BioinfoFieldExtractor
Class GenericSequence

java.lang.Object
  BioinfoFieldExtractor.GenericSequence

public class GenericSequence
extends java.lang.Object

This class is a replacement of ConsensusSeq class. This class is used to store information of a generic sequence resulted from multiple sequence alignment. A generic message is a sequence of message blocks. Each message block is either a static data filed, or a data value. We identify the following primitive data values: booleanInt (ie 0 or 1), short, int, long, double, char, string If the message block is a value block then it also contains a list of sample data extracted from the messages. These data can be used in fuzzing.

Author:

Serge Gorbunov

Nested Class Summary

class

GenericSequence.MessageBlock

Constructor Summary

GenericSequence()

Method Summary

void	addConstantDataMsgBlock(java.util.ArrayList<java.lang.Integer> data)
void	addMessageBlock(GenericSequence.MessageBlock b)
GenericSequence.MessageBlock	addValueDataMsgBlock(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> sampleData, int type, int length)
java.util.ArrayList<GenericSequence.MessageBlock>	getGenericSequence()
int	getTotalNumOfSamples()
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GenericSequence

public GenericSequence()

Method Detail

addMessageBlock

public void addMessageBlock(GenericSequence.MessageBlock b)

getGenericSequence

public java.util.ArrayList<GenericSequence.MessageBlock> getGenericSequence()

addConstantDataMsgBlock

public void addConstantDataMsgBlock(java.util.ArrayList<java.lang.Integer> data)

addValueDataMsgBlock

public GenericSequence.MessageBlock addValueDataMsgBlock(java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> sampleData,
                                                         int type,
                                                         int length)

getTotalNumOfSamples

public int getTotalNumOfSamples()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object