Loading data - Revision history

Keilwagen at 13:46, 2 December 2009

2009-12-02T13:46:13Z

← Older revision		Revision as of 13:46, 2 December 2009
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	'''~~Loading~~ DNA-sequences from a ~~plain text~~ file:'''		'''Most simple way for loading DNA-sequences from a FastA file:'''
	<source lang="java5">		<source lang="java5">
	//create a DNA-alphabet		Sample data = new DNASample( home+"myfile.fa" );
			</source>

			'''Loading DNA-sequences from a FastA file:'''
			<source lang="java5">//create a DNA-alphabet
	AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );		AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );

	//create a Sample using the alphabet from above		//create a Sample using the alphabet from above in FastA-format
	~~Sample~~ data = new Sample( container, new ~~StringExtractor( new File~~("myfile.~~txt~~"), ~~100~~ ) );		data = new Sample( container, new SparseStringExtractor( home+"myfile.fa", StringExtractor.FASTA ));
	</source>		</source>

			'''Loading DNA-sequences from a plain text file:'''
	'''Loading DNA-sequences from a ~~FastA~~ file:'''
	<source lang="java5">		<source lang="java5">
	//create a DNA-alphabet		//create a DNA-alphabet
	AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );		AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );

	//create a Sample using the alphabet from above ~~in FastA-format~~		//create a Sample using the alphabet from above
	~~Sample~~ data = new Sample( container, new ~~StringExtractor( new File~~("myfile.txt"~~), 100, StringExtractor.FASTA~~ ) );		data = new Sample( container, new SparseStringExtractor( home+"myfile.txt" ));
	</source>		</source>

Grau at 09:29, 29 October 2008

2008-10-29T09:29:20Z

← Older revision		Revision as of 09:29, 29 October 2008
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	<source lang="java5">		<source lang="java5">
	//defining the ids, we want to obtain from NCBI Genbank:		//defining the ids, we want to obtain from NCBI Genbank:
	~~Set<String> ids~~ = new ~~HashSet<String>~~();		GenbankRichSequenceDB db = new GenbankRichSequenceDB();
	~~ids.add( "NC_003070" );~~
	~~ids.add( "NC_003071"~~ );

	~~GenbankRichSequenceDB db~~ = new ~~GenbankRichSequenceDB~~();		SimpleSequenceIterator it = new SimpleSequenceIterator(
	~~RichSequenceDB db2 =~~ db.~~getRichSequences~~( ~~ids~~ );		db.getRichSequence( "NC_001284.2" ),
	~~//getting a SequenceIterator~~		db.getRichSequence( "NC_000932.1" )
	~~SequenceIterator it = db2~~.~~sequenceIterator~~();		);

	//conversion to Jstacs Sample		//conversion to Jstacs Sample
	Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null );		Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null );
	</source>		</source>

Grau at 08:15, 29 October 2008

2008-10-29T08:15:31Z

← Older revision		Revision as of 08:15, 29 October 2008
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	//create a Sample using the alphabet from above		//create a Sample using the alphabet from above
	Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100 )		Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100 ) );
	</source>		</source>

Line 15:		Line 15:

	//create a Sample using the alphabet from above in FastA-format		//create a Sample using the alphabet from above in FastA-format
	Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100, StringExtractor.FASTA )		Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100, StringExtractor.FASTA ) );
	</source>		</source>

Grau at 12:21, 7 September 2008

2008-09-07T12:21:49Z

← Older revision		Revision as of 12:21, 7 September 2008
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	'''Loading DNA-sequences from a plain text file:'''		'''Loading DNA-sequences from a plain text file:'''
	<source lang="~~java~~">		<source lang="java5">
	//create a DNA-alphabet		//create a DNA-alphabet
	AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );		AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
Line 10:		Line 10:

	'''Loading DNA-sequences from a FastA file:'''		'''Loading DNA-sequences from a FastA file:'''
	<source lang="~~java~~">		<source lang="java5">
	//create a DNA-alphabet		//create a DNA-alphabet
	AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );		AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );
Line 20:		Line 20:

	'''Creating a Sample from a BioJava SequenceIterator:'''		'''Creating a Sample from a BioJava SequenceIterator:'''
	<source lang="~~java~~">		<source lang="java5">
	//defining the ids, we want to obtain from NCBI Genbank:		//defining the ids, we want to obtain from NCBI Genbank:
	Set<String> ids = new HashSet<String>();		Set<String> ids = new HashSet<String>();

Grau at 12:13, 7 September 2008

2008-09-07T12:13:49Z

← Older revision		Revision as of 12:13, 7 September 2008
Line 8:		Line 8:
	</source>		</source>

	~~<hr />~~
	'''Loading DNA-sequences from a FastA file:'''		'''Loading DNA-sequences from a FastA file:'''
	<source lang="java">		<source lang="java">
Line 18:		Line 18:
	</source>		</source>

	~~<hr />~~
	'''Creating a Sample from a BioJava SequenceIterator:'''		'''Creating a Sample from a BioJava SequenceIterator:'''
	<source lang="java">		<source lang="java">

Grau: New page: '''Loading DNA-sequences from a plain text file:''' //create a DNA-alphabet AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() ); //create a Sam...

2008-09-07T12:13:34Z

New page: '''Loading DNA-sequences from a plain text file:''' <source lang="java"> //create a DNA-alphabet AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() ); //create a Sam...

New page

'''Loading DNA-sequences from a plain text file:'''
<source lang="java">
//create a DNA-alphabet
AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );

//create a Sample using the alphabet from above
Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100 )
</source>

<hr />
'''Loading DNA-sequences from a FastA file:'''
<source lang="java">
//create a DNA-alphabet
AlphabetContainer container = new AlphabetContainer( new DNAAlphabet() );

//create a Sample using the alphabet from above in FastA-format
Sample data = new Sample( container, new StringExtractor( new File("myfile.txt"), 100, StringExtractor.FASTA )
</source>

<hr />
'''Creating a Sample from a BioJava SequenceIterator:'''
<source lang="java">
//defining the ids, we want to obtain from NCBI Genbank:
Set<String> ids = new HashSet<String>();
ids.add( "NC_003070" );
ids.add( "NC_003071" );

GenbankRichSequenceDB db = new GenbankRichSequenceDB();
RichSequenceDB db2 = db.getRichSequences( ids );
//getting a SequenceIterator
SequenceIterator it = db2.sequenceIterator();

//conversion to Jstacs Sample
Sample data = BioJavaAdapter.sequenceIteratorToSample( it, null );
</source>