A B C D F G I J L M N O P R S T U W

A

ABOUT - Static variable in class jaligner.ui.images.ToolbarIcons

About icon

AlignCommandLine - class jaligner.ui.AlignCommandLine.

Command line interface for JAligner.

AlignCommandLine() - Constructor for class jaligner.ui.AlignCommandLine

AlignWindow - class jaligner.ui.AlignWindow.

Graphical user inteface for JAligner.

AlignWindow() - Constructor for class jaligner.ui.AlignWindow

Constructor

Alignment - class jaligner.Alignment.

Holds the output of a pairwise sequences alignment.

Alignment() - Constructor for class jaligner.Alignment

Constructor for Alignment

acidAt(int) - Method in class jaligner.Sequence

Returns the acid at specific location in the sequence

align(Sequence, Sequence, Matrix, float) - Static method in class jaligner.NeedlemanWunsch

Aligns two sequences by Needleman-Wunsch (global)

align(Sequence, Sequence, Matrix, float, float) - Static method in class jaligner.NeedlemanWunschGotoh

Aligns two sequences by Needleman-Wunsch (global)

align(Sequence, Sequence, Matrix, float, float) - Static method in class jaligner.SmithWatermanGotoh

Aligns two sequences by Smith-Waterman (local)

B

BUFFER_SIZE - Static variable in class jaligner.ui.filechooser.FileChooser

Buffer size while reading from or write to a file (4 KB)

C

CLOSE - Static variable in class jaligner.ui.images.ToolbarIcons

Close icon

CLUSTAL - class jaligner.formats.CLUSTAL.

CLUSTAL format.

CLUSTAL() - Constructor for class jaligner.formats.CLUSTAL

Constructor

COPY - Static variable in class jaligner.ui.images.ToolbarIcons

Copy icon

CUT - Static variable in class jaligner.ui.images.ToolbarIcons

Cut icon

Cell - class jaligner.Cell.

A cell in a similarity matrix, to hold row, column and score.

Cell() - Constructor for class jaligner.Cell

Constructor

ClipboardHandler - interface jaligner.ui.clipboard.ClipboardHandler.

Abstract class to handle setting and getting "text" contents of the system clipboard.

ClipboardHandlerAWT - class jaligner.ui.clipboard.ClipboardHandlerAWT.

Sets and gets the contents of the system clipboard.

ClipboardHandlerAWT() - Constructor for class jaligner.ui.clipboard.ClipboardHandlerAWT

ClipboardHandlerFactory - class jaligner.ui.clipboard.ClipboardHandlerFactory.

A factory for ClipboardHandler.

ClipboardHandlerJNLP - class jaligner.ui.clipboard.ClipboardHandlerJNLP.

Sets and gets the contents of the system clipboard.

ClipboardHandlerJNLP() - Constructor for class jaligner.ui.clipboard.ClipboardHandlerJNLP

ClipboardListener - interface jaligner.ui.clipboard.ClipboardListener.

Listener interface to get notified with the clipboard contents.

ClipboardPoller - class jaligner.ui.clipboard.ClipboardPoller.

Checks the system clipboard to notifies a listener with current contents.

ClipboardPoller(ClipboardListener) - Constructor for class jaligner.ui.clipboard.ClipboardPoller

Constructor

Commons - class jaligner.util.Commons.

Global constants/variables/settings

Commons() - Constructor for class jaligner.util.Commons

calculateScore() - Method in class jaligner.Alignment

Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).

changedUpdate(DocumentEvent) - Method in class jaligner.ui.AlignWindow

Implements changedUpdate of DocumentListener

checkScore() - Method in class jaligner.Alignment

Check if the calculated score matches the field score.

clipboardCheck(String) - Method in class jaligner.ui.AlignWindow

Implements the notify method of the interface ClipboardListener

clipboardCheck(String) - Method in interface jaligner.ui.clipboard.ClipboardListener

Notifies the listener with the current contents of the clipboard.

close() - Method in class jaligner.ui.logging.DocumentHandler

compare(Object, Object) - Method in class jaligner.matrix.MatricesCompartor

copy(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Copies the selected text to the system clipboard.

cut(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Copies the selected text to the system clipboad and then deletes it from the text component.

D

DELETE - Static variable in class jaligner.ui.images.ToolbarIcons

Delete icon

DIAGONAL - Static variable in class jaligner.Directions

Traceback direction diagonal

Directions - class jaligner.Directions.

Traceback directions.

Directions() - Constructor for class jaligner.Directions

DocumentHandler - class jaligner.ui.logging.DocumentHandler.

Logging handler of JTextPane.

DocumentHandler(JTextPane) - Constructor for class jaligner.ui.logging.DocumentHandler

Constructor

delete(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Deletes the selected text in a text component.

F

FASTA - class jaligner.formats.FASTA.

FASTA format.

FASTA() - Constructor for class jaligner.formats.FASTA

Constructor for FASTA.

FileChooser - class jaligner.ui.filechooser.FileChooser.

Opens and saves files.

FileChooser() - Constructor for class jaligner.ui.filechooser.FileChooser

FileChooserException - exception jaligner.ui.filechooser.FileChooserException.

File chooser exception

FileChooserException(String) - Constructor for class jaligner.ui.filechooser.FileChooserException

FileChooserFactory - class jaligner.ui.filechooser.FileChooserFactory.

A factory for FileChooser.

FileChooserJNLP - class jaligner.ui.filechooser.FileChooserJNLP.

Opens and saves files.

FileChooserJNLP() - Constructor for class jaligner.ui.filechooser.FileChooserJNLP

FileChooserTrusted - class jaligner.ui.filechooser.FileChooserTrusted.

Opens and saves files.

FileChooserTrusted() - Constructor for class jaligner.ui.filechooser.FileChooserTrusted

Format - class jaligner.formats.Format.

Abstract format

Format() - Constructor for class jaligner.formats.Format

FormatFactory - class jaligner.formats.FormatFactory.

Formats factory.

flush() - Method in class jaligner.ui.logging.DocumentHandler

format(String[], String[]) - Method in class jaligner.formats.CLUSTAL

Returns CLUSTAL format

format(Alignment) - Method in class jaligner.formats.CLUSTAL

Returns CLUSTAL format of the alignment

format(Sequence) - Method in class jaligner.formats.FASTA

Returns the name, description and sequence combined in one string.

format(Alignment) - Method in class jaligner.formats.FASTA

format(Alignment) - Method in class jaligner.formats.Format

Formats alignment

format(Alignment) - Method in class jaligner.formats.Pair

Formats an alignment object to the Pair_FORMAT format

format(LogRecord) - Method in class jaligner.ui.logging.RecordFormatter

This method is called for every log records

G

GAP - Static variable in class jaligner.Alignment

Gap character

GAP - Static variable in class jaligner.Markups

Markup line gap character

GIFS_HOME - Static variable in class jaligner.ui.images.ToolbarIcons

Path to the gifs folder

generate(float, float) - Static method in class jaligner.matrix.MatrixGenerator

Returns scoring matrix from a fixed match/mismatch scoring scheme.

generate(int) - Static method in class jaligner.test.RandomSequenceGenerator

Returns random sequence

getClipboardHandler() - Static method in class jaligner.ui.clipboard.ClipboardHandlerFactory

Returns an instance of a concrete ClipboardHandler.

getCol() - Method in class jaligner.Cell

getContents() - Method in interface jaligner.ui.clipboard.ClipboardHandler

Returns the contents of the system of the clipboard

getContents() - Method in class jaligner.ui.clipboard.ClipboardHandlerAWT

Gets the contents of the system clipboard

getContents() - Method in class jaligner.ui.clipboard.ClipboardHandlerJNLP

Gets the contents of the system clipboard

getCurrentRelease() - Static method in class jaligner.util.Commons

Returns the current release version of JAligner

getDescription() - Method in class jaligner.Sequence

Returns the sequence description

getDirection() - Method in class jaligner.TracebackNode

getExtend() - Method in class jaligner.Alignment

getFileChooser() - Static method in class jaligner.ui.filechooser.FileChooserFactory

Returns an instance of a concrete FileChooser.

getFileSeparator() - Static method in class jaligner.util.Commons

Returns system file separator.

getFormat(String) - Method in class jaligner.formats.FormatFactory

Returns an instance of Format.

getFormats() - Method in class jaligner.formats.FormatFactory

Returns a list of registered formats

getGaps() - Method in class jaligner.Alignment

getHead(Handler) - Method in class jaligner.ui.logging.RecordFormatter

This method is called just after the handler using this formatter is created

getId() - Method in class jaligner.Sequence

Returns the sequence id

getId() - Method in class jaligner.formats.Format

Returns format id

getId() - Method in class jaligner.matrix.Matrix

getIdentity() - Method in class jaligner.Alignment

getInputStream() - Method in class jaligner.ui.filechooser.NamedInputStream

getInstance() - Static method in class jaligner.formats.FormatFactory

Returns an instance for FormatFactory.

getJAlignerInfo() - Static method in class jaligner.util.Commons

Returns information about JAligner

getLength() - Method in class jaligner.TracebackNode

getLineSeparator() - Static method in class jaligner.util.Commons

Returns system line separator.

getMarkupLine() - Method in class jaligner.Alignment

getMatrix() - Method in class jaligner.Alignment

getName() - Method in class jaligner.ui.filechooser.NamedInputStream

getName1() - Method in class jaligner.Alignment

getName2() - Method in class jaligner.Alignment

getOpen() - Method in class jaligner.Alignment

getOriginalSequence1() - Method in class jaligner.Alignment

Returns original Sequence #1

getOriginalSequence2() - Method in class jaligner.Alignment

Returns original Sequence #2

getRow() - Method in class jaligner.Cell

getScore() - Method in class jaligner.Alignment

getScore() - Method in class jaligner.Cell

getScore(char, char) - Method in class jaligner.matrix.Matrix

getScores() - Method in class jaligner.matrix.Matrix

getSequence() - Method in class jaligner.Sequence

Returns the sequence string

getSequence1() - Method in class jaligner.Alignment

getSequence2() - Method in class jaligner.Alignment

getSimilarity() - Method in class jaligner.Alignment

getStart1() - Method in class jaligner.Alignment

getStart2() - Method in class jaligner.Alignment

getSummary() - Method in class jaligner.Alignment

Returns a summary for alignment

getTail(Handler) - Method in class jaligner.ui.logging.RecordFormatter

This method is called just after the handler using this formatter is closed

getType() - Method in class jaligner.Sequence

Returns the sequence type (nucleic or protein)

getUserDirectory() - Method in class jaligner.ui.filechooser.FileChooser

Gets the current user working directory

getUserDirectory() - Static method in class jaligner.util.Commons

Returns user's current directory.

I

IDENTITY - Static variable in class jaligner.Markups

Markup line identity character

insertUpdate(DocumentEvent) - Method in class jaligner.ui.AlignWindow

Implements insertUpdate of DocumentListener

isJnlp() - Static method in class jaligner.util.Commons

Returns true if jnlp is enabled

J

jaligner - package jaligner

Core classes for the implementation of Smith-Waterman-Gotoh algorithm

jaligner.example - package jaligner.example

Example for using API of JAligner to perform pairwise sequence alignment.

jaligner.formats - package jaligner.formats

Group of formats for output alignments.

jaligner.matrix - package jaligner.matrix

Scoring matrices package.

jaligner.test - package jaligner.test

Testing package.

jaligner.ui - package jaligner.ui

Command line and graphical user interface.

jaligner.ui.clipboard - package jaligner.ui.clipboard

Clipboard handling for JNLP and AWT.

jaligner.ui.filechooser - package jaligner.ui.filechooser

File loading and storing.

jaligner.ui.images - package jaligner.ui.images

Images used in the toolbar.

jaligner.ui.logging - package jaligner.ui.logging

Logging package.

jaligner.ui.util - package jaligner.ui.util

Text component utilites package.

jaligner.util - package jaligner.util

Utility classes for helping core and GUI classes.

L

LEFT - Static variable in class jaligner.Directions

Traceback direction left

length() - Method in class jaligner.Sequence

Returns the length of the sequence

list(boolean) - Static method in class jaligner.matrix.MatrixLoader

Returns a list of the scoring matrices in the matrices home directory

list() - Static method in class jaligner.matrix.MatrixLoader

Returns a list of the scoring matrices in the matrices home directory

load(String) - Static method in class jaligner.matrix.MatrixLoader

Loads scoring matrix from Jar file or file system.

load(NamedInputStream) - Static method in class jaligner.matrix.MatrixLoader

Loads scoring matrix from InputStream

loadP53Human() - Static method in class jaligner.example.SmithWatermanGotohExample

loadP53Mouse() - Static method in class jaligner.example.SmithWatermanGotohExample

M

MISMATCH - Static variable in class jaligner.Markups

Markup line mismatch character

Markups - class jaligner.Markups.

Markups line characters.

Markups() - Constructor for class jaligner.Markups

MatricesCompartor - class jaligner.matrix.MatricesCompartor.

Comparator to sort the scoring matrices by their names.

MatricesCompartor() - Constructor for class jaligner.matrix.MatricesCompartor

Matrix - class jaligner.matrix.Matrix.

Scoring matrix.

Matrix(String, float[][]) - Constructor for class jaligner.matrix.Matrix

MatrixGenerator - class jaligner.matrix.MatrixGenerator.

A utility class to generate a scoring matrix from a fixed match and mismatch scoring scheme.

MatrixGenerator() - Constructor for class jaligner.matrix.MatrixGenerator

MatrixLoader - class jaligner.matrix.MatrixLoader.

Scoring matrices loader from a jar file or a file system.

MatrixLoader() - Constructor for class jaligner.matrix.MatrixLoader

MatrixLoaderException - exception jaligner.matrix.MatrixLoaderException.

MatrixLoaderException(String) - Constructor for class jaligner.matrix.MatrixLoaderException

main(String[]) - Static method in class jaligner.example.NeedlemanWunschExample

main(String[]) - Static method in class jaligner.example.NeedlemanWunschGotohExample

main(String[]) - Static method in class jaligner.example.SmithWatermanGotohExample

main(String[]) - Static method in class jaligner.test.NeedlemanWunschGotohTester

main(String[]) - Static method in class jaligner.test.NeedlemanWunschTester

main(String[]) - Static method in class jaligner.test.RandomSequenceGenerator

Displays 10 random protein sequences with length 50.

main(String[]) - Static method in class jaligner.test.SmithWatermanGotohTester

main(String[]) - Static method in class jaligner.ui.AlignCommandLine

main(String[]) - Static method in class jaligner.ui.AlignWindow

N

NUCLEIC - Static variable in class jaligner.Sequence

Sequence type nucleic.

NamedInputStream - class jaligner.ui.filechooser.NamedInputStream.

NamedInputStream(String, InputStream) - Constructor for class jaligner.ui.filechooser.NamedInputStream

NeedlemanWunsch - class jaligner.NeedlemanWunsch.

An implementation of the Needleman-Wunsch algorithm for biological global pairwise sequence alignment.

NeedlemanWunschExample - class jaligner.example.NeedlemanWunschExample.

Example of using JAligner API to perform global pairwise sequence alignment with Needleman-Wunsch algorithm NeedlemanWunsch.

NeedlemanWunschExample() - Constructor for class jaligner.example.NeedlemanWunschExample

NeedlemanWunschGotoh - class jaligner.NeedlemanWunschGotoh.

An implementation of the Needleman-Wunsch algorithm with Gotoh's improvement for biological global pairwise sequence alignment.

NeedlemanWunschGotohExample - class jaligner.example.NeedlemanWunschGotohExample.

Example of using JAligner API to perform global pairwise sequence alignment with NeedlemanWunschGotoh.

NeedlemanWunschGotohExample() - Constructor for class jaligner.example.NeedlemanWunschGotohExample

NeedlemanWunschGotohTester - class jaligner.test.NeedlemanWunschGotohTester.

Testing the scores of the alignments of NeedlemanWunschGotoh.

NeedlemanWunschGotohTester() - Constructor for class jaligner.test.NeedlemanWunschGotohTester

NeedlemanWunschTester - class jaligner.test.NeedlemanWunschTester.

Testing the scores of the alignments of NeedlemanWunsch.

NeedlemanWunschTester() - Constructor for class jaligner.test.NeedlemanWunschTester

nextFocusAction - Variable in class jaligner.ui.AlignWindow

O

OPEN - Static variable in class jaligner.ui.images.ToolbarIcons

Open icon

open() - Method in class jaligner.ui.filechooser.FileChooser

Shows a dialog to select a file

open() - Method in class jaligner.ui.filechooser.FileChooserJNLP

Shows a dialog to select a file.

open() - Method in class jaligner.ui.filechooser.FileChooserTrusted

Shows a dialog to select a file.

open(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Opens a file and puts the contents of the file in a text component.

P

PASTE - Static variable in class jaligner.ui.images.ToolbarIcons

Paste icon

PRINT - Static variable in class jaligner.ui.images.ToolbarIcons

Print icon

PROTEIN - Static variable in class jaligner.Sequence

Sequence type protein.

Pair - class jaligner.formats.Pair.

Pair format.

Pair() - Constructor for class jaligner.formats.Pair

Constructor

PrintJobMointor - class jaligner.ui.util.PrintJobMointor.

Mointor for print job.

parse(String) - Static method in class jaligner.util.SequenceParser

Returns a parsed Sequence from a string.

parse(File) - Static method in class jaligner.util.SequenceParser

Returns a Sequence parsed and loaded from a file

paste(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Copies the text contents of the system clipboard to the text component.

prevFocusAction - Variable in class jaligner.ui.AlignWindow

print(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Prints the contents of a text component.

publish(LogRecord) - Method in class jaligner.ui.logging.DocumentHandler

R

RandomSequenceGenerator - class jaligner.test.RandomSequenceGenerator.

This class contains a random generator for protein sequences.

RandomSequenceGenerator() - Constructor for class jaligner.test.RandomSequenceGenerator

RecordFormatter - class jaligner.ui.logging.RecordFormatter.

Logging record formatter

RecordFormatter() - Constructor for class jaligner.ui.logging.RecordFormatter

registerFormat(Format) - Method in class jaligner.formats.FormatFactory

Registers format.

removeUpdate(DocumentEvent) - Method in class jaligner.ui.AlignWindow

Implements removeUpdate of DocumentListener

run() - Method in class jaligner.ui.clipboard.ClipboardPoller

Runs the thread

S

SAVE - Static variable in class jaligner.ui.images.ToolbarIcons

Save icon

SIMILARITY - Static variable in class jaligner.Markups

Markup line similarity character

SIZE - Static variable in class jaligner.matrix.Matrix

The size of the scoring matrix.

STOP - Static variable in class jaligner.Directions

Traceback direction stop

Sequence - class jaligner.Sequence.

A basic (nucleic or protein) sequence.

Sequence() - Constructor for class jaligner.Sequence

Constructor

Sequence(String) - Constructor for class jaligner.Sequence

Constructor

Sequence(String, String, String, int) - Constructor for class jaligner.Sequence

Constructor

SequenceParser - class jaligner.util.SequenceParser.

SequenceParser to sequences from different formats.

SequenceParser() - Constructor for class jaligner.util.SequenceParser

SequenceParserException - exception jaligner.util.SequenceParserException.

SequenceParserException(String) - Constructor for class jaligner.util.SequenceParserException

SmithWatermanGotoh - class jaligner.SmithWatermanGotoh.

An implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment.

SmithWatermanGotohExample - class jaligner.example.SmithWatermanGotohExample.

Example of using JAligner API to align P53 human aganist P53 mouse using Smith-Waterman-Gotoh algorithm.

SmithWatermanGotohExample() - Constructor for class jaligner.example.SmithWatermanGotohExample

SmithWatermanGotohTester - class jaligner.test.SmithWatermanGotohTester.

Testing the scores of the alignments of SmithWatermanGotoh.

SmithWatermanGotohTester() - Constructor for class jaligner.test.SmithWatermanGotohTester

save(InputStream, String) - Method in class jaligner.ui.filechooser.FileChooser

Saves an input stream to a file

save(InputStream, String) - Method in class jaligner.ui.filechooser.FileChooserJNLP

Saves an input stream to a file.

save(InputStream, String) - Method in class jaligner.ui.filechooser.FileChooserTrusted

Saves an input stream to a file.

save(JTextComponent, String) - Static method in class jaligner.ui.util.TextComponentUtil

Saves the contents of a text component to a file.

save(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Saves the contents of a text component to a file.

selectAll(JTextComponent) - Static method in class jaligner.ui.util.TextComponentUtil

Selects all contents of a text component.

set(int, int, float) - Method in class jaligner.Cell

Sets the row, column and score of the cell.

setCol(int) - Method in class jaligner.Cell

setContents(String) - Method in interface jaligner.ui.clipboard.ClipboardHandler

Sets the contents of the system of the clipboard

setContents(String) - Method in class jaligner.ui.clipboard.ClipboardHandlerAWT

Sets the contents of the system clipboard

setContents(String) - Method in class jaligner.ui.clipboard.ClipboardHandlerJNLP

Sets the contents of the system clipboard

setDescription(String) - Method in class jaligner.Sequence

Sets the sequence description

setDiagonal() - Method in class jaligner.TracebackNode

Sets the direction to diagonal

setExtend(float) - Method in class jaligner.Alignment

setGaps(int) - Method in class jaligner.Alignment

setId(String) - Method in class jaligner.Sequence

Sets the sequence id

setId(String) - Method in class jaligner.formats.Format

Sets format id

setIdentity(int) - Method in class jaligner.Alignment

setJnlp(boolean) - Static method in class jaligner.util.Commons

Sets the JNLP flag to true of false

setLeft(int) - Method in class jaligner.TracebackNode

Sets the direction to left

setMarkupLine(char[]) - Method in class jaligner.Alignment

setMatrix(Matrix) - Method in class jaligner.Alignment

setName1(String) - Method in class jaligner.Alignment

setName2(String) - Method in class jaligner.Alignment

setOpen(float) - Method in class jaligner.Alignment

setOriginalSequence1(Sequence) - Method in class jaligner.Alignment

setOriginalSequence2(Sequence) - Method in class jaligner.Alignment

setRow(int) - Method in class jaligner.Cell

setScore(float) - Method in class jaligner.Alignment

setScore(float) - Method in class jaligner.Cell

setSequence(String) - Method in class jaligner.Sequence

Sets the sequence string

setSequence1(char[]) - Method in class jaligner.Alignment

setSequence2(char[]) - Method in class jaligner.Alignment

setSimilarity(int) - Method in class jaligner.Alignment

setStart1(int) - Method in class jaligner.Alignment

setStart2(int) - Method in class jaligner.Alignment

setStop() - Method in class jaligner.TracebackNode

Sets the direction to stop

setType(int) - Method in class jaligner.Sequence

Sets the sequence type (nucleic or protein)

setUp(int) - Method in class jaligner.TracebackNode

Sets the direction to up

setUserDirectory(String) - Method in class jaligner.ui.filechooser.FileChooser

Sets the user working directory

start() - Method in class jaligner.ui.clipboard.ClipboardPoller

Starts the thread

subsequence(int, int) - Method in class jaligner.Sequence

Returns a subsequence

T

TextComponentUtil - class jaligner.ui.util.TextComponentUtil.

Text component (e.g.

TextComponentUtil() - Constructor for class jaligner.ui.util.TextComponentUtil

TextComponentUtilException - exception jaligner.ui.util.TextComponentUtilException.

TextComponentUtilException(String) - Constructor for class jaligner.ui.util.TextComponentUtilException

ToolbarIcons - class jaligner.ui.images.ToolbarIcons.

Toolbar icons

ToolbarIcons() - Constructor for class jaligner.ui.images.ToolbarIcons

TracebackNode - class jaligner.TracebackNode.

Traceback node

TracebackNode() - Constructor for class jaligner.TracebackNode

Constructor

toArray() - Method in class jaligner.Sequence

Returns the sequence as an array of characters.

toString() - Method in class jaligner.Sequence

Returns the sequence id and the sequence string

U

UP - Static variable in class jaligner.Directions

Traceback direction up

W

waitForPrintJob() - Method in class jaligner.ui.util.PrintJobMointor

Waits for print job

A B C D F G I J L M N O P R S T U W