| Package | Description |
|---|---|
| org.biojava.bio |
The core classes that will be used throughout the bio packages.
|
| org.biojava.bio.annodb |
Databases of generic structured data (annotation) objects.
|
| org.biojava.bio.program.formats |
Experimental parsers using the tagvalue framework.
|
| org.biojava.bio.program.tagvalue |
Process files as streams of records, each with tags with values.
|
| org.biojava.bio.program.unigene |
Objects for representing Unigene clusters.
|
| Class and Description |
|---|
| ChangeTable
A mapping between keys and actions to turn old values into new values.
|
| PropertyChanger
Interface for objects that change tag names or properties systematically.
|
| Class and Description |
|---|
| Index2Model |
ParserListener
ParserListener is an immutable pairing of a parser and
listener. |
| TagValueListener
An object that wishes to be informed of events during the parsing of a file.
|
| Class and Description |
|---|
| ChangeTable.Changer
Callback used to produce a new value from an old one.
|
ParserListener
ParserListener is an immutable pairing of a parser and
listener. |
| TagValueListener
An object that wishes to be informed of events during the parsing of a file.
|
| Class and Description |
|---|
| BoundaryFinder |
| ChangeTable
A mapping between keys and actions to turn old values into new values.
|
| ChangeTable.Changer
Callback used to produce a new value from an old one.
|
| ChangeTable.Splitter
Callback used to produce a list of values from a single old one.
|
| Index2Model |
| LineSplitParser
A parser that splits a line into tag/value at a given column number.
|
ParserListener
ParserListener is an immutable pairing of a parser and
listener. |
| PropertyChanger
Interface for objects that change tag names or properties systematically.
|
| SimpleTagValueWrapper
Helper class to wrap one TagValueListener inside another one.
|
| StateMachine.BasicState
Implementation of a State in a state machine
|
| StateMachine.State
Interface for a State within this StateMachine
|
| StateMachine.Transition
class to represent a State Transition
|
| StateMachine.TransitionTable
Table of Transition destination States
and their corresponding Tags.
|
| TagValue
Utility class for representing tag-value pairs for TagValueParser
implementors.
|
| TagValueContext
Communication interface between Parser and a TagValueListener that allows
listeners to request that a parser/listener pair be pushed onto the stack to
handle the current tag.
|
| TagValueListener
An object that wishes to be informed of events during the parsing of a file.
|
| TagValueParser
Tokenize single records (lines of text, objects) into a tag and a value.
|
| TagValueWrapper
Interface for TagValueListeners that wrap other TagValueListeners
|
| Class and Description |
|---|
ParserListener
ParserListener is an immutable pairing of a parser and
listener. |
| TagValueListener
An object that wishes to be informed of events during the parsing of a file.
|