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Fix #321. Optimized completeGroup() for large groups. #323

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Merged
sbliven merged 1 commit into from
Sep 15, 2015
Merged

Fix #321. Optimized completeGroup() for large groups. #323

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38 changes: 26 additions & 12 deletions ...va-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,9 @@
package org.biojava.nbio.structure.symmetry.core;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

/**
*
Expand All @@ -47,24 +49,36 @@ public int getOrder() {


/**
* Starts with an incomplete set of group generators in `permutations` and
* expands it to include all possible combinations.
*
* Ways to complete group:
* - combinations of permutations pi x pj
* - combinations with itself p^k
*
*/
public void completeGroup() {
int n = permutations.size();
for (int i = 0; i < permutations.size(); i++) {
for (int j = i; j < permutations.size(); j++) {
List<Integer> p = combine(permutations.get(i), permutations.get(j));
addPermutation(p);
// System.out.println("complete group: adding " + p);
}
}
// repeat iteratively until no new permutation are created
if (permutations.size() > n) {
completeGroup();
}
// Copy initial set to allow permutations to grow
List<List<Integer>> gens = new ArrayList<List<Integer>>(permutations);
// Keep HashSet version of permutations for fast lookup.
Set<List<Integer>> known = new HashSet<List<Integer>>(permutations);
//breadth-first search through the map of all members
List<List<Integer>> currentLevel = new ArrayList<List<Integer>>(permutations);
while( currentLevel.size() > 0) {
List<List<Integer>> nextLevel = new ArrayList<List<Integer>>();
for( List<Integer> p : currentLevel) {
for(List<Integer> gen : gens) {
List<Integer> y = combine(p,gen);
if(!known.contains(y)) {
nextLevel.add(y);
//bypass addPermutation(y) for performance
permutations.add(y);
known.add(y);
}
}
}
currentLevel = nextLevel;
}
}

public String toString() {
Expand Down