| 1 | // ==================================================================== // |
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| 2 | // // |
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| 3 | // File : awt_parsimony_defaults.hxx // |
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| 4 | // Purpose : control behavior of parsimony // |
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| 5 | // // |
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| 6 | // // |
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| 7 | // Coded by Ralf Westram (coder@reallysoft.de) in July 2003 // |
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| 8 | // Copyright Department of Microbiology (Technical University Munich) // |
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| 9 | // // |
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| 10 | // Visit our web site at: http://www.arb-home.de/ // |
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| 11 | // // |
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| 12 | // // |
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| 13 | // ==================================================================== // |
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| 14 | |
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| 15 | #ifndef AWT_PARSIMONY_DEFAULTS_HXX |
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| 16 | #define AWT_PARSIMONY_DEFAULTS_HXX |
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| 17 | |
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| 18 | // -------------------------------------------------------------------------------- |
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| 19 | // Defines for PARSIMONY behavior |
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| 20 | |
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| 21 | // When MULTIPLE_GAPS_ARE_MULTIPLE_MUTATIONS is 'undefined' it compiles |
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| 22 | // an EXPERIMENTAL VERSION of parsimony that counts multiple |
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| 23 | // consequetive gaps as one mutation. |
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| 24 | // Our tests show that this method produces bad trees. |
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| 25 | // |
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| 26 | // Recommended setting is 'defined'. |
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| 27 | |
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| 28 | #define MULTIPLE_GAPS_ARE_MULTIPLE_MUTATIONS |
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| 29 | |
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| 30 | |
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| 31 | // When PROPAGATE_GAPS_UPWARDS is defined, gaps are propagates upwards |
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| 32 | // and they may match against gaps in neighbour sequences. |
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| 33 | // |
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| 34 | // Recommended setting is 'defined'. |
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| 35 | |
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| 36 | #define PROPAGATE_GAPS_UPWARDS |
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| 37 | |
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| 38 | // -------------------------------------------------------------------------------- |
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| 39 | // Do not change these settings! |
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| 40 | // -------------------------------------------------------------------------------- |
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| 41 | |
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| 42 | #else |
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| 43 | #error awt_parsimony_defaults.hxx included twice |
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| 44 | #endif // AWT_PARSIMONY_DEFAULTS_HXX |
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