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


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.


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.


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().


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.


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:47 2013 for Mauve by doxygen 1.3.6