetSamples();

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