org::gel::mauve::contigs::ContigMauveAlignFrame Class Reference

Collaboration diagram for org::gel::mauve::contigs::ContigMauveAlignFrame:

[legend]List of all members.

Public Member Functions
void	addButtonActionPerformed (ActionEvent e)
void	addSequence (String file)
void	alignButtonActionPerformed (ActionEvent e)
	ContigMauveAlignFrame (Mauve mauve, ContigOrderer orderer, boolean gui)
void	displayFileInput ()
void	initComponents ()
void	outputButtonActionPerformed (ActionEvent e)
void	setArgs (Hashtable< String, String > args)
void	setVisible (boolean show)
Protected Member Functions
String[]	makeAlignerCommand ()
Protected Attributes
File	current_dir
boolean	first
Hashtable< String, String >	more_args
ContigOrderer	orderer

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Constructor & Destructor Documentation

org::gel::mauve::contigs::ContigMauveAlignFrame::ContigMauveAlignFrame (  Mauve  mauve, ContigOrderer  orderer, boolean  gui )  [inline]

Definition at line 28 of file ContigMauveAlignFrame.java. References initComponents().

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Member Function Documentation

void org::gel::mauve::contigs::ContigMauveAlignFrame::addButtonActionPerformed (  ActionEvent  e  )  [inline]

Definition at line 158 of file ContigMauveAlignFrame.java.

void org::gel::mauve::contigs::ContigMauveAlignFrame::addSequence (  String  file  )  [inline]

Definition at line 126 of file ContigMauveAlignFrame.java. Referenced by org::gel::mauve::contigs::ContigOrderer::initParams().

void org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed (  ActionEvent  e  )  [inline]

Definition at line 131 of file ContigMauveAlignFrame.java. References org::gel::mauve::contigs::ContigOrderer::copyInputFiles(), current_dir, org::gel::mauve::contigs::ContigOrderer::directory, orderer, org::gel::mauve::contigs::ContigOrderer::reference, and org::gel::mauve::contigs::ContigOrderer::unordered. Referenced by org::gel::mauve::contigs::ContigOrderer::startAlignment().

void org::gel::mauve::contigs::ContigMauveAlignFrame::displayFileInput (   )  [inline]

Definition at line 111 of file ContigMauveAlignFrame.java. References org::gel::mauve::contigs::ContigOrderer::count, current_dir, org::gel::mauve::contigs::ContigOrderer::DIR_STUB, org::gel::mauve::contigs::ContigOrderer::getAlignDir(), and orderer. Referenced by org::gel::mauve::contigs::ContigOrderer::startAlignment().

void org::gel::mauve::contigs::ContigMauveAlignFrame::initComponents (   )  [inline]

Definition at line 34 of file ContigMauveAlignFrame.java. Referenced by ContigMauveAlignFrame().

String [] org::gel::mauve::contigs::ContigMauveAlignFrame::makeAlignerCommand (   )  [inline, protected]

Definition at line 74 of file ContigMauveAlignFrame.java. References more_args.

void org::gel::mauve::contigs::ContigMauveAlignFrame::outputButtonActionPerformed (  ActionEvent  e  )  [inline]

Definition at line 163 of file ContigMauveAlignFrame.java.

void org::gel::mauve::contigs::ContigMauveAlignFrame::setArgs (  Hashtable< String, String >  args  )  [inline]

Definition at line 59 of file ContigMauveAlignFrame.java. References more_args. Referenced by org::gel::mauve::contigs::ContigOrderer::initParams().

void org::gel::mauve::contigs::ContigMauveAlignFrame::setVisible (  boolean  show  )  [inline]

Definition at line 98 of file ContigMauveAlignFrame.java. References org::gel::mauve::contigs::ContigOrderer::count, org::gel::mauve::contigs::ContigOrderer::iterations, orderer, and org::gel::mauve::contigs::ContigOrderer::start. Referenced by org::gel::mauve::contigs::ContigOrderer::startAlignment().

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Member Data Documentation

File org::gel::mauve::contigs::ContigMauveAlignFrame::current_dir [protected]

Definition at line 25 of file ContigMauveAlignFrame.java. Referenced by alignButtonActionPerformed(), and displayFileInput().

boolean org::gel::mauve::contigs::ContigMauveAlignFrame::first [protected]

Definition at line 24 of file ContigMauveAlignFrame.java.

Hashtable<String, String> org::gel::mauve::contigs::ContigMauveAlignFrame::more_args [protected]

Definition at line 26 of file ContigMauveAlignFrame.java. Referenced by makeAlignerCommand(), and setArgs().

ContigOrderer org::gel::mauve::contigs::ContigMauveAlignFrame::orderer [protected]

Definition at line 23 of file ContigMauveAlignFrame.java. Referenced by alignButtonActionPerformed(), displayFileInput(), and setVisible().

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The documentation for this class was generated from the following file:

• src/org/gel/mauve/contigs/ContigMauveAlignFrame.java

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