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org::gel::mauve::LcbViewerModel Class Reference

Inheritance diagram for org::gel::mauve::LcbViewerModel:

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Collaboration diagram for org::gel::mauve::LcbViewerModel:

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List of all members.

Public Member Functions

void addMatch (Match m)
 Add a match to the list of matches.

void alignView (Genome g, long coord)
void alignView (Genome g, long left, long right)
 aligns the display to a particular position of a particular sequence.

LCB getDeletedRightNeighbor (LCB lcb, Genome g, long pos)
LCB[] getDelLcbList ()
boolean getDrawLcbBounds ()
boolean getFillLcbBoxes ()
LCB[] getFullLcbList ()
long[] getHighlightArray (Genome g)
LCB getLCB (int match_start, int match_end)
Vector getLcbChangePoints ()
long getLcbCount ()
List getLCBRange (Genome g, long start_coord, long end_coord)
 Finds all LCBs that intersect the specified coordinate range in the current view.

LCB getLeftmostDeletedLCB (Genome g)
LCB getLeftmostVisibleLCB (Genome g)
long getMinLCBWeight ()
boolean getSplitLcbByCtg ()
LCB[] getSplitLcbList ()
LCB getVisibleLcb (int index)
int getVisibleLcbCount ()
LCB[] getVisibleLcbList ()
LCB getVisibleRightNeighbor (LCB lcb, Genome g, long pos)
void initModelLCBs ()
boolean isNwayLcbList ()
void launchGrimmMGR ()
 Uses currently visible LCBs to launch a DCJ window.

 LcbViewerModel (File src)
void sanityCheck ()
void setDelLcbList (LCB[] delLcbList)
void setDrawLcbBounds (boolean value)
void setFillLcbBoxes (boolean value)
void setLcbChangePoints (Vector v)
void setLcbCount (long lcbCount)
void setMinLCBWeight (long lcb_minimum_weight)
void setSplitLcbByCtg (boolean value)
void setSplitLcbList (LCB[] list)
void setVisibleLcb (int index, LCB lcb)
void setVisibleLcbList (LCB[] lcbList)
void updateHighlight (Genome g, long leftCoordinate, long rightCoordinate)
void updateHighlight (Genome g, long coordinate)
void updateLCBweight (int min_weight, boolean temporary)

Protected Member Functions

void referenceUpdated ()

Package Functions

void setFullLcbList (LCB[] fullLcbList)

Private Attributes

LCB[] delLcbList = new LCB [0]
boolean displaySplitLCBs = false
boolean drawLCBbounds = true
boolean fillLCBboxes = false
LCB[] fullLcbList = new LCB [0]
long highlightCoordinateRight = -1
Vector lcb_change_points
long lcbCount = 0
long minimumLCBWeight
boolean nway_lcb_list = false
List originalMatchLcbs = new ArrayList ()
LCB[] splitLcbList = new LCB[0]
LCB[] visibleLcbList = new LCB [0]

Detailed Description

Author:
Paul Infield-Harm
Data model for viewer.

Definition at line 20 of file LcbViewerModel.java.

Constructor & Destructor Documentation

org::gel::mauve::LcbViewerModel::LcbViewerModel (  File  src  )  [inline]
 

Definition at line 53 of file LcbViewerModel.java.

Member Function Documentation

void org::gel::mauve::LcbViewerModel::addMatch (  Match  m  )  [inline]
 

Add a match to the list of matches.

Parameters:
m match to add

Reimplemented from org::gel::mauve::BaseViewerModel.

Definition at line 498 of file LcbViewerModel.java.

References org::gel::mauve::Match::lcb, and originalMatchLcbs.

void org::gel::mauve::LcbViewerModel::alignView (  Genome  g,
long  coord
)  [inline]
 

Reimplemented in org::gel::mauve::XmfaViewerModel.

Definition at line 366 of file LcbViewerModel.java.

References alignView().

void org::gel::mauve::LcbViewerModel::alignView (  Genome  g,
long  left,
long  right
)  [inline]
 

aligns the display to a particular position of a particular sequence.

typically called by RRSequencePanel when the user clicks a part of the sequence.

Definition at line 346 of file LcbViewerModel.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::Match::getLength(), org::gel::mauve::BaseViewerModel::getMatchRange(), org::gel::mauve::Match::getReverse(), org::gel::mauve::Genome::getSortedMatches(), org::gel::mauve::Match::getStart(), and org::gel::mauve::Genome::length.

Referenced by alignView(), and org::gel::mauve::gui::sequence::MatchPanel::mouseClicked().

LCB org::gel::mauve::LcbViewerModel::getDeletedRightNeighbor (  LCB  lcb,
Genome  g,
long  pos
)  [inline]
 

Definition at line 124 of file LcbViewerModel.java.

References delLcbList, org::gel::mauve::LCB::getRightAdjacency(), and org::gel::mauve::LCB::getRightEnd().

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

LCB [] org::gel::mauve::LcbViewerModel::getDelLcbList (   )  [inline]
 

Returns:
Returns the list of deleted LCBs that should not be shown.

Definition at line 174 of file LcbViewerModel.java.

References delLcbList.

boolean org::gel::mauve::LcbViewerModel::getDrawLcbBounds (   )  [inline]
 

Definition at line 510 of file LcbViewerModel.java.

References drawLCBbounds.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), and org::gel::mauve::gui::sequence::MatchPanel::formatBoxes().

boolean org::gel::mauve::LcbViewerModel::getFillLcbBoxes (   )  [inline]
 

Definition at line 521 of file LcbViewerModel.java.

References fillLCBboxes.

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

LCB [] org::gel::mauve::LcbViewerModel::getFullLcbList (   )  [inline]
 

Returns:
Returns the sequence coordinates of the complete set of LCB boundaries.

Definition at line 159 of file LcbViewerModel.java.

References fullLcbList.

Referenced by org::gel::mauve::color::BackboneLcbColor::apply(), org::gel::mauve::color::LCBColorScheme::computeLCBColors(), org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs(), org::gel::mauve::XmfaViewerModel::init(), org::gel::mauve::ModelBuilder::initMauveLCBs(), and initModelLCBs().

long [] org::gel::mauve::LcbViewerModel::getHighlightArray (  Genome  g  )  [inline]
 

Definition at line 312 of file LcbViewerModel.java.

References org::gel::mauve::BaseViewerModel::getHighlightCoordinate(), org::gel::mauve::BaseViewerModel::getHighlightGenome(), org::gel::mauve::Match::getLength(), org::gel::mauve::BaseViewerModel::getMatchRange(), org::gel::mauve::Match::getReverse(), org::gel::mauve::Genome::getSortedMatches(), org::gel::mauve::Match::getStart(), and highlightCoordinateRight.

LCB org::gel::mauve::LcbViewerModel::getLCB (  int  match_start,
int  match_end
)  [inline]
 

Definition at line 193 of file LcbViewerModel.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::BaseViewerModel::getGenomeByViewingIndex(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::Match::getLength(), org::gel::mauve::BaseViewerModel::getMatch(), org::gel::mauve::Match::getReverse(), org::gel::mauve::LCB::getRightEnd(), org::gel::mauve::BaseViewerModel::getSequenceCount(), org::gel::mauve::Match::getStart(), org::gel::mauve::LCB::keep, org::gel::mauve::LCB::setLeftEnd(), org::gel::mauve::LCB::setReverse(), org::gel::mauve::LCB::setRightEnd(), and org::gel::mauve::LCB::weight.

Vector org::gel::mauve::LcbViewerModel::getLcbChangePoints (   )  [inline]
 

Definition at line 450 of file LcbViewerModel.java.

References lcb_change_points.

Referenced by org::gel::mauve::gui::RearrangementPanel::initLCBTools(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

long org::gel::mauve::LcbViewerModel::getLcbCount (   )  [inline]
 

Returns:
Returns the lcbCount.

Definition at line 189 of file LcbViewerModel.java.

References lcbCount.

Referenced by org::gel::mauve::color::LCBColorScheme::computeLCBColors(), org::gel::mauve::gui::RearrangementPanel::initLCBTools(), org::gel::mauve::assembly::AssemblyScorer::numLCBs(), and org::gel::mauve::analysis::SnpExporter::SuppressWarnings().

List org::gel::mauve::LcbViewerModel::getLCBRange (  Genome  g,
long  start_coord,
long  end_coord
)  [inline]
 

Finds all LCBs that intersect the specified coordinate range in the current view.

Parameters:
start_coord The first coordinate of the intersection range
end_coord The last coordinate of the intersection range
lcbs An int array of the intersecting LCB indices

Definition at line 429 of file LcbViewerModel.java.

References org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getRightEnd(), getVisibleLcb(), and getVisibleLcbCount().

LCB org::gel::mauve::LcbViewerModel::getLeftmostDeletedLCB (  Genome  g  )  [inline]
 

Definition at line 138 of file LcbViewerModel.java.

References delLcbList, and org::gel::mauve::LCB::getLeftAdjacency().

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

LCB org::gel::mauve::LcbViewerModel::getLeftmostVisibleLCB (  Genome  g  )  [inline]
 

Definition at line 100 of file LcbViewerModel.java.

References org::gel::mauve::LCB::getLeftAdjacency(), and visibleLcbList.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

long org::gel::mauve::LcbViewerModel::getMinLCBWeight (   )  [inline]
 

Definition at line 446 of file LcbViewerModel.java.

References minimumLCBWeight.

Referenced by org::gel::mauve::gui::RearrangementPanel::initLCBTools().

boolean org::gel::mauve::LcbViewerModel::getSplitLcbByCtg (   )  [inline]
 

Definition at line 536 of file LcbViewerModel.java.

References displaySplitLCBs.

LCB [] org::gel::mauve::LcbViewerModel::getSplitLcbList (   )  [inline]
 

Definition at line 544 of file LcbViewerModel.java.

References splitLcbList.

Referenced by org::gel::mauve::assembly::AssemblyScorer::printBlockInfo().

LCB org::gel::mauve::LcbViewerModel::getVisibleLcb (  int  index  )  [inline]
 

Definition at line 84 of file LcbViewerModel.java.

References visibleLcbList.

Referenced by org::gel::mauve::color::LCBColorScheme::apply(), org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), getLCBRange(), org::gel::mauve::gui::LCBStatusBar::highlightChanged(), org::gel::mauve::gui::LcbLinePanel::paint(), and sanityCheck().

int org::gel::mauve::LcbViewerModel::getVisibleLcbCount (   )  [inline]
 

Definition at line 92 of file LcbViewerModel.java.

References visibleLcbList.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawLcbBounds(), getLCBRange(), org::gel::mauve::gui::RearrangementPanel::initLCBTools(), org::gel::mauve::gui::LcbLinePanel::LcbLinePanel(), org::gel::mauve::gui::LcbLinePanel::paint(), sanityCheck(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

LCB [] org::gel::mauve::LcbViewerModel::getVisibleLcbList (   )  [inline]
 

Returns:
Returns the sequence coordinates of currently viewed LCB boundaries.

Definition at line 80 of file LcbViewerModel.java.

References visibleLcbList.

Referenced by org::gel::mauve::analysis::PermutationExporter::getSplitLCBs(), and org::gel::mauve::ModelBuilder::initMauveLCBs().

LCB org::gel::mauve::LcbViewerModel::getVisibleRightNeighbor (  LCB  lcb,
Genome  g,
long  pos
)  [inline]
 

Definition at line 109 of file LcbViewerModel.java.

References org::gel::mauve::LCB::getRightAdjacency(), org::gel::mauve::LCB::getRightEnd(), and visibleLcbList.

Referenced by org::gel::mauve::gui::sequence::MatchPanel::drawXmfa().

void org::gel::mauve::LcbViewerModel::initModelLCBs (   )  [inline]
 

Definition at line 548 of file LcbViewerModel.java.

References getFullLcbList(), lcb_change_points, nway_lcb_list, setLcbChangePoints(), setMinLCBWeight(), setVisibleLcb(), setVisibleLcbList(), and org::gel::mauve::LCB::weight.

Referenced by org::gel::mauve::ModelBuilder::buildModel(), and org::gel::mauve::XmfaViewerModel::init().

boolean org::gel::mauve::LcbViewerModel::isNwayLcbList (   )  [inline]
 

Definition at line 96 of file LcbViewerModel.java.

References nway_lcb_list.

Referenced by org::gel::mauve::gui::RearrangementPanel::haveNwayLcbData().

void org::gel::mauve::LcbViewerModel::launchGrimmMGR (   )  [inline]
 

Uses currently visible LCBs to launch a DCJ window.

Definition at line 642 of file LcbViewerModel.java.

References org::gel::mauve::Genome::getChromosomes(), org::gel::mauve::LCB::getLeftAdjacency(), org::gel::mauve::LCB::getLeftEnd(), org::gel::mauve::LCB::getReverse(), org::gel::mauve::LCB::getRightAdjacency(), org::gel::mauve::BaseViewerModel::getSequenceCount(), and visibleLcbList.

Referenced by org::gel::mauve::gui::RearrangementPanel::actionPerformed().

void org::gel::mauve::LcbViewerModel::referenceUpdated (   )  [inline, protected]
 

Reimplemented from org::gel::mauve::BaseViewerModel.

Reimplemented in org::gel::mauve::XmfaViewerModel.

Definition at line 287 of file LcbViewerModel.java.

References delLcbList, fullLcbList, org::gel::mauve::LCB::setReference(), and visibleLcbList.

Referenced by updateLCBweight().

void org::gel::mauve::LcbViewerModel::sanityCheck (   )  [inline]
 

Definition at line 458 of file LcbViewerModel.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::LCB::getLeftAdjacency(), org::gel::mauve::BaseViewerModel::getMatch(), org::gel::mauve::BaseViewerModel::getMatchCount(), org::gel::mauve::LCB::getRightAdjacency(), org::gel::mauve::BaseViewerModel::getSequenceCount(), getVisibleLcb(), getVisibleLcbCount(), org::gel::mauve::LCB::id, and org::gel::mauve::Match::lcb.

void org::gel::mauve::LcbViewerModel::setDelLcbList (  LCB[]  delLcbList  )  [inline]
 

Parameters:
delLcbList list of deleted LCBs that should not be shown.

Definition at line 167 of file LcbViewerModel.java.

Referenced by org::gel::mauve::XmfaViewerModel::init(), and org::gel::mauve::ModelBuilder::initMauveLCBs().

void org::gel::mauve::LcbViewerModel::setDrawLcbBounds (  boolean  value  )  [inline]
 

Definition at line 503 of file LcbViewerModel.java.

References drawLCBbounds, and org::gel::mauve::BaseViewerModel::fireDrawingSettingsEvent().

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed().

void org::gel::mauve::LcbViewerModel::setFillLcbBoxes (  boolean  value  )  [inline]
 

Definition at line 514 of file LcbViewerModel.java.

References fillLCBboxes, and org::gel::mauve::BaseViewerModel::fireDrawingSettingsEvent().

Referenced by org::gel::mauve::gui::StyleMenu::actionPerformed(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

void org::gel::mauve::LcbViewerModel::setFullLcbList (  LCB[]  fullLcbList  )  [inline, package]
 

Parameters:
fullLcbList sequence coordinates of the complete set of LCB boundaries.

Definition at line 151 of file LcbViewerModel.java.

Referenced by org::gel::mauve::XmfaViewerModel::init().

void org::gel::mauve::LcbViewerModel::setLcbChangePoints (  Vector  v  )  [inline]
 

Definition at line 454 of file LcbViewerModel.java.

Referenced by initModelLCBs().

void org::gel::mauve::LcbViewerModel::setLcbCount (  long  lcbCount  )  [inline]
 

Parameters:
lcbCount The lcbCount to set.

Definition at line 182 of file LcbViewerModel.java.

Referenced by org::gel::mauve::XmfaViewerModel::init().

void org::gel::mauve::LcbViewerModel::setMinLCBWeight (  long  lcb_minimum_weight  )  [inline]
 

Definition at line 442 of file LcbViewerModel.java.

Referenced by initModelLCBs(), and updateLCBweight().

void org::gel::mauve::LcbViewerModel::setSplitLcbByCtg (  boolean  value  )  [inline]
 

Definition at line 525 of file LcbViewerModel.java.

References displaySplitLCBs, org::gel::mauve::BaseViewerModel::fireDrawingSettingsEvent(), fullLcbList, minimumLCBWeight, splitLcbList, updateLCBweight(), and visibleLcbList.

void org::gel::mauve::LcbViewerModel::setSplitLcbList (  LCB[]  list  )  [inline]
 

Definition at line 540 of file LcbViewerModel.java.

References splitLcbList.

Referenced by org::gel::mauve::XmfaViewerModel::init().

void org::gel::mauve::LcbViewerModel::setVisibleLcb (  int  index,
LCB  lcb
)  [inline]
 

Definition at line 88 of file LcbViewerModel.java.

References visibleLcbList.

Referenced by initModelLCBs().

void org::gel::mauve::LcbViewerModel::setVisibleLcbList (  LCB[]  lcbList  )  [inline]
 

Parameters:
lcbList sequence coordinates of currently viewed LCB boundaries.

Definition at line 72 of file LcbViewerModel.java.

Referenced by org::gel::mauve::ModelBuilder::initMauveLCBs(), and initModelLCBs().

void org::gel::mauve::LcbViewerModel::updateHighlight (  Genome  g,
long  leftCoordinate,
long  rightCoordinate
)  [inline]
 

Definition at line 62 of file LcbViewerModel.java.

References highlightCoordinateRight.

void org::gel::mauve::LcbViewerModel::updateHighlight (  Genome  g,
long  coordinate
)  [inline]
 

Reimplemented from org::gel::mauve::BaseViewerModel.

Reimplemented in org::gel::mauve::XmfaViewerModel.

Definition at line 57 of file LcbViewerModel.java.

References highlightCoordinateRight.

void org::gel::mauve::LcbViewerModel::updateLCBweight (  int  min_weight,
boolean  temporary
)  [inline]
 

Definition at line 370 of file LcbViewerModel.java.

References org::gel::mauve::ColorScheme::apply(), delLcbList, org::gel::mauve::BaseViewerModel::fireWeightEvent(), fullLcbList, org::gel::mauve::BaseViewerModel::getColorScheme(), org::gel::mauve::BaseViewerModel::getMatch(), org::gel::mauve::BaseViewerModel::getMatchCount(), org::gel::mauve::Match::lcb, originalMatchLcbs, referenceUpdated(), org::gel::mauve::BaseViewerModel::setColorScheme(), setMinLCBWeight(), and visibleLcbList.

Referenced by setSplitLcbByCtg(), and org::gel::mauve::gui::RearrangementPanel::stateChanged().

Member Data Documentation

LCB [] org::gel::mauve::LcbViewerModel::delLcbList = new LCB [0] [private]
 

Definition at line 31 of file LcbViewerModel.java.

Referenced by getDeletedRightNeighbor(), getDelLcbList(), getLeftmostDeletedLCB(), referenceUpdated(), and updateLCBweight().

boolean org::gel::mauve::LcbViewerModel::displaySplitLCBs = false [private]
 

Definition at line 47 of file LcbViewerModel.java.

Referenced by getSplitLcbByCtg(), and setSplitLcbByCtg().

boolean org::gel::mauve::LcbViewerModel::drawLCBbounds = true [private]
 

Definition at line 43 of file LcbViewerModel.java.

Referenced by getDrawLcbBounds(), and setDrawLcbBounds().

boolean org::gel::mauve::LcbViewerModel::fillLCBboxes = false [private]
 

Definition at line 45 of file LcbViewerModel.java.

Referenced by getFillLcbBoxes(), and setFillLcbBoxes().

LCB [] org::gel::mauve::LcbViewerModel::fullLcbList = new LCB [0] [private]
 

Definition at line 25 of file LcbViewerModel.java.

Referenced by getFullLcbList(), referenceUpdated(), setSplitLcbByCtg(), and updateLCBweight().

long org::gel::mauve::LcbViewerModel::highlightCoordinateRight = -1 [private]
 

Definition at line 49 of file LcbViewerModel.java.

Referenced by getHighlightArray(), and updateHighlight().

Vector org::gel::mauve::LcbViewerModel::lcb_change_points [private]
 

Definition at line 37 of file LcbViewerModel.java.

Referenced by getLcbChangePoints(), and initModelLCBs().

long org::gel::mauve::LcbViewerModel::lcbCount = 0 [private]
 

Definition at line 39 of file LcbViewerModel.java.

Referenced by getLcbCount().

long org::gel::mauve::LcbViewerModel::minimumLCBWeight [private]
 

Definition at line 41 of file LcbViewerModel.java.

Referenced by getMinLCBWeight(), and setSplitLcbByCtg().

boolean org::gel::mauve::LcbViewerModel::nway_lcb_list = false [private]
 

Definition at line 51 of file LcbViewerModel.java.

Referenced by initModelLCBs(), and isNwayLcbList().

List org::gel::mauve::LcbViewerModel::originalMatchLcbs = new ArrayList () [private]
 

Definition at line 33 of file LcbViewerModel.java.

Referenced by addMatch(), and updateLCBweight().

LCB [] org::gel::mauve::LcbViewerModel::splitLcbList = new LCB[0] [private]
 

Definition at line 28 of file LcbViewerModel.java.

Referenced by getSplitLcbList(), setSplitLcbByCtg(), and setSplitLcbList().

LCB [] org::gel::mauve::LcbViewerModel::visibleLcbList = new LCB [0] [private]
 

Definition at line 22 of file LcbViewerModel.java.

Referenced by getLeftmostVisibleLCB(), getVisibleLcb(), getVisibleLcbCount(), getVisibleLcbList(), getVisibleRightNeighbor(), launchGrimmMGR(), referenceUpdated(), setSplitLcbByCtg(), setVisibleLcb(), and updateLCBweight().

The documentation for this class was generated from the following file:
Generated on Tue May 21 06:03:08 2013 for Mauve by doxygen 1.3.6