QueryParameterStruct Struct Reference

#include <SSAHAMain.h>

List of all members.

Public Attributes

string queryName
string queryType
string queryFormat
string subjectName
string subjectType
string subjectFormat
int queryStart
int queryEnd
int wordLength
int stepLength
int maxStore
int minPrint
int maxGap
int maxInsert
int numRepeats
int sortMatches
int doAlignment
int substituteThreshold
int bandExtension
string queryReplace
string subjectReplace
string logMode
string saveName
bool parserFriendly
bool packHits
bool reverseQuery
bool runQuery
bool printHashStats

Friends

ostream & operator<< (ostream &os, const QueryParameterStruct &qps)

Detailed Description

Definition at line 50 of file SSAHAMain.h.

Friends And Related Function Documentation

ostream& operator<< ( ostream &  os,
const QueryParameterStruct &  qps 
) [friend]

Definition at line 81 of file SSAHAMain.h.

00082   {
00083     return os << "queryName:\t" << qps.queryName   
00084        << "\nqueryType:\t" << qps.queryType   
00085        << "\nqueryFormat:\t" << qps.queryFormat   
00086        << "\nsubjectName:\t" << qps.subjectName 
00087        << "\nsubjectType:\t" << qps.subjectType  
00088        << "\nsubjectFormat:\t" << qps.subjectFormat  
00089        << "\nqueryStart:\t" << qps.queryStart  
00090        << "\nqueryEnd:\t" << qps.queryEnd  
00091        << "\nwordLength:\t" << qps.wordLength  
00092        << "\nstepLength:\t" << qps.stepLength   
00093        << "\nmaxStore:\t" << qps.maxStore    
00094        << "\nminPrint:\t" << qps.minPrint     
00095        << "\nmaxGap:  \t" << qps.maxGap     
00096        << "\nmaxInsert:\t" << qps.maxInsert     
00097        << "\nnumRepeats:\t" << qps.numRepeats
00098        << "\nsortMatches:\t" << qps.sortMatches
00099        << "\ndoAlignment:\t" << qps.doAlignment
00100        << "\nsubstituteThreshold:\t" << qps.substituteThreshold
00101        << "\nbandExtension:\t" << qps.bandExtension
00102       //       << "\nreportMode:\t" << qps.reportMode  
00103        << "\nqueryReplace:\t" << qps.queryReplace  
00104        << "\nsubjectReplace:\t" << qps.subjectReplace  
00105        << "\nlogMode:\t" << qps.logMode  
00106        << "\nsaveName:\t" << qps.saveName    
00107        << "\nparserFriendly:\t" 
00108        << (( qps.parserFriendly ) ? (string)"true" : (string)"false") 
00109        << "\npackHits:\t" 
00110        << (( qps.packHits ) ? (string)"true" : (string)"false") 
00111        << "\nreverseQuery:\t" 
00112        << (( qps.reverseQuery ) ? (string)"true" : (string)"false") 
00113        << "\nrunQuery:\t" 
00114        << (( qps.runQuery ) ? (string)"true" : (string)"false") 
00115        << "\nprintHashStats:\t" 
00116        << (( qps.printHashStats ) ? (string)"true" : (string)"false") 
00117        << "\n";
00118   } // ~operator<<

Member Data Documentation

string QueryParameterStruct::queryName

Definition at line 52 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::queryType

Definition at line 53 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::queryFormat

Definition at line 54 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::subjectName

Definition at line 55 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::subjectType

Definition at line 56 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::subjectFormat

Definition at line 57 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::queryStart

Definition at line 58 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::queryEnd

Definition at line 59 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::wordLength

Definition at line 60 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::stepLength

Definition at line 61 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::maxStore

Definition at line 62 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::minPrint

Definition at line 63 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::maxGap

Definition at line 64 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::maxInsert

Definition at line 65 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::numRepeats

Definition at line 66 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::sortMatches

Definition at line 67 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::doAlignment

Definition at line 68 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::substituteThreshold

Definition at line 69 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

int QueryParameterStruct::bandExtension

Definition at line 70 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::queryReplace

Definition at line 71 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::subjectReplace

Definition at line 72 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

string QueryParameterStruct::logMode

Definition at line 74 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine(), and processQuery().

string QueryParameterStruct::saveName

Definition at line 75 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

bool QueryParameterStruct::parserFriendly

Definition at line 76 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

bool QueryParameterStruct::packHits

Definition at line 77 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

bool QueryParameterStruct::reverseQuery

Definition at line 78 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

bool QueryParameterStruct::runQuery

Definition at line 79 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

bool QueryParameterStruct::printHashStats

Definition at line 80 of file SSAHAMain.h.

Referenced by CommandLineArg::parseCommandLine().

The documentation for this struct was generated from the following file:
Generated on Fri Dec 21 13:19:31 2007 for ssaha by  doxygen 1.5.2