org::gel::mauve::Match Class Reference

Records an ungapped local alignment among multiple sequences. More...

List of all members.

Public Member Functions
void	copyArrays (LCB lcb, long[] starts, long[] lengths, boolean[] reverse, int seq_count)
long	getLength (int sourceIndex)
long	getLength (Genome g)
boolean	getReverse (int sourceIndex)
boolean	getReverse (Genome g)
long	getStart (int sourceIndex)
long	getStart (Genome g)
	Match (Match m)
	Match (int sequenceCount)
long	offset ()
	Compute and return the generalized offset.
void	setLength (int sourceIndex, long length)
void	setLength (Genome g, long length)
void	setReverse (int sourceIndex, boolean r)
void	setReverse (Genome g, boolean r)
void	setStart (int sourceIndex, long start)
void	setStart (Genome g, long start)
Public Attributes
Color	color
boolean	highlighted = false
int	lcb = 0
Static Public Attributes
final int	NO_MATCH = 0
Static Package Attributes
final long	serialVersionUID = 1

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Detailed Description

Records an ungapped local alignment among multiple sequences.

Sequence coordinates start at 1 and a coordinate of 0 indicates that the alignment is undefined in that sequence.

Definition at line 13 of file Match.java.

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Constructor & Destructor Documentation

org::gel::mauve::Match::Match (  int  sequenceCount  )  [inline]

Definition at line 31 of file Match.java.

org::gel::mauve::Match::Match (  Match  m  )  [inline]

Definition at line 38 of file Match.java. References color, and lcb.

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Member Function Documentation

void org::gel::mauve::Match::copyArrays (  LCB  lcb, long[]  starts, long[]  lengths, boolean[]  reverse, int  seq_count )  [inline]

Definition at line 163 of file Match.java. Referenced by org::gel::mauve::LCB::LCB().

long org::gel::mauve::Match::getLength (  int  sourceIndex  )  [inline]

Deprecated: Parameters: sourceIndex  Returns: Definition at line 90 of file Match.java.

long org::gel::mauve::Match::getLength (  Genome  g  )  [inline]

Definition at line 80 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes(), org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::XMFAAlignment::getLCB(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::BaseViewerModel::getMatchRange(), org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::XMFAAlignment::revCompify(), and org::gel::mauve::XMFAAlignment::SuppressWarnings().

boolean org::gel::mauve::Match::getReverse (  int  sourceIndex  )  [inline]

Deprecated: Parameters: sourceIndex  Returns: Definition at line 120 of file Match.java.

boolean org::gel::mauve::Match::getReverse (  Genome  g  )  [inline]

Definition at line 110 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::BaseViewerModel::correctMatchReversals(), org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes(), org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::LcbViewerModel::getLCB(), and org::gel::mauve::XMFAAlignment::revCompify().

long org::gel::mauve::Match::getStart (  int  sourceIndex  )  [inline]

Deprecated: Parameters: sourceIndex  Returns: Definition at line 61 of file Match.java.

long org::gel::mauve::Match::getStart (  Genome  g  )  [inline]

Definition at line 51 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::LcbViewerModel::alignView(), org::gel::mauve::BaseViewerModel::alignView(), org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::BaseViewerModel::correctMatchReversals(), org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes(), org::gel::mauve::LcbViewerModel::getHighlightArray(), org::gel::mauve::XMFAAlignment::getLCB(), org::gel::mauve::LcbViewerModel::getLCB(), org::gel::mauve::BaseViewerModel::getMatchRange(), org::gel::mauve::XMFAAlignment::getRange(), org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::ModelBuilder::readMums(), org::gel::mauve::XMFAAlignment::revCompify(), and org::gel::mauve::XMFAAlignment::SuppressWarnings().

long org::gel::mauve::Match::offset (   )  [inline]

Compute and return the generalized offset. Definition at line 141 of file Match.java. References NO_MATCH. Referenced by org::gel::mauve::color::OffsetColorScheme::apply(), and org::gel::mauve::color::OffsetColorScheme::initOffsets().

void org::gel::mauve::Match::setLength (  int  sourceIndex, long  length )  [inline]

Deprecated: Parameters: sourceIndex  length  Definition at line 105 of file Match.java.

void org::gel::mauve::Match::setLength (  Genome  g, long  length )  [inline]

Definition at line 95 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::ModelBuilder::readMums(), and org::gel::mauve::XMFAAlignment::SuppressWarnings().

void org::gel::mauve::Match::setReverse (  int  sourceIndex, boolean  r )  [inline]

Deprecated: Parameters: sourceIndex  r  Definition at line 135 of file Match.java.

void org::gel::mauve::Match::setReverse (  Genome  g, boolean  r )  [inline]

Definition at line 125 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::BaseViewerModel::correctMatchReversals(), org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::ModelBuilder::readMums(), and org::gel::mauve::XMFAAlignment::SuppressWarnings().

void org::gel::mauve::Match::setStart (  int  sourceIndex, long  start )  [inline]

Deprecated: Parameters: sourceIndex  start  Definition at line 75 of file Match.java.

void org::gel::mauve::Match::setStart (  Genome  g, long  start )  [inline]

Definition at line 66 of file Match.java. References org::gel::mauve::Genome::getSourceIndex(). Referenced by org::gel::mauve::BaseViewerModel::getMatchRange(), org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::ModelBuilder::readMums(), and org::gel::mauve::XMFAAlignment::SuppressWarnings().

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Member Data Documentation

Color org::gel::mauve::Match::color

Definition at line 18 of file Match.java. Referenced by org::gel::mauve::color::OffsetColorScheme::apply(), org::gel::mauve::color::NormalizedOffsetColorScheme::apply(), org::gel::mauve::color::NormalizedMultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityTypeColorScheme::apply(), org::gel::mauve::color::MultiplicityColorScheme::apply(), org::gel::mauve::color::LCBColorScheme::apply(), org::gel::mauve::LCBlist::filterLCBs(), and Match().

boolean org::gel::mauve::Match::highlighted = false

Definition at line 20 of file Match.java. Referenced by org::gel::mauve::BaseViewerModel::addMatchHighlight(), org::gel::mauve::BaseViewerModel::clearMatchHighlights(), and org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes().

int org::gel::mauve::Match::lcb = 0

Definition at line 22 of file Match.java. Referenced by org::gel::mauve::LcbViewerModel::addMatch(), org::gel::mauve::color::LCBColorScheme::apply(), org::gel::mauve::gui::sequence::MatchPanel::drawMatchBoxes(), org::gel::mauve::LCBlist::filterLCBs(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), Match(), org::gel::mauve::ModelBuilder::readMauveAlignment(), org::gel::mauve::LcbViewerModel::sanityCheck(), and org::gel::mauve::LcbViewerModel::updateLCBweight().

final int org::gel::mauve::Match::NO_MATCH = 0 [static]

Definition at line 16 of file Match.java. Referenced by org::gel::mauve::BaseViewerModel::getMatchRange(), offset(), org::gel::mauve::ModelBuilder::readMauveAlignment(), and org::gel::mauve::ModelBuilder::readMums().

final long org::gel::mauve::Match::serialVersionUID = 1 [static, package]

Definition at line 15 of file Match.java.

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

• src/org/gel/mauve/Match.java

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