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Generate Exhaustive Permutations

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Illustrates generation of exhaustive permutation of symbols given the symbolic bases.

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Generate Exhaustive Permutations
--------------------------------------------------
[1] main executing reference usage: usage_generateExhaustivePermutation

The objective is to illustrate generation of exhaustive permutation of symbols given the symbolic bases.
The method of generation is a kronecker-akin approach. The indexRepresentedPermutations may be mapped to any symbols provided.

Sample output:
Given bases = 'AB';
lengthOf1PatternSeq = 3;

< symbols >
AAA
AAB
ABA
ABB
BAA
BAB
BBA
BBB

< indexRepresentedPermutations >
1 1 1
1 1 2
1 2 1
1 2 2
2 1 1
2 1 2
2 2 1
2 2 2

Given bases = '01';
lengthOf1PatternSeq = 4;

< symbols >
0000
0001
0010
0011
0100
0101
0110
0111
1000
1001
1010
1011
1100
1101
1110
1111

< indexRepresentedPermutations >
1 1 1 1
1 1 1 2
1 1 2 1
1 1 2 2
1 2 1 1
1 2 1 2
1 2 2 1
1 2 2 2
2 1 1 1
2 1 1 2
2 1 2 1
2 1 2 2
2 2 1 1
2 2 1 2
2 2 2 1
2 2 2 2
--------------------------------------------------
[2] main executing reference usage: usage_computePermutationSeqForSpecificIndex
Obtain a sequence of permutation by direct computation, instead of extracting from a pre-generated exhaustive sequence of prescribed order.
This accelerate the process and saves memory space.

Sample output:

The sequence is CGGGCAG.
The sequence indexed extracted from exhaustive list is CGGGCAG from index: 4044.
==========================================
The sequence is CCCTATC.
The sequence indexed extracted from exhaustive list is CCCTATC from index: 101.
==========================================
The sequence is CCTGGAC.
The sequence indexed extracted from exhaustive list is CCTGGAC from index: 505.
==========================================
The sequence is CCGGATA.
The sequence indexed extracted from exhaustive list is CCGGATA from index: 999.
==========================================

* Caveat : Illustrative Purposes
- may run out of memory when lengthOf1PatternSeq >= 10;
- note as well that lengthOf1PatternSeq has to be >= length(bases)
- uncomment variables for display, eg. indexRepresentedPermutations

If the demo has more elegant presentation, please do not hesitate to suggest and send feedback to author.
Email: promethevx@yahoo.com.

Thank you.

Regards,
Michael Chan JT

Comments and Ratings (2)

Michael Chan

Michael Chan (view profile)

Hi Forrest,

For a length of 64, at usage_generateExhaustivePermutation.m

% Caveat: may run out of memory when >= 10;
% note as well that lengthOf1PatternSeq has to be >= length(bases)
lengthOf1PatternSeq = 64;

and

bases = 'ABCD';

Please note the caveat of memory issue, unless your machine has large memory capacity. However, you may wish to run by parts, ie. using another sample usage (computePermutationSeqForSpecificIndex.m), the usage is illustrated by: usage_computePermutationSeqForSpecificIndex.m

You may also convert it to C or java. It can be faster, however, in C, please note on the use of 'malloc' (memory allocation).

Forrest

I have 4 letters... A,B,C,D. I need all possible combos of this, 64. Can you explain how I would install and run this code? I attempted to, and got an error below.

??? Input argument "bases" is undefined.

Error in ==> generateExhaustivePermutation at 9
numberOfUniqueBases = length(bases);"

Updates

1.1

Added an option to derive a permutated sequence for a specific index for speed and memory conservation.

MATLAB Release
MATLAB 7.10 (R2010a)
Acknowledgements

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