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

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

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

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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)

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.


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.


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().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:59 2013 for Mauve by doxygen 1.3.6