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

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

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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

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.


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().


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().


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