org::gel::mauve::assembly::AssemblyScorer Class Reference

Collaboration diagram for org::gel::mauve::assembly::AssemblyScorer:

Collaboration graph
[legend]
List of all members.

Public Member Functions

 AssemblyScorer (ContigOrderer co, File outDir, String basename)
 AssemblyScorer (ContigOrderer co, File outDir)
 AssemblyScorer (File alnmtFile, File outDir, String basename)
 AssemblyScorer (File alnmtFile, File outDir)
 AssemblyScorer (XmfaViewerModel model)
void completeAlignment (int retcode)
Gap[] getAssemblyGaps ()
int getBPdist ()
BrokenCDS[] getBrokenCDS ()
long getContigN50 ()
long getContigN90 ()
DCJ getDCJ ()
int getDCJdist ()
Chromosome[] getExtraContigs ()
int getInterLcbBoundaryCount ()
Chromosome[] getInverted ()
long getMaxContigLength ()
long getMinContigLength ()
Map< Chromosome, Integer > getMisAssemblies ()
int getMiscalled ()
Chromosome[] getMissingChromosomes ()
XmfaViewerModel getModel ()
Gap[] getReferenceGaps ()
int getSCJdist ()
int getSharedBoundaryCount ()
SNP[] getSNPs ()
int[][] getSubs ()
int getUncalled ()
boolean hasBrokenCDS ()
long numBasesAssembly ()
long numBasesReference ()
int numBlocks ()
int numBrokenCDS ()
int numCompleteCDS ()
int numContigs ()
int numLCBs ()
long numReplicons ()
double percentExtraBases ()
double percentMissedBases ()
void setMiscalled (int miscalled)
void setUncalled (int uncalled)
void summarizeBaseCalls ()
long totalExtraBases ()
long totalMissedBases ()
double typeIadjErr ()
double typeIIadjErr ()

Static Public Member Functions

void calculateMissingGC (AssemblyScorer asmScore, File outDir, String basename)
int[][] countSubstitutions (SNP[] snps)
 Returns a 4x4 matrix of counts of substitution types between genome src_i and src_j.

void printInfo (AssemblyScorer sa, PrintStream miscallOut, PrintStream uncallOut, PrintStream gapOut)
 Prints the SNP and gap data from this AssemblyScorer object out to the respective PrintStreams.

void printInfo (AssemblyScorer sa, File outDir, String baseName, boolean batch)
void printMissingRegions (AssemblyScorer asmScore, File outDir, String basename)

Static Public Attributes

final int MINIMUM_REPORTABLE_MISSING_LENGTH = 20

Static Package Functions

double countGC (byte[] rawseq)
int getBaseIdx (char c) throws IllegalArgumentException
String subsToString (AssemblyScorer assScore)

Private Member Functions

void computeAdjacencyErrors ()
void computeBrokenCDS ()
void computeContigSizeStats ()
synchronized void loadInfo ()
 computes info.


Static Private Member Functions

String getReferenceChromosomes (AssemblyScorer sa)
void printBlockInfo (PrintStream out, XmfaViewerModel model)

Private Attributes

File alnmtFile
Gap[] assGaps
String basename
boolean batch
BrokenCDS[] brokenCDS
CDSErrorExporter cdsEE
ContigOrderer co
long contigN50 = -1
long contigN90 = -1
DCJ dcj
Chromosome[] extraCtgs
boolean getBrokenCDS = true
Vector< ChromosomeinvCtgs
long maxContigLength = -1
 contig stats

long minContigLength = -1
Map< Chromosome, Integer > misAsm
int miscalled
Chromosome[] missingChroms
XmfaViewerModel model
int numInterLcbBnds
int numMisAssemblies
int numSharedBnds
File outputDir
Gap[] refGaps
SNP[] snps
int[][] subs
Vector< AdjacencytypeI
 extra adjacencies

Vector< AdjacencytypeII
 missing adjacencies

int uncalled

Static Private Attributes

int A = 0
int C = 1
int G = 3
int T = 2

Constructor & Destructor Documentation

org::gel::mauve::assembly::AssemblyScorer::AssemblyScorer XmfaViewerModel  model  )  [inline]
 

Definition at line 87 of file AssemblyScorer.java.

References loadInfo().

org::gel::mauve::assembly::AssemblyScorer::AssemblyScorer File  alnmtFile,
File  outDir
[inline]
 

Definition at line 92 of file AssemblyScorer.java.

References basename, and batch.

org::gel::mauve::assembly::AssemblyScorer::AssemblyScorer File  alnmtFile,
File  outDir,
String  basename
[inline]
 

Definition at line 99 of file AssemblyScorer.java.

org::gel::mauve::assembly::AssemblyScorer::AssemblyScorer ContigOrderer  co,
File  outDir
[inline]
 

Definition at line 104 of file AssemblyScorer.java.

References batch.

org::gel::mauve::assembly::AssemblyScorer::AssemblyScorer ContigOrderer  co,
File  outDir,
String  basename
[inline]
 

Definition at line 110 of file AssemblyScorer.java.


Member Function Documentation

void org::gel::mauve::assembly::AssemblyScorer::calculateMissingGC AssemblyScorer  asmScore,
File  outDir,
String  basename
[inline, static]
 

Definition at line 514 of file AssemblyScorer.java.

References countGC(), getAssemblyGaps(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::XmfaViewerModel::getLCBAndColumn(), org::gel::mauve::Genome::getLength(), getModel(), org::gel::mauve::XmfaViewerModel::getXmfa(), and org::gel::mauve::XMFAAlignment::readRawSequence().

void org::gel::mauve::assembly::AssemblyScorer::completeAlignment int  retcode  )  [inline]
 

Definition at line 115 of file AssemblyScorer.java.

References alnmtFile, basename, batch, co, loadInfo(), outputDir, and printInfo().

void org::gel::mauve::assembly::AssemblyScorer::computeAdjacencyErrors  )  [inline, private]
 

Definition at line 141 of file AssemblyScorer.java.

References dcj, org::gel::mauve::dcjx::Adjacency::getFirstBlockEnd(), org::gel::mauve::dcjx::Adjacency::getSecondBlockEnd(), typeI, and typeII.

Referenced by loadInfo().

void org::gel::mauve::assembly::AssemblyScorer::computeBrokenCDS  )  [inline, private]
 

Definition at line 299 of file AssemblyScorer.java.

References assGaps, brokenCDS, cdsEE, org::gel::mauve::Genome::getAnnotationSequence(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::BaseViewerModel::getGenomes(), refGaps, and snps.

Referenced by loadInfo().

void org::gel::mauve::assembly::AssemblyScorer::computeContigSizeStats  )  [inline, private]
 

Definition at line 264 of file AssemblyScorer.java.

References contigN50, contigN90, org::gel::mauve::Genome::getChromosomes(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), maxContigLength, and minContigLength.

Referenced by loadInfo().

double org::gel::mauve::assembly::AssemblyScorer::countGC byte[]  rawseq  )  [inline, static, package]
 

Definition at line 577 of file AssemblyScorer.java.

Referenced by calculateMissingGC().

int [][] org::gel::mauve::assembly::AssemblyScorer::countSubstitutions SNP[]  snps  )  [inline, static]
 

Returns a 4x4 matrix of counts of substitution types between genome src_i and src_j.

A C T G A - C - T - G -
Parameters:
snps 
Returns:
a 4x4 matrix of substitution counts

Definition at line 623 of file AssemblyScorer.java.

References getBaseIdx(), and subs.

Gap [] org::gel::mauve::assembly::AssemblyScorer::getAssemblyGaps  )  [inline]
 

Definition at line 350 of file AssemblyScorer.java.

References assGaps.

Referenced by calculateMissingGC(), and org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::getBaseIdx char  c  )  throws IllegalArgumentException [inline, static, package]
 

Definition at line 639 of file AssemblyScorer.java.

Referenced by countSubstitutions().

int org::gel::mauve::assembly::AssemblyScorer::getBPdist  )  [inline]
 

Definition at line 398 of file AssemblyScorer.java.

References dcj.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

BrokenCDS [] org::gel::mauve::assembly::AssemblyScorer::getBrokenCDS  )  [inline]
 

Definition at line 378 of file AssemblyScorer.java.

References brokenCDS.

long org::gel::mauve::assembly::AssemblyScorer::getContigN50  )  [inline]
 

Definition at line 468 of file AssemblyScorer.java.

References contigN50.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

long org::gel::mauve::assembly::AssemblyScorer::getContigN90  )  [inline]
 

Definition at line 472 of file AssemblyScorer.java.

References contigN90.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

DCJ org::gel::mauve::assembly::AssemblyScorer::getDCJ  )  [inline]
 

Definition at line 342 of file AssemblyScorer.java.

References dcj.

int org::gel::mauve::assembly::AssemblyScorer::getDCJdist  )  [inline]
 

Definition at line 394 of file AssemblyScorer.java.

References dcj.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

Chromosome [] org::gel::mauve::assembly::AssemblyScorer::getExtraContigs  )  [inline]
 

Definition at line 354 of file AssemblyScorer.java.

References extraCtgs.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::getInterLcbBoundaryCount  )  [inline]
 

Definition at line 505 of file AssemblyScorer.java.

References numInterLcbBnds.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

Chromosome [] org::gel::mauve::assembly::AssemblyScorer::getInverted  )  [inline]
 

Definition at line 422 of file AssemblyScorer.java.

References invCtgs.

long org::gel::mauve::assembly::AssemblyScorer::getMaxContigLength  )  [inline]
 

Definition at line 464 of file AssemblyScorer.java.

References maxContigLength.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

long org::gel::mauve::assembly::AssemblyScorer::getMinContigLength  )  [inline]
 

Definition at line 476 of file AssemblyScorer.java.

References minContigLength.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

Map<Chromosome, Integer> org::gel::mauve::assembly::AssemblyScorer::getMisAssemblies  )  [inline]
 

Definition at line 418 of file AssemblyScorer.java.

References misAsm.

int org::gel::mauve::assembly::AssemblyScorer::getMiscalled  )  [inline]
 

Definition at line 322 of file AssemblyScorer.java.

References miscalled.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

Chromosome [] org::gel::mauve::assembly::AssemblyScorer::getMissingChromosomes  )  [inline]
 

Definition at line 358 of file AssemblyScorer.java.

References missingChroms.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

XmfaViewerModel org::gel::mauve::assembly::AssemblyScorer::getModel  )  [inline]
 

Definition at line 338 of file AssemblyScorer.java.

Referenced by calculateMissingGC(), getReferenceChromosomes(), org::gel::mauve::assembly::ScoreAssembly::getSumText(), and printMissingRegions().

String org::gel::mauve::assembly::AssemblyScorer::getReferenceChromosomes AssemblyScorer  sa  )  [inline, static, private]
 

Definition at line 728 of file AssemblyScorer.java.

References org::gel::mauve::Genome::getChromosomes(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), getModel(), org::gel::mauve::Chromosome::getName(), and org::gel::mauve::Chromosome::getStart().

Referenced by printInfo().

Gap [] org::gel::mauve::assembly::AssemblyScorer::getReferenceGaps  )  [inline]
 

Definition at line 346 of file AssemblyScorer.java.

References refGaps.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText(), and printMissingRegions().

int org::gel::mauve::assembly::AssemblyScorer::getSCJdist  )  [inline]
 

Definition at line 390 of file AssemblyScorer.java.

References dcj.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::getSharedBoundaryCount  )  [inline]
 

Definition at line 501 of file AssemblyScorer.java.

References numSharedBnds.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

SNP [] org::gel::mauve::assembly::AssemblyScorer::getSNPs  )  [inline]
 

Definition at line 362 of file AssemblyScorer.java.

References snps.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int [][] org::gel::mauve::assembly::AssemblyScorer::getSubs  )  [inline]
 

Definition at line 366 of file AssemblyScorer.java.

References subs.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText(), and subsToString().

int org::gel::mauve::assembly::AssemblyScorer::getUncalled  )  [inline]
 

Definition at line 330 of file AssemblyScorer.java.

References uncalled.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

boolean org::gel::mauve::assembly::AssemblyScorer::hasBrokenCDS  )  [inline]
 

Definition at line 370 of file AssemblyScorer.java.

References brokenCDS.

synchronized void org::gel::mauve::assembly::AssemblyScorer::loadInfo  )  [inline, private]
 

computes info.

sorts gaps and snps

Definition at line 206 of file AssemblyScorer.java.

References assGaps, computeAdjacencyErrors(), computeBrokenCDS(), computeContigSizeStats(), extraCtgs, getBrokenCDS, org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), missingChroms, numInterLcbBnds, numSharedBnds, refGaps, org::gel::mauve::BaseViewerModel::setReference(), snps, and summarizeBaseCalls().

Referenced by AssemblyScorer(), and completeAlignment().

long org::gel::mauve::assembly::AssemblyScorer::numBasesAssembly  )  [inline]
 

Definition at line 439 of file AssemblyScorer.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), and org::gel::mauve::Genome::getLength().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

long org::gel::mauve::assembly::AssemblyScorer::numBasesReference  )  [inline]
 

Definition at line 443 of file AssemblyScorer.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), and org::gel::mauve::Genome::getLength().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::numBlocks  )  [inline]
 

Definition at line 402 of file AssemblyScorer.java.

References dcj.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::numBrokenCDS  )  [inline]
 

Definition at line 382 of file AssemblyScorer.java.

References cdsEE.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::numCompleteCDS  )  [inline]
 

Definition at line 386 of file AssemblyScorer.java.

References cdsEE.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::numContigs  )  [inline]
 

Definition at line 430 of file AssemblyScorer.java.

References org::gel::mauve::Genome::getChromosomes(), and org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

int org::gel::mauve::assembly::AssemblyScorer::numLCBs  )  [inline]
 

Definition at line 426 of file AssemblyScorer.java.

References org::gel::mauve::LcbViewerModel::getLcbCount().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

long org::gel::mauve::assembly::AssemblyScorer::numReplicons  )  [inline]
 

Definition at line 434 of file AssemblyScorer.java.

References org::gel::mauve::Genome::getChromosomes(), and org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

double org::gel::mauve::assembly::AssemblyScorer::percentExtraBases  )  [inline]
 

Returns:
numExtraBases/totalNumBases

Definition at line 484 of file AssemblyScorer.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::Genome::getLength(), and refGaps.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

double org::gel::mauve::assembly::AssemblyScorer::percentMissedBases  )  [inline]
 

Definition at line 447 of file AssemblyScorer.java.

References assGaps, org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), and org::gel::mauve::Genome::getLength().

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

void org::gel::mauve::assembly::AssemblyScorer::printBlockInfo PrintStream  out,
XmfaViewerModel  model
[inline, static, private]
 

Definition at line 741 of file AssemblyScorer.java.

References org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), and org::gel::mauve::LcbViewerModel::getSplitLcbList().

Referenced by printInfo().

void org::gel::mauve::assembly::AssemblyScorer::printInfo AssemblyScorer  sa,
PrintStream  miscallOut,
PrintStream  uncallOut,
PrintStream  gapOut
[inline, static]
 

Prints the SNP and gap data from this AssemblyScorer object out to the respective PrintStreams.


NOTE: snpOut and gapOut can take null values

Parameters:
sa the AssemblyScorer to print info for
snpOut stream to print SNP info to
gapOut stream to print gap info to

Definition at line 779 of file AssemblyScorer.java.

References assGaps, refGaps, and snps.

void org::gel::mauve::assembly::AssemblyScorer::printInfo AssemblyScorer  sa,
File  outDir,
String  baseName,
boolean  batch
[inline, static]
 

Definition at line 676 of file AssemblyScorer.java.

References getReferenceChromosomes(), model, and printBlockInfo().

Referenced by completeAlignment().

void org::gel::mauve::assembly::AssemblyScorer::printMissingRegions AssemblyScorer  asmScore,
File  outDir,
String  basename
[inline, static]
 

Definition at line 654 of file AssemblyScorer.java.

References getModel(), getReferenceGaps(), org::gel::mauve::XmfaViewerModel::getSequenceRange(), and MINIMUM_REPORTABLE_MISSING_LENGTH.

void org::gel::mauve::assembly::AssemblyScorer::setMiscalled int  miscalled  )  [inline]
 

Definition at line 326 of file AssemblyScorer.java.

void org::gel::mauve::assembly::AssemblyScorer::setUncalled int  uncalled  )  [inline]
 

Definition at line 334 of file AssemblyScorer.java.

String org::gel::mauve::assembly::AssemblyScorer::subsToString AssemblyScorer  assScore  )  [inline, static, package]
 

Definition at line 591 of file AssemblyScorer.java.

References getSubs(), and subs.

void org::gel::mauve::assembly::AssemblyScorer::summarizeBaseCalls  )  [inline]
 

Definition at line 289 of file AssemblyScorer.java.

References snps, and subs.

Referenced by loadInfo().

long org::gel::mauve::assembly::AssemblyScorer::totalExtraBases  )  [inline]
 

Definition at line 493 of file AssemblyScorer.java.

References refGaps.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

long org::gel::mauve::assembly::AssemblyScorer::totalMissedBases  )  [inline]
 

Definition at line 456 of file AssemblyScorer.java.

References assGaps.

Referenced by org::gel::mauve::assembly::ScoreAssembly::getSumText().

double org::gel::mauve::assembly::AssemblyScorer::typeIadjErr  )  [inline]
 

Definition at line 406 of file AssemblyScorer.java.

References dcj, and typeI.

double org::gel::mauve::assembly::AssemblyScorer::typeIIadjErr  )  [inline]
 

Definition at line 412 of file AssemblyScorer.java.

References dcj, and typeII.


Member Data Documentation

int org::gel::mauve::assembly::AssemblyScorer::A = 0 [static, private]
 

Definition at line 81 of file AssemblyScorer.java.

File org::gel::mauve::assembly::AssemblyScorer::alnmtFile [private]
 

Definition at line 43 of file AssemblyScorer.java.

Referenced by completeAlignment().

Gap [] org::gel::mauve::assembly::AssemblyScorer::assGaps [private]
 

Definition at line 51 of file AssemblyScorer.java.

Referenced by computeBrokenCDS(), getAssemblyGaps(), loadInfo(), percentMissedBases(), printInfo(), and totalMissedBases().

String org::gel::mauve::assembly::AssemblyScorer::basename [private]
 

Definition at line 46 of file AssemblyScorer.java.

Referenced by AssemblyScorer(), and completeAlignment().

boolean org::gel::mauve::assembly::AssemblyScorer::batch [private]
 

Definition at line 45 of file AssemblyScorer.java.

Referenced by AssemblyScorer(), and completeAlignment().

BrokenCDS [] org::gel::mauve::assembly::AssemblyScorer::brokenCDS [private]
 

Definition at line 54 of file AssemblyScorer.java.

Referenced by computeBrokenCDS(), getBrokenCDS(), and hasBrokenCDS().

int org::gel::mauve::assembly::AssemblyScorer::C = 1 [static, private]
 

Definition at line 82 of file AssemblyScorer.java.

CDSErrorExporter org::gel::mauve::assembly::AssemblyScorer::cdsEE [private]
 

Definition at line 55 of file AssemblyScorer.java.

Referenced by computeBrokenCDS(), numBrokenCDS(), and numCompleteCDS().

ContigOrderer org::gel::mauve::assembly::AssemblyScorer::co [private]
 

Definition at line 42 of file AssemblyScorer.java.

Referenced by completeAlignment().

long org::gel::mauve::assembly::AssemblyScorer::contigN50 = -1 [private]
 

Definition at line 77 of file AssemblyScorer.java.

Referenced by computeContigSizeStats(), and getContigN50().

long org::gel::mauve::assembly::AssemblyScorer::contigN90 = -1 [private]
 

Definition at line 78 of file AssemblyScorer.java.

Referenced by computeContigSizeStats(), and getContigN90().

DCJ org::gel::mauve::assembly::AssemblyScorer::dcj [private]
 

Definition at line 56 of file AssemblyScorer.java.

Referenced by computeAdjacencyErrors(), getBPdist(), getDCJ(), getDCJdist(), getSCJdist(), numBlocks(), typeIadjErr(), and typeIIadjErr().

Chromosome [] org::gel::mauve::assembly::AssemblyScorer::extraCtgs [private]
 

Definition at line 52 of file AssemblyScorer.java.

Referenced by getExtraContigs(), and loadInfo().

int org::gel::mauve::assembly::AssemblyScorer::G = 3 [static, private]
 

Definition at line 84 of file AssemblyScorer.java.

boolean org::gel::mauve::assembly::AssemblyScorer::getBrokenCDS = true [private]
 

Definition at line 57 of file AssemblyScorer.java.

Referenced by loadInfo().

Vector<Chromosome> org::gel::mauve::assembly::AssemblyScorer::invCtgs [private]
 

Definition at line 68 of file AssemblyScorer.java.

Referenced by getInverted().

long org::gel::mauve::assembly::AssemblyScorer::maxContigLength = -1 [private]
 

contig stats

Definition at line 76 of file AssemblyScorer.java.

Referenced by computeContigSizeStats(), and getMaxContigLength().

long org::gel::mauve::assembly::AssemblyScorer::minContigLength = -1 [private]
 

Definition at line 79 of file AssemblyScorer.java.

Referenced by computeContigSizeStats(), and getMinContigLength().

final int org::gel::mauve::assembly::AssemblyScorer::MINIMUM_REPORTABLE_MISSING_LENGTH = 20 [static]
 

Definition at line 653 of file AssemblyScorer.java.

Referenced by printMissingRegions().

Map<Chromosome,Integer> org::gel::mauve::assembly::AssemblyScorer::misAsm [private]
 

Definition at line 69 of file AssemblyScorer.java.

Referenced by getMisAssemblies().

int org::gel::mauve::assembly::AssemblyScorer::miscalled [private]
 

Definition at line 72 of file AssemblyScorer.java.

Referenced by getMiscalled().

Chromosome [] org::gel::mauve::assembly::AssemblyScorer::missingChroms [private]
 

Definition at line 53 of file AssemblyScorer.java.

Referenced by getMissingChromosomes(), and loadInfo().

XmfaViewerModel org::gel::mauve::assembly::AssemblyScorer::model [private]
 

Definition at line 47 of file AssemblyScorer.java.

Referenced by printInfo().

int org::gel::mauve::assembly::AssemblyScorer::numInterLcbBnds [private]
 

Definition at line 61 of file AssemblyScorer.java.

Referenced by getInterLcbBoundaryCount(), and loadInfo().

int org::gel::mauve::assembly::AssemblyScorer::numMisAssemblies [private]
 

Definition at line 70 of file AssemblyScorer.java.

int org::gel::mauve::assembly::AssemblyScorer::numSharedBnds [private]
 

Definition at line 59 of file AssemblyScorer.java.

Referenced by getSharedBoundaryCount(), and loadInfo().

File org::gel::mauve::assembly::AssemblyScorer::outputDir [private]
 

Definition at line 44 of file AssemblyScorer.java.

Referenced by completeAlignment().

Gap [] org::gel::mauve::assembly::AssemblyScorer::refGaps [private]
 

Definition at line 50 of file AssemblyScorer.java.

Referenced by computeBrokenCDS(), getReferenceGaps(), loadInfo(), percentExtraBases(), printInfo(), and totalExtraBases().

SNP [] org::gel::mauve::assembly::AssemblyScorer::snps [private]
 

Definition at line 49 of file AssemblyScorer.java.

Referenced by computeBrokenCDS(), getSNPs(), loadInfo(), printInfo(), and summarizeBaseCalls().

int [][] org::gel::mauve::assembly::AssemblyScorer::subs [private]
 

Definition at line 48 of file AssemblyScorer.java.

Referenced by countSubstitutions(), getSubs(), subsToString(), and summarizeBaseCalls().

int org::gel::mauve::assembly::AssemblyScorer::T = 2 [static, private]
 

Definition at line 83 of file AssemblyScorer.java.

Vector<Adjacency> org::gel::mauve::assembly::AssemblyScorer::typeI [private]
 

extra adjacencies

Definition at line 64 of file AssemblyScorer.java.

Referenced by computeAdjacencyErrors(), and typeIadjErr().

Vector<Adjacency> org::gel::mauve::assembly::AssemblyScorer::typeII [private]
 

missing adjacencies

Definition at line 67 of file AssemblyScorer.java.

Referenced by computeAdjacencyErrors(), and typeIIadjErr().

int org::gel::mauve::assembly::AssemblyScorer::uncalled [private]
 

Definition at line 73 of file AssemblyScorer.java.

Referenced by getUncalled().


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