Uses of Class
edu.upenn.gloDB.Sequence

Packages that use Sequence
edu.upenn.gloDB   
edu.upenn.gloDB.gui   
edu.upenn.gloDB.io   
edu.upenn.gloDB.parser   
 

Uses of Sequence in edu.upenn.gloDB
 

Methods in edu.upenn.gloDB that return Sequence
static Sequence ObjectHandles.getSequence(java.lang.String id)
          Returns the Sequence object for the given ID.
 Sequence Feature.getSource()
          Returns the underlying Sequence object.
 Sequence AbstractFeature.getSource()
          Returns the underlying Sequence object.
 

Methods in edu.upenn.gloDB with parameters of type Sequence
static void ObjectHandles.addSequence(Sequence sequence)
          Add a Sequence to the sequencePool.
 java.util.TreeSet Track.featuresBySource(Sequence sequence)
          Get the set of Features based on the Sequence object.
static void ObjectHandles.removeSequence(Sequence sequence)
          Removes the Sequence object for sequencePool and other relevant lists.
 

Constructors in edu.upenn.gloDB with parameters of type Sequence
AbstractFeature(Sequence source)
          Set the source when the Feature is created.
ExactFeature(int start, int stop, Sequence source)
          Create a new ExactFeature object and add it to the set of Feature objects.
ExactFeature(int start, int stop, Sequence source, boolean addToPool)
          Create a new ExactFeature object and add the newly created ExactFeature object to the set of Feature objects if addToPool is true.
FuzzyFeature(int start, int startExt, int stop, int stopExt, Sequence source)
          Create a new FuzzyFeature object and add it to the set of Feature objects.
FuzzyFeature(int start, int startExt, int stop, int stopExt, Sequence source, boolean addToPool)
          Create a new FuzzyFeature object and add the newly created FuzzyFeature object to the set of Feature objects if addToPool is true.
 

Uses of Sequence in edu.upenn.gloDB.gui
 

Fields in edu.upenn.gloDB.gui declared as Sequence
private  Sequence SequenceBrowser.BrowserFrame.sequence
           
 

Methods in edu.upenn.gloDB.gui that return Sequence
static Sequence GUISequenceIO.newSequence()
           
 

Uses of Sequence in edu.upenn.gloDB.io
 

Methods in edu.upenn.gloDB.io that return Sequence
 Sequence SequenceFile.load(java.lang.String filename)
          Load the first sequence in the data file and return the resulting Sequence object.
 Sequence FASTASequence.load(java.lang.String filename)
          Load the first sequence in the FASTA file and return the resulting Sequence object.
 Sequence SequenceFile.load(java.lang.String filename, java.lang.String id)
          Load the first sequence in the data file and return the resulting Sequence object.
 Sequence FASTASequence.load(java.lang.String filename, java.lang.String id)
          Load the first sequence in the FASTA file and return the resulting Sequence object.
 Sequence SequenceFile.load(java.lang.String filename, java.lang.String id, FASTAParser parser)
          Load the first Sequence in the data file and return the resulting Sequence object.
 Sequence FASTASequence.load(java.lang.String filename, java.lang.String id, FASTAParser parser)
          Load the first sequence in the FASTA file and return the resulting Sequence object.
 

Uses of Sequence in edu.upenn.gloDB.parser
 

Fields in edu.upenn.gloDB.parser declared as Sequence
private  Sequence Operation.sequence
          If not null, then ignore all other Sequences when testing for Feature matches.
 

Methods in edu.upenn.gloDB.parser that return Sequence
 Sequence Parser.sequenceRef()
           
 

Methods in edu.upenn.gloDB.parser with parameters of type Sequence
 void Operation.setSequence(Sequence seq)
          This will remove all Features from "track" that are not on "sequence".
 




Copyright 2012 Stephen Fisher and Junhyong Kim, University of Pennsylvania. All Rights Reserved.