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

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

[legend]Collaboration diagram for org::gel::mauve::summary::output::OverviewFileWriter:

[legend]List of all members.

Public Member Functions
	OverviewFileWriter (SegmentDataProcessor proc)
void	printGeneInformation ()
void	writeHeaderInfo ()
Static Public Attributes
final String	NUM_BASE_PAIRS = "num_bp"
final String	NUMBER_GENES = "num_genes"
final String	NUMBER_ISLANDS = "num_islands"
final String	PERCENT_TOTAL = "percent"
final String	UNKNOWN = "unknown"
Protected Member Functions
String	getData (int column, int row)
	Returns the data that should be printed in the specified row and column.
void	initSubClassParticulars (Hashtable args)
	Convenience method for inheriting classes to set variables necessary from the constructor.
boolean	moreRowsToPrint ()
	called from printData.
void	performCalculations ()
Vector	setColumnHeaders ()
	Gets the names of the columns.
void	setMinSize ()
boolean	shouldPrintRow (int row)
Protected Attributes
long[]	bp_data
long	cur_multiplicity
double[]	double_totals
Segment[]	firsts
int[][]	gene_data
int[]	island_data
long[]	lengths
long[]	long_totals
int	min_size
int[]	num_genes
int[]	num_segments
SegmentDataProcessor	processor
int	sequence
int	total

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Constructor & Destructor Documentation

org::gel::mauve::summary::output::OverviewFileWriter::OverviewFileWriter (  SegmentDataProcessor  proc  )  [inline]

Definition at line 37 of file OverviewFileWriter.java.

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Member Function Documentation

String org::gel::mauve::summary::output::OverviewFileWriter::getData (  int  column, int  row )  [inline, protected, virtual]

Returns the data that should be printed in the specified row and column. It is up to sub-classes to track where to get the data from, as the format is not intended to be standardized. Parameters: column  The header representing which column this data is for row  An int that may be useful for identifying what data is desired. It gets incremented every time printDataRow () is called. Implements org::gel::mauve::summary::output::AbstractTabbedDataWriter. Definition at line 115 of file OverviewFileWriter.java. References bp_data, double_totals, gene_data, island_data, lengths, long_totals, num_genes, num_segments, and total.

void org::gel::mauve::summary::output::OverviewFileWriter::initSubClassParticulars (  Hashtable  args  )  [inline, protected]

Convenience method for inheriting classes to set variables necessary from the constructor. Parameters: args  Contains objects necessary to successfully initialize a subclass. NOTE: can be null value Reimplemented from org::gel::mauve::summary::output::AbstractTabbedDataWriter. Definition at line 41 of file OverviewFileWriter.java. References bp_data, cur_multiplicity, org::gel::mauve::summary::output::AbstractTabbedDataWriter::doneWritingFile(), gene_data, island_data, lengths, num_genes, num_segments, printGeneInformation(), setMinSize(), and writeHeaderInfo().

boolean org::gel::mauve::summary::output::OverviewFileWriter::moreRowsToPrint (   )  [inline, protected, virtual]

called from printData. Used to determine when to stop attempting to print rows. Returns: True if there is more tabbed data to print, false otherwise Implements org::gel::mauve::summary::output::AbstractTabbedDataWriter. Definition at line 190 of file OverviewFileWriter.java. References bp_data, cur_multiplicity, double_totals, island_data, long_totals, num_genes, performCalculations(), and total. Referenced by printGeneInformation().

void org::gel::mauve::summary::output::OverviewFileWriter::performCalculations (   )  [inline, protected]

Definition at line 68 of file OverviewFileWriter.java. References bp_data, org::gel::mauve::analysis::Segment::END, org::gel::mauve::analysis::Segment::getSegmentLength(), island_data, org::gel::mauve::analysis::Segment::multiplicityType(), org::gel::mauve::analysis::Segment::nexts, and num_segments. Referenced by moreRowsToPrint().

void org::gel::mauve::summary::output::OverviewFileWriter::printGeneInformation (   )  [inline]

Definition at line 107 of file OverviewFileWriter.java. References moreRowsToPrint(), org::gel::mauve::summary::output::AbstractTabbedDataWriter::printData(), and org::gel::mauve::summary::output::AbstractTabbedDataWriter::printHeaders(). Referenced by initSubClassParticulars().

Vector org::gel::mauve::summary::output::OverviewFileWriter::setColumnHeaders (   )  [inline, protected, virtual]

Gets the names of the columns. Implements org::gel::mauve::summary::output::AbstractTabbedDataWriter. Definition at line 214 of file OverviewFileWriter.java. References double_totals, long_totals, NUM_BASE_PAIRS, NUMBER_GENES, NUMBER_ISLANDS, and PERCENT_TOTAL.

void org::gel::mauve::summary::output::OverviewFileWriter::setMinSize (   )  [inline, protected]

Definition at line 62 of file OverviewFileWriter.java. Referenced by initSubClassParticulars().

boolean org::gel::mauve::summary::output::OverviewFileWriter::shouldPrintRow (  int  row  )  [inline, protected, virtual]

Implements org::gel::mauve::summary::output::AbstractTabbedDataWriter. Definition at line 228 of file OverviewFileWriter.java. References cur_multiplicity, and island_data.

void org::gel::mauve::summary::output::OverviewFileWriter::writeHeaderInfo (   )  [inline]

Definition at line 80 of file OverviewFileWriter.java. Referenced by initSubClassParticulars().

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Member Data Documentation

long [] org::gel::mauve::summary::output::OverviewFileWriter::bp_data [protected]

Definition at line 23 of file OverviewFileWriter.java. Referenced by getData(), initSubClassParticulars(), moreRowsToPrint(), and performCalculations().

long org::gel::mauve::summary::output::OverviewFileWriter::cur_multiplicity [protected]

Definition at line 34 of file OverviewFileWriter.java. Referenced by initSubClassParticulars(), moreRowsToPrint(), and shouldPrintRow().

double [] org::gel::mauve::summary::output::OverviewFileWriter::double_totals [protected]

Definition at line 25 of file OverviewFileWriter.java. Referenced by getData(), moreRowsToPrint(), and setColumnHeaders().

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

Definition at line 30 of file OverviewFileWriter.java.

int [][] org::gel::mauve::summary::output::OverviewFileWriter::gene_data [protected]

Definition at line 21 of file OverviewFileWriter.java. Referenced by getData(), and initSubClassParticulars().

int [] org::gel::mauve::summary::output::OverviewFileWriter::island_data [protected]

Definition at line 22 of file OverviewFileWriter.java. Referenced by getData(), initSubClassParticulars(), moreRowsToPrint(), performCalculations(), and shouldPrintRow().

long [] org::gel::mauve::summary::output::OverviewFileWriter::lengths [protected]

Definition at line 29 of file OverviewFileWriter.java. Referenced by getData(), and initSubClassParticulars().

long [] org::gel::mauve::summary::output::OverviewFileWriter::long_totals [protected]

Definition at line 24 of file OverviewFileWriter.java. Referenced by getData(), moreRowsToPrint(), and setColumnHeaders().

int org::gel::mauve::summary::output::OverviewFileWriter::min_size [protected]

Definition at line 35 of file OverviewFileWriter.java.

final String org::gel::mauve::summary::output::OverviewFileWriter::NUM_BASE_PAIRS = "num_bp" [static]

Definition at line 17 of file OverviewFileWriter.java. Referenced by setColumnHeaders().

int [] org::gel::mauve::summary::output::OverviewFileWriter::num_genes [protected]

Definition at line 27 of file OverviewFileWriter.java. Referenced by getData(), initSubClassParticulars(), and moreRowsToPrint().

int [] org::gel::mauve::summary::output::OverviewFileWriter::num_segments [protected]

Definition at line 28 of file OverviewFileWriter.java. Referenced by getData(), initSubClassParticulars(), and performCalculations().

final String org::gel::mauve::summary::output::OverviewFileWriter::NUMBER_GENES = "num_genes" [static]

Definition at line 15 of file OverviewFileWriter.java. Referenced by setColumnHeaders().

final String org::gel::mauve::summary::output::OverviewFileWriter::NUMBER_ISLANDS = "num_islands" [static]

Definition at line 16 of file OverviewFileWriter.java. Referenced by setColumnHeaders().

final String org::gel::mauve::summary::output::OverviewFileWriter::PERCENT_TOTAL = "percent" [static]

Definition at line 18 of file OverviewFileWriter.java. Referenced by setColumnHeaders().

SegmentDataProcessor org::gel::mauve::summary::output::OverviewFileWriter::processor [protected]

Definition at line 13 of file OverviewFileWriter.java.

int org::gel::mauve::summary::output::OverviewFileWriter::sequence [protected]

Definition at line 32 of file OverviewFileWriter.java.

int org::gel::mauve::summary::output::OverviewFileWriter::total [protected]

Definition at line 33 of file OverviewFileWriter.java. Referenced by getData(), and moreRowsToPrint().

final String org::gel::mauve::summary::output::OverviewFileWriter::UNKNOWN = "unknown" [static]

Definition at line 19 of file OverviewFileWriter.java.

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

• src/org/gel/mauve/summary/output/OverviewFileWriter.java

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