org::gel::mauve::format::DelegatingSequence Class Reference

Inheritance diagram for org::gel::mauve::format::DelegatingSequence:

[legend]Collaboration diagram for org::gel::mauve::format::DelegatingSequence:

[legend]List of all members.

Public Member Functions
void	addChangeListener (ChangeListener cl, ChangeType ct)
void	addChangeListener (ChangeListener cl)
boolean	containsFeature (Feature f)
int	countFeatures ()
Feature	createFeature (Template ft) throws BioException, ChangeVetoException
	DelegatingSequence (Sequence s, SupportedFormat format, File source, int index) throws FileNotFoundException
void	edit (Edit edit) throws IllegalAlphabetException, ChangeVetoException
Iterator	features ()
FeatureHolder	filter (FeatureFilter fc)
FeatureHolder	filter (FeatureFilter fc, boolean recurse)
Alphabet	getAlphabet ()
Annotation	getAnnotation ()
String	getName ()
FeatureFilter	getSchema ()
String	getURN ()
boolean	isUnchanging (ChangeType ct)
Iterator	iterator ()
int	length ()
void	removeChangeListener (ChangeListener cl, ChangeType ct)
void	removeChangeListener (ChangeListener cl)
void	removeFeature (Feature f) throws ChangeVetoException, BioException
String	seqString ()
SymbolList	subList (int start, int end) throws IndexOutOfBoundsException
String	subStr (int start, int end) throws IndexOutOfBoundsException
Symbol	symbolAt (int index) throws IndexOutOfBoundsException
List	toList ()
Protected Member Functions
void	completeInit (Sequence s)
void	init (Sequence s)
SimpleStrandedFeature	makeThinFeature (StrandedFeature f, FilterCacheSpec spec)
Static Protected Member Functions
SimpleStrandedFeature	makeThinFeature (Sequence sequence, StrandedFeature f, FilterCacheSpec spec)
Protected Attributes
Alphabet	alphabet
Annotation	annotation
boolean	circular
int	featureCount
Map	filterCache = new HashMap ()
SupportedFormat	format
int	length
String	name
int	sequenceIndex
File	source
String	urn
Package Attributes
Changeable	ch = new Unchangeable ()
SymbolList	packedList = null
Private Member Functions
void	addToCache (Sequence s, FilterCacheSpec filterCacheSpec)
FeatureHolder	getCachedFilterResults (FeatureFilter ff)

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Constructor & Destructor Documentation

org::gel::mauve::format::DelegatingSequence::DelegatingSequence (  Sequence  s, SupportedFormat  format, File  source, int  index )  throws FileNotFoundException [inline]

Definition at line 65 of file DelegatingSequence.java. References init(), and source.

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Member Function Documentation

void org::gel::mauve::format::DelegatingSequence::addChangeListener (  ChangeListener  cl, ChangeType  ct )  [inline]

Definition at line 132 of file DelegatingSequence.java. References ch.

void org::gel::mauve::format::DelegatingSequence::addChangeListener (  ChangeListener  cl  )  [inline]

Deprecated: Definition at line 128 of file DelegatingSequence.java. References ch.

void org::gel::mauve::format::DelegatingSequence::addToCache (  Sequence  s, FilterCacheSpec  filterCacheSpec )  [inline, private]

Definition at line 236 of file DelegatingSequence.java. References org::gel::mauve::FilterCacheSpec::filter, filterCache, and makeThinFeature(). Referenced by getCachedFilterResults(), and init().

void org::gel::mauve::format::DelegatingSequence::completeInit (  Sequence  s  )  [inline, protected]

Definition at line 105 of file DelegatingSequence.java. Referenced by init().

boolean org::gel::mauve::format::DelegatingSequence::containsFeature (  Feature  f  )  [inline]

Definition at line 339 of file DelegatingSequence.java. References sequenceIndex, and source.

int org::gel::mauve::format::DelegatingSequence::countFeatures (   )  [inline]

Definition at line 204 of file DelegatingSequence.java. References featureCount.

Feature org::gel::mauve::format::DelegatingSequence::createFeature (  Template  ft  )  throws BioException, ChangeVetoException [inline]

Definition at line 329 of file DelegatingSequence.java.

void org::gel::mauve::format::DelegatingSequence::edit (  Edit  edit  )  throws IllegalAlphabetException, ChangeVetoException [inline]

Definition at line 199 of file DelegatingSequence.java.

Iterator org::gel::mauve::format::DelegatingSequence::features (   )  [inline]

Definition at line 208 of file DelegatingSequence.java. References sequenceIndex, and source.

FeatureHolder org::gel::mauve::format::DelegatingSequence::filter (  FeatureFilter  fc  )  [inline]

Definition at line 313 of file DelegatingSequence.java. References getCachedFilterResults(), sequenceIndex, and source.

FeatureHolder org::gel::mauve::format::DelegatingSequence::filter (  FeatureFilter  fc, boolean  recurse )  [inline]

Definition at line 213 of file DelegatingSequence.java. References getCachedFilterResults(), sequenceIndex, and source.

Alphabet org::gel::mauve::format::DelegatingSequence::getAlphabet (   )  [inline]

Definition at line 166 of file DelegatingSequence.java. References packedList.

Annotation org::gel::mauve::format::DelegatingSequence::getAnnotation (   )  [inline]

Definition at line 157 of file DelegatingSequence.java. References annotation.

FeatureHolder org::gel::mauve::format::DelegatingSequence::getCachedFilterResults (  FeatureFilter  ff  )  [inline, private]

Definition at line 227 of file DelegatingSequence.java. References addToCache(), filterCache, sequenceIndex, and source. Referenced by filter().

String org::gel::mauve::format::DelegatingSequence::getName (   )  [inline]

Reimplemented in org::gel::mauve::format::RichDelegatingSequence. Definition at line 111 of file DelegatingSequence.java.

FeatureFilter org::gel::mauve::format::DelegatingSequence::getSchema (   )  [inline]

Definition at line 344 of file DelegatingSequence.java. References sequenceIndex, and source.

String org::gel::mauve::format::DelegatingSequence::getURN (   )  [inline]

Definition at line 115 of file DelegatingSequence.java. References urn.

void org::gel::mauve::format::DelegatingSequence::init (  Sequence  s  )  [inline, protected]

Definition at line 76 of file DelegatingSequence.java. References addToCache(), alphabet, annotation, completeInit(), featureCount, packedList, and urn. Referenced by DelegatingSequence().

boolean org::gel::mauve::format::DelegatingSequence::isUnchanging (  ChangeType  ct  )  [inline]

Definition at line 148 of file DelegatingSequence.java. References ch.

Iterator org::gel::mauve::format::DelegatingSequence::iterator (   )  [inline]

Definition at line 182 of file DelegatingSequence.java. References packedList.

int org::gel::mauve::format::DelegatingSequence::length (   )  [inline]

Definition at line 170 of file DelegatingSequence.java.

SimpleStrandedFeature org::gel::mauve::format::DelegatingSequence::makeThinFeature (  Sequence  sequence, StrandedFeature  f, FilterCacheSpec  spec )  [inline, static, protected]

Parameters: f  Returns: Exceptions: ChangeVetoException  Make a slimmed-down copy of the feature for caching. Definition at line 270 of file DelegatingSequence.java. References org::gel::mauve::FilterCacheSpec::getAnnotations().

SimpleStrandedFeature org::gel::mauve::format::DelegatingSequence::makeThinFeature (  StrandedFeature  f, FilterCacheSpec  spec )  [inline, protected]

Definition at line 258 of file DelegatingSequence.java. Referenced by addToCache().

void org::gel::mauve::format::DelegatingSequence::removeChangeListener (  ChangeListener  cl, ChangeType  ct )  [inline]

Definition at line 144 of file DelegatingSequence.java. References ch.

void org::gel::mauve::format::DelegatingSequence::removeChangeListener (  ChangeListener  cl  )  [inline]

Deprecated: Definition at line 140 of file DelegatingSequence.java. References ch.

void org::gel::mauve::format::DelegatingSequence::removeFeature (  Feature  f  )  throws ChangeVetoException, BioException [inline]

Definition at line 334 of file DelegatingSequence.java.

String org::gel::mauve::format::DelegatingSequence::seqString (   )  [inline]

Definition at line 191 of file DelegatingSequence.java. References packedList.

SymbolList org::gel::mauve::format::DelegatingSequence::subList (  int  start, int  end )  throws IndexOutOfBoundsException [inline]

Definition at line 186 of file DelegatingSequence.java.

String org::gel::mauve::format::DelegatingSequence::subStr (  int  start, int  end )  throws IndexOutOfBoundsException [inline]

Definition at line 195 of file DelegatingSequence.java. References packedList.

Symbol org::gel::mauve::format::DelegatingSequence::symbolAt (  int  index  )  throws IndexOutOfBoundsException [inline]

Definition at line 174 of file DelegatingSequence.java. References packedList.

List org::gel::mauve::format::DelegatingSequence::toList (   )  [inline]

Definition at line 178 of file DelegatingSequence.java. References packedList.

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Member Data Documentation

Alphabet org::gel::mauve::format::DelegatingSequence::alphabet [protected]

Definition at line 44 of file DelegatingSequence.java. Referenced by org::gel::mauve::format::DelegatingSequence::DelegatingSublist::getAlphabet(), and init().

Annotation org::gel::mauve::format::DelegatingSequence::annotation [protected]

Definition at line 42 of file DelegatingSequence.java. Referenced by getAnnotation(), and init().

Changeable org::gel::mauve::format::DelegatingSequence::ch = new Unchangeable () [package]

Definition at line 61 of file DelegatingSequence.java. Referenced by org::gel::mauve::format::DelegatingSequence::DelegatingSublist::addChangeListener(), addChangeListener(), isUnchanging(), org::gel::mauve::format::DelegatingSequence::DelegatingSublist::removeChangeListener(), and removeChangeListener().

boolean org::gel::mauve::format::DelegatingSequence::circular [protected]

Definition at line 58 of file DelegatingSequence.java.

int org::gel::mauve::format::DelegatingSequence::featureCount [protected]

Definition at line 52 of file DelegatingSequence.java. Referenced by countFeatures(), and init().

Map org::gel::mauve::format::DelegatingSequence::filterCache = new HashMap () [protected]

Definition at line 54 of file DelegatingSequence.java. Referenced by addToCache(), and getCachedFilterResults().

SupportedFormat org::gel::mauve::format::DelegatingSequence::format [protected]

Definition at line 56 of file DelegatingSequence.java.

int org::gel::mauve::format::DelegatingSequence::length [protected]

Definition at line 46 of file DelegatingSequence.java.

String org::gel::mauve::format::DelegatingSequence::name [protected]

Definition at line 48 of file DelegatingSequence.java.

SymbolList org::gel::mauve::format::DelegatingSequence::packedList = null [package]

Definition at line 63 of file DelegatingSequence.java. Referenced by getAlphabet(), init(), iterator(), org::gel::mauve::format::DelegatingSequence::DelegatingSublist::seqString(), seqString(), subStr(), symbolAt(), and toList().

int org::gel::mauve::format::DelegatingSequence::sequenceIndex [protected]

Definition at line 40 of file DelegatingSequence.java. Referenced by containsFeature(), features(), filter(), getCachedFilterResults(), and getSchema().

File org::gel::mauve::format::DelegatingSequence::source [protected]

Definition at line 38 of file DelegatingSequence.java. Referenced by containsFeature(), DelegatingSequence(), features(), filter(), getCachedFilterResults(), and getSchema().

String org::gel::mauve::format::DelegatingSequence::urn [protected]

Definition at line 50 of file DelegatingSequence.java. Referenced by getURN(), and init().

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

• src/org/gel/mauve/format/DelegatingSequence.java

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