org::gel::mauve::gui::AlignFrame Class Reference

A dialog box implementing a graphical interface to the command-line mauveAligner tool. More...

Inheritance diagram for org::gel::mauve::gui::AlignFrame:

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Collaboration diagram for org::gel::mauve::gui::AlignFrame:

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List of all members.

Public Member Functions

void addButtonActionPerformed (java.awt.event.ActionEvent e)
void addNotify ()
void alignButtonActionPerformed (java.awt.event.ActionEvent evt)
 Read the user's genome alignment parameters and start the alignment using the command line mauveAligner tool.

 AlignFrame (Mauve mauve, boolean gui)
 AlignFrame (Mauve mauve)
void cancelButtonActionPerformed (java.awt.event.ActionEvent evt)
void collinearCheckBoxActionPerformed (java.awt.event.ActionEvent e)
void completeAlignment (int retcode)
void defaultSeedCheckBoxActionPerformed (java.awt.event.ActionEvent e)
void determineLCBsCheckBoxActionPerformed (java.awt.event.ActionEvent e)
boolean getCollinear ()
int getMinLcbWeight ()
String getOutput ()
boolean getRecursive ()
int getSeedWeight ()
String[] getSequences ()
void initComponents ()
boolean isLCBSearchEnabled ()
void outputButtonActionPerformed (java.awt.event.ActionEvent e)
void removeButtonActionPerformed (java.awt.event.ActionEvent e)
void setOutput (String filename)
void setVisible (boolean show)

Static Public Member Functions

String getBinaryPath (String name)
void printCommand (String[] cmd, PrintStream out)
 Prints an aligner command in an easily readable format.


Public Attributes

JButton alignButton = new JButton()
JButton cancelButton = new JButton()

Protected Member Functions

String[] makeAlignerCommand ()
void printCommand (String[] mauve_cmd)

Protected Attributes

JButton addButton = new JButton()
JFileChooser fc
 < contains the various parameter panels

java.awt.Frame frame
JScrollPane listScrollPane = new JScrollPane()
Mauve mauve
JTextField minLcbWeightText = new JTextField()
JButton outputButton = new JButton()
JTextField outputFileText = new JTextField()
JLabel outputLabel = new JLabel()
String read_filename
JButton removeButton = new JButton()
JSlider seedLengthSlider = new JSlider()
JList sequenceList = null
DefaultListModel sequenceListModel = new DefaultListModel()
JPanel sequencesPanel = new JPanel()
AlignWorker worker

Package Functions

File getDefaultFile () throws IOException
void thisWindowClosed (java.awt.event.WindowEvent e)
void thisWindowClosing (java.awt.event.WindowEvent e)

Package Attributes

JTabbedPane alignmentOptionPane = new JTabbedPane()
JCheckBox collinearCheckBox = new JCheckBox()
Dimension d
JCheckBox defaultSeedCheckBox = new JCheckBox()
JCheckBox determineLCBsCheckBox = new JCheckBox()
JLabel minLcbWeightLabel = new JLabel()
JPanel parameterPanel = new JPanel()
JPanel parentPanel = new JPanel()
JCheckBox recursiveCheckBox = new JCheckBox()
JLabel seedLengthLabel = new JLabel()
JLabel sequencesLabel = new JLabel()

Private Attributes

boolean mShown = false

Detailed Description

A dialog box implementing a graphical interface to the command-line mauveAligner tool.

Allows the user to manipulate various alignment options. Originally created with Metrowerks java gui designer.

Definition at line 41 of file AlignFrame.java.


Constructor & Destructor Documentation

org::gel::mauve::gui::AlignFrame::AlignFrame Mauve  mauve  )  [inline]
 

Definition at line 84 of file AlignFrame.java.

org::gel::mauve::gui::AlignFrame::AlignFrame Mauve  mauve,
boolean  gui
[inline]
 

Definition at line 88 of file AlignFrame.java.


Member Function Documentation

void org::gel::mauve::gui::AlignFrame::addButtonActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 608 of file AlignFrame.java.

References sequenceList, and sequenceListModel.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::addNotify  )  [inline]
 

Definition at line 518 of file AlignFrame.java.

References mShown.

void org::gel::mauve::gui::AlignFrame::alignButtonActionPerformed java.awt.event.ActionEvent  evt  )  [inline]
 

Read the user's genome alignment parameters and start the alignment using the command line mauveAligner tool.

This function translates information entered into the GUI aligner front-end into a command line for mauveAligner.

Definition at line 428 of file AlignFrame.java.

References alignButton, cancelButton, getOutput(), makeAlignerCommand(), org::gel::mauve::gui::AlignWorker::mauve_cmd, outputFileText, org::gel::mauve::gui::SwingWorker::start(), and worker.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::cancelButtonActionPerformed java.awt.event.ActionEvent  evt  )  [inline]
 

Definition at line 491 of file AlignFrame.java.

References alignButton, cancelButton, org::gel::mauve::gui::AlignWorker::interrupt(), and worker.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::collinearCheckBoxActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Reimplemented in org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 592 of file AlignFrame.java.

References collinearCheckBox, determineLCBsCheckBox, minLcbWeightLabel, and minLcbWeightText.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::completeAlignment int  retcode  )  [inline]
 

Implements org::gel::mauve::gui::AlignmentProcessListener.

Definition at line 465 of file AlignFrame.java.

References alignButton, cancelButton, org::gel::mauve::gui::AlignWorker::getKilled(), org::gel::mauve::gui::Mauve::loadFile(), mauve, read_filename, setVisible(), and worker.

void org::gel::mauve::gui::AlignFrame::defaultSeedCheckBoxActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 557 of file AlignFrame.java.

References defaultSeedCheckBox, seedLengthLabel, and seedLengthSlider.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::determineLCBsCheckBoxActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Reimplemented in org::gel::mauve::gui::MauveAlignFrame, and org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 571 of file AlignFrame.java.

References collinearCheckBox, determineLCBsCheckBox, minLcbWeightLabel, minLcbWeightText, and recursiveCheckBox.

Referenced by initComponents().

String org::gel::mauve::gui::AlignFrame::getBinaryPath String  name  )  [inline, static]
 

Definition at line 357 of file AlignFrame.java.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

boolean org::gel::mauve::gui::AlignFrame::getCollinear  )  [inline]
 

Definition at line 655 of file AlignFrame.java.

References collinearCheckBox.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

File org::gel::mauve::gui::AlignFrame::getDefaultFile  )  throws IOException [inline, package]
 

Reimplemented in org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 348 of file AlignFrame.java.

int org::gel::mauve::gui::AlignFrame::getMinLcbWeight  )  [inline]
 

Definition at line 673 of file AlignFrame.java.

References minLcbWeightText.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

String org::gel::mauve::gui::AlignFrame::getOutput  )  [inline]
 

Definition at line 685 of file AlignFrame.java.

References outputFileText.

Referenced by alignButtonActionPerformed(), org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

boolean org::gel::mauve::gui::AlignFrame::getRecursive  )  [inline]
 

Definition at line 650 of file AlignFrame.java.

References recursiveCheckBox.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

int org::gel::mauve::gui::AlignFrame::getSeedWeight  )  [inline]
 

Definition at line 660 of file AlignFrame.java.

References defaultSeedCheckBox, and seedLengthSlider.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

String [] org::gel::mauve::gui::AlignFrame::getSequences  )  [inline]
 

Definition at line 696 of file AlignFrame.java.

References sequenceListModel.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand(), and org::gel::mauve::gui::MauveAlignFrame::makeAlignerCommand().

void org::gel::mauve::gui::AlignFrame::initComponents  )  [inline]
 

Reimplemented in org::gel::mauve::gui::MauveAlignFrame, and org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 102 of file AlignFrame.java.

References addButton, addButtonActionPerformed(), alignButton, alignButtonActionPerformed(), alignmentOptionPane, cancelButton, cancelButtonActionPerformed(), collinearCheckBox, collinearCheckBoxActionPerformed(), d, defaultSeedCheckBox, defaultSeedCheckBoxActionPerformed(), determineLCBsCheckBox, determineLCBsCheckBoxActionPerformed(), listScrollPane, minLcbWeightLabel, minLcbWeightText, outputButton, outputButtonActionPerformed(), outputFileText, outputLabel, parameterPanel, parentPanel, recursiveCheckBox, removeButton, removeButtonActionPerformed(), seedLengthLabel, seedLengthSlider, sequenceList, sequenceListModel, sequencesLabel, sequencesPanel, thisWindowClosed(), and thisWindowClosing().

Referenced by org::gel::mauve::gui::MauveFrame::doAlign(), and org::gel::mauve::gui::MauveFrame::doProgressiveAlign().

boolean org::gel::mauve::gui::AlignFrame::isLCBSearchEnabled  )  [inline]
 

Reimplemented in org::gel::mauve::gui::MauveAlignFrame.

Definition at line 668 of file AlignFrame.java.

References determineLCBsCheckBox.

Referenced by org::gel::mauve::gui::ProgressiveMauveAlignFrame::makeAlignerCommand().

String [] org::gel::mauve::gui::AlignFrame::makeAlignerCommand  )  [inline, protected]
 

Reimplemented in org::gel::mauve::gui::MauveAlignFrame, and org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 498 of file AlignFrame.java.

Referenced by alignButtonActionPerformed().

void org::gel::mauve::gui::AlignFrame::outputButtonActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 636 of file AlignFrame.java.

References outputFileText.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::printCommand String[]  mauve_cmd  )  [inline, protected]
 

Definition at line 503 of file AlignFrame.java.

void org::gel::mauve::gui::AlignFrame::printCommand String[]  cmd,
PrintStream  out
[inline, static]
 

Prints an aligner command in an easily readable format.

Parameters:
cmd the command to print
out the output stream to print to

Definition at line 413 of file AlignFrame.java.

void org::gel::mauve::gui::AlignFrame::removeButtonActionPerformed java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 627 of file AlignFrame.java.

References sequenceList, and sequenceListModel.

Referenced by initComponents().

void org::gel::mauve::gui::AlignFrame::setOutput String  filename  )  [inline]
 

Definition at line 690 of file AlignFrame.java.

References outputFileText.

void org::gel::mauve::gui::AlignFrame::setVisible boolean  show  )  [inline]
 

Definition at line 703 of file AlignFrame.java.

Referenced by completeAlignment(), org::gel::mauve::gui::MauveFrame::doAlign(), and org::gel::mauve::gui::MauveFrame::doProgressiveAlign().

void org::gel::mauve::gui::AlignFrame::thisWindowClosed java.awt.event.WindowEvent  e  )  [inline, package]
 

Definition at line 551 of file AlignFrame.java.

References cancelButton, org::gel::mauve::gui::AlignWorker::interrupt(), and worker.

Referenced by org::gel::mauve::gui::MauveFrame::doAlign(), org::gel::mauve::gui::MauveFrame::doProgressiveAlign(), and initComponents().

void org::gel::mauve::gui::AlignFrame::thisWindowClosing java.awt.event.WindowEvent  e  )  [inline, package]
 

Definition at line 539 of file AlignFrame.java.

References cancelButton.

Referenced by initComponents().


Member Data Documentation

JButton org::gel::mauve::gui::AlignFrame::addButton = new JButton() [protected]
 

Definition at line 64 of file AlignFrame.java.

Referenced by initComponents().

JButton org::gel::mauve::gui::AlignFrame::alignButton = new JButton()
 

Definition at line 60 of file AlignFrame.java.

Referenced by alignButtonActionPerformed(), cancelButtonActionPerformed(), completeAlignment(), and initComponents().

JTabbedPane org::gel::mauve::gui::AlignFrame::alignmentOptionPane = new JTabbedPane() [package]
 

Definition at line 73 of file AlignFrame.java.

Referenced by initComponents().

JButton org::gel::mauve::gui::AlignFrame::cancelButton = new JButton()
 

Definition at line 61 of file AlignFrame.java.

Referenced by alignButtonActionPerformed(), cancelButtonActionPerformed(), completeAlignment(), initComponents(), thisWindowClosed(), and thisWindowClosing().

JCheckBox org::gel::mauve::gui::AlignFrame::collinearCheckBox = new JCheckBox() [package]
 

Definition at line 58 of file AlignFrame.java.

Referenced by collinearCheckBoxActionPerformed(), determineLCBsCheckBoxActionPerformed(), getCollinear(), and initComponents().

Dimension org::gel::mauve::gui::AlignFrame::d [package]
 

Reimplemented in org::gel::mauve::gui::MauveAlignFrame, and org::gel::mauve::gui::ProgressiveMauveAlignFrame.

Definition at line 79 of file AlignFrame.java.

Referenced by initComponents().

JCheckBox org::gel::mauve::gui::AlignFrame::defaultSeedCheckBox = new JCheckBox() [package]
 

Definition at line 51 of file AlignFrame.java.

Referenced by defaultSeedCheckBoxActionPerformed(), getSeedWeight(), and initComponents().

JCheckBox org::gel::mauve::gui::AlignFrame::determineLCBsCheckBox = new JCheckBox() [package]
 

Definition at line 52 of file AlignFrame.java.

Referenced by collinearCheckBoxActionPerformed(), determineLCBsCheckBoxActionPerformed(), initComponents(), and isLCBSearchEnabled().

JFileChooser org::gel::mauve::gui::AlignFrame::fc [protected]
 

< contains the various parameter panels

Definition at line 76 of file AlignFrame.java.

java.awt.Frame org::gel::mauve::gui::AlignFrame::frame [protected]
 

Definition at line 47 of file AlignFrame.java.

JScrollPane org::gel::mauve::gui::AlignFrame::listScrollPane = new JScrollPane() [protected]
 

Definition at line 77 of file AlignFrame.java.

Referenced by initComponents().

Mauve org::gel::mauve::gui::AlignFrame::mauve [protected]
 

Definition at line 81 of file AlignFrame.java.

Referenced by completeAlignment().

JLabel org::gel::mauve::gui::AlignFrame::minLcbWeightLabel = new JLabel() [package]
 

Definition at line 56 of file AlignFrame.java.

Referenced by collinearCheckBoxActionPerformed(), determineLCBsCheckBoxActionPerformed(), and initComponents().

JTextField org::gel::mauve::gui::AlignFrame::minLcbWeightText = new JTextField() [protected]
 

Definition at line 57 of file AlignFrame.java.

Referenced by collinearCheckBoxActionPerformed(), determineLCBsCheckBoxActionPerformed(), getMinLcbWeight(), and initComponents().

boolean org::gel::mauve::gui::AlignFrame::mShown = false [private]
 

Definition at line 516 of file AlignFrame.java.

Referenced by addNotify().

JButton org::gel::mauve::gui::AlignFrame::outputButton = new JButton() [protected]
 

Definition at line 67 of file AlignFrame.java.

Referenced by initComponents().

JTextField org::gel::mauve::gui::AlignFrame::outputFileText = new JTextField() [protected]
 

Definition at line 66 of file AlignFrame.java.

Referenced by alignButtonActionPerformed(), getOutput(), initComponents(), outputButtonActionPerformed(), and setOutput().

JLabel org::gel::mauve::gui::AlignFrame::outputLabel = new JLabel() [protected]
 

Definition at line 69 of file AlignFrame.java.

Referenced by initComponents().

JPanel org::gel::mauve::gui::AlignFrame::parameterPanel = new JPanel() [package]
 

Definition at line 50 of file AlignFrame.java.

Referenced by initComponents().

JPanel org::gel::mauve::gui::AlignFrame::parentPanel = new JPanel() [package]
 

Definition at line 72 of file AlignFrame.java.

Referenced by initComponents().

String org::gel::mauve::gui::AlignFrame::read_filename [protected]
 

Definition at line 44 of file AlignFrame.java.

Referenced by completeAlignment().

JCheckBox org::gel::mauve::gui::AlignFrame::recursiveCheckBox = new JCheckBox() [package]
 

Definition at line 55 of file AlignFrame.java.

Referenced by determineLCBsCheckBoxActionPerformed(), getRecursive(), and initComponents().

JButton org::gel::mauve::gui::AlignFrame::removeButton = new JButton() [protected]
 

Definition at line 65 of file AlignFrame.java.

Referenced by initComponents().

JLabel org::gel::mauve::gui::AlignFrame::seedLengthLabel = new JLabel() [package]
 

Definition at line 54 of file AlignFrame.java.

Referenced by defaultSeedCheckBoxActionPerformed(), and initComponents().

JSlider org::gel::mauve::gui::AlignFrame::seedLengthSlider = new JSlider() [protected]
 

Definition at line 53 of file AlignFrame.java.

Referenced by defaultSeedCheckBoxActionPerformed(), getSeedWeight(), and initComponents().

JList org::gel::mauve::gui::AlignFrame::sequenceList = null [protected]
 

Definition at line 68 of file AlignFrame.java.

Referenced by addButtonActionPerformed(), initComponents(), and removeButtonActionPerformed().

DefaultListModel org::gel::mauve::gui::AlignFrame::sequenceListModel = new DefaultListModel() [protected]
 

Definition at line 78 of file AlignFrame.java.

Referenced by addButtonActionPerformed(), getSequences(), initComponents(), and removeButtonActionPerformed().

JLabel org::gel::mauve::gui::AlignFrame::sequencesLabel = new JLabel() [package]
 

Definition at line 70 of file AlignFrame.java.

Referenced by initComponents().

JPanel org::gel::mauve::gui::AlignFrame::sequencesPanel = new JPanel() [protected]
 

Definition at line 63 of file AlignFrame.java.

Referenced by initComponents().

AlignWorker org::gel::mauve::gui::AlignFrame::worker [protected]
 

Definition at line 82 of file AlignFrame.java.

Referenced by alignButtonActionPerformed(), cancelButtonActionPerformed(), completeAlignment(), and thisWindowClosed().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:01 2013 for Mauve by doxygen 1.3.6