org::gel::mauve::summary::output::SegmentDataProcessor Class Reference

Inheritance diagram for org::gel::mauve::summary::output::SegmentDataProcessor:

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Collaboration diagram for org::gel::mauve::summary::output::SegmentDataProcessor:

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List of all members.

Public Member Functions

long multiplicityForGenome (int index)
 SegmentDataProcessor (Hashtable map)

Static Public Member Functions

long multiplicityForGenome (int index, int count)

Protected Member Functions

void addDataLinks ()
void addUniques ()
void assignIDs ()
void compressBackboneSegments ()
void findContigsInUniques ()
int getReferenceSequence ()
List getSegmentsSortedBySeq (int sequence)
void init ()
Vector makeDefaultStartEndColumnHeaders ()

Protected Attributes

long all_seq_multiplicity
Vector backbone
int backbone_min
int count
Segment current
Segment[] firsts
int reference = -1

Constructor & Destructor Documentation

org::gel::mauve::summary::output::SegmentDataProcessor::SegmentDataProcessor Hashtable  map  )  [inline]
 

Definition at line 32 of file SegmentDataProcessor.java.

References init().


Member Function Documentation

void org::gel::mauve::summary::output::SegmentDataProcessor::addDataLinks  )  [inline, protected]
 

Definition at line 132 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::nexts, and org::gel::mauve::analysis::Segment::prevs.

Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::addUniques  )  [inline, protected]
 

Definition at line 155 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::nexts, org::gel::mauve::analysis::Segment::prevs, and org::gel::mauve::analysis::Segment::right.

Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::assignIDs  )  [inline, protected]
 

Definition at line 81 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::END, multiplicityForGenome(), org::gel::mauve::analysis::Segment::multiplicityType(), org::gel::mauve::analysis::Segment::nexts, and org::gel::mauve::analysis::Segment::typed_id.

Referenced by init().

void org::gel::mauve::summary::output::SegmentDataProcessor::compressBackboneSegments  )  [inline, protected]
 

Definition at line 204 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::append(), org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::multiplicityType(), org::gel::mauve::analysis::Segment::nexts, org::gel::mauve::analysis::Segment::prevs, org::gel::mauve::analysis::Segment::remove(), org::gel::mauve::analysis::Segment::reverse, and org::gel::mauve::analysis::Segment::right.

void org::gel::mauve::summary::output::SegmentDataProcessor::findContigsInUniques  )  [inline, protected]
 

Definition at line 65 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::END, org::gel::mauve::contigs::ContigHandler::fixSegmentByContigs(), multiplicityForGenome(), org::gel::mauve::analysis::Segment::multiplicityType(), and org::gel::mauve::analysis::Segment::nexts.

int org::gel::mauve::summary::output::SegmentDataProcessor::getReferenceSequence  )  [inline, protected]
 

Definition at line 110 of file SegmentDataProcessor.java.

References org::gel::mauve::analysis::Segment::reverse.

List org::gel::mauve::summary::output::SegmentDataProcessor::getSegmentsSortedBySeq int  sequence  )  [inline, protected]
 

Definition at line 280 of file SegmentDataProcessor.java.

void org::gel::mauve::summary::output::SegmentDataProcessor::init  )  [inline, protected]
 

Definition at line 42 of file SegmentDataProcessor.java.

References addDataLinks(), addUniques(), assignIDs(), and org::gel::mauve::analysis::Segment::END.

Referenced by SegmentDataProcessor().

Vector org::gel::mauve::summary::output::SegmentDataProcessor::makeDefaultStartEndColumnHeaders  )  [inline, protected]
 

Definition at line 260 of file SegmentDataProcessor.java.

Referenced by org::gel::mauve::summary::output::AbstractMatchDataWriter::setColumnHeaders().

long org::gel::mauve::summary::output::SegmentDataProcessor::multiplicityForGenome int  index,
int  count
[inline, static]
 

Definition at line 104 of file SegmentDataProcessor.java.

long org::gel::mauve::summary::output::SegmentDataProcessor::multiplicityForGenome int  index  )  [inline]
 

Definition at line 100 of file SegmentDataProcessor.java.

Referenced by assignIDs(), findContigsInUniques(), and org::gel::mauve::summary::output::AbstractIslandWriter::printData().


Member Data Documentation

long org::gel::mauve::summary::output::SegmentDataProcessor::all_seq_multiplicity [protected]
 

Definition at line 30 of file SegmentDataProcessor.java.

Vector org::gel::mauve::summary::output::SegmentDataProcessor::backbone [protected]
 

Definition at line 28 of file SegmentDataProcessor.java.

int org::gel::mauve::summary::output::SegmentDataProcessor::backbone_min [protected]
 

Definition at line 20 of file SegmentDataProcessor.java.

int org::gel::mauve::summary::output::SegmentDataProcessor::count [protected]
 

Definition at line 18 of file SegmentDataProcessor.java.

Segment org::gel::mauve::summary::output::SegmentDataProcessor::current [protected]
 

Definition at line 26 of file SegmentDataProcessor.java.

Segment [] org::gel::mauve::summary::output::SegmentDataProcessor::firsts [protected]
 

Definition at line 24 of file SegmentDataProcessor.java.

int org::gel::mauve::summary::output::SegmentDataProcessor::reference = -1 [protected]
 

Definition at line 22 of file SegmentDataProcessor.java.

Referenced by org::gel::mauve::summary::output::AbstractMatchDataWriter::initSubClassParticulars().


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