Serialized Form


Package edu.upenn.gloDB

Class edu.upenn.gloDB.AbstractFeature extends java.lang.Object implements Serializable

Serialized Fields

source

java.lang.String source
The contig that underlies the positions.


attributes

java.lang.String attributes
This is similar to "qualifiers" in GenBank. ex: scores, strand (+/-), phase (within codon). Each key/value pair is delimited by a ";". the keys and values are separated by "=". ex: "scores=.; strand=+". Key based attribute searches are case sensitive.

Notes:
Should any of these be hardcoded as fields?

Class edu.upenn.gloDB.ExactFeature extends AbstractFeature implements Serializable

Serialized Fields

start

int start
The initial position defining this Feature.


stop

int stop
The last position defining this Feature.

Class edu.upenn.gloDB.FuzzyFeature extends AbstractFeature implements Serializable

Serialized Fields

start

int start
The initial position defining this Feature.


startExt

int startExt
The number of the positions defining the start position.


stop

int stop
The last position defining this Feature.


stopExt

int stopExt
The number of the positions defining the stop position.

Class edu.upenn.gloDB.GloDBException extends java.lang.RuntimeException implements Serializable

Class edu.upenn.gloDB.InvalidIDException extends GloDBException implements Serializable


Package edu.upenn.gloDB.gui

Class edu.upenn.gloDB.gui.FieldEditDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

thisDialog

FieldEditDialog thisDialog

save

java.util.ArrayList<E> save

textFields

java.util.ArrayList<E> textFields

okB

javax.swing.JButton okB

cancelB

javax.swing.JButton cancelB

Class edu.upenn.gloDB.gui.ObjectSelectorDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

thisDialog

ObjectSelectorDialog thisDialog

output

java.util.ArrayList<E> output

objectL

javax.swing.JList objectL

selectB

javax.swing.JButton selectB

cancelB

javax.swing.JButton cancelB

Class edu.upenn.gloDB.gui.QueryBuilder extends javax.swing.JFrame implements Serializable

Serialized Fields

OPERATORS

java.lang.String[] OPERATORS

queryTF

javax.swing.JTextField queryTF

table

javax.swing.JTable table

tableModel

QueryBuilder.ListTableModel tableModel

trackID

java.lang.String trackID

updateB

javax.swing.JButton updateB

groupB

javax.swing.JButton groupB

ungroupB

javax.swing.JButton ungroupB

deleteB

javax.swing.JButton deleteB

deleteAllB

javax.swing.JButton deleteAllB

copyB

javax.swing.JButton copyB

computeB

javax.swing.JButton computeB

newB

javax.swing.JButton newB

operatorL

javax.swing.JList operatorL

negateChB

javax.swing.JCheckBox negateChB

trackL

javax.swing.JList trackL

sequenceChB

javax.swing.JCheckBox sequenceChB

sequenceCB

javax.swing.JComboBox sequenceCB

minWidthTF

javax.swing.JTextField minWidthTF

maxWidthTF

javax.swing.JTextField maxWidthTF

minSeqPosTF

javax.swing.JTextField minSeqPosTF

maxSeqPosTF

javax.swing.JTextField maxSeqPosTF

minRepeatTF

javax.swing.JTextField minRepeatTF

maxRepeatTF

javax.swing.JTextField maxRepeatTF

minWithinTF

javax.swing.JTextField minWithinTF

maxWithinTF

javax.swing.JTextField maxWithinTF

minPosTF

javax.swing.JTextField minPosTF

maxPosTF

javax.swing.JTextField maxPosTF

thisFrame

QueryBuilder thisFrame

Class edu.upenn.gloDB.gui.ViewHTML extends javax.swing.JFrame implements Serializable

Serialized Fields

thisFrame

ViewHTML thisFrame

htmlText

ViewHTML.HTMLEditorPane htmlText

Class edu.upenn.gloDB.gui.ViewParserDefs extends javax.swing.JFrame implements Serializable

Serialized Fields

thisFrame

ViewParserDefs thisFrame

Package edu.upenn.gloDB.parser

Class edu.upenn.gloDB.parser.ParseException extends java.lang.Exception implements Serializable

Serialized Fields

specialConstructor

boolean specialConstructor
This variable determines which constructor was used to create this object and thereby affects the semantics of the "getMessage" method (see below).


currentToken

Token currentToken
This is the last token that has been consumed successfully. If this object has been created due to a parse error, the token followng this token will (therefore) be the first error token.


expectedTokenSequences

int[][] expectedTokenSequences
Each entry in this array is an array of integers. Each array of integers represents a sequence of tokens (by their ordinal values) that is expected at this point of the parse.


tokenImage

java.lang.String[] tokenImage
This is a reference to the "tokenImage" array of the generated parser within which the parse error occurred. This array is defined in the generated ...Constants interface.


eol

java.lang.String eol
The end of line string for this machine.

Class edu.upenn.gloDB.parser.TokenMgrError extends java.lang.Error implements Serializable

Serialized Fields

errorCode

int errorCode
Indicates the reason why the exception is thrown. It will have one of the above 4 values.




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