org::gel::mauve::contigs::ContigOrderer Class Reference

Inheritance diagram for org::gel::mauve::contigs::ContigOrderer:

[legend]Collaboration diagram for org::gel::mauve::contigs::ContigOrderer:

[legend]List of all members.

Public Member Functions
void	addAlignmentProcessListener (AlignmentProcessListener listener)
	ContigOrderer (String[] args, Vector frames)
	ContigOrderer (String[] args, Vector frames, boolean gui)
void	copyInputFiles ()
File	getAlignDir ()
File	getAlignmentFile ()
boolean	getFiles ()
void	init (String[] args, Vector frames, boolean gui)
void	initGUI ()
void	initParams (String[] args)
void	renameLastAlignment ()
void	reorderDone ()
boolean	shouldReorder ()
Static Public Member Functions
void	main (String[] args)
Static Public Attributes
final String	ALIGN_START = "Start from alignment file."
final int	DEFAULT_ITERATIONS = 15
final String	DIR_STUB = "alignment"
final String	SEQ_START = "Start from sequence files."
Protected Member Functions
File	makeAlignDir ()
boolean	orderRepeated ()
void	setFilesFromAlignStart ()
void	startAlignment (boolean show_message)
Protected Attributes
ContigMauveAlignFrame	align
File	align_dir
boolean	align_start
int	count = 1
File	directory
boolean	gui
int	iterations = DEFAULT_ITERATIONS
MauveFrame	parent
Vector	past_orders
File	reference
ContigReorderer	reorderer
int	start = 0
File	unordered
Static Protected Attributes
final String	DRAFT_FILE = "-draft"
final String	OUTPUT_DIR = "-output"
final String	REF_FILE = "-ref"
Private Member Functions
void	fireAlignmentEvent ()
Private Attributes
EventListenerList	alnListeners
File	alnmtFile

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Constructor & Destructor Documentation

org::gel::mauve::contigs::ContigOrderer::ContigOrderer (  String[]  args, Vector  frames, boolean  gui )  [inline]

Definition at line 49 of file ContigOrderer.java. References init(), initGUI(), and initParams(). Referenced by main().

org::gel::mauve::contigs::ContigOrderer::ContigOrderer (  String[]  args, Vector  frames )  [inline]

Definition at line 57 of file ContigOrderer.java.

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Member Function Documentation

void org::gel::mauve::contigs::ContigOrderer::addAlignmentProcessListener (  AlignmentProcessListener  listener  )  [inline]

Definition at line 293 of file ContigOrderer.java. References alnListeners.

void org::gel::mauve::contigs::ContigOrderer::copyInputFiles (   )  [inline]

Definition at line 309 of file ContigOrderer.java. References makeAlignDir(), reference, and unordered. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed().

void org::gel::mauve::contigs::ContigOrderer::fireAlignmentEvent (   )  [inline, private]

Definition at line 297 of file ContigOrderer.java. References alnListeners. Referenced by reorderDone().

File org::gel::mauve::contigs::ContigOrderer::getAlignDir (   )  [inline]

Definition at line 336 of file ContigOrderer.java. References count, DIR_STUB, and directory. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::displayFileInput(), getFiles(), initParams(), makeAlignDir(), renameLastAlignment(), and reorderDone().

File org::gel::mauve::contigs::ContigOrderer::getAlignmentFile (   )  [inline]

Definition at line 306 of file ContigOrderer.java.

boolean org::gel::mauve::contigs::ContigOrderer::getFiles (   )  [inline]

Definition at line 158 of file ContigOrderer.java. References directory, getAlignDir(), and parent. Referenced by initGUI().

void org::gel::mauve::contigs::ContigOrderer::init (  String[]  args, Vector  frames, boolean  gui )  [inline]

Definition at line 114 of file ContigOrderer.java. References align, alnListeners, DEFAULT_ITERATIONS, iterations, past_orders, org::gel::mauve::contigs::ContigReorderer::ref_ind, org::gel::mauve::contigs::ContigReorderer::reorder_ind, and reorderer. Referenced by ContigOrderer().

void org::gel::mauve::contigs::ContigOrderer::initGUI (   )  [inline]

Definition at line 105 of file ContigOrderer.java. References getFiles(), org::gel::mauve::contigs::ContigReorderer::init(), iterations, reorderer, and startAlignment(). Referenced by ContigOrderer().

void org::gel::mauve::contigs::ContigOrderer::initParams (  String[]  args  )  [inline]

Definition at line 61 of file ContigOrderer.java. References org::gel::mauve::contigs::ContigMauveAlignFrame::addSequence(), align, directory, DRAFT_FILE, getAlignDir(), gui, OUTPUT_DIR, REF_FILE, org::gel::mauve::contigs::ContigMauveAlignFrame::setArgs(), and startAlignment(). Referenced by ContigOrderer().

void org::gel::mauve::contigs::ContigOrderer::main (  String[]  args  )  [inline, static]

Definition at line 341 of file ContigOrderer.java. References ContigOrderer().

File org::gel::mauve::contigs::ContigOrderer::makeAlignDir (   )  [inline, protected]

Definition at line 324 of file ContigOrderer.java. References count, getAlignDir(), and iterations. Referenced by copyInputFiles(), and reorderDone().

boolean org::gel::mauve::contigs::ContigOrderer::orderRepeated (   )  [inline, protected]

Definition at line 285 of file ContigOrderer.java. References org::gel::mauve::contigs::ContigReorderer::ordered, past_orders, and reorderer. Referenced by reorderDone().

void org::gel::mauve::contigs::ContigOrderer::renameLastAlignment (   )  [inline]

Definition at line 231 of file ContigOrderer.java. References DIR_STUB, directory, and getAlignDir().

void org::gel::mauve::contigs::ContigOrderer::reorderDone (   )  [inline]

Definition at line 237 of file ContigOrderer.java. References org::gel::mauve::contigs::ContigReorderer::active, align_dir, align_start, alnListeners, count, directory, org::gel::mauve::contigs::ContigReorderer::feature_file, fireAlignmentEvent(), org::gel::mauve::contigs::ContigReorderer::fix, getAlignDir(), gui, org::gel::mauve::contigs::ContigReorderer::inverted_from_start, iterations, makeAlignDir(), org::gel::mauve::contigs::ContigReorderer::ordered, orderRepeated(), parent, past_orders, reference, reorderer, startAlignment(), and unordered. Referenced by org::gel::mauve::contigs::ContigReorderer::initModelData().

void org::gel::mauve::contigs::ContigOrderer::setFilesFromAlignStart (   )  [inline, protected]

Definition at line 209 of file ContigOrderer.java. References align_dir, org::gel::mauve::contigs::ContigReorderer::file, org::gel::mauve::contigs::ContigReorderer::fix, org::gel::mauve::gui::MauveFrame::getFeatureImporter(), org::gel::mauve::gui::MauveFrame::getModel(), org::gel::mauve::XMFAAlignment::getName(), parent, reference, reorderer, and unordered. Referenced by shouldReorder().

boolean org::gel::mauve::contigs::ContigOrderer::shouldReorder (   )  [inline]

Definition at line 222 of file ContigOrderer.java. References align_start, count, iterations, and setFilesFromAlignStart(). Referenced by org::gel::mauve::contigs::ContigReorderer::initModelData().

void org::gel::mauve::contigs::ContigOrderer::startAlignment (  boolean  show_message  )  [inline, protected]

Definition at line 134 of file ContigOrderer.java. References align, org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed(), org::gel::mauve::contigs::ContigMauveAlignFrame::displayFileInput(), gui, and org::gel::mauve::contigs::ContigMauveAlignFrame::setVisible(). Referenced by initGUI(), initParams(), and reorderDone().

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Member Data Documentation

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

Definition at line 35 of file ContigOrderer.java. Referenced by init(), initParams(), and startAlignment().

File org::gel::mauve::contigs::ContigOrderer::align_dir [protected]

Definition at line 29 of file ContigOrderer.java. Referenced by reorderDone(), and setFilesFromAlignStart().

boolean org::gel::mauve::contigs::ContigOrderer::align_start [protected]

Definition at line 40 of file ContigOrderer.java. Referenced by reorderDone(), and shouldReorder().

final String org::gel::mauve::contigs::ContigOrderer::ALIGN_START = "Start from alignment file." [static]

Definition at line 38 of file ContigOrderer.java.

EventListenerList org::gel::mauve::contigs::ContigOrderer::alnListeners [private]

Definition at line 46 of file ContigOrderer.java. Referenced by addAlignmentProcessListener(), fireAlignmentEvent(), init(), and reorderDone().

File org::gel::mauve::contigs::ContigOrderer::alnmtFile [private]

Definition at line 47 of file ContigOrderer.java.

int org::gel::mauve::contigs::ContigOrderer::count = 1 [protected]

Definition at line 31 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::displayFileInput(), getAlignDir(), makeAlignDir(), reorderDone(), org::gel::mauve::contigs::ContigMauveAlignFrame::setVisible(), and shouldReorder().

final int org::gel::mauve::contigs::ContigOrderer::DEFAULT_ITERATIONS = 15 [static]

Definition at line 36 of file ContigOrderer.java. Referenced by init().

final String org::gel::mauve::contigs::ContigOrderer::DIR_STUB = "alignment" [static]

Definition at line 30 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::displayFileInput(), getAlignDir(), and renameLastAlignment().

File org::gel::mauve::contigs::ContigOrderer::directory [protected]

Definition at line 26 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed(), getAlignDir(), getFiles(), initParams(), renameLastAlignment(), and reorderDone().

final String org::gel::mauve::contigs::ContigOrderer::DRAFT_FILE = "-draft" [static, protected]

Definition at line 45 of file ContigOrderer.java. Referenced by initParams().

boolean org::gel::mauve::contigs::ContigOrderer::gui [protected]

Definition at line 42 of file ContigOrderer.java. Referenced by initParams(), reorderDone(), and startAlignment().

int org::gel::mauve::contigs::ContigOrderer::iterations = DEFAULT_ITERATIONS [protected]

Definition at line 37 of file ContigOrderer.java. Referenced by init(), initGUI(), makeAlignDir(), reorderDone(), org::gel::mauve::contigs::ContigMauveAlignFrame::setVisible(), and shouldReorder().

final String org::gel::mauve::contigs::ContigOrderer::OUTPUT_DIR = "-output" [static, protected]

Definition at line 43 of file ContigOrderer.java. Referenced by initParams().

MauveFrame org::gel::mauve::contigs::ContigOrderer::parent [protected]

Definition at line 34 of file ContigOrderer.java. Referenced by getFiles(), reorderDone(), and setFilesFromAlignStart().

Vector org::gel::mauve::contigs::ContigOrderer::past_orders [protected]

Definition at line 41 of file ContigOrderer.java. Referenced by init(), orderRepeated(), and reorderDone().

final String org::gel::mauve::contigs::ContigOrderer::REF_FILE = "-ref" [static, protected]

Definition at line 44 of file ContigOrderer.java. Referenced by initParams().

File org::gel::mauve::contigs::ContigOrderer::reference [protected]

Definition at line 28 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed(), copyInputFiles(), reorderDone(), and setFilesFromAlignStart().

ContigReorderer org::gel::mauve::contigs::ContigOrderer::reorderer [protected]

Definition at line 33 of file ContigOrderer.java. Referenced by init(), initGUI(), orderRepeated(), reorderDone(), and setFilesFromAlignStart().

final String org::gel::mauve::contigs::ContigOrderer::SEQ_START = "Start from sequence files." [static]

Definition at line 39 of file ContigOrderer.java.

int org::gel::mauve::contigs::ContigOrderer::start = 0 [protected]

Definition at line 32 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::setVisible().

File org::gel::mauve::contigs::ContigOrderer::unordered [protected]

Definition at line 27 of file ContigOrderer.java. Referenced by org::gel::mauve::contigs::ContigMauveAlignFrame::alignButtonActionPerformed(), copyInputFiles(), reorderDone(), and setFilesFromAlignStart().

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

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

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