This is the complete list of members for Alignment, including all inherited members.
| Alignment() | Alignment | |
| Alignment(Alignment &) | Alignment | |
| alignmentInfo | Alignment | |
| alignmentSummaryHTML(const Alignment &trimmedAlig, const char *const destFile) | Alignment | |
| alignmentSummarySVG(Alignment &trimmedAlig, const char *destFile, int blocks) | Alignment | |
| calculateColIdentity(float *columnIdentity) | Alignment | |
| calculateSeqOverlap() | Alignment | |
| checkCorrespondence(std::string *names, int *lenghts, int totalInputSequences, int multiple) | Alignment | |
| Cleaning | Alignment | |
| dataType | Alignment | private |
| filename | Alignment | |
| fillMatrices(bool aligned, bool checkInvalidChars=true) | Alignment | |
| getAlignmentType() const | Alignment | |
| getNumAminos() | Alignment | |
| getNumSpecies() | Alignment | |
| getSequenceNameOrder(std::string *names, int *orderVector) | Alignment | |
| getSequences(std::string *names) | Alignment | |
| getSequences(std::string *names, int *lenghts) | Alignment | |
| getSequences(std::string *names, std::string *sequences, int *lenghts) | Alignment | |
| getTranslationCDS(Alignment *proteinAlignment) | Alignment | |
| identities | Alignment | |
| isAligned | Alignment | |
| isFileAligned() | Alignment | |
| numberOfResidues | Alignment | |
| numberOfSequences | Alignment | |
| originalNumberOfResidues | Alignment | |
| originalNumberOfSequences | Alignment | |
| overlaps | Alignment | |
| prepareCodingSequence(bool splitByStopCodon, bool ignoreStopCodon, Alignment *proteinAlignment) | Alignment | |
| printAlignmentInfo(std::ostream &output) | Alignment | |
| printSeqIdentity() | Alignment | |
| printSeqOverlap() | Alignment | |
| saveResidues | Alignment | |
| saveSequences | Alignment | |
| SeqRef | Alignment | |
| seqsInfo | Alignment | |
| seqsName | Alignment | |
| sequences | Alignment | |
| SequencesMatrix | Alignment | |
| setBlockSize(int blockSize) | Alignment | |
| setKeepSequencesFlag(bool newFlagValue) | Alignment | |
| setWindowsSize(int ghWindow, int shWindow) | Alignment | |
| Statistics | Alignment | |
| statSVG(const char *const destFile) | Alignment | |
| updateSequencesAndResiduesNums(bool countSequences=true, bool countResidues=true) | Alignment | |
| ~Alignment() | Alignment | |
1.8.13