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

- a -

• add() : match< T >
• addToKISTable() : PREPRO< GENOME_TYPE >

- b -

• binary_search() : KISES< GENOME_TYPE >

- c -

• check_it() : CleanFile< GENOME_TYPE >
• checkE() : CleanFile< GENOME_TYPE >
• checkK() : CleanFile< GENOME_TYPE >
• checkO() : CleanFile< GENOME_TYPE >
• checkS() : CleanFile< GENOME_TYPE >
• checkStitchedHits() : PREPRO< GENOME_TYPE >
• CleanFile() : CleanFile< GENOME_TYPE >
• copy_it() : CleanFile< GENOME_TYPE >
• copy_title() : CleanFile< GENOME_TYPE >

- d -

• dirty : SEQ< GENOME_TYPE >

- e -

• elm : match< T >
• End : SEQ< GENOME_TYPE >
• end1 : lightKIS< GENOME_TYPE >
• end2 : lightKIS< GENOME_TYPE >
• extractBP() : PREPRO< GENOME_TYPE >
• extractBPCoords() : PREPRO< GENOME_TYPE >
• extractGaps() : PREPRO< GENOME_TYPE >
• extractGapsFromHits() : PREPRO< GENOME_TYPE >

- f -

• fileN : CleanFile< GENOME_TYPE >
• fileName1 : PREPRO< GENOME_TYPE >
• fileName2 : PREPRO< GENOME_TYPE >
• find() : KISES< GENOME_TYPE >
• find_KISes() : KISES< GENOME_TYPE >

- g -

• gAlign() : PREPRO< GENOME_TYPE >
• GAOnStitchedHits() : PREPRO< GENOME_TYPE >
• genome1 : PREPRO< GENOME_TYPE >
• genome2 : PREPRO< GENOME_TYPE >
• get_Coords() : lightKIS< GENOME_TYPE >, KIS< GENOME_TYPE >
• get_dirty() : SEQ< GENOME_TYPE >
• get_elm() : match< T >
• get_end() : SEQ< GENOME_TYPE >
• get_info() : SEQ< GENOME_TYPE >
• get_KO() : SEQ< GENOME_TYPE >
• get_match() : match< T >
• get_or() : CleanFile< GENOME_TYPE >
• get_Orientation() : lightKIS< GENOME_TYPE >, KIS< GENOME_TYPE >
• get_orientation() : SEQ< GENOME_TYPE >
• get_start() : SEQ< GENOME_TYPE >
• getCleanRes() : CleanFile< GENOME_TYPE >
• getGene() : PREPRO< GENOME_TYPE >
• getGenome() : PREPRO< GENOME_TYPE >
• getName() : lightKIS< GENOME_TYPE >
• getValid() : lightKIS< GENOME_TYPE >

- i -

• info : SEQ< GENOME_TYPE >
• insert_seg() : KIS< GENOME_TYPE >
• intersection() : CleanFile< GENOME_TYPE >
• isdigit() : CleanFile< GENOME_TYPE >
• isspace() : CleanFile< GENOME_TYPE >
• itr : KIS< GENOME_TYPE >, CleanFile< GENOME_TYPE >

- k -

• KIS() : KIS< GENOME_TYPE >
• KISES() : KISES< GENOME_TYPE >
• KO : SEQ< GENOME_TYPE >

- l -

• labelIt() : PREPRO< GENOME_TYPE >
• lAlign() : PREPRO< GENOME_TYPE >
• legalize_it() : CleanFile< GENOME_TYPE >
• lightKIS() : lightKIS< GENOME_TYPE >

- m -

• MakeLegal() : CleanFile< GENOME_TYPE >
• mtch : match< T >

- n -

• name : lightKIS< GENOME_TYPE >
• nameIt() : lightKIS< GENOME_TYPE >

- o -

• operator()() : lightKISComp2< GENOME_TYPE >, lightKISComp1< GENOME_TYPE >, GeneComp< GENOME_TYPE >
• operator<() : SEQ< GENOME_TYPE >, match< T >, lightKIS< GENOME_TYPE >
• operator=() : SEQ< GENOME_TYPE >, lightKIS< GENOME_TYPE >, KIS< GENOME_TYPE >
• operator==() : SEQ< GENOME_TYPE >, lightKIS< GENOME_TYPE >
• operator>() : SEQ< GENOME_TYPE >, lightKIS< GENOME_TYPE >
• Orientation : SEQ< GENOME_TYPE >, lightKIS< GENOME_TYPE >
• orientation : KIS< GENOME_TYPE >

- p -

• PREPRO() : PREPRO< GENOME_TYPE >
• print() : PREPRO< GENOME_TYPE >, KIS< GENOME_TYPE >
• printToFile() : PREPRO< GENOME_TYPE >

- r -

• refineGapTable() : PREPRO< GENOME_TYPE >
• refineHitTable() : PREPRO< GENOME_TYPE >
• refineKISTable() : PREPRO< GENOME_TYPE >
• res : KISES< GENOME_TYPE >

- s -

• seg1 : KIS< GENOME_TYPE >
• seg2 : KIS< GENOME_TYPE >
• segments : CleanFile< GENOME_TYPE >
• SEQ() : SEQ< GENOME_TYPE >
• set_dirty() : SEQ< GENOME_TYPE >
• set_end() : SEQ< GENOME_TYPE >
• set_info() : SEQ< GENOME_TYPE >
• set_KO() : SEQ< GENOME_TYPE >
• set_match() : match< T >
• set_orientation() : SEQ< GENOME_TYPE >
• set_start() : SEQ< GENOME_TYPE >
• setValid() : lightKIS< GENOME_TYPE >
• skipspaces() : CleanFile< GENOME_TYPE >
• Start : SEQ< GENOME_TYPE >
• start1 : lightKIS< GENOME_TYPE >
• start2 : lightKIS< GENOME_TYPE >
• stitch() : PREPRO< GENOME_TYPE >
• stitchHits() : PREPRO< GENOME_TYPE >
• string2GENOMEType() : CleanFile< GENOME_TYPE >

- t -

• Tokenize() : CleanFile< GENOME_TYPE >
• toString() : PREPRO< GENOME_TYPE >
• transformSeq() : PREPRO< GENOME_TYPE >

- u -

• unionHits() : PREPRO< GENOME_TYPE >
• unionKis() : KIS< GENOME_TYPE >
• update() : lightKIS< GENOME_TYPE >

- v -

• valid : lightKIS< GENOME_TYPE >

- ~ -

• ~CleanFile() : CleanFile< GENOME_TYPE >
• ~KIS() : KIS< GENOME_TYPE >
• ~KISES() : KISES< GENOME_TYPE >
• ~SEQ() : SEQ< GENOME_TYPE >

---