org.irisa.genouest.logol
Class Treatment

java.lang.Object
  extended by org.irisa.genouest.logol.Treatment

public class Treatment
extends java.lang.Object

This class generate some Prolog code based on parser result.
The LogolVariable contains all data needed to get intelligent parsing.

Version:
1.0
Author:
osallou

Field Summary
static HashMapCounter counters
           
static Model currentModel
           
static int dataType
          Type of sequence data to analyse.
static double DEFAULTMAXDISTANCE
          Maximum distance to use when looking for a word and distance is not yet known.
static java.util.Vector<java.lang.String> definitions
           
static java.lang.String filename
           
static java.lang.String installPath
          Installation path
static int isAny
           
static java.lang.String isAnyMax
           
static java.lang.String isAnyMin
           
static int maxLength
          Maximum length of a variable X
static long maxResultSize
          Maximum length of a complete match
static int maxSpacerLength
          Maximum length of a spacer .*
static int minLength
          Minimum length of a variable X
static java.util.Vector<Model> models
           
static int parentStrategy
          Strategy to apply when looking for parents.
static java.lang.String query
          Query e.g.
static boolean saveAny
          Decides if previous spacer must be saved
static java.lang.String suffixSearchPath
          Path to suffixSearch shell
static java.lang.String uID
           
static java.util.HashMap<java.lang.Integer,LogolVariable> varInfo
           
static java.lang.String workingDir
           
 
Constructor Summary
Treatment()
           
 
Method Summary
 java.lang.String get(LogolVariable lvar, int countVar)
          Creates Prolog query for the current variable
static int getParseStep()
          get the current step of parsing
static void reset()
           
static void setParseStep(int step)
          Defines current step
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dataType

public static int dataType
Type of sequence data to analyse. 0: DNA 1: RNA 2: Protein


saveAny

public static boolean saveAny
Decides if previous spacer must be saved


counters

public static HashMapCounter counters

models

public static java.util.Vector<Model> models

definitions

public static java.util.Vector<java.lang.String> definitions

query

public static java.lang.String query
Query e.g. sequence of models


varInfo

public static java.util.HashMap<java.lang.Integer,LogolVariable> varInfo

uID

public static java.lang.String uID

workingDir

public static java.lang.String workingDir

filename

public static java.lang.String filename

currentModel

public static Model currentModel

DEFAULTMAXDISTANCE

public static double DEFAULTMAXDISTANCE
Maximum distance to use when looking for a word and distance is not yet known. Default is 1 e.g. 100%.


isAny

public static int isAny

isAnyMin

public static java.lang.String isAnyMin

isAnyMax

public static java.lang.String isAnyMax

minLength

public static int minLength
Minimum length of a variable X


maxLength

public static int maxLength
Maximum length of a variable X


maxSpacerLength

public static int maxSpacerLength
Maximum length of a spacer .*


maxResultSize

public static long maxResultSize
Maximum length of a complete match


parentStrategy

public static int parentStrategy
Strategy to apply when looking for parents. 0: Get all parents at first X, then compare with next when reached. All solutions are evaluated once. 1: Save parent as equal to first match in string. Then evaluate all parents for each next call (interesting if applying a strategy limiting. number of possibilities


installPath

public static java.lang.String installPath
Installation path


suffixSearchPath

public static java.lang.String suffixSearchPath
Path to suffixSearch shell

Constructor Detail

Treatment

public Treatment()
Method Detail

reset

public static void reset()

getParseStep

public static int getParseStep()
get the current step of parsing

Returns:
the current step id

setParseStep

public static void setParseStep(int step)
Defines current step

Parameters:
step - See Constants

get

public java.lang.String get(LogolVariable lvar,
                            int countVar)
Creates Prolog query for the current variable

Parameters:
lvar - variable to analyse
countVar - id of the current variable
Returns:
Prolog string
Throws:
GrammarException