A B C D E F G H I J K L M N O P Q R S T U V W _

A

about - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
AbstractFeature - Class in edu.upenn.gloDB
AbstractFeature.
AbstractFeature(Sequence) - Constructor for class edu.upenn.gloDB.AbstractFeature
Set the source when the Feature is created.
accept(File) - Method in class edu.upenn.gloDB.gui.ViewHTML.HTMLFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.FASTASequence.FASTAFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.FASTATrack.FASTAFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.GenBankTrack.GenBankFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.GFFTrack.GFFFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.GloDBTrack.GloDBFilter
 
accept(File) - Method in class edu.upenn.gloDB.io.HTMLFile.HTMLFilter
 
actionPerformed(ActionEvent) - Method in class edu.upenn.gloDB.gui.Root.RootFrame
Handle menu items.
add_escapes(String) - Method in exception edu.upenn.gloDB.parser.ParseException
Used to convert raw characters to their escaped version when these raw version cannot be used as part of an ASCII string literal.
addAttribute(String, String) - Method in class edu.upenn.gloDB.AbstractFeature
Add an attribute.
addAttribute(String) - Method in class edu.upenn.gloDB.AbstractFeature
Add an attribute (key/value pair).
addAttribute(Object, Object) - Method in class edu.upenn.gloDB.Sequence
Add a sequence attribute.
addAttribute(Object, Object) - Method in class edu.upenn.gloDB.Track
Add an attribute.
addAttributeB - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
addAttributeB - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
addEscapes(String) - Static method in error edu.upenn.gloDB.parser.TokenMgrError
Replaces unprintable characters by their espaced (or unicode escaped) equivalents in the given string
addFeature(Feature) - Static method in class edu.upenn.gloDB.ObjectHandles
Add a Feature to the featurePool.
addFeature(Feature) - Method in class edu.upenn.gloDB.Track
Adds a Feature to 'features'.
addFeature(Feature, boolean) - Method in class edu.upenn.gloDB.Track
Adds a Feature to 'features'.
addFeatures(TreeSet) - Method in class edu.upenn.gloDB.Track
This will add 'features' to the current feature set.
addLength(int, int, int, int) - Method in class edu.upenn.gloDB.parser.Parser
Deal with length/from values.
addLoaderArg(Object, Object) - Method in class edu.upenn.gloDB.Sequence
Add a sequence parserArg.
addMenuItem(JMenuItem, JMenu, String, int, ImageIcon) - Method in class edu.upenn.gloDB.gui.Root.RootFrame
Add specified item to specified menu.
addRepeat(int, int, int, int) - Method in class edu.upenn.gloDB.parser.Parser
Deal with repeat/within values.
addRow(QueryElement) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Append a new row to the end of the table.
addRowAt(QueryElement, int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Add new row to table.
addSequence(Sequence) - Static method in class edu.upenn.gloDB.ObjectHandles
Add a Sequence to the sequencePool.
addSequenceFileType(SequenceFile) - Static method in class edu.upenn.gloDB.io.FileIO
Adds the Seqeunce file type to the list of possible types.
addToGroup(Object) - Method in class edu.upenn.gloDB.gui.QueryElement
'element' is assumed to be a QueryElement.
addTrack(Track) - Static method in class edu.upenn.gloDB.ObjectHandles
Add a Tracks to the trackPool.
addTrackFileType(TrackFile) - Static method in class edu.upenn.gloDB.io.FileIO
Adds the Track file type to the list of possible types.
adjustBeginLineColumn(int, int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
Method to adjust line and column numbers for the start of a token.
allTracks() - Method in class edu.upenn.gloDB.parser.Parser
 
allTRACKS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
AND - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
arg - Variable in class edu.upenn.gloDB.parser.Parser.JJCalls
 
argsTF - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.EditSourcePanel
 
ASSIGN - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
attributeL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
attributeL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
attributes - Variable in class edu.upenn.gloDB.AbstractFeature
This is similar to "qualifiers" in GenBank.
attributes - Variable in class edu.upenn.gloDB.Sequence
Metadata related to the sequence.
attributes - Variable in class edu.upenn.gloDB.Track
This is similar to "qualifiers" in GenBank (ex: scores, strand (+/-), phase (within codon)).
available - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 

B

backup(int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
bAND - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
beginColumn - Variable in class edu.upenn.gloDB.parser.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
beginLine - Variable in class edu.upenn.gloDB.parser.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
BeginToken() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
bMINUS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
bNOT - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
bOR - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
browserFrame - Static variable in class edu.upenn.gloDB.gui.SequenceBrowser
 
browserFrame - Static variable in class edu.upenn.gloDB.gui.TrackBrowser
 
browseSequences - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
browseTracks - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
bufcolumn - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
buffer - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
bufline - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
bufpos - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
bufsize - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 

C

cancelB - Variable in class edu.upenn.gloDB.gui.FieldEditDialog
 
cancelB - Variable in class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
cData - Variable in class edu.upenn.gloDB.Sequence
 
clearHistory - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
clearMessages - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
clone() - Method in class edu.upenn.gloDB.gui.QueryElement
Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone() - Method in class edu.upenn.gloDB.parser.Operation
Create a shallow clone (just clone the structure, not the Objects) of the existing object.
clone() - Method in class edu.upenn.gloDB.Track
Create a shallow clone of the existing object (clone the structure but not the Objects).
cloneMerged() - Method in class edu.upenn.gloDB.Track
Create a shallow clone of the existing object (clone the structure but not the Objects).
cloneTrack(boolean) - Method in class edu.upenn.gloDB.Track
Create a shallow clone of the existing object (clone the structure but not the Objects).
cluster(Track, int, int) - Static method in class edu.upenn.gloDB.FeatureUtils
Deprecated. replaced with cluster.py
cluster(String, int, int) - Method in class edu.upenn.gloDB.Track
Deprecated. replaced with cluster.py
column - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
columnNames - Variable in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
 
compare(Object, Object) - Method in class edu.upenn.gloDB.Track.FeatureMaxComparator
Compares this object with the specified object for order.
compareFeatures(Feature, Feature) - Static method in class edu.upenn.gloDB.FeatureUtils
Compares two Features for order.
compareTo(Object) - Method in class edu.upenn.gloDB.ExactFeature
Compares this object with the specified object for order.
compareTo(Object) - Method in interface edu.upenn.gloDB.Feature
Compares this object with the specified object for order.
compareTo(Object) - Method in class edu.upenn.gloDB.FuzzyFeature
Compares this object with the specified object for order.
compareTo(Object) - Method in class edu.upenn.gloDB.Track
Compares this object with the specified object for order.
compressString(String) - Static method in class edu.upenn.gloDB.GloDBUtils
 
compute(String) - Static method in class edu.upenn.gloDB.parser.ParserUtils
This will parse the input string to create the operations array, then compute the operations and assign the results to the Track indicated.
computeB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
console - Static variable in class edu.upenn.gloDB.GloDBMain
 
contained(Feature, int, int) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns a new Feature containing the region in 'feature' that is bounded by minB/maxB.
contains(int) - Method in class edu.upenn.gloDB.ExactFeature
Returns '-1' if this Feature exists after the integer 'pos', returns '0' if 'pos' is contained in this Feature, and '1' if 'pos' occurs after this Feature.
contains(Feature) - Method in class edu.upenn.gloDB.ExactFeature
Returns 'true' if the Feature 'feature' exists within this Feature.
contains(int) - Method in interface edu.upenn.gloDB.Feature
Returns '-1' if this Feature exists after the integer 'pos', returns '0' if 'pos' is contained in this Feature, and '1' if 'pos' occurs after this Feature.
contains(Feature) - Method in interface edu.upenn.gloDB.Feature
Returns 'true' if the Feature 'feature' exists in this Feature.
contains(Feature, int) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns '-1' if 'feature' exists after the integer 'pos', returns '0' if 'pos' is contained in 'feature', and '1' if 'pos' occurs after 'feature'.
contains(Feature, Feature) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns 'true' if the second Feature ('featureB') is contained in the first Feature ('featureA').
contains(int) - Method in class edu.upenn.gloDB.FuzzyFeature
Returns '-1' if this Feature exists after the integer 'pos', returns '0' if 'pos' is contained in this Feature, and '1' if 'pos' occurs after this Feature.
contains(Feature) - Method in class edu.upenn.gloDB.FuzzyFeature
Returns 'true' if the Feature 'feature' is contained in this Feature.
contains(int) - Method in class edu.upenn.gloDB.Sequence
Returns 'true' if the position 'pos' is contained in this Sequence object.
contains(Feature) - Method in class edu.upenn.gloDB.Sequence
Returns 'true' if 'feature' is contained in this Sequence object.
contains(int) - Method in class edu.upenn.gloDB.Track
Returns '-1' if this Track exists after the integer 'pos', returns '0' if 'pos' is contained in this Track, and '1' if 'pos' occurs after this Track.
contains(Feature) - Method in class edu.upenn.gloDB.Track
Returns 'true' if 'feature' exists in this Track.
contains(String) - Method in class edu.upenn.gloDB.Track
Returns 'true' if this Track contains any Features on 'source'.
containsAttribute(String) - Method in class edu.upenn.gloDB.AbstractFeature
Returns true if attribute 'key' exists.
containsAttribute(String) - Method in interface edu.upenn.gloDB.Feature
Returns true if attribute 'key' exists.
containsAttribute(Object) - Method in class edu.upenn.gloDB.Sequence
Returns true if attribute 'key' exists.
containsAttribute(Object) - Method in class edu.upenn.gloDB.Track
Returns true if attribute 'key' exists.
containsSequence(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Returns true if the Sequence object exists in the sequencePool.
containsTrack(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Returns true if the Track object exists in the trackPool.
contiguousL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
convertConstant(int) - Static method in class edu.upenn.gloDB.GloDBUtils
Convert from the integer constant value to a string equivalent.
convertConstant(int) - Static method in class edu.upenn.gloDB.io.FileIO
Convert from the integer constant value to a string equivalent.
copyB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
copyHistory - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
createString(int) - Static method in class edu.upenn.gloDB.GloDBMain
 
curChar - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
curLexState - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
currentToken - Variable in exception edu.upenn.gloDB.parser.ParseException
This is the last token that has been consumed successfully.

D

data - Variable in class edu.upenn.gloDB.Sequence
The sequence raw data as an unformatted string.
DataFile - Interface in edu.upenn.gloDB.io
Interface for files that contain Features or Sequences (ie.
dataLength - Variable in class edu.upenn.gloDB.Sequence
 
dataLoaded - Variable in class edu.upenn.gloDB.Sequence
This is a flag for whether data has been loaded.
dataLoader - Variable in class edu.upenn.gloDB.Sequence
This is the object that will handle getting the data for this Sequence.
debug - Static variable in class edu.upenn.gloDB.parser.ParserUtils
 
debugSolveAll - Static variable in class edu.upenn.gloDB.parser.ParserUtils
 
debugSolveOps - Static variable in class edu.upenn.gloDB.parser.ParserUtils
 
debugStream - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
DEFAULT - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
defaultLexState - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
delAttribute(String) - Method in class edu.upenn.gloDB.AbstractFeature
Remove an attribute.
delAttribute(Object) - Method in class edu.upenn.gloDB.Sequence
Remove an attribute.
delAttribute(Object) - Method in class edu.upenn.gloDB.Track
Remove an attribute.
delAttributeB - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
delAttributeB - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
deleteAllB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
deleteB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
densityRepeat(Operation) - Method in class edu.upenn.gloDB.parser.Parser
 
DESC - Variable in class edu.upenn.gloDB.io.FASTASequence
 
DESC - Variable in class edu.upenn.gloDB.io.FASTATrack
 
DESC - Variable in class edu.upenn.gloDB.io.GenBankTrack
 
DESC - Variable in class edu.upenn.gloDB.io.GFFTrack
 
DESC - Variable in class edu.upenn.gloDB.io.GloDBTrack
 
disable_tracing() - Method in class edu.upenn.gloDB.parser.Parser
 
displaySequence - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
displayTrack - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
Done() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 

E

editAttributeB - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
editAttributeB - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
edu.upenn.gloDB - package edu.upenn.gloDB
 
edu.upenn.gloDB.gui - package edu.upenn.gloDB.gui
 
edu.upenn.gloDB.io - package edu.upenn.gloDB.io
 
edu.upenn.gloDB.parser - package edu.upenn.gloDB.parser
 
enable_tracing() - Method in class edu.upenn.gloDB.parser.Parser
 
endColumn - Variable in class edu.upenn.gloDB.parser.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
endLine - Variable in class edu.upenn.gloDB.parser.Token
beginLine and beginColumn describe the position of the first character of this token; endLine and endColumn describe the position of the last character of this token.
EOF - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
eol - Variable in exception edu.upenn.gloDB.parser.ParseException
The end of line string for this machine.
EOL - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
equals(Object) - Method in class edu.upenn.gloDB.ExactFeature
This will return true if the features are equal and the sources are the same.
equals(Object) - Method in interface edu.upenn.gloDB.Feature
This will return true if the features are equal and the sources are the same.
equals(Object) - Method in class edu.upenn.gloDB.FuzzyFeature
This will return true if the features are equal and the sources are the same.
EQUALS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
erase() - Method in class edu.upenn.gloDB.Track
Erases all Track information, except for the ID.
ERROR - Static variable in class edu.upenn.gloDB.GloDBUtils
 
errorCode - Variable in error edu.upenn.gloDB.parser.TokenMgrError
Indicates the reason why the exception is thrown.
ExactFeature - Class in edu.upenn.gloDB
These objects store exact positions bounding a Feature.
ExactFeature(int, int, Sequence) - Constructor for class edu.upenn.gloDB.ExactFeature
Create a new ExactFeature object and add it to the set of Feature objects.
ExactFeature(int, int, Sequence, boolean) - Constructor for class edu.upenn.gloDB.ExactFeature
Create a new ExactFeature object and add the newly created ExactFeature object to the set of Feature objects if addToPool is true.
ExpandBuff(boolean) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
expectedTokenSequences - Variable in exception edu.upenn.gloDB.parser.ParseException
Each entry in this array is an array of integers.
expr(ArrayList) - Method in class edu.upenn.gloDB.parser.Parser
 
EXT - Variable in class edu.upenn.gloDB.io.FASTASequence
 
EXT - Variable in class edu.upenn.gloDB.io.FASTATrack
 
EXT - Variable in class edu.upenn.gloDB.io.GenBankTrack
 
EXT - Variable in class edu.upenn.gloDB.io.GFFTrack
 
EXT - Variable in class edu.upenn.gloDB.io.GloDBTrack
 

F

FASTA - Static variable in class edu.upenn.gloDB.io.FileIO
 
FASTAParser - Interface in edu.upenn.gloDB.io
Interface for parsing of FASTA headers.
FASTAParserDefault - Class in edu.upenn.gloDB.io
The default parser for FASTA headers.
FASTAParserDefault() - Constructor for class edu.upenn.gloDB.io.FASTAParserDefault
 
FASTAParserFly - Class in edu.upenn.gloDB.io
Parses the header line at the beginning of each sequence.
FASTAParserFly() - Constructor for class edu.upenn.gloDB.io.FASTAParserFly
 
FASTAParserMinimal - Class in edu.upenn.gloDB.io
Parses the header line at the beginning of each FASTA sequence.
FASTAParserMinimal() - Constructor for class edu.upenn.gloDB.io.FASTAParserMinimal
 
FASTASequence - Class in edu.upenn.gloDB.io
Import Sequence data from a FASTA file.
FASTASequence() - Constructor for class edu.upenn.gloDB.io.FASTASequence
 
FASTASequence.FASTAFilter - Class in edu.upenn.gloDB.io
FASTA specific FileFilter.
FASTASequence.FASTAFilter() - Constructor for class edu.upenn.gloDB.io.FASTASequence.FASTAFilter
 
FASTATrack - Class in edu.upenn.gloDB.io
Import Track data from a FASTA file.
FASTATrack() - Constructor for class edu.upenn.gloDB.io.FASTATrack
 
FASTATrack.FASTAFilter - Class in edu.upenn.gloDB.io
FASTA specific FileFilter.
FASTATrack.FASTAFilter() - Constructor for class edu.upenn.gloDB.io.FASTATrack.FASTAFilter
 
Feature - Interface in edu.upenn.gloDB
Feature interface.
FEATURE - Static variable in class edu.upenn.gloDB.GloDBUtils
 
feature() - Method in class edu.upenn.gloDB.parser.Parser
 
featureIterator() - Method in class edu.upenn.gloDB.Track
Returns an Iterator over 'features'.
featureL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
features - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
features - Variable in class edu.upenn.gloDB.Track
TreeSet of Feature objects comprising the Track.
featuresBySource(Sequence) - Method in class edu.upenn.gloDB.Track
Get the set of Features based on the Sequence object.
featuresBySource(String) - Method in class edu.upenn.gloDB.Track
Get the set of Features based on the Sequence ID.
FeatureUtils - Class in edu.upenn.gloDB
FeatureUtils.
FeatureUtils() - Constructor for class edu.upenn.gloDB.FeatureUtils
 
FEEDBACK - Static variable in class edu.upenn.gloDB.GloDBUtils
 
FieldEditDialog - Class in edu.upenn.gloDB.gui
This class is used to present a modal dialog for editing text in the 'text' HashMap.
FieldEditDialog(String, String[], ArrayList) - Constructor for class edu.upenn.gloDB.gui.FieldEditDialog
 
fileChooser - Static variable in class edu.upenn.gloDB.gui.GUIUtils
 
fileFilter - Variable in class edu.upenn.gloDB.io.FASTASequence
 
fileFilter - Variable in class edu.upenn.gloDB.io.FASTATrack
 
fileFilter - Variable in class edu.upenn.gloDB.io.GenBankTrack
 
fileFilter - Variable in class edu.upenn.gloDB.io.GFFTrack
 
fileFilter - Variable in class edu.upenn.gloDB.io.GloDBTrack
 
FileIO - Class in edu.upenn.gloDB.io
Import and export utilities.
FileIO() - Constructor for class edu.upenn.gloDB.io.FileIO
 
FillBuff() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
filter - Static variable in class edu.upenn.gloDB.gui.GUISequenceIO
Define 'filter' as a static global variable so that it persists across instances of the fileChoosers and thus will 'remember' what the user last used.
filter - Static variable in class edu.upenn.gloDB.gui.GUITrackIO
Define 'filter' as a static global variable so that it persists across instances of the fileChoosers and thus will 'remember' what the user last used.
filterOnAttribute(String, String) - Method in class edu.upenn.gloDB.Track
This will remove all Features from this Track that do not contain the specified attribute.
filterOnLength() - Method in class edu.upenn.gloDB.parser.Operation
This will remove all Features from "track" that are not within the 'minLength'/'maxLength' boundaries.
filterOnLength(int, int) - Method in class edu.upenn.gloDB.Track
This will remove all Features from this Track that are outside of the specifed range.
filterOnRepeat() - Method in class edu.upenn.gloDB.parser.Operation
This will remove all Features from "track" that are not within the 'minRepeat/maxRepeat' and 'minWithin/maxWithin' boundaries.
filterOnRepeat(int, int, int, int) - Method in class edu.upenn.gloDB.Track
This will remove all Features from this Track that do not conform to the repeat criterion.
filterOnSeqPos() - Method in class edu.upenn.gloDB.parser.Operation
This will remove all Features from "track" that are not within the 'minSeqPos'/'maxSeqPos' boundaries.
filterOnSeqPos(int, int) - Method in class edu.upenn.gloDB.Track
This will remove all Features from this Track that are not within the 'min'/'max' boundaries.
filterOnSequence() - Method in class edu.upenn.gloDB.parser.Operation
This will remove all Features from "track" that are not on "sequence".
filterOnSequence(String) - Method in class edu.upenn.gloDB.Track
This will remove all Features from this Track that do not exist on the specified Sequence.
first - Variable in class edu.upenn.gloDB.parser.Parser.JJCalls
 
firstFeature() - Method in class edu.upenn.gloDB.parser.Operation
Restart the Tracks iterator and return the first Feature.
flip() - Method in class edu.upenn.gloDB.ExactFeature
Inverts the positions, returning a new Feature object.
flip() - Method in interface edu.upenn.gloDB.Feature
Inverts the positions, returning a new Feature object.
flip() - Method in class edu.upenn.gloDB.FuzzyFeature
Inverts the positions, returning a new Feature object.
flip() - Method in class edu.upenn.gloDB.Track
Inverts the positions of each feature in the Track.
format(String) - Method in class edu.upenn.gloDB.io.GFFTrack
Format all Features into a GFF like string.
FORMAT_WIDTH - Static variable in class edu.upenn.gloDB.Sequence
This is the number of characters to print out per line when formatting the output in getDataFormatted().
formatParsed() - Method in class edu.upenn.gloDB.parser.Parser
 
FROM - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
FuzzyFeature - Class in edu.upenn.gloDB
These objects code Features that don't have definite boundaries.
FuzzyFeature(int, int, int, int, Sequence) - Constructor for class edu.upenn.gloDB.FuzzyFeature
Create a new FuzzyFeature object and add it to the set of Feature objects.
FuzzyFeature(int, int, int, int, Sequence, boolean) - Constructor for class edu.upenn.gloDB.FuzzyFeature
Create a new FuzzyFeature object and add the newly created FuzzyFeature object to the set of Feature objects if addToPool is true.
fxn_AND(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
AND : all F in T1 which also exists in T2.
fxn_bAND(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
&& (bAND) : all positions in T1 that overlap with positions in T2.
fxn_bMINUS(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
bMINUS : all positions in T1 that don't exist in T2.
fxn_bOR(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
OR : all F in T1 and T2.
fxn_MINUS(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
MINUS : all F in T1 that don't overlap with F in T2.
fxn_OR(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
OR : all F in T1 and T2.
fxn_POS(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
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.
fxn_sAND(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
sAND : all features in T1 which exactly overlap features in T2.
fxn_sMINUS(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
sMINUS : all features in T1 that don't exactly overlap features in T2.

G

gen - Variable in class edu.upenn.gloDB.parser.Parser.JJCalls
 
GENBANK - Static variable in class edu.upenn.gloDB.io.FileIO
 
GenBankTrack - Class in edu.upenn.gloDB.io
Import/Export Track data from/to GenBank files.
GenBankTrack() - Constructor for class edu.upenn.gloDB.io.GenBankTrack
 
GenBankTrack.GenBankFilter - Class in edu.upenn.gloDB.io
GenBank specific FileFilter.
GenBankTrack.GenBankFilter() - Constructor for class edu.upenn.gloDB.io.GenBankTrack.GenBankFilter
 
generateParseException() - Method in class edu.upenn.gloDB.parser.Parser
 
GenomeBrowser - Class in edu.upenn.gloDB.io
Import/Export Track data from/to Genome Browser.
GenomeBrowser() - Constructor for class edu.upenn.gloDB.io.GenomeBrowser
 
getAttribute(String) - Method in class edu.upenn.gloDB.AbstractFeature
Get value for attribute 'key'.
getAttribute(String) - Method in interface edu.upenn.gloDB.Feature
Get value for attribute 'key'.
getAttribute(Object) - Method in class edu.upenn.gloDB.Sequence
Get a sequence attribute.
getAttribute(Object) - Method in class edu.upenn.gloDB.Track
Get value for attribute 'key'.
getAttributes() - Method in class edu.upenn.gloDB.AbstractFeature
Get the attributes.
getAttributes() - Method in interface edu.upenn.gloDB.Feature
Get the Feature attributes.
getAttributes() - Method in class edu.upenn.gloDB.Sequence
Get the sequence attributes.
getAttributes() - Method in class edu.upenn.gloDB.Track
Get the attributes.
getAttributesMap() - Method in class edu.upenn.gloDB.AbstractFeature
Get the attributes as HashMap.
getAttributesMap() - Method in interface edu.upenn.gloDB.Feature
Get the Feature attributes as HashMap.
getBeginColumn() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getBeginLine() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getClassName(Object) - Static method in class edu.upenn.gloDB.GloDBUtils
Get the class name without any package info.
getColumn() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
Deprecated.  
getColumnCount() - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
 
getColumnName(int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
 
getData() - Method in class edu.upenn.gloDB.ExactFeature
Returns the Sequence data from start to stop.
getData() - Method in interface edu.upenn.gloDB.Feature
Returns the underlying sequence data.
getData() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the Sequence data from start to stopExt.
getData(HashMap) - Method in class edu.upenn.gloDB.io.FASTASequence
Return the Sequence data as a String.
getData() - Method in class edu.upenn.gloDB.Sequence
Returns the Sequence data as a single unformatted string.
getData(HashMap) - Method in interface edu.upenn.gloDB.SequenceLoader
Return the Sequence data as a string.
getData() - Method in class edu.upenn.gloDB.Track
Returns the sequence data.
getDataBounded(int, int) - Method in class edu.upenn.gloDB.Sequence
Returns the sequence data between position '(min-1)' and position 'max'.
getDataBoundedFormatted(int, int) - Method in class edu.upenn.gloDB.Sequence
Returns the bounded sequence data with "\n" inserted every FORMAT_WIDTH characters.
getDataFASTA() - Method in class edu.upenn.gloDB.Track
Returns the sequence data formatted as a multi-sequence FASTA file.
getDataFormatted() - Method in class edu.upenn.gloDB.ExactFeature
Returns the Sequence data from start to stop, with "\n" inserted every Sequence.FORMAT_WIDTH characters (usually 50 to 80 chars).
getDataFormatted() - Method in interface edu.upenn.gloDB.Feature
Returns the Sequence data, with "\n" inserted every Sequence.FORMAT_WIDTH characters (usually 50 to 80 chars).
getDataFormatted() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the Sequence data from start to stopExt, with "\n" inserted every 80 characters.
getDataFormatted() - Method in class edu.upenn.gloDB.Sequence
Returns the sequence data with "\n" inserted every FORMAT_WIDTH characters.
getDataFormatted() - Method in class edu.upenn.gloDB.Track
Returns the sequence data formatted with "\n" inserted every Sequence.FORMAT_WIDTH characters and blank lines inserted between sequences.
getDataLoader() - Method in class edu.upenn.gloDB.Sequence
Returns the parser for the Sequence source.
getDataType(int, String) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the DataFile based on the file type and type description.
getDataTypes(int) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the DataFiles based on the file type.
getDesc() - Method in interface edu.upenn.gloDB.io.DataFile
Get a description of the file type.
getDesc() - Method in class edu.upenn.gloDB.io.FASTASequence
 
getDesc() - Method in class edu.upenn.gloDB.io.FASTATrack
 
getDesc() - Method in class edu.upenn.gloDB.io.GenBankTrack
 
getDesc() - Method in class edu.upenn.gloDB.io.GFFTrack
 
getDesc() - Method in class edu.upenn.gloDB.io.GloDBTrack
 
getDescription() - Method in class edu.upenn.gloDB.gui.ViewHTML.HTMLFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.FASTASequence.FASTAFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.FASTATrack.FASTAFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.GenBankTrack.GenBankFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.GFFTrack.GFFFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.GloDBTrack.GloDBFilter
 
getDescription() - Method in class edu.upenn.gloDB.io.HTMLFile.HTMLFilter
 
getEndColumn() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getEndLine() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getExt() - Method in interface edu.upenn.gloDB.io.DataFile
Get an array of file extensions.
getExt() - Method in class edu.upenn.gloDB.io.FASTASequence
 
getExt() - Method in class edu.upenn.gloDB.io.FASTATrack
 
getExt() - Method in class edu.upenn.gloDB.io.GenBankTrack
 
getExt() - Method in class edu.upenn.gloDB.io.GFFTrack
 
getExt() - Method in class edu.upenn.gloDB.io.GloDBTrack
 
getFeatures() - Method in class edu.upenn.gloDB.Track
Get the features, sorted by their min values.
getFeaturesByMax() - Method in class edu.upenn.gloDB.Track
Get the features, sorted by their max values.
getFileFilter() - Method in interface edu.upenn.gloDB.io.DataFile
Get a FileFilter for use in the GUI.
getFileFilter() - Method in class edu.upenn.gloDB.io.FASTASequence
 
getFileFilter() - Method in class edu.upenn.gloDB.io.FASTATrack
 
getFileFilter() - Method in class edu.upenn.gloDB.io.GenBankTrack
 
getFileFilter() - Method in class edu.upenn.gloDB.io.GFFTrack
 
getFileFilter() - Method in class edu.upenn.gloDB.io.GloDBTrack
 
getFilename(File) - Static method in class edu.upenn.gloDB.gui.GUIUtils
On Windows machines the path contains "\\", however, when converted to a String, this becomes "\".
getGroup() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getGroup() - Method in class edu.upenn.gloDB.parser.Operation
Gets the array of Operations.
getHTML() - Method in class edu.upenn.gloDB.gui.ViewHTML.HTMLEditorPane
 
getID() - Method in class edu.upenn.gloDB.gui.QueryBuilder
 
getID() - Method in interface edu.upenn.gloDB.io.DataFile
Get the file ID.
getID() - Method in class edu.upenn.gloDB.io.FASTASequence
 
getID() - Method in class edu.upenn.gloDB.io.FASTATrack
 
getID() - Method in class edu.upenn.gloDB.io.GenBankTrack
 
getID() - Method in class edu.upenn.gloDB.io.GFFTrack
 
getID() - Method in class edu.upenn.gloDB.io.GloDBTrack
 
getId() - Method in class edu.upenn.gloDB.parser.Parser
 
getID() - Method in class edu.upenn.gloDB.Sequence
Get the id.
getID() - Method in class edu.upenn.gloDB.Track
Get the ID.
GetImage() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getLine() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
Deprecated.  
getLoaderArg(Object) - Method in class edu.upenn.gloDB.Sequence
Get a sequence parserArg.
getLoaderArgs() - Method in class edu.upenn.gloDB.Sequence
Get the sequence loaderArgs.
getMax() - Method in class edu.upenn.gloDB.ExactFeature
Returns the maximum position of the Feature.
getMax() - Method in interface edu.upenn.gloDB.Feature
Returns the maximum position of the Feature.
getMax() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the maximum position of the Feature.
getMax() - Method in class edu.upenn.gloDB.Sequence
Returns the maximum position of the Sequence on the chromosome.
getMax() - Method in class edu.upenn.gloDB.Track
Returns the maximum stop position in the Track.
getMaxLength() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMaxPos() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMaxRepeat() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMaxSeqPos() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMaxWithin() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMessage() - Method in exception edu.upenn.gloDB.parser.ParseException
This method has the standard behavior when this object has been created using the standard constructors.
getMessage() - Method in error edu.upenn.gloDB.parser.TokenMgrError
You can also modify the body of this method to customize your error messages.
getMin() - Method in class edu.upenn.gloDB.ExactFeature
Returns the initial position of the Feature.
getMin() - Method in interface edu.upenn.gloDB.Feature
Returns the initial position of the Feature.
getMin() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the initial position of the Feature.
getMin() - Method in class edu.upenn.gloDB.Sequence
Returns the initial position of the Sequence on the chromosome.
getMin() - Method in class edu.upenn.gloDB.Track
Returns the minimum start position in the Track.
getMinLength() - Method in class edu.upenn.gloDB.gui.QueryElement
Most often need these as Strings
getMinPos() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMinRepeat() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMinSeqPos() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getMinWithin() - Method in class edu.upenn.gloDB.gui.QueryElement
 
getNextToken() - Method in class edu.upenn.gloDB.parser.Parser
 
getNextToken() - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
getOffset() - Method in class edu.upenn.gloDB.Sequence
Returns the Sequence starting position on the chromosome.
getOperation(Operation) - Static method in class edu.upenn.gloDB.parser.ParserUtils
For Operations that contain groups, this will solve the group and store the resulting TreeSet of Tracks in the Operation.
getOperatorVal(int) - Static method in class edu.upenn.gloDB.gui.QueryElement
Returns the string equivalent to the operator index value.
getOperatorVal() - Method in class edu.upenn.gloDB.gui.QueryElement
Returns the string equivalent to the operator index value.
getRow(int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Returns the QueryElement that represents the specified row in the table.
getRowCount() - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
 
getSequence(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Returns the Sequence object for the given ID.
getSequenceFileType(String) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the SequenceFile based on the file type description.
getSequenceFileType(int) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the SequenceFile based on the file type ID.
getSequenceFileTypes() - Static method in class edu.upenn.gloDB.io.FileIO
Returns the set of Sequence file types.
getSequenceList() - Static method in class edu.upenn.gloDB.ObjectHandles
Get the sequenceList.
getSequencePool() - Static method in class edu.upenn.gloDB.ObjectHandles
Get the sequencePool.
getSource() - Method in class edu.upenn.gloDB.AbstractFeature
Returns the underlying Sequence object.
getSource() - Method in interface edu.upenn.gloDB.Feature
Returns the underlying Sequence object.
getSourceID() - Method in class edu.upenn.gloDB.AbstractFeature
Returns the underlying Sequence object's ID.
getSourceID() - Method in interface edu.upenn.gloDB.Feature
Returns the underlying Sequence object's ID.
getSources() - Method in class edu.upenn.gloDB.Track
Get the map of source Sequences to Features.
getSourceSet() - Method in class edu.upenn.gloDB.Track
Get the set of source Sequence objects.
getStart() - Method in class edu.upenn.gloDB.ExactFeature
Returns the start position.
getStart() - Method in interface edu.upenn.gloDB.Feature
Returns the start position of the Feature.
getStart() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the start position.
getStartExt() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the startExt position.
getStop() - Method in class edu.upenn.gloDB.ExactFeature
Returns the stop position.
getStop() - Method in interface edu.upenn.gloDB.Feature
Returns the maximum position of the Feature.
getStop() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the stop position.
getStopExt() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the stopExt.
GetSuffix(int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
getSystemProperty(String) - Static method in class edu.upenn.gloDB.GloDBMain
 
getToken(int) - Method in class edu.upenn.gloDB.parser.Parser
 
getTrack(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Returns the Track object for the given ID.
getTrackBySequenceList(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Get the trackList that contains all Tracks with the given Sequence.
getTrackFileType(String) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the TrackFile based on the file type description.
getTrackFileType(int) - Static method in class edu.upenn.gloDB.io.FileIO
Returns the TrackFile based on the file type ID.
getTrackFileTypes() - Static method in class edu.upenn.gloDB.io.FileIO
Returns the set of Track file types.
getTrackList() - Static method in class edu.upenn.gloDB.ObjectHandles
Get the trackList.
getTrackPool() - Static method in class edu.upenn.gloDB.ObjectHandles
Get the trackPool.
getType() - Method in class edu.upenn.gloDB.AbstractFeature
Returns Feature type (see GloDBUtils)
getType() - Method in class edu.upenn.gloDB.parser.Operation
Get the Operation type: 0 = POS, 1 = AND, 2 = nAND, 3 = OR, 4 = LESS 10 = ., 11 = &&, 12 = ^&&, 13 = ||, 14 = -
getType(int) - Static method in class edu.upenn.gloDB.parser.Operator
Return the representative String for a type value.
getType() - Method in class edu.upenn.gloDB.Sequence
Returns Feature type (see GloDBUtils)
getValueAt(int, int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Operator, Negate, Track, Qualifiers
getVerbose() - Static method in class edu.upenn.gloDB.GloDBUtils
Get the VERBOSE flag.
GFF - Static variable in class edu.upenn.gloDB.io.FileIO
 
GFFTrack - Class in edu.upenn.gloDB.io
Import/Export Track data from/to GFF files.
GFFTrack() - Constructor for class edu.upenn.gloDB.io.GFFTrack
 
GFFTrack.GFFFilter - Class in edu.upenn.gloDB.io
GFF specific FileFilter.
GFFTrack.GFFFilter() - Constructor for class edu.upenn.gloDB.io.GFFTrack.GFFFilter
 
GLODB - Static variable in class edu.upenn.gloDB.io.FileIO
 
GloDBException - Exception in edu.upenn.gloDB
A wrapper for all GloDB exceptions.
GloDBException() - Constructor for exception edu.upenn.gloDB.GloDBException
Create a new GloDBException without a message.
GloDBException(String) - Constructor for exception edu.upenn.gloDB.GloDBException
Create a new GloDBException with a message.
GloDBMain - Class in edu.upenn.gloDB
GloDBMain program.
GloDBMain() - Constructor for class edu.upenn.gloDB.GloDBMain
 
GloDBTrack - Class in edu.upenn.gloDB.io
Import/Export Track data from/to GloDB files.
GloDBTrack() - Constructor for class edu.upenn.gloDB.io.GloDBTrack
 
GloDBTrack.GloDBFilter - Class in edu.upenn.gloDB.io
GloDB specific FileFilter.
GloDBTrack.GloDBFilter() - Constructor for class edu.upenn.gloDB.io.GloDBTrack.GloDBFilter
 
GloDBUtils - Class in edu.upenn.gloDB
GloDBUtils.
GloDBUtils() - Constructor for class edu.upenn.gloDB.GloDBUtils
 
group - Variable in class edu.upenn.gloDB.gui.QueryElement
Group of QueryElements (ie Tracks).
group - Variable in class edu.upenn.gloDB.parser.Operation
If this Operation is a 'group' (ie '()'), then instead of containing a SortedSet of Features, it will contain an array of Operations.
group() - Method in class edu.upenn.gloDB.parser.Parser
 
groupB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
groupIterator() - Method in class edu.upenn.gloDB.gui.QueryElement
 
groupIterator() - Method in class edu.upenn.gloDB.parser.Operation
Returns an iterator over the group list, null if empty group.
groupSize() - Method in class edu.upenn.gloDB.gui.QueryElement
 
guiMessages - Static variable in class edu.upenn.gloDB.GloDBUtils
If not null, all error and warning messages will be sent here.
GUISequenceIO - Class in edu.upenn.gloDB.gui
Static methods used throughout the GUI.
GUISequenceIO() - Constructor for class edu.upenn.gloDB.gui.GUISequenceIO
 
GUITrackIO - Class in edu.upenn.gloDB.gui
Static methods used to handle Track IO.
GUITrackIO() - Constructor for class edu.upenn.gloDB.gui.GUITrackIO
 
GUIUtils - Class in edu.upenn.gloDB.gui
Static methods used throughout the GUI.
GUIUtils() - Constructor for class edu.upenn.gloDB.gui.GUIUtils
 

H

hasNextFeature() - Method in class edu.upenn.gloDB.parser.Operation
Return true if there are more Features in 'iterator'.
helpTopics - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
history - Static variable in class edu.upenn.gloDB.gui.Root
This will contain all commands that the GUI generates and sends to the console to be run.
history - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
HOOK - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
HTMLFile - Class in edu.upenn.gloDB.io
Save URL, HTML text, or InputStream as HTML file.
HTMLFile() - Constructor for class edu.upenn.gloDB.io.HTMLFile
 
HTMLFile.HTMLFilter - Class in edu.upenn.gloDB.io
HTML FileFilter.
HTMLFile.HTMLFilter() - Constructor for class edu.upenn.gloDB.io.HTMLFile.HTMLFilter
 
htmlText - Variable in class edu.upenn.gloDB.gui.ViewHTML
 
hyperlinkUpdate(HyperlinkEvent) - Method in class edu.upenn.gloDB.gui.ViewHTML.Hyperactive
 

I

ID - Variable in class edu.upenn.gloDB.io.FASTASequence
 
ID - Variable in class edu.upenn.gloDB.io.FASTATrack
 
ID - Variable in class edu.upenn.gloDB.io.GenBankTrack
 
ID - Variable in class edu.upenn.gloDB.io.GFFTrack
 
ID - Variable in class edu.upenn.gloDB.io.GloDBTrack
 
id - Variable in class edu.upenn.gloDB.parser.Parser
The ID of the new Track object.
id - Variable in class edu.upenn.gloDB.Sequence
This is a unique name for the sequence, that is used by the parser to identify the sequence.
id - Variable in class edu.upenn.gloDB.Track
This is a unique name for the Track, that is used by the parser to identify the Track.
idTF - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.newSequencePanel
 
ignore - Variable in class edu.upenn.gloDB.parser.Operation
Flag for whether the mapped Feature should be included in the output.
ignore() - Method in class edu.upenn.gloDB.parser.Parser
 
IGNORE - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
IGNORE_ATTRIBUTES - Static variable in class edu.upenn.gloDB.GloDBUtils
This flag is used in FeatureUtils.compareFeatures() to compare two Features.
ignoreAttributes() - Static method in class edu.upenn.gloDB.GloDBUtils
Get the IGNORE_ATTRIBUTES flag.
image - Variable in class edu.upenn.gloDB.parser.Token
The string image of the token.
inBuf - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
initialize() - Method in class edu.upenn.gloDB.parser.Operation
 
input_stream - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
INPUTSTREAM - Static variable in class edu.upenn.gloDB.gui.ViewHTML
 
inputStream - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
INTEGER - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
INVALID_LEXICAL_STATE - Static variable in error edu.upenn.gloDB.parser.TokenMgrError
Tried to change to an invalid lexical state.
InvalidIDException - Exception in edu.upenn.gloDB
 
InvalidIDException() - Constructor for exception edu.upenn.gloDB.InvalidIDException
Create a new InvalidIDException without a message.
InvalidIDException(String) - Constructor for exception edu.upenn.gloDB.InvalidIDException
Create a new InvalidIDException with a message.
ISBATCH - Static variable in class edu.upenn.gloDB.GloDBMain
 
isContiguous(TreeSet) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns 'true' if the set of Features does not contain gaps between Features.
isContiguous() - Method in class edu.upenn.gloDB.Track
Returns 'true' if the Track does not contain gaps between Features.
isDataLoaded() - Method in class edu.upenn.gloDB.Sequence
Returns true if data was loaded.
isEmpty(String) - Static method in class edu.upenn.gloDB.GloDBUtils
Returns true if 'str' is empty (ignores spaces) or null.
isGroup() - Method in class edu.upenn.gloDB.parser.Operation
Returns true if this Operation is a group.
isGrouped() - Method in class edu.upenn.gloDB.gui.QueryElement
 
isIgnore() - Method in class edu.upenn.gloDB.parser.Operation
Gets the ignore flag.
isNegate() - Method in class edu.upenn.gloDB.parser.Operation
Flag for whether to invert the output Track, treating the Track as a mask over the Sequence (ie binary operation).
isOrderOperator(int) - Static method in class edu.upenn.gloDB.gui.QueryElement
Returns the string equivalent to the operator index value.
isOrderOperator(String) - Static method in class edu.upenn.gloDB.gui.QueryElement
Returns the string equivalent to the operator index value.
isSingleSource() - Method in class edu.upenn.gloDB.Track
Returns 'true' if the Features contained in the Track all refer to the same sequence.
items - Variable in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Stores the QueryElements that are in the table.
iterator - Variable in class edu.upenn.gloDB.parser.Operation
An Iterator over 'Track'.

J

jj_2_1(int) - Method in class edu.upenn.gloDB.parser.Parser
 
jj_2_rtns - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_3_1() - Method in class edu.upenn.gloDB.parser.Parser
 
jj_3R_3() - Method in class edu.upenn.gloDB.parser.Parser
 
jj_3R_4() - Method in class edu.upenn.gloDB.parser.Parser
 
jj_add_error_token(int, int) - Method in class edu.upenn.gloDB.parser.Parser
 
jj_consume_token(int) - Method in class edu.upenn.gloDB.parser.Parser
 
jj_endpos - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_expentries - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_expentry - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_gc - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_gen - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_input_stream - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_kind - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_la - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_la1 - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_la1_0 - Static variable in class edu.upenn.gloDB.parser.Parser
 
jj_la1_0() - Static method in class edu.upenn.gloDB.parser.Parser
 
jj_la1_1 - Static variable in class edu.upenn.gloDB.parser.Parser
 
jj_la1_1() - Static method in class edu.upenn.gloDB.parser.Parser
 
jj_lastpos - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_lasttokens - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_ls - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_nt - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_ntk - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_ntk() - Method in class edu.upenn.gloDB.parser.Parser
 
jj_rescan - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_rescan_token() - Method in class edu.upenn.gloDB.parser.Parser
 
jj_save(int, int) - Method in class edu.upenn.gloDB.parser.Parser
 
jj_scan_token(int) - Method in class edu.upenn.gloDB.parser.Parser
 
jj_scanpos - Variable in class edu.upenn.gloDB.parser.Parser
 
jj_semLA - Variable in class edu.upenn.gloDB.parser.Parser
 
jjAddStates(int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjCheckNAdd(int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjCheckNAddStates(int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjCheckNAddStates(int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjCheckNAddTwoStates(int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjFillToken() - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjmatchedKind - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjmatchedPos - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveNfa_0(int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa0_0() - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa10_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa1_0(long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa2_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa3_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa4_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa5_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa6_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa7_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa8_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjMoveStringLiteralDfa9_0(long, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjnewStateCnt - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjnextStates - Static variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjround - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjrounds - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjStartNfa_0(int, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjStartNfaWithStates_0(int, int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjstateSet - Variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjStopAtPos(int, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjStopStringLiteralDfa_0(int, long) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjstrLiteralImages - Static variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjtoSkip - Static variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
jjtoToken - Static variable in class edu.upenn.gloDB.parser.ParserTokenManager
 

K

kind - Variable in class edu.upenn.gloDB.parser.Token
An integer that describes the kind of this token.

L

length() - Method in class edu.upenn.gloDB.ExactFeature
Returns the number of positions contained in the Feature ((stop - start) + 1).
length() - Method in interface edu.upenn.gloDB.Feature
Returns the number of positions contained in the Feature.
length() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the maximum number of positions contained in the Feature (((stop + stopExt) - start) + 1).
length(Operation) - Method in class edu.upenn.gloDB.parser.Parser
 
LENGTH - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
length() - Method in class edu.upenn.gloDB.Sequence
Returns the length of the data string.
length() - Method in class edu.upenn.gloDB.Track
Returns the number of positions contained in the Track.
lengthL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
lengthL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
LEXICAL_ERROR - Static variable in error edu.upenn.gloDB.parser.TokenMgrError
Lexical error occured.
LexicalError(boolean, int, int, int, String, char) - Static method in error edu.upenn.gloDB.parser.TokenMgrError
Returns a detailed message for the Error when it is thrown by the token manager to indicate a lexical error.
lexStateNames - Static variable in class edu.upenn.gloDB.parser.ParserTokenManager
 
lGROUP - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
line - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
lLENGTH - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
lLENGTH2 - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
load(String) - Method in class edu.upenn.gloDB.io.FASTASequence
Load the first sequence in the FASTA file and return the resulting Sequence object.
load(String, String) - Method in class edu.upenn.gloDB.io.FASTASequence
Load the first sequence in the FASTA file and return the resulting Sequence object.
load(String, String, FASTAParser) - Method in class edu.upenn.gloDB.io.FASTASequence
Load the first sequence in the FASTA file and return the resulting Sequence object.
load(String) - Method in class edu.upenn.gloDB.io.FASTATrack
Load all Features in the FASTA file into a single Track and return the resulting Track object.
load(String, String) - Method in class edu.upenn.gloDB.io.FASTATrack
Load all Features in the FASTA file into a single Track and return the resulting Track object.
load(String) - Method in class edu.upenn.gloDB.io.GenBankTrack
Load all Features in the GenBank file into a single Track and return the resulting Track object.
load(String, String) - Method in class edu.upenn.gloDB.io.GenBankTrack
Load all Features in the GenBank file into a single Track and return the resulting Track object.
load(String) - Method in class edu.upenn.gloDB.io.GFFTrack
Load all Features in the GFF file into a single Track and return the resulting Track object.
load(String, String) - Method in class edu.upenn.gloDB.io.GFFTrack
Load all Features in the GFF file into a single Track and return the resulting Track object.
load(String) - Method in class edu.upenn.gloDB.io.GloDBTrack
Load all Features in the GloDB file into a single Track and return the resulting Track object.
load(String, String) - Method in class edu.upenn.gloDB.io.GloDBTrack
Load all Features in the GloDB file into a single Track and return the resulting Track object.
load(String) - Method in interface edu.upenn.gloDB.io.SequenceFile
Load the first sequence in the data file and return the resulting Sequence object.
load(String, String) - Method in interface edu.upenn.gloDB.io.SequenceFile
Load the first sequence in the data file and return the resulting Sequence object.
load(String, String, FASTAParser) - Method in interface edu.upenn.gloDB.io.SequenceFile
Load the first Sequence in the data file and return the resulting Sequence object.
load(String) - Method in interface edu.upenn.gloDB.io.TrackFile
Load all Features in the data file into a single Track and return the resulting Track object.
load(String, String) - Method in interface edu.upenn.gloDB.io.TrackFile
Load all Features in the data file into a single Track and return the resulting Track object.
loadAll(String) - Method in class edu.upenn.gloDB.io.FASTASequence
Load all Sequences in the FASTA file and return a Set containing the resulting Sequence objects.
loadAll(String, FASTAParser) - Method in class edu.upenn.gloDB.io.FASTASequence
Load all Sequences in the FASTA file and return a set containing the resulting Sequence objects.
loadAll(String) - Method in interface edu.upenn.gloDB.io.SequenceFile
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.
loadAll(String, FASTAParser) - Method in interface edu.upenn.gloDB.io.SequenceFile
Load all Sequences in the data file and return a HashSet containing the resulting Sequence objects.
loadData() - Method in class edu.upenn.gloDB.Sequence
This will load the data from 'dataLoader' if data is currently empty.
loadDataL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
loaderArgs - Variable in class edu.upenn.gloDB.Sequence
This is a map of key:value pairs needed to load the data from the data source, as defined by 'dataLoader': URL, file, database, etc.
loaderTF - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.EditSourcePanel
 
loadSequence() - Static method in class edu.upenn.gloDB.gui.GUISequenceIO
Use a FileChooser to select a Sequence file to load.
loadSequence - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
loadTrack() - Static method in class edu.upenn.gloDB.gui.GUITrackIO
Use a FileChooser to select a Track file to load.
loadTrack - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
lookingAhead - Variable in class edu.upenn.gloDB.parser.Parser
 
LOOP_DETECTED - Static variable in error edu.upenn.gloDB.parser.TokenMgrError
Detected (and bailed out of) an infinite loop in the token manager.
lREPEAT - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
lSET - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 

M

main(String[]) - Static method in class edu.upenn.gloDB.GloDBMain
 
matched - Variable in class edu.upenn.gloDB.parser.Operation
Number of times the Operation has been matched.
MAX_FEATURES - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
This is the total number of features that will be displayed in the feature list.
maxL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
maxL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
maxLength() - Method in class edu.upenn.gloDB.FuzzyFeature
This is the same as length().
maxLength - Variable in class edu.upenn.gloDB.gui.QueryElement
Maximum acceptible Feature width.
maxLength - Variable in class edu.upenn.gloDB.parser.Operation
Maximum acceptible Feature width.
maxNextCharInd - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
maxPos - Variable in class edu.upenn.gloDB.gui.QueryElement
Maximum ordered position ('POS').
maxPos - Variable in class edu.upenn.gloDB.parser.Operation
Maximum number of positions since the previous Track.
maxPosTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
maxRepeat - Variable in class edu.upenn.gloDB.gui.QueryElement
Maximum number of repeating features.
maxRepeat - Variable in class edu.upenn.gloDB.parser.Operation
Maximum number of repeating features.
maxRepeatTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
maxSeqPos - Variable in class edu.upenn.gloDB.gui.QueryElement
Maximum acceptible position within 'sequence'.
maxSeqPos - Variable in class edu.upenn.gloDB.parser.Operation
Maximum acceptible position within 'sequence'.
maxSeqPosTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
maxWidthTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
maxWithin - Variable in class edu.upenn.gloDB.gui.QueryElement
Maximum number of positions between repeating features.
maxWithin - Variable in class edu.upenn.gloDB.parser.Operation
Maximum number of positions between repeating features.
maxWithinTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
mergeContiguous(Track) - Static method in class edu.upenn.gloDB.FeatureUtils
This will merge all overlapping Features in the track, creating new Feature objects as necessary.
mergeContiguous() - Method in class edu.upenn.gloDB.Track
This will merge all overlapping Features in the Track, creating new Feature objects as necessary.
messages - Static variable in class edu.upenn.gloDB.gui.Root
This will contain all error and warning messages.
messages - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
minL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
minL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
minLength() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the minimum number of positions contained in the Feature ((stop - start) + 1).
minLength - Variable in class edu.upenn.gloDB.gui.QueryElement
Minimum acceptible Feature width.
minLength - Variable in class edu.upenn.gloDB.parser.Operation
Minimum acceptible Feature width.
minPos - Variable in class edu.upenn.gloDB.gui.QueryElement
Minimum ordered position ('POS').
minPos - Variable in class edu.upenn.gloDB.parser.Operation
Minimum number of positions since the previous Track.
minPosTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
minRepeat - Variable in class edu.upenn.gloDB.gui.QueryElement
Minimum number of repeating features.
minRepeat - Variable in class edu.upenn.gloDB.parser.Operation
Minimum number of repeating features.
minRepeatTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
minSeqPos - Variable in class edu.upenn.gloDB.gui.QueryElement
Minimum acceptible position within 'sequence'.
minSeqPos - Variable in class edu.upenn.gloDB.parser.Operation
Minimum acceptible position within 'sequence'.
minSeqPosTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
MINUS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
minWidthTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
minWithin - Variable in class edu.upenn.gloDB.gui.QueryElement
Minimum number of positions between repeating features.
minWithin - Variable in class edu.upenn.gloDB.parser.Operation
Minimum number of positions between repeating features.
minWithinTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 

N

negate - Variable in class edu.upenn.gloDB.gui.QueryElement
Negate?
negate - Variable in class edu.upenn.gloDB.parser.Operation
Flag for whether to invert the output Track, treating the Track as a mask over the Sequence (ie binary operation).
negate() - Method in class edu.upenn.gloDB.parser.Parser
 
negate(Track) - Static method in class edu.upenn.gloDB.parser.ParserUtils
This will perform a 'binary' inversion of the Features in the Track.
negateChB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
newB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
newSequence() - Static method in class edu.upenn.gloDB.gui.GUISequenceIO
 
newSequence - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
newSequenceLoader(String) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Present a dialog box for changing sequence loader.
newToken(int) - Static method in class edu.upenn.gloDB.parser.Token
Returns a new Token object, by default.
next - Variable in class edu.upenn.gloDB.parser.Parser.JJCalls
 
next - Variable in class edu.upenn.gloDB.parser.Token
A reference to the next regular (non-special) token from the input stream.
nextFeature() - Method in class edu.upenn.gloDB.parser.Operation
Return the next Feature in iterator.
nINTEGER - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
noRepeats() - Method in class edu.upenn.gloDB.Track
This will return a copy of the track without any duplicate features (based on start/stop values).
numFeatures() - Method in class edu.upenn.gloDB.parser.Operation
Returns the number of Features contained in Operation.
numFeatures() - Method in class edu.upenn.gloDB.Track
Returns the number of Features contained in the Track.
numFeaturesL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
numSources() - Method in class edu.upenn.gloDB.Track
Returns the number of Sources spanned by the Track.
nValue() - Method in class edu.upenn.gloDB.parser.Parser
 

O

OBJECT - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
ObjectHandles - Class in edu.upenn.gloDB
ObjectHandles.
ObjectHandles() - Constructor for class edu.upenn.gloDB.ObjectHandles
 
objectL - Variable in class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
ObjectSelectorDialog - Class in edu.upenn.gloDB.gui
This class is used to present a modal dialog for selecting an item from the 'objects' array and includes the selected item in the 'out' arraylist.
ObjectSelectorDialog(String, Object[], ArrayList) - Constructor for class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
offset - Variable in class edu.upenn.gloDB.Sequence
This is the starting position for this Sequence on the chromosome.
offsetL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
okB - Variable in class edu.upenn.gloDB.gui.FieldEditDialog
 
openFileChooser(int, FileFilter) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Create a file chooser for opening files.
Operation - Class in edu.upenn.gloDB.parser
These objects store the operations parsed by the parser.
Operation() - Constructor for class edu.upenn.gloDB.parser.Operation
Create a new Operation object, used by clone() below.
Operation(ArrayList) - Constructor for class edu.upenn.gloDB.parser.Operation
Create a new Operation object containing a group.
Operation(Track) - Constructor for class edu.upenn.gloDB.parser.Operation
Create a new Operation object with a Track.
Operation(Set) - Constructor for class edu.upenn.gloDB.parser.Operation
Create a new Operation object with a set of Tracks.
operator - Variable in class edu.upenn.gloDB.gui.QueryElement
Index for type of operation to be performed.
Operator - Class in edu.upenn.gloDB.parser
Methods for processing the different types of operators.
Operator() - Constructor for class edu.upenn.gloDB.parser.Operator
 
operator() - Method in class edu.upenn.gloDB.parser.Parser
 
operatorL - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
operatorRepeat(Operation) - Method in class edu.upenn.gloDB.parser.Parser
 
OPERATORS - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
OPERATORS - Static variable in class edu.upenn.gloDB.gui.QueryElement
 
opExpr() - Method in class edu.upenn.gloDB.parser.Parser
 
OR - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
oRepeat() - Method in class edu.upenn.gloDB.parser.Parser
 
origHTML - Variable in class edu.upenn.gloDB.gui.ViewHTML.HTMLEditorPane
 
output - Variable in class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
overlap(Feature) - Method in class edu.upenn.gloDB.ExactFeature
Returns the overlapping region between the two Features.
overlap(Feature) - Method in interface edu.upenn.gloDB.Feature
Returns the overlapping region between the two Features.
overlap(Feature, Feature) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns the overlapping region between the two Features.
overlap(Feature) - Method in class edu.upenn.gloDB.FuzzyFeature
Returns the overlapping region between the two Features.
overlaps(Feature) - Method in class edu.upenn.gloDB.ExactFeature
Returns 'true' if the Feature 'feature' has a position that overlaps this Feature.
overlaps(Feature) - Method in interface edu.upenn.gloDB.Feature
Returns 'true' if the Feature 'feature' has at least one position that overlaps positions in this Feature.
overlaps(Feature, Track) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns 'true' if the Feature and Track overlap.
overlaps(Feature, Feature) - Static method in class edu.upenn.gloDB.FeatureUtils
Returns 'true' if the Features have overlapping positions.
overlaps(Feature) - Method in class edu.upenn.gloDB.FuzzyFeature
Returns 'true' if the feature 'featCk' has positions that overlap positions in this feature.
overlaps(Feature) - Method in class edu.upenn.gloDB.Track
Returns 'true' if the Feature 'featureB' overlaps at least one Feature in this Track.
overlaps(Track) - Method in class edu.upenn.gloDB.Track
Returns 'true' if a Feature in trackB overlaps at least one Feature in this Track.

P

parsed - Variable in class edu.upenn.gloDB.parser.Parser
An ArrayList containing the parsed Tracks.
ParseException - Exception in edu.upenn.gloDB.parser
This exception is thrown when parse errors are encountered.
ParseException(Token, int[][], String[]) - Constructor for exception edu.upenn.gloDB.parser.ParseException
This constructor is used by the method "generateParseException" in the generated parser.
ParseException() - Constructor for exception edu.upenn.gloDB.parser.ParseException
The following constructors are for use by you for whatever purpose you can think of.
ParseException(String) - Constructor for exception edu.upenn.gloDB.parser.ParseException
 
parseHeader(String) - Method in interface edu.upenn.gloDB.io.FASTAParser
 
parseHeader(String) - Method in class edu.upenn.gloDB.io.FASTAParserDefault
As the default parser, do not process the header at all, except to remove the leading '>'.
parseHeader(String) - Method in class edu.upenn.gloDB.io.FASTAParserFly
 
parseHeader(String) - Method in class edu.upenn.gloDB.io.FASTAParserMinimal
 
parseLine() - Method in class edu.upenn.gloDB.parser.Parser
 
Parser - Class in edu.upenn.gloDB.parser
The parser is created using javacc.
Parser(String) - Constructor for class edu.upenn.gloDB.parser.Parser
Construct a new Parser using trackPool as the set Tracks to search.
Parser(InputStream) - Constructor for class edu.upenn.gloDB.parser.Parser
 
Parser(Reader) - Constructor for class edu.upenn.gloDB.parser.Parser
 
Parser(ParserTokenManager) - Constructor for class edu.upenn.gloDB.parser.Parser
 
Parser.JJCalls - Class in edu.upenn.gloDB.parser
 
Parser.JJCalls() - Constructor for class edu.upenn.gloDB.parser.Parser.JJCalls
 
Parser.LookaheadSuccess - Error in edu.upenn.gloDB.parser
 
Parser.LookaheadSuccess() - Constructor for error edu.upenn.gloDB.parser.Parser.LookaheadSuccess
 
ParserConstants - Interface in edu.upenn.gloDB.parser
 
parserDefs - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
ParserTokenManager - Class in edu.upenn.gloDB.parser
 
ParserTokenManager(SimpleCharStream) - Constructor for class edu.upenn.gloDB.parser.ParserTokenManager
 
ParserTokenManager(SimpleCharStream, int) - Constructor for class edu.upenn.gloDB.parser.ParserTokenManager
 
ParserUtils - Class in edu.upenn.gloDB.parser
Methods to process the Operations ArrayList produced by the parser.
ParserUtils() - Constructor for class edu.upenn.gloDB.parser.ParserUtils
 
PLUS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
POS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
position() - Method in class edu.upenn.gloDB.parser.Parser
 
POSITIONS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
post(String) - Static method in class edu.upenn.gloDB.io.GenomeBrowser
 
prevCharIsCR - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
prevCharIsLF - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
printError(String) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the error message to either the gui or stderr.
printMsg(String) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the message to either the gui or stderr.
printMsg(String, int) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the message to either the gui or stderr.
printMsg(String, boolean) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the message to either the gui or stderr.
printMsg(String, int, boolean) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the message to either the gui or stderr.
printWarning(String) - Static method in class edu.upenn.gloDB.GloDBUtils
Display the warning message to either the gui or stderr.
processOperation(Track, Operation) - Static method in class edu.upenn.gloDB.parser.Operator
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.

Q

QueryBuilder - Class in edu.upenn.gloDB.gui
Browse existing Tracks.
QueryBuilder() - Constructor for class edu.upenn.gloDB.gui.QueryBuilder
 
QueryBuilder(String) - Constructor for class edu.upenn.gloDB.gui.QueryBuilder
 
QueryBuilder.ListTableModel - Class in edu.upenn.gloDB.gui
 
QueryBuilder.ListTableModel() - Constructor for class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
 
QueryElement - Class in edu.upenn.gloDB.gui
Contains query info for either a single Track or a group of QueryElements (ie Tracks).
QueryElement() - Constructor for class edu.upenn.gloDB.gui.QueryElement
Create a new QueryElement object.
QueryElement(String) - Constructor for class edu.upenn.gloDB.gui.QueryElement
Create a new QueryElement object.
queryTF - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
queryTracks - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
quit - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 

R

random - Static variable in class edu.upenn.gloDB.io.GenomeBrowser
 
random - Static variable in class edu.upenn.gloDB.Sequence
Used to create random ids.
random - Static variable in class edu.upenn.gloDB.Track
Used to create random IDs.
randomID(String) - Static method in class edu.upenn.gloDB.Sequence
 
randomID(String) - Static method in class edu.upenn.gloDB.Track
Uses 'base' to create a random ID string that doesn't already exist in the trackPool.
randomString() - Static method in class edu.upenn.gloDB.io.GenomeBrowser
 
readChar() - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
rebuildTrack(Track) - Static method in class edu.upenn.gloDB.ObjectHandles
Rebuilds the Track relevant lists.
ReInit(InputStream) - Method in class edu.upenn.gloDB.parser.Parser
 
ReInit(Reader) - Method in class edu.upenn.gloDB.parser.Parser
 
ReInit(ParserTokenManager) - Method in class edu.upenn.gloDB.parser.Parser
 
ReInit(SimpleCharStream) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
ReInit(SimpleCharStream, int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
ReInit(Reader, int, int, int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInit(Reader, int, int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInit(Reader) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInit(InputStream, int, int, int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInit(InputStream) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInit(InputStream, int, int) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
ReInitRounds() - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
reloadData() - Method in class edu.upenn.gloDB.Sequence
This will load the data from 'dataLoader' if overwriting the current value of data.
removeAllRows() - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Removes all rows from the table.
removeFeature(Feature) - Method in class edu.upenn.gloDB.Track
Removes a Feature from 'features'.
removeRow(int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Removes the QueryElement that represents the specified row in the table.
removeRows(int[]) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Removes the QueryElements that represent the rows specified.
removeRows(int, int) - Method in class edu.upenn.gloDB.gui.QueryBuilder.ListTableModel
Removes the QueryElements that represent the specified row in the table.
removeSequence(Sequence) - Static method in class edu.upenn.gloDB.ObjectHandles
Removes the Sequence object for sequencePool and other relevant lists.
removeTrack(String) - Static method in class edu.upenn.gloDB.ObjectHandles
Removes the Track object for trackPool and other relevant lists.
removeTrack(Track) - Static method in class edu.upenn.gloDB.ObjectHandles
Removes the Track object for trackPool and other relevant lists.
renameTrack(String) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Present a dialog box for renaming a particular Track.
renameTrack(String, String) - Static method in class edu.upenn.gloDB.ObjectHandles
Changes the Track's ID in trackPool, trackList, and trackBySequenceList.
renameTrack(Track, String) - Static method in class edu.upenn.gloDB.ObjectHandles
Changes the Track's ID in trackPool, trackList, and trackBySequenceList.
REPEATED - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
resetGloDBDefaults() - Static method in class edu.upenn.gloDB.GloDBUtils
RE-set GloDB user defaults.
resetGUIDefaults() - Static method in class edu.upenn.gloDB.gui.GUIUtils
RE-set GUI user defaults.
resetTrack() - Method in class edu.upenn.gloDB.parser.Operation
Restart iterator.
rGROUP - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
rLENGTH - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
Root - Class in edu.upenn.gloDB.gui
Base window for GUI.
Root() - Constructor for class edu.upenn.gloDB.gui.Root
 
Root.RootFrame - Class in edu.upenn.gloDB.gui
 
Root.RootFrame() - Constructor for class edu.upenn.gloDB.gui.Root.RootFrame
 
rootFrame - Static variable in class edu.upenn.gloDB.gui.Root
 
rREPEAT - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
rSET - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
run(HashMap, HashMap) - Method in class edu.upenn.gloDB.parser.Parser
Performs the parsing.
runCommand(String, boolean) - Static method in class edu.upenn.gloDB.gui.Root
This will add the String to the history and if 'toConsole', then run the command through the console.
runGC() - Static method in class edu.upenn.gloDB.GloDBMain
 

S

s_runtime - Static variable in class edu.upenn.gloDB.GloDBMain
 
sAND - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
save - Variable in class edu.upenn.gloDB.gui.FieldEditDialog
 
save(String) - Method in class edu.upenn.gloDB.io.FASTASequence
Save the Seqeuence to a file based on it's ID.
save(String, String, boolean) - Method in class edu.upenn.gloDB.io.FASTASequence
Save the Sequence data.
save(String) - Method in class edu.upenn.gloDB.io.FASTATrack
Save the Track to a file based on it's ID.
save(String, String, boolean) - Method in class edu.upenn.gloDB.io.FASTATrack
Save all Features in a FASTA file.
save(String) - Method in class edu.upenn.gloDB.io.GenBankTrack
Save the Track to a file based on it's ID.
save(String, String, boolean) - Method in class edu.upenn.gloDB.io.GenBankTrack
Save all Features in a GloDB file.
save(String) - Method in class edu.upenn.gloDB.io.GFFTrack
Save the Track to a file based on it's ID.
save(String, String, boolean) - Method in class edu.upenn.gloDB.io.GFFTrack
Save all Features in a GFF file.
save(String) - Method in class edu.upenn.gloDB.io.GloDBTrack
Save the Track to a file based on it's ID.
save(String, String, boolean) - Method in class edu.upenn.gloDB.io.GloDBTrack
Save all Features in a GloDB file.
save(String) - Method in interface edu.upenn.gloDB.io.SequenceFile
Save the Sequence object to a file based on it's ID.
save(String, String, boolean) - Method in interface edu.upenn.gloDB.io.SequenceFile
Save the Sequence object data.
save(String) - Method in interface edu.upenn.gloDB.io.TrackFile
Save the Track to a file based on it's ID.
save(String, String, boolean) - Method in interface edu.upenn.gloDB.io.TrackFile
Save the object data.
saveFileChooser(int, FileFilter) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Use a JFileChooser the get the file info for saving a Sequence.
saveFileChooser() - Method in class edu.upenn.gloDB.gui.ViewHTML
Use a JFileChooser the get the file info for saving HTML to a file.
saveFileChooser() - Static method in class edu.upenn.gloDB.io.HTMLFile
Use a JFileChooser the get the file info for saving HTML to a file.
saveInputStream(InputStream) - Static method in class edu.upenn.gloDB.io.HTMLFile
 
saveInputStream(InputStream, String, boolean) - Static method in class edu.upenn.gloDB.io.HTMLFile
 
saveSequence(String) - Static method in class edu.upenn.gloDB.gui.GUISequenceIO
Use a FileChooser to save the given Sequence, returning the filename.
saveSequence - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
saveText(String, boolean) - Method in class edu.upenn.gloDB.gui.ViewHTML
Save the html text to a file.
saveText(String) - Static method in class edu.upenn.gloDB.io.HTMLFile
Save the html text to a file.
saveText(String, String, boolean) - Static method in class edu.upenn.gloDB.io.HTMLFile
Save the html text to a file.
saveTrack(String) - Static method in class edu.upenn.gloDB.gui.GUITrackIO
Use a FileChooser to save the given Track, returning the filename.
saveTrack - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
saveURL(URL) - Static method in class edu.upenn.gloDB.io.HTMLFile
 
saveURL(URL, String, boolean) - Static method in class edu.upenn.gloDB.io.HTMLFile
 
selectB - Variable in class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
selectHistory - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
selectSequence(String) - Method in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
selectTrack(String) - Method in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
SEPARATOR - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
SEQUENCE - Static variable in class edu.upenn.gloDB.GloDBUtils
 
sequence - Variable in class edu.upenn.gloDB.gui.QueryElement
Sequence ID.
sequence - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
sequence - Variable in class edu.upenn.gloDB.parser.Operation
If not null, then ignore all other Sequences when testing for Feature matches.
sequence(Operation) - Method in class edu.upenn.gloDB.parser.Parser
 
SEQUENCE - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
Sequence - Class in edu.upenn.gloDB
Sequence.
Sequence() - Constructor for class edu.upenn.gloDB.Sequence
Create a new Sequence object and add it to the set of Sequence objects.
Sequence(String) - Constructor for class edu.upenn.gloDB.Sequence
Create a new Sequence object with the specified id, and add it to the set of Sequence objects.
Sequence(boolean) - Constructor for class edu.upenn.gloDB.Sequence
Create a new Sequence object and add the newly created Sequence object to the set of sequence objects if addToPool is true.
Sequence(boolean, String) - Constructor for class edu.upenn.gloDB.Sequence
Create a new Sequence object and add the newly created Sequence object to the set of sequence objects if addToPool is true.
SequenceBrowser - Class in edu.upenn.gloDB.gui
Browse existing Sequences.
SequenceBrowser() - Constructor for class edu.upenn.gloDB.gui.SequenceBrowser
 
SequenceBrowser.BrowserFrame - Class in edu.upenn.gloDB.gui
 
SequenceBrowser.BrowserFrame() - Constructor for class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
SequenceBrowser.BrowserFrame.EditSourcePanel - Class in edu.upenn.gloDB.gui
Displays the Sequence data.
SequenceBrowser.BrowserFrame.EditSourcePanel() - Constructor for class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.EditSourcePanel
 
SequenceBrowser.BrowserFrame.newSequencePanel - Class in edu.upenn.gloDB.gui
Handle newSequence dialog.
SequenceBrowser.BrowserFrame.newSequencePanel() - Constructor for class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.newSequencePanel
 
SequenceBrowser.BrowserFrame.ViewSequencePanel - Class in edu.upenn.gloDB.gui
Displays the Sequence data.
SequenceBrowser.BrowserFrame.ViewSequencePanel() - Constructor for class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.ViewSequencePanel
 
sequenceCB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
sequenceCB - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
sequenceChB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
SequenceFile - Interface in edu.upenn.gloDB.io
Interface for files that contain Sequences (ie.
sequenceFileTypes - Static variable in class edu.upenn.gloDB.io.FileIO
This HashSet is used to store references to SequenceFile types.
sequenceIterator() - Static method in class edu.upenn.gloDB.ObjectHandles
Returns a iterator over all Sequences in sequencePool.
sequenceL - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
sequenceList - Static variable in class edu.upenn.gloDB.ObjectHandles
This is a duplicate list of Sequences in the sequencePool.
SequenceLoader - Interface in edu.upenn.gloDB
Interface for objects that load sequence data (ie.
sequencePool - Static variable in class edu.upenn.gloDB.ObjectHandles
The set of all existing Sequences.
sequencePool - Variable in class edu.upenn.gloDB.parser.Parser
The set of Sequences to be used.
sequenceRef() - Method in class edu.upenn.gloDB.parser.Parser
 
sequences - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
sequenceSelected(String) - Method in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
This will update the SequenceBrowser for the currently selected Sequence.
sequenceSelector() - Static method in class edu.upenn.gloDB.gui.GUIUtils
Present a dialog box for selecting a particular Sequence.
setAttributes(String) - Method in class edu.upenn.gloDB.AbstractFeature
Set the attributes.
setAttributes(HashMap) - Method in class edu.upenn.gloDB.AbstractFeature
Set the attributes using a HashMap.
setAttributes(String) - Method in interface edu.upenn.gloDB.Feature
Set the Feature attributes.
setAttributes(HashMap) - Method in interface edu.upenn.gloDB.Feature
Set the Feature attributes from a HashMap.
setAttributes(HashMap) - Method in class edu.upenn.gloDB.Sequence
Set the sequence attributes.
setAttributes(HashMap) - Method in class edu.upenn.gloDB.Track
Set the attributes.
setData(String) - Method in class edu.upenn.gloDB.Sequence
Set the Sequence data, expecting a single unformatted string.
setDataLoader(SequenceLoader) - Method in class edu.upenn.gloDB.Sequence
Set the Sequence source parser.
setDebugStream(PrintStream) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 
setFeatures(TreeSet) - Method in class edu.upenn.gloDB.Track
This will replace 'features' with the TreeSet argument.
setGroup(ArrayList) - Method in class edu.upenn.gloDB.gui.QueryElement
If null value, then will set group to a new ArrayList().
setGroup(ArrayList) - Method in class edu.upenn.gloDB.parser.Operation
Sets the array of Operations.
setID(String) - Method in class edu.upenn.gloDB.gui.QueryBuilder
 
setID(String) - Method in class edu.upenn.gloDB.Track
Set the ID.
setID(String, boolean) - Method in class edu.upenn.gloDB.Track
Set the ID.
setIgnore(boolean) - Method in class edu.upenn.gloDB.parser.Operation
Sets the ignore flag.
setIgnoreAttributes(boolean) - Static method in class edu.upenn.gloDB.GloDBUtils
Set the IGNORE_ATTRIBUTES flag.
setLength(int, int) - Method in class edu.upenn.gloDB.parser.Operation
This will set the min/max Length for all Features in "track".
setLoaderArgs(HashMap) - Method in class edu.upenn.gloDB.Sequence
Set the sequence loaderArgs.
setMaxLength(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMaxPos(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMaxRepeat(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMaxSeqPos(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMaxWithin(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMinLength(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMinPos(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMinRepeat(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMinSeqPos(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setMinWithin(String) - Method in class edu.upenn.gloDB.gui.QueryElement
 
setNegate(boolean) - Method in class edu.upenn.gloDB.parser.Operation
Flag for whether to invert the output Track, treating the Track as a mask over the Sequence (ie binary operation).
setOffset(int) - Method in class edu.upenn.gloDB.Sequence
Set the Sequence starting position on the chromosome.
setRepeat(int, int) - Method in class edu.upenn.gloDB.parser.Operation
This will set the min/max Repeat for all Features in "track".
setRepeat(int, int, int, int) - Method in class edu.upenn.gloDB.parser.Operation
 
setSeqPos(int, int) - Method in class edu.upenn.gloDB.parser.Operation
This will set the min/max seqquence position for all Features in "track".
setSequence(Sequence) - Method in class edu.upenn.gloDB.parser.Operation
This will remove all Features from "track" that are not on "sequence".
setShowAllFiles(boolean) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Set the SHOW_ALL_FILES flag.
setSystemProperty(String, String) - Static method in class edu.upenn.gloDB.GloDBMain
 
setText(String) - Method in class edu.upenn.gloDB.gui.ViewHTML.HTMLEditorPane
 
setType(int) - Method in class edu.upenn.gloDB.parser.Operation
Set the Operation type: 0 = POS, 1 = AND, 2 = nAND, 3 = OR, 4 = LESS 10 = ., 11 = &&, 12 = ^&&, 13 = ||, 14 = -
setup(Object, int) - Method in class edu.upenn.gloDB.gui.ViewHTML
 
setUseFileExtensions(boolean) - Static method in class edu.upenn.gloDB.gui.GUIUtils
Set the USE_FILE_EXTENSIONS flag.
setVerbose(int) - Static method in class edu.upenn.gloDB.GloDBUtils
Set the VERBOSE flag.
show() - Static method in class edu.upenn.gloDB.gui.Root
 
show() - Static method in class edu.upenn.gloDB.gui.SequenceBrowser
 
show(String) - Static method in class edu.upenn.gloDB.gui.SequenceBrowser
 
show() - Static method in class edu.upenn.gloDB.gui.TrackBrowser
 
show(String) - Static method in class edu.upenn.gloDB.gui.TrackBrowser
 
SHOW_ALL_FILES - Static variable in class edu.upenn.gloDB.gui.GUIUtils
By using global static variables, these values will persist across instances of the open/save fileChoosers.
showAllFiles() - Static method in class edu.upenn.gloDB.gui.GUIUtils
 
showMessages - Static variable in class edu.upenn.gloDB.gui.Root
Flag whether to display messages in the 'messages' panel.
SimpleCharStream - Class in edu.upenn.gloDB.parser
An implementation of interface CharStream, where the stream is assumed to contain only ASCII characters (without unicode processing).
SimpleCharStream(Reader, int, int, int) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
SimpleCharStream(Reader, int, int) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
SimpleCharStream(Reader) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
SimpleCharStream(InputStream, int, int, int) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
SimpleCharStream(InputStream, int, int) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
SimpleCharStream(InputStream) - Constructor for class edu.upenn.gloDB.parser.SimpleCharStream
 
sizeOf() - Static method in class edu.upenn.gloDB.GloDBMain
A simple class to experiment with your JVM's garbage collector and memory sizes for various data types.
sMINUS - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
solveOps(ArrayList) - Static method in class edu.upenn.gloDB.parser.ParserUtils
This will run solveOpsRecurse() which will recursively solve the Operations in the ArrayList 'ops'.
solveOps(ArrayList, String) - Static method in class edu.upenn.gloDB.parser.ParserUtils
This will run solveOpsRecurse() which will recursively solve the Operations in the ArrayList 'ops'.
solveOpsRecurse(ArrayList) - Static method in class edu.upenn.gloDB.parser.ParserUtils
This will solve the Operations in the ArrayList 'ops', calling itself to recursively resolve groups of Operations.
sortByMax(TreeSet) - Static method in class edu.upenn.gloDB.Track
Sort the Feature TreeSet by max values.
source - Variable in class edu.upenn.gloDB.AbstractFeature
The contig that underlies the positions.
sources - Variable in class edu.upenn.gloDB.Track
Map of Sequence object IDs to Features.
SP0 - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
SP1 - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
specialConstructor - Variable in exception edu.upenn.gloDB.parser.ParseException
This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).
specialToken - Variable in class edu.upenn.gloDB.parser.Token
This field is used to access special tokens that occur prior to this token, but after the immediately preceding regular (non-special) token.
STAR - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
start - Variable in class edu.upenn.gloDB.ExactFeature
The initial position defining this Feature.
start - Variable in class edu.upenn.gloDB.FuzzyFeature
The initial position defining this Feature.
startExt - Variable in class edu.upenn.gloDB.FuzzyFeature
The number of the positions defining the start position.
STATIC_LEXER_ERROR - Static variable in error edu.upenn.gloDB.parser.TokenMgrError
An attempt wass made to create a second instance of a static token manager.
staticFlag - Static variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
statusBar - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
statusBar - Static variable in class edu.upenn.gloDB.gui.Root
 
statusBar - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
statusBar - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
stop - Variable in class edu.upenn.gloDB.ExactFeature
The last position defining this Feature.
stop - Variable in class edu.upenn.gloDB.FuzzyFeature
The last position defining this Feature.
stopExt - Variable in class edu.upenn.gloDB.FuzzyFeature
The number of the positions defining the stop position.
stripDescriptor(String) - Method in class edu.upenn.gloDB.parser.Parser
Chop off preceeding descriptor.
SURL - Static variable in class edu.upenn.gloDB.io.GenomeBrowser
 
SwitchTo(int) - Method in class edu.upenn.gloDB.parser.ParserTokenManager
 

T

table - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
tableModel - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
TEXT - Static variable in class edu.upenn.gloDB.gui.ViewHTML
 
textFields - Variable in class edu.upenn.gloDB.gui.FieldEditDialog
 
thisDialog - Variable in class edu.upenn.gloDB.gui.FieldEditDialog
 
thisDialog - Variable in class edu.upenn.gloDB.gui.ObjectSelectorDialog
 
thisFrame - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
thisFrame - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.EditSourcePanel
 
thisFrame - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.newSequencePanel
 
thisFrame - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
thisFrame - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.ViewSequencePanel
 
thisFrame - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
thisFrame - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame.ViewSequencePanel
 
thisFrame - Variable in class edu.upenn.gloDB.gui.ViewHTML
 
thisFrame - Variable in class edu.upenn.gloDB.gui.ViewParserDefs
 
TIMES - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
toArray() - Method in class edu.upenn.gloDB.gui.QueryElement
Creates an array with the fields in the following order: "operator, negate, group, track, sequence, min/max length, min/max pos".
toggleShowMessages - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
token - Variable in class edu.upenn.gloDB.parser.Parser
 
Token - Class in edu.upenn.gloDB.parser
Describes the input token stream.
Token() - Constructor for class edu.upenn.gloDB.parser.Token
 
token_source - Variable in class edu.upenn.gloDB.parser.Parser
 
tokenBegin - Variable in class edu.upenn.gloDB.parser.SimpleCharStream
 
tokenImage - Variable in exception edu.upenn.gloDB.parser.ParseException
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred.
tokenImage - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
TokenMgrError - Error in edu.upenn.gloDB.parser
 
TokenMgrError() - Constructor for error edu.upenn.gloDB.parser.TokenMgrError
 
TokenMgrError(String, int) - Constructor for error edu.upenn.gloDB.parser.TokenMgrError
 
TokenMgrError(boolean, int, int, int, String, char, int) - Constructor for error edu.upenn.gloDB.parser.TokenMgrError
 
toString() - Method in class edu.upenn.gloDB.AbstractFeature
Returns description and Feature information.
toString() - Method in class edu.upenn.gloDB.ExactFeature
Only basic Feature information.
toString() - Method in interface edu.upenn.gloDB.Feature
Only returns basic Feature information.
toString() - Method in class edu.upenn.gloDB.FuzzyFeature
Only returns basic Feature information.
toString() - Method in class edu.upenn.gloDB.gui.QueryElement
Returns QueryElement information for debugging purposes.
toString() - Method in class edu.upenn.gloDB.io.FASTASequence
 
toString() - Method in class edu.upenn.gloDB.parser.Operation
Returns Operation information for debugging purposes.
toString() - Method in class edu.upenn.gloDB.parser.Parser
Returns the string to be parsed and the same string having been parsed information.
toString() - Method in class edu.upenn.gloDB.parser.Token
Returns the image.
toString() - Method in class edu.upenn.gloDB.Sequence
Returns attributes information.
toString() - Method in class edu.upenn.gloDB.Track
Only returns Feature start/stop position information.
toStringFull() - Method in class edu.upenn.gloDB.ExactFeature
Returns all Feature information.
toStringFull() - Method in interface edu.upenn.gloDB.Feature
Returns all Feature information, except the data.
toStringFull() - Method in class edu.upenn.gloDB.FuzzyFeature
Returns all Feature information.
toStringFull() - Method in class edu.upenn.gloDB.Track
Returns all description and Feature information.
toStringMin() - Method in class edu.upenn.gloDB.ExactFeature
Only returns start/stop position information.
toStringMin() - Method in interface edu.upenn.gloDB.Feature
Only returns Feature start/stop information.
toStringMin() - Method in class edu.upenn.gloDB.FuzzyFeature
Only returns start/stop position information.
toStringMore() - Method in class edu.upenn.gloDB.Track
Only returns Feature start/stop position information.
toStringQualifiers() - Method in class edu.upenn.gloDB.gui.QueryElement
Returns a String that contains the qualifiers (Sequence, Length, and SeqPos) formatted for a query.
TRACK - Static variable in class edu.upenn.gloDB.GloDBUtils
 
track - Variable in class edu.upenn.gloDB.gui.QueryElement
Track ID.
track - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
track - Variable in class edu.upenn.gloDB.parser.Operation
SortedSet of Features to be searched.
track(int) - Method in class edu.upenn.gloDB.parser.Parser
 
TRACK - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 
Track - Class in edu.upenn.gloDB
Tracks are collections of Features and allow accessing the Features as a sorted Set (sorted by source and position information) or grouped by the Feature source information.
Track() - Constructor for class edu.upenn.gloDB.Track
Create a new Track object and add it to the trackPool.
Track(String) - Constructor for class edu.upenn.gloDB.Track
Create a new Track object with the specified ID, and add it to the trackPool.
Track(boolean) - Constructor for class edu.upenn.gloDB.Track
Create a new Track object and add the newly create Track object to the trackPool if addToPool is true.
Track(boolean, String) - Constructor for class edu.upenn.gloDB.Track
Create a new Track object and add the newly create Track object to the trackPool if addToPool is true.
Track.FeatureMaxComparator - Class in edu.upenn.gloDB
 
Track.FeatureMaxComparator() - Constructor for class edu.upenn.gloDB.Track.FeatureMaxComparator
 
trackAssign() - Method in class edu.upenn.gloDB.parser.Parser
 
TrackBrowser - Class in edu.upenn.gloDB.gui
Browse existing Tracks.
TrackBrowser() - Constructor for class edu.upenn.gloDB.gui.TrackBrowser
 
TrackBrowser.BrowserFrame - Class in edu.upenn.gloDB.gui
 
TrackBrowser.BrowserFrame() - Constructor for class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
TrackBrowser.BrowserFrame.ViewSequencePanel - Class in edu.upenn.gloDB.gui
Displays the Sequence data.
TrackBrowser.BrowserFrame.ViewSequencePanel() - Constructor for class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame.ViewSequencePanel
 
trackBySequenceList - Static variable in class edu.upenn.gloDB.ObjectHandles
This is a list of all Tracks in the trackPool, that contain each Sequence.
trackCB - Variable in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
 
TrackFile - Interface in edu.upenn.gloDB.io
Interface for files that contain Features or Sequences (ie.
trackFileTypes - Static variable in class edu.upenn.gloDB.io.FileIO
This HashSet is used to store references to TrackFile types.
trackID - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
trackIterator() - Static method in class edu.upenn.gloDB.ObjectHandles
Returns a iterator over all Tracks in trackPool.
trackL - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
trackL - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
trackList - Static variable in class edu.upenn.gloDB.ObjectHandles
This is a duplicate list of Tracks in the trackPool.
trackPool - Static variable in class edu.upenn.gloDB.ObjectHandles
The HashMap of all existing Tracks.
trackPool - Variable in class edu.upenn.gloDB.parser.Parser
The set of Tracks to be used.
trackRef() - Method in class edu.upenn.gloDB.parser.Parser
 
tracks - Variable in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
 
trackSelected(String) - Method in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
This will update the TrackBrowser for the currently selected Track.
trackSelector() - Static method in class edu.upenn.gloDB.gui.GUIUtils
Present a dialog box for selecting a particular Track.
type - Variable in class edu.upenn.gloDB.parser.Operation
Flag for the type of operation to be performed with the preceeding Operation.

U

uncompressString(byte[]) - Static method in class edu.upenn.gloDB.GloDBUtils
 
ungroupB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
updateAttributes() - Method in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame
This is separate from sequenceSelected() so it can be called separately for when the attributes are changed in the attribute panel.
updateAttributes() - Method in class edu.upenn.gloDB.gui.TrackBrowser.BrowserFrame
This is separate from trackSelected() so it can be called separately for when the attributes are changed in the attribute panel.
updateB - Variable in class edu.upenn.gloDB.gui.QueryBuilder
 
updateEditPanel(QueryElement) - Method in class edu.upenn.gloDB.gui.QueryBuilder
 
UpdateLineColumn(char) - Method in class edu.upenn.gloDB.parser.SimpleCharStream
 
updateQuery() - Method in class edu.upenn.gloDB.gui.QueryBuilder
Updates the query text field based on the current list items.
updateQueryElement(QueryElement) - Method in class edu.upenn.gloDB.gui.QueryBuilder
 
updateValues() - Method in class edu.upenn.gloDB.gui.SequenceBrowser.BrowserFrame.EditSourcePanel
 
URL - Static variable in class edu.upenn.gloDB.gui.ViewHTML
 
USE_COMPRESSION - Static variable in class edu.upenn.gloDB.Sequence
When true then sequence data will be stored in the Sequence object in a compressed format.
USE_FILE_EXTENSIONS - Static variable in class edu.upenn.gloDB.gui.GUIUtils
 
usedMemory() - Static method in class edu.upenn.gloDB.GloDBMain
 
useFileExtensions() - Static method in class edu.upenn.gloDB.gui.GUIUtils
 
userDefaults - Static variable in class edu.upenn.gloDB.GloDBMain
User established properties.

V

validOperation(ArrayList) - Method in class edu.upenn.gloDB.parser.Parser
Test if 'ops' contains any Operations that lack a Feature.
value() - Method in class edu.upenn.gloDB.parser.Parser
 
VERBOSE - Static variable in class edu.upenn.gloDB.GloDBUtils
Amount of detailed feedback: 2 = lots, 1 = no warnings, 0 = no feedback.
viewAPI - Variable in class edu.upenn.gloDB.gui.Root.RootFrame
 
ViewHTML - Class in edu.upenn.gloDB.gui
Browse HTML file or text.
ViewHTML(URL) - Constructor for class edu.upenn.gloDB.gui.ViewHTML
 
ViewHTML(String) - Constructor for class edu.upenn.gloDB.gui.ViewHTML
 
ViewHTML(InputStream) - Constructor for class edu.upenn.gloDB.gui.ViewHTML
 
ViewHTML.HTMLEditorPane - Class in edu.upenn.gloDB.gui
This class is meant to wrap the JEditorPane because the JEditorPane munges up the HTML source when it stores the text.
ViewHTML.HTMLEditorPane() - Constructor for class edu.upenn.gloDB.gui.ViewHTML.HTMLEditorPane
 
ViewHTML.HTMLFilter - Class in edu.upenn.gloDB.gui
HTML FileFilter.
ViewHTML.HTMLFilter() - Constructor for class edu.upenn.gloDB.gui.ViewHTML.HTMLFilter
 
ViewHTML.Hyperactive - Class in edu.upenn.gloDB.gui
 
ViewHTML.Hyperactive() - Constructor for class edu.upenn.gloDB.gui.ViewHTML.Hyperactive
 
ViewParserDefs - Class in edu.upenn.gloDB.gui
View parser definitions.
ViewParserDefs() - Constructor for class edu.upenn.gloDB.gui.ViewParserDefs
 
viewTrack(String) - Static method in class edu.upenn.gloDB.io.GenomeBrowser
Posts 'track' to Genome Browser.

W

WARNING - Static variable in class edu.upenn.gloDB.GloDBUtils
 
WITHIN - Static variable in interface edu.upenn.gloDB.parser.ParserConstants
 

_

_runGC() - Static method in class edu.upenn.gloDB.GloDBMain
 

A B C D E F G H I J K L M N O P Q R S T U V W _


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