private void setSequence(String sequence) { // Check for nulls if (sequence == null) { throw new IllegalArgumentException("'sequence' is null"); } // Remove white space and convert to lower-case sequence = WHITESPACE_PATTERN.matcher(sequence).replaceAll(""); sequence = sequence.toLowerCase(); // Check if (!SEQUENCE_PATTERN.matcher(sequence).matches()) { throw new IllegalArgumentException("'sequence' is not a nucleotide sequence [" + sequence + "]"); } this.sequence = sequence; List<String> chunks = CHUNKER.chunkIntoList(sequence); this.sequenceFirstChunk = CHUNKER.firstChunk(chunks); this.sequenceChunks = CHUNKER.latterChunks(chunks); }
private void setSequence(String sequence) { // Check for nulls if (sequence == null) { throw new IllegalArgumentException("'sequence' is null"); } // Remove white space and convert to upper case sequence = WHITESPACE_PATTERN.matcher(sequence).replaceAll(""); sequence = sequence.toUpperCase(); // Check amino acid if (!AMINO_ACID_PATTERN.matcher(sequence).matches()) { throw new IllegalArgumentException("'sequence' is not an amino acid sequence [" + sequence + "]"); } if (!AMINO_ACID_WITHOUT_ASTERIX_PATTERN.matcher(sequence).matches()) { throw new IllegalArgumentException("You have submitted a protein sequence which contains an asterix (*). This may be from an ORF prediction program. " + "'*' is not a valid IUPAC amino acid character and amino acid sequences which go through our pipeline should not contain it. Please strip out " + "all asterix characters from your sequence and resubmit your search."); } this.sequence = sequence; List<String> chunks = CHUNKER.chunkIntoList(sequence); this.sequenceFirstChunk = CHUNKER.firstChunk(chunks); this.sequenceChunks = CHUNKER.latterChunks(chunks); }
private void setDescription(String description) { this.description = description; List<String> chunks = CHUNKER.chunkIntoList(description); descriptionFirstChunk = CHUNKER.firstChunk(chunks); descriptionChunks = CHUNKER.latterChunks(chunks); }
private void setDescription(String description) { this.description = description; List<String> chunks = CHUNKER.chunkIntoList(description); descriptionFirstChunk = CHUNKER.firstChunk(chunks); descriptionChunks = CHUNKER.latterChunks(chunks); }
private void setException(String exception) { this.exception = exception; List<String> chunks = CHUNKER.chunkIntoList(exception); this.exceptionFirstChunk = CHUNKER.firstChunk(chunks); this.exceptionChunks = CHUNKER.latterChunks(chunks); }
private void setDefinition(String definition) { this.definition = definition; List<String> chunks = CHUNKER.chunkIntoList(definition); definitionFirstChunk = CHUNKER.firstChunk(chunks); definitionChunks = CHUNKER.latterChunks(chunks); }
private void setDescription(String description) { this.description = description; List<String> chunks = CHUNKER.chunkIntoList(description); descriptionFirstChunk = CHUNKER.firstChunk(chunks); descriptionChunks = CHUNKER.latterChunks(chunks); }
private void setAbstract(String text) { this.abstractText = text; List<String> chunks = CHUNKER.chunkIntoList(abstractText); abstractFirstChunk = CHUNKER.firstChunk(chunks); abstractChunks = CHUNKER.latterChunks(chunks); }
private void setAbstract(String text) { this.abstractText = text; List<String> chunks = CHUNKER.chunkIntoList(abstractText); abstractFirstChunk = CHUNKER.firstChunk(chunks); abstractChunks = CHUNKER.latterChunks(chunks); }