Here is a list of all functions with links to the classes they belong to:

- c -

• chainIndexToStoichiomLetter() : MultimerHandler
• checkMSAFormatAndReturnRowIndexIntervalsCorrespondingToChains() : MultimerHandler
• checkRepeatedChainAndReturnOneSegment() : MultimerHandler
• checkRequiredFlags() : FlagHandler
• checkRowCorrespondsOnlyToOneChainAndReturnChainIndex() : MultimerHandler
• containsInvalidLetters() : MSAReader

- f -

• FlagHandler() : FlagHandler

- g -

• generateIdForSequences() : MSAWriter
• getBooleanValue() : FlagHandler
• getFileArrayValue() : FlagHandler
• getFlagValue() : FlagHandler
• getFloatValue() : FlagHandler
• getHeteromerMSAs() : MultimerHandler
• getHetoromerMSAs() : MultimerHandler
• getHomomerIndividualMSA() : MultimerHandler
• getIntArrayValue() : FlagHandler
• getIntValue() : FlagHandler
• getNonZeroIntValue() : FlagHandler
• getSequenceSegment() : MultimerHandler

- i -

• includesInPairedMSA() : MultimerHandler
• isHeteromerFormat() : MultimerHandler
• isHomomerFormat() : MultimerHandler
• isUnaligned() : MSAReader

- m -

• makeUppercase() : MSAReader
• MSAReader() : MSAReader, MSAReader_a2m, MSAReader_a3m, MSAReader_aln, MSAReader_clustal, MSAReader_fasta, MSAReader_pfam, MSAReader_sto
• MSAWriter() : MSAWriter, MSAWriter_a2m, MSAWriter_a3m, MSAWriter_aln, MSAWriter_clustal, MSAWriter_fasta, MSAWriter_pfam, MSAWriter_sto
• MultimerHandler() : MultimerHandler

- p -

• processFlags() : FlagHandler

- r -

• read() : MSAReader
• readFile() : MSAReader, MSAReader_a2m, MSAReader_a3m, MSAReader_aln, MSAReader_clustal, MSAReader_fasta, MSAReader_pfam, MSAReader_sto

- v -

• validateSequences() : MSAReader

- w -

• write() : MSAWriter
• writeFile() : MSAWriter, MSAWriter_a2m, MSAWriter_a3m, MSAWriter_aln, MSAWriter_clustal, MSAWriter_fasta, MSAWriter_pfam, MSAWriter_sto