| alig | Cleaner | private |
| Alignment class | Cleaner | friend |
| blockSize | Cleaner | |
| calculateRelaxedSeqIdentity() | Cleaner | |
| calculateRepresentativeSeq(float maximumIdent) | Cleaner | |
| calculateSeqIdentity() | Cleaner | |
| calculateSpuriousVector(float overlap, float *spuriousVector) | Cleaner | |
| clean(float baseLine, float GapsPct, float conservationPct, bool complementary) | Cleaner | |
| clean2ndSlope(bool complementary) | Cleaner | |
| cleanByCutValueFallBehind(float cut, float baseLine, const float *ValueVect, bool complementary) | Cleaner | |
| cleanByCutValueOverpass(double cut, float baseLine, const int *gInCol, bool complementary) | Cleaner | |
| cleanByCutValueOverpassOrEquals(double cutGaps, const int *gInCol, float baseLine, float cutCons, const float *MDK_Win, bool complementary) | Cleaner | |
| cleanCombMethods(bool complementary, bool variable) | Cleaner | |
| cleanCompareFile(float cutpoint, float baseLine, float *vectValues, bool complementary) | Cleaner | |
| cleanConservation(float baseLine, float conservationPct, bool complementary) | Cleaner | |
| Cleaner(Alignment *parent) | Cleaner | explicitprivate |
| Cleaner(Alignment *parent, Cleaner *mold) | Cleaner | private |
| cleanGaps(float baseLine, float gapsPct, bool complementary) | Cleaner | |
| cleanNoAllGaps(bool complementary) | Cleaner | |
| cleanOverlapSeq(float minimumOverlap, float *overlapSeq, bool complementary) | Cleaner | |
| cleanSpuriousSeq(float overlapColumn, float minimumOverlap, bool complementary) | Cleaner | |
| cleanStrict(int gapCut, const int *gInCol, float simCut, const float *MDK_W, bool complementary, bool variable) | Cleaner | |
| computeComplementaryAlig(bool residues, bool sequences) | Cleaner | |
| getClustering(float identityThreshold) | Cleaner | |
| getCutPointClusters(int clusterNumber) | Cleaner | |
| keepSequences | Cleaner | |
| left_boundary | Cleaner | |
| removeAllGapsSeqsAndCols(bool seqs=true, bool cols=true) | Cleaner | |
| removeColumns(int *columns, int init, int size, bool complementary) | Cleaner | |
| removeDuplicates() | Cleaner | |
| removeOnlyTerminal() | Cleaner | |
| removeSequences(int *seqs, int init, int size, bool complementary) | Cleaner | |
| removeSmallerBlocks(int blockSize, Alignment &original) | Cleaner | |
| right_boundary | Cleaner | |
| selectMethod() | Cleaner | |
| setBoundaries(int *boundaries) | Cleaner | |
| setTrimTerminalGapsFlag(bool terminalOnly_) | Cleaner | |
| terminalGapOnly | Cleaner | |
1.8.13