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

What do lines 51/52 really look like?
".. results nothing as an output" Nothing as in "", or null, or absolutely nothing happens (in which case is the CPU busy or idle)?

Sorry,

Corrected the code.

The output is some thing like

qwer :

This is the only part where I'm getting nothing, as rest of the result of the parser is as I'm expected.

If I change the length to 2000, it shows the characters upto 2000. If I change length to 12000, then again there is no result.


I think it has to do something with the datatype (may be)

Does it continue after the quer : or is that the end of the output? Is it possible that it's just running in Order(n^2) or worse time, and it will work eventually?

Arrays and String etc in Java are limited by the VM memory size - but if you were running out of memory you should get an Exception.

That is the end of the output. I don't see any exceptions and also the result as well.

Surprisingly, the parser is going to the next element in no time.

To be honest, I'm no expert on SAX, but I#m having a quiet afternoon, and nobody else is answering, so...

I found a number of notes like this one re SAX:

The characters method can be called multiple times for a single tag, and you have to collect the characters across the multiple calls rather than expecting them all to arrive at once.

You code seems to assume a single callback, because it resets the bgenomeSequence flag on the first callback. I think you should only reset bgenomeSequence when you get the corresponding endElement call, and allow for multiple characters callbacks inbetween.

To be honest, I'm no expert on SAX, but I#m having a quiet afternoon, and nobody else is answering, so...

I found a number of notes like this one re SAX:


You code seems to assume a single callback, because it resets the bgenomeSequence flag on the first callback. I think you should only reset bgenomeSequence when you get the corresponding endElement call, and allow for multiple characters callbacks inbetween.

thanks, will try it. Just in case if somebody want to have a detailed look how the xml file appears, here it is

http://www.4shared.com/folder/8jRp_m3n/_online.html

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