Package edu.msu.cme.rdp.multicompare.visitors

Examples of edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor

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        options.addOption(new Option(CmdOptions.METADATA_SHORT_OPT, CmdOptions.METADATA_LONG_OPT, true, CmdOptions.METADATA_DESC));
    }
  

    public static void printResults(ConcretRoot<MCTaxon> root, List<MCSample> samples, PrintStream heirOut, PrintStream bootstrapOut) throws IOException {
        DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(heirOut, samples);
        root.topDownVisit(printVisitor);
        for (MCSample sample : samples) {
            MCSamplePrintUtil.printBootstrapCountTable(bootstrapOut, sample);
        }
    }
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        MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
        MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format, min_bootstrap_words);
        assign_out.close();
        if ( hier_out != null){
            DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, samples);
            result.getRoot().topDownVisit(printVisitor);
            hier_out.close();
            if ( multiClassifier.hasCopyNumber()){
                // print copy number corrected counts
                File cn_corrected_s =  new File (hier_out_filename.getParentFile(), "cnadjusted_" + hier_out_filename.getName());
                PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
                printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
                result.getRoot().topDownVisit(printVisitor);
                cn_corrected_hier_out.close();
            }
        }
       
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            for ( int i = 1; i < args.length; i++){
                theObj.processOneHierFile(args[i]);
            }

            PrintStream hier_out = new PrintStream(outFile);
            DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, theObj.getResult().getSamples());
            theObj.getResult().getRoot().topDownVisit(printVisitor);
            hier_out.close();
        }catch (Exception ex){
            outFile.delete();
            throw ex;
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        if ( taxonFilterFile != null){
            taxonFilter = readTaxonFilterFile(taxonFilterFile);
        }
       
        MultiClassifier multiClassifier = new MultiClassifier(train_propfile, gene);
        DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(heir_out, samples);
        MultiClassifierResult result = multiClassifier.multiClassificationParser(samples, conf, assign_out, format, rank, taxonFilter);

        result.getRoot().topDownVisit(printVisitor);

        assign_out.close();
        heir_out.close();
        if ( multiClassifier.hasCopyNumber()){
            // print copy number corrected counts
            File cn_corrected_s =  new File (new File(hier_out_filename).getParentFile(), "cncorrected_" + hier_out_filename);
            PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
            printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
            result.getRoot().topDownVisit(printVisitor);
            cn_corrected_hier_out.close();
        }
       
    }
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Related Classes of edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor

  • edu.msu.cme.rdp.multicompare.Main
  • edu.msu.cme.rdp.multicompare.MergeTaxonCount
  • edu.msu.cme.rdp.multicompare.Reprocess
  • edu.msu.cme.rdp.multicompare.taxon.MCTaxon
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