Hi all,
I'm currently using SAX to parse an xml file. Recenlty I have encountered a problem where, one of the element consist of more than 50,000 characters (a DNA sequence ) and the SAX results nothing as an output.
The code which I'm using is
public void getCommand() {
try {
// open file dialogue
JFrame frame = null;
String filename = File.separator+"tmp";
JFileChooser fc = new JFileChooser(new File(filename));
// Show open dialog; this method does not return until the dialog is closed
fc.showOpenDialog(frame);
File selFile = fc.getSelectedFile();
selFile = fc.getSelectedFile();
f = selFile.toString();
String tempFile = f;
// end file dialogue
//System.exit (0);
SAXParserFactory factory = SAXParserFactory.newInstance();
SAXParser saxParser = factory.newSAXParser();
DefaultHandler handler = new DefaultHandler() {
boolean bgenomeSequence = false;
public void startElement(String uri, String localName,String qName,
Attributes attributes) throws SAXException {
if (qName.equalsIgnoreCase("qwer")) {
bgenomeSequence = true;
}
}
public void endElement(String uri, String localName,
String qName) throws SAXException {
// System.out.println("End Element :" + qName);
}
public void characters(char ch[], int start, long length) throws SAXException {
if (bgenomeSequence) {
System.out.println("qwer : " + new String(ch, start, int(length)));
bgenomeSequence = false;
}
}
};
saxParser.parse(""+tempFile+"", handler);
} catch (Exception e) {
e.printStackTrace();
}
}The sample xml file where I'm encountering error,
<sequence123>
<source id="1">
<label>input sequence1</label>
<qwer>gatcggcaggatcagctcgagcacatcatcagccacccgggggccctgatcggcttctcggacgcgggggcacacctgcggcagatggcgcactacaatttcccgctgcgtatgctcttccgggtccaggaggcggcgcgggagggacgagaggtcatgcccatcgagcgcgcgatctggcgcctcacgggcgagctgggcgattggttcggaatcgcggcggggacactcgcaccggggcggcaggccgacgtggtggtgctcgatccggcgggcatcgatggtgcggtggagaaggtgcacgaggagcccatggagggcttctccggcatggtgcggctggtgcgtcgaaacccgcgggccgtgcgcgcggtgctcgtgaacgggaacctcgcggtgcgtgatggcgaggtgctccccgatgtcggcaagcgcccgggcttcgggcggctgctgcgcgcgcaggaaacccgtggcacaagggcttgaggctgccgcgcagacgatgtgtctgtaagaagtgccttgcagtgaaaagaaatcctcgcgctcgcgttcgctgcggtggagcggatcggacgcctgacggtacgatgccacacctgcggctgcgcccgatctgccgtgcggggccgtcgtcaccggggaacgaatccatgctcgtgcgccgcaccctgccgttcatcgccctctcgtcgaccctctggcttctgggctgcggtgaagtgcgggtcgtcgacgccaggtccggtgagcaggacgaccacgtccccccgtcgcccccctctggcccctgccagctgacgttcgcgttgcccttcggcggcgtgggtaggggactcgaggtctcgaacgatggccgcaccgtgagcagcttgagcgccaccgagatgctgcaggggagcgtcggacgggtagggggacggtggtacttcgaggtcaccgtcgacaccttggccgacggcgtgtggtgggctcagaacatcggcatcggcacgcccgacgggattcgcacgatgggaggcagcagcgggggactgagcgcgctcctcaacagcggggggagcctgatgcccggtttcggctcacccgagcccttcttcggtgaggccttcggtacgggagacgtcatcggggtggcagccgatctggacgaagggcgcgtctttttcagcaggaatggcgtctggctgaacgcaggcgatccgctccaggggacgagaggtgtgccgatcatcgtgctgcctggcgtcgacgcctactacccggcggtcggggtctccgagggcgacacgctgaccatcaacctgagcggcgacttcgtgcatgcgataccagcgggctatgcccccttcgccgccggcctcaccggcgatgaagacgggcactgcatcgacgtcggcgccggtggaatgccagcatctccagcgcccgtgcaggcgacctgctcggcggcctacgagttcacgagttacgcagctccccagggcagcggcgaagagctacacgtcgtcggcatctacgagccttccacgggcgtaggcggacaggtcgacgtccacatcgaacgctcgggagacatgacgctggccctcacggcctacgtggcgacatcgttccgtgtgacggtcgcccccggggcaaacctcgggcgcatcgttctttcgagctacgaaccctcctccgtcgacgcgcctctcggcgtcacggtgagcagccatgtcttcgagggcaatggccgctacctgggagggggattcgaatggccctcttcggagacgagcgaactgatctccgccgtggaagaggagaccgagctgaagctgagcagcttcagtggttgctatgcgggaagccaattcacgctgaccaactgagtggctcgcttcgcgtggagagattcgttgggcgtccttcacgacaggaggacgggagggcgtcacggtcgtcctggtcacggcgtgctgataacagaacccattcgcagaccatgagtgccagggggtcatcgattcgcttgctgggtgcccgcgagatccgcctgggcaagcggttggatgcaatgttgacactgggaccggggggaagtagcaactggcggattgcagcatacctgcaagcgatggcgccctgcttcatcggcatggaacgagaacctggcacgcggccgcgtcctgttcgcgcgcagcgcaccggcgggcagggcgtcggggaggcttcgtcgaggaggagcgttcaccggaacgcagaaaaggagctacgtggagacccaccatgatccgtttccggtggtgtgggacgaccccgatgacgctcaggccttctgggtcgtcaacgtcgtccactgccctgcgccgatgagccgtctcgatttcgacctgcgcatgcgcccgatgctgcgcgggaccaatcgggtttacgagcactacggggtccccatccggctggctccgacgttgatccacgggttcgtctaccagaagctcatcagcctggaggtcacggccgatgagctccctgccatcctgagccgggccgacgcggcagtgcgtcacactggaaccgatctcgagggcgcctgggagcgccgctggctgccggagatcaagtcccatctcgctcacctctcggcattcgatctgagcggcgcaccgctgcctgtgctcctcgagcatctcgtggatgtggagcagcggatggagcgcctctggcagctgcacacggagctgctcacgccggtgctcgtcgcgctgaacgacttcgacgagatgtaccgtgacctctttccggaggcgaagccgctcgaggtgtatcagctgctctcgggctttcccaacaagaccgtcgaggcaaacctccgcctgtgggatctgggacgacgagcggcgcagaccccctcccttcgcactctcctcgcgcgggatctgggcgggagacggacggaggcccccgagcgcaccacggccgacgtgctcgccgcactctcggagttccccgaaggacgcgcgttgctgcaggacatcgaggcctacgtcggcacgtatggcgagcgcaatgatgacctctacatcgatcgtcccacgtggatcgaggacaccacacctgtgctgaatggactgcgtgaggctgtcgcgcaggccgatcgggacctcgctggtgaactccagcgccaggcggagcagcgagagacacggctgagcgaggtgcggtcgcggctcgcatccctccctcgtccggtggtggacgagttcgacgcactcctgaaagcggcccagacggcgacggtgctgagcgaggagcaccacttctggatcgactgcaagatcacctaccacgccaggcgggtgggcctggagctgggcaggcgcctcgcgcaacgtggcttgctggagcgcgccgaagacgtgttccagttgacgctcgcagaactggtggctcgccagcatgccccgctcgaagacgctccactgaaggtgctggtcgccgagcgtgaagccgagagggcccgctcttcaggggtcacgcctcctccctttctcggcgttccacggcccatcttgccgatggactgcgcgatcatgcgcgcaggattcaagttcaacggaggcccgatggggccccccagtgcgggcgatctccggggaatgccgggttccagcgggacggtgcgcggccctgtacggatcgtgcgcacccagagggacgccgactcgctccggccaaacgacatcctcgtcgccccgttcacgctgccttcctggacgccctatttcgcgagcgtggcaggggtggtcaccaacatcggcggcaccttgtgccacgcggccgtcgtcgcgcgggagtacggcattcccgccgtcgtcggcacgcagacggcgaccgagacgctccgtgatggtcagctcgtcgaggtcgacggagacgcgggtatcgtccgtgtgctgagttcgtgaggtcgagtttttcatgagagacatgacggcgtcgggcctgaaggcgtggcttgtcgcccgtgtcgcggcgatcagcgggagcgatcctcaccagattgatgcccggcagcggttcggacgccacggaatcgactcgttgcatgcgacccggctcatcgcggagctgtccacgcgcctggagcgatcgctctcaccgacactgatctgggagtacccgaccatcgaggcactcgcagcgcatctcggcggcgagacgcaacgcatcgaggaagcgagcgtgggcgctggagaaatcggcgcagcgacgtacggggccggcgagcccattgcgatcgtgggaatggcttgccgcttccctggcgcacctgacgaggcgtcgttctgggacctcctccgtgacggcgtggacgcggtcggtgtcgtgccgtccgaccgaggctgggacgaagcgctcgttgcagccggtgtcgatcgggcagagcgggacaaggtgcgacgcggtgccttcctggaccgggtcgacgcattcgatcccttcttcttcggcatctcccctcgggaggcgatgtcgatggatccgcagcaacggctgatgctcgagctgtgctgggaggcgctggagagagcaggaattccgccacgcttgctcgcgggcagcccggcaggcgtcttcgccggggccatctggtccgactacgaggccctcatgtaccgcggcgcagcaggtgcgctggatcagtatgcggtgacgggggcgcaccacagcatcatcgccaaccgcatctcgtacctcctcggcctccaggggccgagcctttccgtcgacacggcttgctcctcggggctcgtggtcgtgcacctcgcttgcgagagcttgcgccgcggcgagtgcaatgtggccctggcaggagccgtgaacctcaacctgctgccggagagcgccgtcgccatggcacgcttcggcgcgctctcaccggacggacgttgctataccttcgatggccgcgcgaacggctacgttcgcggggagggggcaggcgt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</source>
</sequence123>It would be really helpful if some gives an idea how to read this.
thanks a lot
