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org::gel::mauve::gui::ProgressiveMauveAlignFrame Class Reference

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

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

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List of all members.

Public Member Functions

void collinearCheckBoxActionPerformed (java.awt.event.ActionEvent e)
void determineLCBsCheckBoxActionPerformed (java.awt.event.ActionEvent e)
String getGapExtend ()
String getGapOpen ()
boolean getRefine ()
String[][] getScoreMatrix ()
String getScoreMatrixName ()
boolean getSeedFamilies ()
boolean getSumOfPairs ()
void initComponents ()
void matrixChoiceActionPerformed (java.awt.event.ActionEvent e)
 ProgressiveMauveAlignFrame (Mauve mauve, boolean gui)
 ProgressiveMauveAlignFrame (Mauve mauve)
void recursiveCheckBoxActionPerformed (java.awt.event.ActionEvent e)
void scoreTextActionPerformed (java.awt.event.ActionEvent e)
void setMatrixValues (String[][] mat)
void setScoreEditable (boolean edit)
void stateChanged (ChangeEvent e)
void updateEnabledStates ()

Protected Member Functions

String[] makeAlignerCommand ()

Protected Attributes

JLabel breakpointWeightScaleLabel = new JLabel()
JSlider breakpointWeightScaleSlider = new JSlider()
JTextField breakpointWeightScaleText = new JTextField(5)
JLabel conservationWeightScaleLabel = new JLabel()
JSlider conservationWeightScaleSlider = new JSlider()
JTextField conservationWeightScaleText = new JTextField(5)
Dimension d
JLabel gapExtendLabel = new JLabel()
JTextField gapExtendText = new JTextField()
JLabel gapOpenLabel = new JLabel()
JTextField gapOpenText = new JTextField()
String hoxd_ge = "-30"
String hoxd_go = "-400"
String[][] hoxd_matrix
JComboBox matrixChoice = new JComboBox(new String[] {"HOXD (default)", "Custom"})
JLabel matrixChoiceLabel = new JLabel()
JCheckBox refineCheckBox = new JCheckBox()
JLabel[] scoreLabelCol = new JLabel[4]
JLabel[] scoreLabelRow = new JLabel[4]
String[] scoreLabels = {"A", "C", "G", "T"}
JPanel scorePanel = new JPanel()
JTextField[][] scoreText = new JTextField[4][4]
JCheckBox seedFamiliesCheckBox = new JCheckBox()
JCheckBox sumOfPairsCheckBox = new JCheckBox()

Package Functions

File getDefaultFile () throws IOException

Constructor & Destructor Documentation

org::gel::mauve::gui::ProgressiveMauveAlignFrame::ProgressiveMauveAlignFrame (  Mauve  mauve  )  [inline]
 

Definition at line 69 of file ProgressiveMauveAlignFrame.java.

org::gel::mauve::gui::ProgressiveMauveAlignFrame::ProgressiveMauveAlignFrame (  Mauve  mauve,
boolean  gui
)  [inline]
 

Definition at line 73 of file ProgressiveMauveAlignFrame.java.

Member Function Documentation

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

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 518 of file ProgressiveMauveAlignFrame.java.

References updateEnabledStates().

Referenced by initComponents().

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

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 512 of file ProgressiveMauveAlignFrame.java.

References updateEnabledStates().

Referenced by initComponents().

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

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 328 of file ProgressiveMauveAlignFrame.java.

String org::gel::mauve::gui::ProgressiveMauveAlignFrame::getGapExtend (   )  [inline]
 

Definition at line 598 of file ProgressiveMauveAlignFrame.java.

References gapExtendText.

Referenced by makeAlignerCommand().

String org::gel::mauve::gui::ProgressiveMauveAlignFrame::getGapOpen (   )  [inline]
 

Definition at line 594 of file ProgressiveMauveAlignFrame.java.

References gapOpenText.

Referenced by makeAlignerCommand().

boolean org::gel::mauve::gui::ProgressiveMauveAlignFrame::getRefine (   )  [inline]
 

Definition at line 568 of file ProgressiveMauveAlignFrame.java.

References refineCheckBox.

Referenced by makeAlignerCommand().

String [][] org::gel::mauve::gui::ProgressiveMauveAlignFrame::getScoreMatrix (   )  [inline]
 

Definition at line 586 of file ProgressiveMauveAlignFrame.java.

References scoreText.

Referenced by makeAlignerCommand().

String org::gel::mauve::gui::ProgressiveMauveAlignFrame::getScoreMatrixName (   )  [inline]
 

Definition at line 582 of file ProgressiveMauveAlignFrame.java.

References matrixChoice.

Referenced by makeAlignerCommand().

boolean org::gel::mauve::gui::ProgressiveMauveAlignFrame::getSeedFamilies (   )  [inline]
 

Definition at line 561 of file ProgressiveMauveAlignFrame.java.

References seedFamiliesCheckBox.

Referenced by makeAlignerCommand().

boolean org::gel::mauve::gui::ProgressiveMauveAlignFrame::getSumOfPairs (   )  [inline]
 

Definition at line 575 of file ProgressiveMauveAlignFrame.java.

References sumOfPairsCheckBox.

Referenced by makeAlignerCommand().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::initComponents (   )  [inline]
 

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 78 of file ProgressiveMauveAlignFrame.java.

References breakpointWeightScaleLabel, breakpointWeightScaleSlider, breakpointWeightScaleText, collinearCheckBoxActionPerformed(), conservationWeightScaleLabel, conservationWeightScaleSlider, conservationWeightScaleText, determineLCBsCheckBoxActionPerformed(), gapExtendLabel, gapExtendText, gapOpenLabel, gapOpenText, hoxd_ge, hoxd_go, hoxd_matrix, matrixChoice, matrixChoiceActionPerformed(), matrixChoiceLabel, recursiveCheckBoxActionPerformed(), refineCheckBox, scoreLabelCol, scoreLabelRow, scoreLabels, scorePanel, scoreText, scoreTextActionPerformed(), seedFamiliesCheckBox, setMatrixValues(), setScoreEditable(), and sumOfPairsCheckBox.

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

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 346 of file ProgressiveMauveAlignFrame.java.

References org::gel::mauve::gui::AlignFrame::getBinaryPath(), org::gel::mauve::gui::AlignFrame::getCollinear(), getGapExtend(), getGapOpen(), org::gel::mauve::gui::AlignFrame::getMinLcbWeight(), org::gel::mauve::gui::AlignFrame::getOutput(), org::gel::mauve::gui::AlignFrame::getRecursive(), getRefine(), getScoreMatrix(), getScoreMatrixName(), getSeedFamilies(), org::gel::mauve::gui::AlignFrame::getSeedWeight(), org::gel::mauve::gui::AlignFrame::getSequences(), getSumOfPairs(), org::gel::mauve::gui::AlignFrame::isLCBSearchEnabled(), and scoreLabels.

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::matrixChoiceActionPerformed (  java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 541 of file ProgressiveMauveAlignFrame.java.

References gapExtendText, gapOpenText, hoxd_ge, hoxd_go, hoxd_matrix, matrixChoice, setMatrixValues(), and setScoreEditable().

Referenced by initComponents().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::recursiveCheckBoxActionPerformed (  java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 523 of file ProgressiveMauveAlignFrame.java.

References updateEnabledStates().

Referenced by initComponents().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::scoreTextActionPerformed (  java.awt.event.ActionEvent  e  )  [inline]
 

Definition at line 556 of file ProgressiveMauveAlignFrame.java.

References matrixChoice.

Referenced by initComponents().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::setMatrixValues (  String  mat[][]  )  [inline]
 

Definition at line 527 of file ProgressiveMauveAlignFrame.java.

References scoreText.

Referenced by initComponents(), and matrixChoiceActionPerformed().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::setScoreEditable (  boolean  edit  )  [inline]
 

Definition at line 533 of file ProgressiveMauveAlignFrame.java.

References gapExtendText, gapOpenText, and scoreText.

Referenced by initComponents(), and matrixChoiceActionPerformed().

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::stateChanged (  ChangeEvent  e  )  [inline]
 

Definition at line 333 of file ProgressiveMauveAlignFrame.java.

References breakpointWeightScaleSlider, and breakpointWeightScaleText.

void org::gel::mauve::gui::ProgressiveMauveAlignFrame::updateEnabledStates (   )  [inline]
 

Definition at line 482 of file ProgressiveMauveAlignFrame.java.

References breakpointWeightScaleLabel, breakpointWeightScaleSlider, breakpointWeightScaleText, conservationWeightScaleLabel, conservationWeightScaleSlider, conservationWeightScaleText, refineCheckBox, and sumOfPairsCheckBox.

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

Member Data Documentation

JLabel org::gel::mauve::gui::ProgressiveMauveAlignFrame::breakpointWeightScaleLabel = new JLabel() [protected]
 

Definition at line 42 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and updateEnabledStates().

JSlider org::gel::mauve::gui::ProgressiveMauveAlignFrame::breakpointWeightScaleSlider = new JSlider() [protected]
 

Definition at line 41 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), stateChanged(), and updateEnabledStates().

JTextField org::gel::mauve::gui::ProgressiveMauveAlignFrame::breakpointWeightScaleText = new JTextField(5) [protected]
 

Definition at line 43 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), stateChanged(), and updateEnabledStates().

JLabel org::gel::mauve::gui::ProgressiveMauveAlignFrame::conservationWeightScaleLabel = new JLabel() [protected]
 

Definition at line 45 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and updateEnabledStates().

JSlider org::gel::mauve::gui::ProgressiveMauveAlignFrame::conservationWeightScaleSlider = new JSlider() [protected]
 

Definition at line 44 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and updateEnabledStates().

JTextField org::gel::mauve::gui::ProgressiveMauveAlignFrame::conservationWeightScaleText = new JTextField(5) [protected]
 

Definition at line 46 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and updateEnabledStates().

Dimension org::gel::mauve::gui::ProgressiveMauveAlignFrame::d [protected]
 

Reimplemented from org::gel::mauve::gui::AlignFrame.

Definition at line 36 of file ProgressiveMauveAlignFrame.java.

JLabel org::gel::mauve::gui::ProgressiveMauveAlignFrame::gapExtendLabel = new JLabel() [protected]
 

Definition at line 67 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

JTextField org::gel::mauve::gui::ProgressiveMauveAlignFrame::gapExtendText = new JTextField() [protected]
 

Definition at line 66 of file ProgressiveMauveAlignFrame.java.

Referenced by getGapExtend(), initComponents(), matrixChoiceActionPerformed(), and setScoreEditable().

JLabel org::gel::mauve::gui::ProgressiveMauveAlignFrame::gapOpenLabel = new JLabel() [protected]
 

Definition at line 65 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

JTextField org::gel::mauve::gui::ProgressiveMauveAlignFrame::gapOpenText = new JTextField() [protected]
 

Definition at line 64 of file ProgressiveMauveAlignFrame.java.

Referenced by getGapOpen(), initComponents(), matrixChoiceActionPerformed(), and setScoreEditable().

String org::gel::mauve::gui::ProgressiveMauveAlignFrame::hoxd_ge = "-30" [protected]
 

Definition at line 63 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and matrixChoiceActionPerformed().

String org::gel::mauve::gui::ProgressiveMauveAlignFrame::hoxd_go = "-400" [protected]
 

Definition at line 62 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and matrixChoiceActionPerformed().

String [][] org::gel::mauve::gui::ProgressiveMauveAlignFrame::hoxd_matrix [protected]
 

Initial value:

 {
                {"91",   "-114", "-31",  "-123"},
                {"-114", "100",  "-125", "-31" },
                {"-31",  "-125", "100",  "-114"},
                {"-123", "-31",  "-114", "91"  }
    }

Definition at line 56 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and matrixChoiceActionPerformed().

JComboBox org::gel::mauve::gui::ProgressiveMauveAlignFrame::matrixChoice = new JComboBox(new String[] {"HOXD (default)", "Custom"}) [protected]
 

Definition at line 50 of file ProgressiveMauveAlignFrame.java.

Referenced by getScoreMatrixName(), initComponents(), matrixChoiceActionPerformed(), and scoreTextActionPerformed().

JLabel org::gel::mauve::gui::ProgressiveMauveAlignFrame::matrixChoiceLabel = new JLabel() [protected]
 

Definition at line 51 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

JCheckBox org::gel::mauve::gui::ProgressiveMauveAlignFrame::refineCheckBox = new JCheckBox() [protected]
 

Definition at line 37 of file ProgressiveMauveAlignFrame.java.

Referenced by getRefine(), initComponents(), and updateEnabledStates().

JLabel [] org::gel::mauve::gui::ProgressiveMauveAlignFrame::scoreLabelCol = new JLabel[4] [protected]
 

Definition at line 54 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

JLabel [] org::gel::mauve::gui::ProgressiveMauveAlignFrame::scoreLabelRow = new JLabel[4] [protected]
 

Definition at line 53 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

String [] org::gel::mauve::gui::ProgressiveMauveAlignFrame::scoreLabels = {"A", "C", "G", "T"} [protected]
 

Definition at line 55 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents(), and makeAlignerCommand().

JPanel org::gel::mauve::gui::ProgressiveMauveAlignFrame::scorePanel = new JPanel() [protected]
 

Definition at line 49 of file ProgressiveMauveAlignFrame.java.

Referenced by initComponents().

JTextField [][] org::gel::mauve::gui::ProgressiveMauveAlignFrame::scoreText = new JTextField[4][4] [protected]
 

Definition at line 52 of file ProgressiveMauveAlignFrame.java.

Referenced by getScoreMatrix(), initComponents(), setMatrixValues(), and setScoreEditable().

JCheckBox org::gel::mauve::gui::ProgressiveMauveAlignFrame::seedFamiliesCheckBox = new JCheckBox() [protected]
 

Definition at line 38 of file ProgressiveMauveAlignFrame.java.

Referenced by getSeedFamilies(), and initComponents().

JCheckBox org::gel::mauve::gui::ProgressiveMauveAlignFrame::sumOfPairsCheckBox = new JCheckBox() [protected]
 

Definition at line 40 of file ProgressiveMauveAlignFrame.java.

Referenced by getSumOfPairs(), initComponents(), and updateEnabledStates().

The documentation for this class was generated from the following file:
Generated on Thu May 23 06:08:20 2013 for Mauve by doxygen 1.3.6