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org::gel::mauve::assembly::ScoreAssembly Class Reference

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

Collaboration graph
[legend]
List of all members.

Public Member Functions

void cancel ()
 ScoreAssembly (XmfaViewerModel model)

Static Public Member Functions

String getSumText (AssemblyScorer assScore, boolean header, boolean singleLine)
void interactive (MauveFrame frame)
void launchWindow (MauveFrame frame)
void main (String[] args)

Package Functions

 SuppressWarnings ("static-access") private static Options getOptions()

Private Member Functions

void addTables ()
synchronized void finish ()
void initWithJTables (XmfaViewerModel model)

Static Private Member Functions

AssemblyScorer getAS (File alnmtFile)
String[] makeAlnCmd (File seq1, File seq2, File output)
void startNewSA (MauveFrame frame)

Private Attributes

AssemblyScorer asmScore
boolean cancel
int fHEIGHT = 510
boolean finished
int fWIDTH = 800
XmfaViewerModel model
JTextArea sumTA
AnalysisDisplayWindow win

Static Private Attributes

String CDS_CMD = "Broken CDS"
String CDS_DESC = "Broken CDS in assembly genome"
final String[] DEFAULT_ARGS
final String error = "Error computing DCJ distances! Please report bug to atritt@ucdavis.edu"
String GAP_CMD = "Gaps"
String GAP_DESC = "Gaps in reference and assembly"
String INV_CMD = "Inverted Contigs"
String INV_DESC = "Incorrectly inverted contigs"
String MIS_CMD = "Mis-assembled Contigs"
String MIS_DESC = "Mis-assembled contigs with the total number of mis-assemblies in each"
HashMap< String, ScoreAssembly > modelMap = new HashMap<String ScoreAssembly>()
HashMap< String, ScoreAssembly > running = new HashMap<String ScoreAssembly>()
String SNP_CMD = "SNPs"
String SNP_DESC = "SNPs between reference and assembly"
String SUM_CMD = "Summary"
String SUM_DESC = "Summary of scoring assembly"
final String temp = "Running..."

Constructor & Destructor Documentation

org::gel::mauve::assembly::ScoreAssembly::ScoreAssembly (  XmfaViewerModel  model  )  [inline]
 

Definition at line 74 of file ScoreAssembly.java.

References initWithJTables().

Member Function Documentation

void org::gel::mauve::assembly::ScoreAssembly::addTables (   )  [inline, private]
 

Definition at line 119 of file ScoreAssembly.java.

void org::gel::mauve::assembly::ScoreAssembly::cancel (   )  [inline]
 

Definition at line 101 of file ScoreAssembly.java.

synchronized void org::gel::mauve::assembly::ScoreAssembly::finish (   )  [inline, private]
 

Definition at line 105 of file ScoreAssembly.java.

AssemblyScorer org::gel::mauve::assembly::ScoreAssembly::getAS (  File  alnmtFile  )  [inline, static, private]
 

Definition at line 383 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::getSumText (  AssemblyScorer  assScore,
boolean  header,
boolean  singleLine
)  [inline, static]
 

Definition at line 167 of file ScoreAssembly.java.

References org::gel::mauve::assembly::AssemblyScorer::getAssemblyGaps(), org::gel::mauve::assembly::AssemblyScorer::getBPdist(), org::gel::mauve::assembly::AssemblyScorer::getContigN50(), org::gel::mauve::assembly::AssemblyScorer::getContigN90(), org::gel::mauve::assembly::AssemblyScorer::getDCJdist(), org::gel::mauve::Genome::getDisplayName(), org::gel::mauve::assembly::AssemblyScorer::getExtraContigs(), org::gel::mauve::BaseViewerModel::getGenomeBySourceIndex(), org::gel::mauve::assembly::AssemblyScorer::getInterLcbBoundaryCount(), org::gel::mauve::assembly::AssemblyScorer::getMaxContigLength(), org::gel::mauve::assembly::AssemblyScorer::getMinContigLength(), org::gel::mauve::assembly::AssemblyScorer::getMiscalled(), org::gel::mauve::assembly::AssemblyScorer::getMissingChromosomes(), org::gel::mauve::assembly::AssemblyScorer::getModel(), org::gel::mauve::assembly::AssemblyScorer::getReferenceGaps(), org::gel::mauve::assembly::AssemblyScorer::getSCJdist(), org::gel::mauve::assembly::AssemblyScorer::getSharedBoundaryCount(), org::gel::mauve::assembly::AssemblyScorer::getSNPs(), org::gel::mauve::assembly::AssemblyScorer::getSubs(), org::gel::mauve::assembly::AssemblyScorer::getUncalled(), org::gel::mauve::assembly::AssemblyScorer::numBasesAssembly(), org::gel::mauve::assembly::AssemblyScorer::numBasesReference(), org::gel::mauve::assembly::AssemblyScorer::numBlocks(), org::gel::mauve::assembly::AssemblyScorer::numBrokenCDS(), org::gel::mauve::assembly::AssemblyScorer::numCompleteCDS(), org::gel::mauve::assembly::AssemblyScorer::numContigs(), org::gel::mauve::assembly::AssemblyScorer::numLCBs(), org::gel::mauve::assembly::AssemblyScorer::numReplicons(), org::gel::mauve::assembly::AssemblyScorer::percentExtraBases(), org::gel::mauve::assembly::AssemblyScorer::percentMissedBases(), org::gel::mauve::assembly::AssemblyScorer::totalExtraBases(), and org::gel::mauve::assembly::AssemblyScorer::totalMissedBases().

void org::gel::mauve::assembly::ScoreAssembly::initWithJTables (  XmfaViewerModel  model  )  [inline, private]
 

Definition at line 81 of file ScoreAssembly.java.

References org::gel::mauve::gui::AnalysisDisplayWindow::addContentPanel(), asmScore, fHEIGHT, fWIDTH, org::gel::mauve::BaseViewerModel::getSrc(), running, SUM_CMD, SUM_DESC, sumTA, temp, and win.

Referenced by ScoreAssembly().

void org::gel::mauve::assembly::ScoreAssembly::interactive (  MauveFrame  frame  )  [inline, static]
 

Definition at line 276 of file ScoreAssembly.java.

References org::gel::mauve::gui::MauveFrame::getModel(), and org::gel::mauve::BaseViewerModel::getSrc().

void org::gel::mauve::assembly::ScoreAssembly::launchWindow (  MauveFrame  frame  )  [inline, static]
 

Definition at line 258 of file ScoreAssembly.java.

References org::gel::mauve::gui::MauveFrame::getModel(), and org::gel::mauve::BaseViewerModel::getSrc().

void org::gel::mauve::assembly::ScoreAssembly::main (  String[]  args  )  [inline, static]
 

Definition at line 296 of file ScoreAssembly.java.

References org::gel::mauve::gui::SwingWorker::start().

String [] org::gel::mauve::assembly::ScoreAssembly::makeAlnCmd (  File  seq1,
File  seq2,
File  output
)  [inline, static, private]
 

Definition at line 395 of file ScoreAssembly.java.

void org::gel::mauve::assembly::ScoreAssembly::startNewSA (  MauveFrame  frame  )  [inline, static, private]
 

Definition at line 272 of file ScoreAssembly.java.

org::gel::mauve::assembly::ScoreAssembly::SuppressWarnings (  "static-access"   )  [inline, package]
 

Definition at line 409 of file ScoreAssembly.java.

References org::gel::mauve::OptionsBuilder::addBoolean().

Member Data Documentation

AssemblyScorer org::gel::mauve::assembly::ScoreAssembly::asmScore [private]
 

Definition at line 66 of file ScoreAssembly.java.

Referenced by initWithJTables().

boolean org::gel::mauve::assembly::ScoreAssembly::cancel [private]
 

Definition at line 72 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::CDS_CMD = "Broken CDS" [static, private]
 

Definition at line 43 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::CDS_DESC = "Broken CDS in assembly genome" [static, private]
 

Definition at line 44 of file ScoreAssembly.java.

final String [] org::gel::mauve::assembly::ScoreAssembly::DEFAULT_ARGS [static, private]
 

Initial value:

 {"--skip-refinement",
                                                                                                        "--weight=200"}

Definition at line 35 of file ScoreAssembly.java.

final String org::gel::mauve::assembly::ScoreAssembly::error = "Error computing DCJ distances! Please report bug to atritt@ucdavis.edu" [static, private]
 

Definition at line 56 of file ScoreAssembly.java.

int org::gel::mauve::assembly::ScoreAssembly::fHEIGHT = 510 [private]
 

Definition at line 64 of file ScoreAssembly.java.

Referenced by initWithJTables().

boolean org::gel::mauve::assembly::ScoreAssembly::finished [private]
 

Definition at line 70 of file ScoreAssembly.java.

int org::gel::mauve::assembly::ScoreAssembly::fWIDTH = 800 [private]
 

Definition at line 62 of file ScoreAssembly.java.

Referenced by initWithJTables().

String org::gel::mauve::assembly::ScoreAssembly::GAP_CMD = "Gaps" [static, private]
 

Definition at line 41 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::GAP_DESC = "Gaps in reference and assembly" [static, private]
 

Definition at line 42 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::INV_CMD = "Inverted Contigs" [static, private]
 

Definition at line 45 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::INV_DESC = "Incorrectly inverted contigs" [static, private]
 

Definition at line 46 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::MIS_CMD = "Mis-assembled Contigs" [static, private]
 

Definition at line 47 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::MIS_DESC = "Mis-assembled contigs with the total number of mis-assemblies in each" [static, private]
 

Definition at line 48 of file ScoreAssembly.java.

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

Definition at line 60 of file ScoreAssembly.java.

HashMap<String,ScoreAssembly> org::gel::mauve::assembly::ScoreAssembly::modelMap = new HashMap<String ScoreAssembly>() [static, private]
 

Definition at line 50 of file ScoreAssembly.java.

HashMap<String,ScoreAssembly> org::gel::mauve::assembly::ScoreAssembly::running = new HashMap<String ScoreAssembly>() [static, private]
 

Definition at line 52 of file ScoreAssembly.java.

Referenced by initWithJTables().

String org::gel::mauve::assembly::ScoreAssembly::SNP_CMD = "SNPs" [static, private]
 

Definition at line 39 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::SNP_DESC = "SNPs between reference and assembly" [static, private]
 

Definition at line 40 of file ScoreAssembly.java.

String org::gel::mauve::assembly::ScoreAssembly::SUM_CMD = "Summary" [static, private]
 

Definition at line 37 of file ScoreAssembly.java.

Referenced by initWithJTables().

String org::gel::mauve::assembly::ScoreAssembly::SUM_DESC = "Summary of scoring assembly" [static, private]
 

Definition at line 38 of file ScoreAssembly.java.

Referenced by initWithJTables().

JTextArea org::gel::mauve::assembly::ScoreAssembly::sumTA [private]
 

Definition at line 58 of file ScoreAssembly.java.

Referenced by initWithJTables().

final String org::gel::mauve::assembly::ScoreAssembly::temp = "Running..." [static, private]
 

Definition at line 54 of file ScoreAssembly.java.

Referenced by initWithJTables().

AnalysisDisplayWindow org::gel::mauve::assembly::ScoreAssembly::win [private]
 

Definition at line 68 of file ScoreAssembly.java.

Referenced by initWithJTables().

The documentation for this class was generated from the following file:
Generated on Wed May 22 06:05:11 2013 for Mauve by doxygen 1.3.6