#Adaptive-FM-index

##What is it? FM-index is a Succinct Data Structure(SDS),SDS can represent an object as implicitly,and in space close to information-theoretic lower bound of the object while supporting operations of the original object efficiently. FM-index and CSA(compressed suffix array) both are implicit expression about SA(suffix array),has the ability of fast pattern matching,and needs little space,and Adaptive-FM-index is more space efficient,comparable with Bzip2,but CSA is a little weake in space.Adaptive-FM-index is a advanced version of the original FM-index,it's faster and smaller,as you can guess, we developed a set of compression methods,for each pieces of data,always select the best one,that's the bigest secret about my works.It works like a mixture of KMP and Bzip2,you can build a fm-index for a document,and then you have mainly there operations in your hands: counting: count how many a pattern occurs in the document. locating: locate all the positions where the pattern occurs. extracting: decompress a piece of the document.

How to use it?

###just for fun step 1:download it or clone it step 2:make step 3:run my_fm ###build your own program step 1:download or clone it step 2:make step 3:include FM.h step 4: g++ your_program.cpp -o xx -fm.a

###example ```cpp #include"fm.h" #include using namespace std; int main() { FM fm("filename"); int num; fm.Counting("the",num); cout<<"pattern the occs "<<num<<" times"<<endl; int * pos=fm.Locating("love",num); cout<<"pattern love occs "<<num<<" times"<<endl; cout<<"all the positions are:"; for(int i=0;i<num;i++) cout<<pos[i]<<endl; delete [] pos;//it's your duty to delete pos. pos=NULL;

	int start=0;
	int len =20;
	unsigned char *sequence =fm.Extracting(start,len);
	cout<<"T[start...start+len-1] is "<<sequence<<endl;
	delete [] sequence;//it's your duty to delete sequence.
	sequence =NULL;

	fm.Save("index.fm");//serialize the fm object to file index.fm
	FM fm2;
	fm2.Load("index.fm");//restore the fm object from file index.fm

	return 0;
}
```

##Structure ##ChangeLog 2014.5.25:
Use the LookupTables,and cross them,it looks helpful,count works faster about 25~35%.

2014.5.27:
If gamma coding don't save much space,only very few,using plain first.it helps,not very significant.

2014.5.28:
Complete the copy constructor,assigment operator,for class FM by using UseCount Tec. It seems WT-Node is not a good name,BitMap is better.

2014.5.30:
Want to computer from head or tail,depending which points is good,working on it Now!

2014.6.1:
It seems that Rank(int pos) works now,and the answer seems right.That's good!. Now working on Rank(int pos,int &bit). And change rename 'WT-Node' to BitMap

2014.6.2:
Computer Rank from head or tail adaptivly, but the result is not good,this may be a result of expanded lookuptables,or bit-reverse function. So we can drop the drawback-lookup tables,and drop the bit-reverse function,only holds:forward-lookuptables and reverse-table,this will reduce space of tables,and bit-reverse can use the reverse-table,so it's may be faster.working on it!

2014.6.3
It does not work to drop backforward-lookup tables and bit-reverse function,So,expanded lookuptables and bit-reverse function is not the suspect of fading performance

2014.6.4
After a long time thinking,it's no need to use reverse-function or reverse-tables. we can map all the gamma value to odd numbers,so the lowest bit will be 1, and it can denote the boundary. The mapping function: f(x)=x+x-1 or f(x)=x+x-3 or f(x) = x+x-5...

2014.6.6:
Rank from head or tail will not save time for any kind of document.if the file is random-like file,the needed block should be small,in this situation,from both points will not help,because time used for decoding is not very significant,and time for prepare-operations will increase.for highly-repetive data the runs are big,the decoding process is good enough,for example,if the block-size is 1024,the runs will be hundreds,so only a few decoding steps is needed.In this situation, form both points will not help too.So let it go,bye!

2014.6.6:
drawbacksearch function has the potential to works faster.Woking on it