Examples of org.broad.igv.feature.tribble.IGVBEDCodec.encode()

Class org.broad.igv.feature.tribble.IGVBEDCodec

Examples of org.broad.igv.feature.tribble.IGVBEDCodec.encode()

org.broad.igv.feature.tribble.IGVBEDCodec.encode()
Encode a feature as a BED string. @param feature - feature to encode @return the encoded string


        int allNumCols = -1;
        if (features != null) {
            IGVBEDCodec codec = new IGVBEDCodec();
            while (features.hasNext()) {
                String data = codec.encode(features.next());


                writer.println(data);


                //We require consistency of output
                int tmpNumCols = data.split("\t").length;

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            pw = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
            pw.println("#gffTags");
            for(Feature feature : features) {


                BasicFeature bf = (BasicFeature) feature;
                String line = codec.encode(bf);
                pw.println(line);
            }




        } catch (IOException e) {

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        }
        try {
            reader = ParsingUtils.openBufferedReader(ifile);
            List<Feature> features = parser.loadFeatures(reader, null, codec);
            for (Feature feat : features) {
                String encoded = outCodec.encode(feat);
                outStream.print(encoded);
                outStream.print('\n');
            }
        } catch (IOException e) {
            log.error(e.getMessage(), e);

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                List<Feature> features = fTrack.getFeatures(range.getChr(), range.getStart(), range.getEnd());
                Predicate<Feature> pred = FeatureUtils.getOverlapPredicate(range.getChr(), range.getStart(), range.getEnd());
                features = CollUtils.filter(features, pred);
                IGVBEDCodec codec = new IGVBEDCodec();
                for (Feature feat : features) {
                    String featString = codec.encode(feat);
                    writer.println(featString);
                }
            }
        }
        writer.flush();

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            }


            for (List<BasicFeature> geneList : genes.values()) {
                for (BasicFeature gene : geneList) {
                    pw.println(codec.encode(gene));
                }
            }
        } finally {
            if (br != null) br.close();
            if (pw != null) pw.close();

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