Uses of Class
edu.upenn.gloDB.Track

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

Uses of Track in edu.upenn.gloDB
 

Methods in edu.upenn.gloDB that return Track
 Track Track.cloneMerged()
          Create a shallow clone of the existing object (clone the structure but not the Objects).
 Track Track.cluster(java.lang.String id, int maxSpace, int threshold)
          Deprecated. replaced with cluster.py
 Track Track.flip()
          Inverts the positions of each feature in the Track.
static Track ObjectHandles.getTrack(java.lang.String id)
          Returns the Track object for the given ID.
 Track Track.noRepeats()
          This will return a copy of the track without any duplicate features (based on start/stop values).
 

Methods in edu.upenn.gloDB with parameters of type Track
static void ObjectHandles.addTrack(Track track)
          Add a Tracks to the trackPool.
static java.util.TreeSet FeatureUtils.cluster(Track track, int maxSpace, int threshold)
          Deprecated. replaced with cluster.py
static java.util.TreeSet FeatureUtils.mergeContiguous(Track track)
          This will merge all overlapping Features in the track, creating new Feature objects as necessary.
static boolean FeatureUtils.overlaps(Feature featureA, Track track)
          Returns 'true' if the Feature and Track overlap.
 boolean Track.overlaps(Track trackB)
          Returns 'true' if a Feature in trackB overlaps at least one Feature in this Track.
static void ObjectHandles.rebuildTrack(Track track)
          Rebuilds the Track relevant lists.
static void ObjectHandles.removeTrack(Track track)
          Removes the Track object for trackPool and other relevant lists.
static void ObjectHandles.renameTrack(Track track, java.lang.String newID)
          Changes the Track's ID in trackPool, trackList, and trackBySequenceList.
 

Uses of Track in edu.upenn.gloDB.gui
 

Fields in edu.upenn.gloDB.gui declared as Track
private  Track TrackBrowser.BrowserFrame.track
           
 

Methods in edu.upenn.gloDB.gui that return Track
static Track GUITrackIO.loadTrack()
          Use a FileChooser to select a Track file to load.
 

Uses of Track in edu.upenn.gloDB.io
 

Methods in edu.upenn.gloDB.io that return Track
 Track TrackFile.load(java.lang.String filename)
          Load all Features in the data file into a single Track and return the resulting Track object.
 Track GloDBTrack.load(java.lang.String filename)
          Load all Features in the GloDB file into a single Track and return the resulting Track object.
 Track GFFTrack.load(java.lang.String filename)
          Load all Features in the GFF file into a single Track and return the resulting Track object.
 Track GenBankTrack.load(java.lang.String filename)
          Load all Features in the GenBank file into a single Track and return the resulting Track object.
 Track FASTATrack.load(java.lang.String filename)
          Load all Features in the FASTA file into a single Track and return the resulting Track object.
 Track TrackFile.load(java.lang.String filename, java.lang.String sourceID)
          Load all Features in the data file into a single Track and return the resulting Track object.
 Track GloDBTrack.load(java.lang.String filename, java.lang.String sourceID)
          Load all Features in the GloDB file into a single Track and return the resulting Track object.
 Track GFFTrack.load(java.lang.String filename, java.lang.String sourceID)
          Load all Features in the GFF file into a single Track and return the resulting Track object.
 Track GenBankTrack.load(java.lang.String filename, java.lang.String seqID)
          Load all Features in the GenBank file into a single Track and return the resulting Track object.
 Track FASTATrack.load(java.lang.String filename, java.lang.String sourceID)
          Load all Features in the FASTA file into a single Track and return the resulting Track object.
 

Uses of Track in edu.upenn.gloDB.parser
 

Fields in edu.upenn.gloDB.parser declared as Track
 Track Operation.track
          SortedSet of Features to be searched.
 

Methods in edu.upenn.gloDB.parser that return Track
static Track ParserUtils.compute(java.lang.String parse)
          This will parse the input string to create the operations array, then compute the operations and assign the results to the Track indicated.
static Track Operator.fxn_AND(Track left, Operation operation)
          AND : all F in T1 which also exists in T2.
static Track Operator.fxn_bAND(Track left, Operation operation)
          && (bAND) : all positions in T1 that overlap with positions in T2.
static Track Operator.fxn_bMINUS(Track left, Operation operation)
          bMINUS : all positions in T1 that don't exist in T2.
static Track Operator.fxn_bOR(Track left, Operation operation)
          OR : all F in T1 and T2.
static Track Operator.fxn_MINUS(Track left, Operation operation)
          MINUS : all F in T1 that don't overlap with F in T2.
static Track Operator.fxn_OR(Track left, Operation operation)
          OR : all F in T1 and T2.
static Track Operator.fxn_POS(Track left, Operation operation)
          POS : all contiguous F in T1 and T2, appropriately spaced For each T2 need to loop through all T1 (on same seq), until past range.
static Track Operator.fxn_sAND(Track left, Operation operation)
          sAND : all features in T1 which exactly overlap features in T2.
static Track Operator.fxn_sMINUS(Track left, Operation operation)
          sMINUS : all features in T1 that don't exactly overlap features in T2.
private static Track ParserUtils.negate(Track track)
          This will perform a 'binary' inversion of the Features in the Track.
(package private) static Track Operator.processOperation(Track left, Operation operation)
          The first argument 'left' is the set of Features on the left hand side of the operation, the second argument 'operation' contains both the operation type and the set of Features on the right hand side of the operation.
static Track ParserUtils.solveOps(java.util.ArrayList ops)
          This will run solveOpsRecurse() which will recursively solve the Operations in the ArrayList 'ops'.
static Track ParserUtils.solveOps(java.util.ArrayList ops, java.lang.String id)
          This will run solveOpsRecurse() which will recursively solve the Operations in the ArrayList 'ops'.
private static Track ParserUtils.solveOpsRecurse(java.util.ArrayList ops)
          This will solve the Operations in the ArrayList 'ops', calling itself to recursively resolve groups of Operations.
 Track Parser.trackRef()
           
 

Methods in edu.upenn.gloDB.parser with parameters of type Track
static Track Operator.fxn_AND(Track left, Operation operation)
          AND : all F in T1 which also exists in T2.
static Track Operator.fxn_bAND(Track left, Operation operation)
          && (bAND) : all positions in T1 that overlap with positions in T2.
static Track Operator.fxn_bMINUS(Track left, Operation operation)
          bMINUS : all positions in T1 that don't exist in T2.
static Track Operator.fxn_bOR(Track left, Operation operation)
          OR : all F in T1 and T2.
static Track Operator.fxn_MINUS(Track left, Operation operation)
          MINUS : all F in T1 that don't overlap with F in T2.
static Track Operator.fxn_OR(Track left, Operation operation)
          OR : all F in T1 and T2.
static Track Operator.fxn_POS(Track left, Operation operation)
          POS : all contiguous F in T1 and T2, appropriately spaced For each T2 need to loop through all T1 (on same seq), until past range.
static Track Operator.fxn_sAND(Track left, Operation operation)
          sAND : all features in T1 which exactly overlap features in T2.
static Track Operator.fxn_sMINUS(Track left, Operation operation)
          sMINUS : all features in T1 that don't exactly overlap features in T2.
private static Track ParserUtils.negate(Track track)
          This will perform a 'binary' inversion of the Features in the Track.
(package private) static Track Operator.processOperation(Track left, Operation operation)
          The first argument 'left' is the set of Features on the left hand side of the operation, the second argument 'operation' contains both the operation type and the set of Features on the right hand side of the operation.
 

Constructors in edu.upenn.gloDB.parser with parameters of type Track
Operation(Track track)
          Create a new Operation object with a Track.
 




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