/** @throws Exception */
public void process() throws Exception {
byte[] lineSep = System.getProperty("line.separator").getBytes();
for (GeneSequence sequence : sequences) {
String header = headerFormat.getHeader(sequence);
os.write('>');
os.write(header.getBytes());
os.write(lineSep);
int compoundCount = 0;
String seq = "";
// GeneSequence currently has a strand attribute to indicate direction
seq = sequence.getSequence5PrimeTo3Prime().getSequenceAsString();
if (showExonUppercase) {
StringBuilder sb = new StringBuilder(seq.toLowerCase());
int geneBioBegin = sequence.getBioBegin();
int geneBioEnd = sequence.getBioEnd();
for (ExonSequence exonSequence : sequence.getExonSequences()) {
int featureBioBegin = 0;
int featureBioEnd = 0;
if (sequence.getStrand() != Strand.NEGATIVE) {
featureBioBegin = exonSequence.getBioBegin() - geneBioBegin;
featureBioEnd = exonSequence.getBioEnd() - geneBioBegin;
} else {
featureBioBegin = geneBioEnd - exonSequence.getBioEnd();
featureBioEnd = geneBioEnd - exonSequence.getBioBegin();
}
if (featureBioBegin < 0
|| featureBioEnd < 0
|| featureBioEnd > sb.length()
|| featureBioBegin > sb.length()) {
System.out.println(
"Bad Feature "
+ sequence.getAccession().toString()
+ " "
+ sequence.getStrand()
+ " "
+ geneBioBegin
+ " "
+ geneBioEnd
+ " "
+ exonSequence.getBioBegin()
+ " "
+ exonSequence.getBioEnd());
} else {
for (int i = featureBioBegin; i <= featureBioEnd; i++) {
char ch = sb.charAt(i);
// probably not the fastest but the safest way if language is not standard ASCII
String temp = ch + "";
ch = temp.toUpperCase().charAt(0);
sb.setCharAt(i, ch);
}
}
}
seq = sb.toString();
}
for (int i = 0; i < seq.length(); i++) {
os.write(seq.charAt(i));
compoundCount++;
if (compoundCount == lineLength) {
os.write(lineSep);
compoundCount = 0;
}
}
// If we had sequence which was a reciprocal of line length
// then don't write the line terminator as this has already written
// it
if ((sequence.getLength() % getLineLength()) != 0) {
os.write(lineSep);
}
}
}
