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

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

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

Inheritance graph
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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

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.


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.


The documentation for this interface was generated from the following file:
Generated on Mon Aug 19 06:03:48 2013 for Mauve by doxygen 1.3.6