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Packages that use Sequence | |
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edu.upenn.gloDB | |
edu.upenn.gloDB.gui | |
edu.upenn.gloDB.io | |
edu.upenn.gloDB.parser |
Uses of Sequence in edu.upenn.gloDB |
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Methods in edu.upenn.gloDB that return Sequence | |
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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 | |
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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 | |
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AbstractFeature(Sequence source)
Set the source when the Feature is created. |
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ExactFeature(int start,
int stop,
Sequence source)
Create a new ExactFeature object and add it to the set of Feature objects. |
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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. |
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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. |
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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 |
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Fields in edu.upenn.gloDB.gui declared as Sequence | |
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private Sequence |
SequenceBrowser.BrowserFrame.sequence
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Methods in edu.upenn.gloDB.gui that return Sequence | |
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static Sequence |
GUISequenceIO.newSequence()
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Uses of Sequence in edu.upenn.gloDB.io |
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Methods in edu.upenn.gloDB.io that return Sequence | |
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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 |
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Fields in edu.upenn.gloDB.parser declared as Sequence | |
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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 | |
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Sequence |
Parser.sequenceRef()
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Methods in edu.upenn.gloDB.parser with parameters of type Sequence | |
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void |
Operation.setSequence(Sequence seq)
This will remove all Features from "track" that are not on "sequence". |
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