org::gel::mauve::backbone::BackboneList Class Reference

Collaboration diagram for org::gel::mauve::backbone::BackboneList:

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List of all members.

Public Member Functions

Backbone getBackbone (Genome g, long position)
Backbone[] getBackboneArray ()
Backbone getNextBackbone (Genome g, long position)
void setBackbone (Backbone[] bb_array)
void setSeqBackbone (Vector seq_bb)
void setXmfa (XMFAAlignment xmfa)

Protected Attributes

Backbone[] bb_array
Vector seq_bb
XMFAAlignment xmfa

Member Function Documentation

Backbone org::gel::mauve::backbone::BackboneList::getBackbone Genome  g,
long  position
[inline]
 

Definition at line 139 of file BackboneList.java.

References org::gel::mauve::backbone::Backbone::getLeftEnd(), getNextBackbone(), and org::gel::mauve::backbone::Backbone::getRightEnd().

Referenced by org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), and org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs().

Backbone [] org::gel::mauve::backbone::BackboneList::getBackboneArray  )  [inline]
 

Definition at line 147 of file BackboneList.java.

References bb_array.

Referenced by org::gel::mauve::color::BackboneMultiplicityColor::apply(), and org::gel::mauve::color::BackboneLcbColor::apply().

Backbone org::gel::mauve::backbone::BackboneList::getNextBackbone Genome  g,
long  position
[inline]
 

Definition at line 87 of file BackboneList.java.

References org::gel::mauve::XMFAAlignment::getLCBAndColumn(), org::gel::mauve::backbone::Backbone::getLeftEnd(), org::gel::mauve::Genome::getLength(), org::gel::mauve::Genome::getSourceIndex(), org::gel::mauve::backbone::Backbone::length, seq_bb, org::gel::mauve::backbone::Backbone::setLcbIndex(), org::gel::mauve::backbone::Backbone::setLeftColumn(), org::gel::mauve::backbone::Backbone::setLeftEnd(), org::gel::mauve::backbone::Backbone::setLength(), org::gel::mauve::backbone::Backbone::setRightEnd(), org::gel::mauve::backbone::Backbone::setSeqs(), and xmfa.

Referenced by org::gel::mauve::SimilarityIndex::calculateIndex(), org::gel::mauve::gui::sequence::MatchPanel::drawXmfa(), getBackbone(), and org::gel::mauve::analysis::OneToOneOrthologExporter::getBackboneSegs().

void org::gel::mauve::backbone::BackboneList::setBackbone Backbone[]  bb_array  )  [inline]
 

Definition at line 79 of file BackboneList.java.

Referenced by org::gel::mauve::backbone::BackboneListBuilder::build().

void org::gel::mauve::backbone::BackboneList::setSeqBackbone Vector  seq_bb  )  [inline]
 

Definition at line 83 of file BackboneList.java.

Referenced by org::gel::mauve::backbone::BackboneListBuilder::build().

void org::gel::mauve::backbone::BackboneList::setXmfa XMFAAlignment  xmfa  )  [inline]
 

Definition at line 75 of file BackboneList.java.

Referenced by org::gel::mauve::backbone::BackboneListBuilder::build().


Member Data Documentation

Backbone [] org::gel::mauve::backbone::BackboneList::bb_array [protected]
 

Definition at line 71 of file BackboneList.java.

Referenced by getBackboneArray().

Vector org::gel::mauve::backbone::BackboneList::seq_bb [protected]
 

Definition at line 69 of file BackboneList.java.

Referenced by getNextBackbone().

XMFAAlignment org::gel::mauve::backbone::BackboneList::xmfa [protected]
 

Definition at line 73 of file BackboneList.java.

Referenced by getNextBackbone().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:03:50 2013 for Mauve by doxygen 1.3.6