org::gel::mauve::summary::ProcessBackboneFile Class Reference

Inheritance diagram for org::gel::mauve::summary::ProcessBackboneFile:

[legend]Collaboration diagram for org::gel::mauve::summary::ProcessBackboneFile:

[legend]List of all members.

Public Member Functions
Vector	getBackboneSegments ()
	ProcessBackboneFile (String file)
	ProcessBackboneFile (Hashtable args)
Static Public Member Functions
void	main (String[] args)
	Main.
void	startProcessor (String file, Hashtable spec_args)
Static Public Attributes
final String	INPUT_FILE = "input_file"
Protected Member Functions
int	getSequenceCount ()
void	init (String file)
void	loadData ()
void	processFirstRow ()
void	storeRow ()
Protected Attributes
Vector	backbone
int	count
StringTokenizer	current_input
String[]	current_row
BufferedReader	in
String	in_file
String	not_header
Iterator	sub_iterator

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Constructor & Destructor Documentation

org::gel::mauve::summary::ProcessBackboneFile::ProcessBackboneFile (  Hashtable  args  )  [inline]

Definition at line 36 of file ProcessBackboneFile.java. References init(), and INPUT_FILE.

org::gel::mauve::summary::ProcessBackboneFile::ProcessBackboneFile (  String  file  )  [inline]

Definition at line 40 of file ProcessBackboneFile.java. References init().

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Member Function Documentation

Vector org::gel::mauve::summary::ProcessBackboneFile::getBackboneSegments (   )  [inline]

Definition at line 153 of file ProcessBackboneFile.java.

int org::gel::mauve::summary::ProcessBackboneFile::getSequenceCount (   )  [inline, protected]

Definition at line 106 of file ProcessBackboneFile.java. References current_input. Referenced by loadData().

void org::gel::mauve::summary::ProcessBackboneFile::init (  String  file  )  [inline, protected]

Definition at line 44 of file ProcessBackboneFile.java. References in_file, and loadData(). Referenced by ProcessBackboneFile().

void org::gel::mauve::summary::ProcessBackboneFile::loadData (   )  [inline, protected]

Definition at line 56 of file ProcessBackboneFile.java. References current_input, getSequenceCount(), not_header, processFirstRow(), and storeRow(). Referenced by init().

void org::gel::mauve::summary::ProcessBackboneFile::main (  String[]  args  )  [inline, static]

Main. Parameters: args  The backbone file to read and create islands from Definition at line 179 of file ProcessBackboneFile.java. References startProcessor().

void org::gel::mauve::summary::ProcessBackboneFile::processFirstRow (   )  [inline, protected]

Definition at line 117 of file ProcessBackboneFile.java. References current_input, and not_header. Referenced by loadData().

void org::gel::mauve::summary::ProcessBackboneFile::startProcessor (  String  file, Hashtable  spec_args )  [inline, static]

Definition at line 157 of file ProcessBackboneFile.java. References INPUT_FILE. Referenced by main().

void org::gel::mauve::summary::ProcessBackboneFile::storeRow (   )  [inline, protected]

Definition at line 92 of file ProcessBackboneFile.java. References org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::reverse, and org::gel::mauve::analysis::Segment::right. Referenced by loadData().

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Member Data Documentation

Vector org::gel::mauve::summary::ProcessBackboneFile::backbone [protected]

Definition at line 30 of file ProcessBackboneFile.java.

int org::gel::mauve::summary::ProcessBackboneFile::count [protected]

Definition at line 32 of file ProcessBackboneFile.java.

StringTokenizer org::gel::mauve::summary::ProcessBackboneFile::current_input [protected]

Definition at line 22 of file ProcessBackboneFile.java. Referenced by getSequenceCount(), loadData(), and processFirstRow().

String [] org::gel::mauve::summary::ProcessBackboneFile::current_row [protected]

Definition at line 34 of file ProcessBackboneFile.java.

BufferedReader org::gel::mauve::summary::ProcessBackboneFile::in [protected]

Definition at line 18 of file ProcessBackboneFile.java.

String org::gel::mauve::summary::ProcessBackboneFile::in_file [protected]

Definition at line 20 of file ProcessBackboneFile.java. Referenced by init().

final String org::gel::mauve::summary::ProcessBackboneFile::INPUT_FILE = "input_file" [static]

Definition at line 28 of file ProcessBackboneFile.java. Referenced by ProcessBackboneFile(), and startProcessor().

String org::gel::mauve::summary::ProcessBackboneFile::not_header [protected]

Definition at line 26 of file ProcessBackboneFile.java. Referenced by loadData(), and processFirstRow().

Iterator org::gel::mauve::summary::ProcessBackboneFile::sub_iterator [protected]

Definition at line 24 of file ProcessBackboneFile.java.

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

• src/org/gel/mauve/summary/ProcessBackboneFile.java

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