org::gel::mauve::SupportedFormat Interface Reference

A definition of a format supported for annotation/feature reading. More...

Inheritance diagram for org::gel::mauve::SupportedFormat:

[legend]List of all members.

Public Member Functions
SequenceIterator	readFile (File file)
Package Functions
String	getChromosomeName (Sequence s)
FilterCacheSpec[]	getFilterCacheSpecs ()
String	getSequenceName (Sequence s)
boolean	isRich ()
	True if this parsing files of this format results in biojavax RichSequence objects.
Sequence	makeDelegate (Sequence s, File source, int index) throws FileNotFoundException
SequenceIterator	makeIterator (File file)
Sequence	readInnerSequence (File file, int index)
void	validate (Sequence s, File file, int index) throws FileNotFoundException

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Detailed Description

A definition of a format supported for annotation/feature reading.

All formats must support delegation, that is, the smart caching of features and such.

Definition at line 14 of file SupportedFormat.java.

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Member Function Documentation

String org::gel::mauve::SupportedFormat::getChromosomeName (  Sequence  s  )  [package]

Parameters: s  Returns: Return a human-readable name for the subsequence. Implemented in org::gel::mauve::format::FastaFormat, and org::gel::mauve::format::GenbankEmblFormat. Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

FilterCacheSpec [] org::gel::mauve::SupportedFormat::getFilterCacheSpecs (   )  [package]

Implemented in org::gel::mauve::format::FastaFormat, and org::gel::mauve::format::GenbankEmblFormat. Referenced by org::gel::mauve::gui::sequence::FeaturePanel::init(), and org::gel::mauve::gui::sequence::FeatureFilterer::initFeatureTypes().

String org::gel::mauve::SupportedFormat::getSequenceName (  Sequence  s  )  [package]

Parameters: s  Returns: Return a human-readable name for the entire sequence. Implemented in org::gel::mauve::format::FastaFormat, and org::gel::mauve::format::GenbankEmblFormat. Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

boolean org::gel::mauve::SupportedFormat::isRich (   )  [package]

True if this parsing files of this format results in biojavax RichSequence objects. Returns: Implemented in org::gel::mauve::format::EmblFormat, org::gel::mauve::format::FastaFormat, org::gel::mauve::format::GenbankFileFormat, org::gel::mauve::format::INSDseqFormat, and org::gel::mauve::format::RawFormat. Referenced by org::gel::mauve::format::BaseFormat::makeIterator().

Sequence org::gel::mauve::SupportedFormat::makeDelegate (  Sequence  s, File  source, int  index )  throws FileNotFoundException [package]

Parameters: s  source  index  - the ordinal of the sequence that should be delegated. Returns: Exceptions: FileNotFoundException  Create a delegate based on the source file. The sequence s must correspond to the contents of the file. Implemented in org::gel::mauve::format::BaseFormat.

SequenceIterator org::gel::mauve::SupportedFormat::makeIterator (  File  file  )  [package]

Parameters: s  source  index  Returns: Exceptions: FileNotFoundException  Referenced by org::gel::mauve::GenomeBuilder::buildGenome().

SequenceIterator org::gel::mauve::SupportedFormat::readFile (  File  file  )

Parameters: reader  Returns: Create a sequenceIterator over the set of sequences within the file. Implemented in org::gel::mauve::format::EmblFormat, org::gel::mauve::format::FastaFormat, org::gel::mauve::format::GenbankFileFormat, and org::gel::mauve::format::INSDseqFormat. Referenced by org::gel::mauve::format::SequenceIteratorCache::getSequence(), and org::gel::mauve::format::BaseFormat::makeIterator().

Sequence org::gel::mauve::SupportedFormat::readInnerSequence (  File  file, int  index )  [package]

Parameters: file  index  Returns: Implemented in org::gel::mauve::format::BaseFormat.

void org::gel::mauve::SupportedFormat::validate (  Sequence  s, File  file, int  index )  throws FileNotFoundException [package]

Parameters: s  file  Exceptions: FileNotFoundException  Do whatever initial validation of sequence or file that is necessary Implemented in org::gel::mauve::format::BaseFormat.

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The documentation for this interface was generated from the following file:

• src/org/gel/mauve/SupportedFormat.java

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