@@ -132,38 +132,6 @@ public void process() throws Exception {
132132
133133 }
134134
135- /*
136- * public static void main(String[] args) { try { FileInputStream is = new
137- * FileInputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds.faa");
138- *
139- *
140- * FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new
141- * FastaReader<ProteinSequence, AminoAcidCompound>(is, new
142- * GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new
143- * ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
144- * LinkedHashMap<String, ProteinSequence> proteinSequences =
145- * fastaReader.process(); is.close();
146- *
147- *
148- * // System.out.println(proteinSequences);
149- *
150- * FileOutputStream fileOutputStream = new
151- * FileOutputStream("/Users/Scooter/scripps/dyadic/c1-454Scaffolds_temp.faa"
152- * );
153- *
154- * BufferedOutputStream bo = new BufferedOutputStream(fileOutputStream);
155- * long start = System.currentTimeMillis(); FastaWriter<ProteinSequence,
156- * AminoAcidCompound> fastaWriter = new FastaWriter<ProteinSequence,
157- * AminoAcidCompound>(bo, proteinSequences.values(), new
158- * GenericFastaHeaderFormat<ProteinSequence, AminoAcidCompound>());
159- * fastaWriter.process(); bo.close(); long end = System.currentTimeMillis();
160- * System.out.println("Took " + (end - start) + " seconds");
161- *
162- * fileOutputStream.close();
163- *
164- *
165- * } catch (Exception e) { e.printStackTrace(); } }
166- */
167135 /**
168136 * @return the lineLength
169137 */
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