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

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

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

Collaboration graph
List of all members.

Public Member Functions

Vector getBackboneSegments ()
 ProcessBackboneFile (String file)
 ProcessBackboneFile (Hashtable args)

Static Public Member Functions

void main (String[] args)

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

Constructor & Destructor Documentation

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

Definition at line 36 of file

References init(), and INPUT_FILE.

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

Definition at line 40 of file

References init().

Member Function Documentation

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

Definition at line 153 of file

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

Definition at line 106 of file

References current_input.

Referenced by loadData().

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

Definition at line 44 of file

References in_file, and loadData().

Referenced by ProcessBackboneFile().

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

Definition at line 56 of file

References current_input, getSequenceCount(), not_header, processFirstRow(), and storeRow().

Referenced by init().

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


args The backbone file to read and create islands from

Definition at line 179 of file

References startProcessor().

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

Definition at line 117 of file

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

References INPUT_FILE.

Referenced by main().

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

Definition at line 92 of file

References org::gel::mauve::analysis::Segment::left, org::gel::mauve::analysis::Segment::reverse, and org::gel::mauve::analysis::Segment::right.

Referenced by loadData().

Member Data Documentation

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

Definition at line 30 of file

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

Definition at line 32 of file

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

Definition at line 22 of file

Referenced by getSequenceCount(), loadData(), and processFirstRow().

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

Definition at line 34 of file

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

Definition at line 18 of file

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

Definition at line 20 of file

Referenced by init().

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

Definition at line 28 of file

Referenced by ProcessBackboneFile(), and startProcessor().

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

Definition at line 26 of file

Referenced by loadData(), and processFirstRow().

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

Definition at line 24 of file

The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:20 2013 for Mauve by doxygen 1.3.6