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Restore MIXTURE to Phase 2 algorithm set
MIXTURE uses a neutral selection strategy (rule-based only, no MAX/MIN bias) and a unique isomorphism pre-check, making it algorithmically distinct from MAX and MIN. It serves as the fallback for reactions where neither maximum nor minimum overlap bias resolves the mapping cleanly. The selection comparator gives MIXTURE lowest priority so it only wins when it produces better coverage/quality than the other three — restoring it cannot degrade results on reactions where RINGS/MIN/MAX succeed.
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Lines changed: 4 additions & 4 deletions

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src/main/java/com/bioinceptionlabs/reactionblast/mapping/CallableAtomMappingTool.java

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -175,13 +175,13 @@ private void generateAtomAtomMapping(
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boolean ringsAlreadyRun = solution.containsKey(RINGS);
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IMappingAlgorithm[] remaining;
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if (minAlreadyRun && ringsAlreadyRun) {
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remaining = new IMappingAlgorithm[]{MAX};
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remaining = new IMappingAlgorithm[]{MAX, MIXTURE};
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} else if (minAlreadyRun) {
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remaining = new IMappingAlgorithm[]{MAX, RINGS};
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remaining = new IMappingAlgorithm[]{MAX, MIXTURE, RINGS};
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} else if (ringsAlreadyRun) {
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remaining = new IMappingAlgorithm[]{MIN, MAX};
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remaining = new IMappingAlgorithm[]{MIN, MAX, MIXTURE};
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} else {
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remaining = new IMappingAlgorithm[]{MIN, MAX, RINGS};
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remaining = new IMappingAlgorithm[]{MIN, MAX, MIXTURE, RINGS};
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}
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try {

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