| 1 | /************************************************************************ |
|---|
| 2 | Global prefs |
|---|
| 3 | Written by Chris Hodges <hodges@in.tum.de>. |
|---|
| 4 | Last change: 02.02.04 |
|---|
| 5 | ************************************************************************/ |
|---|
| 6 | |
|---|
| 7 | #ifndef GLOBALPREFS_H |
|---|
| 8 | #define GLOBALPREFS_H |
|---|
| 9 | |
|---|
| 10 | /* size of alphabet */ |
|---|
| 11 | #define ALPHASIZE 5 |
|---|
| 12 | |
|---|
| 13 | /* How many codes can be stored in a LONG |
|---|
| 14 | -> ALPHASIZE^MAXCODEFITLONG < 2^31 */ |
|---|
| 15 | #define MAXCODEFITLONG 13 |
|---|
| 16 | |
|---|
| 17 | /* index building prefs */ |
|---|
| 18 | |
|---|
| 19 | /* how many characters of a prefix will be observed */ |
|---|
| 20 | #define MAXPREFIXSIZE 5 |
|---|
| 21 | |
|---|
| 22 | /* how big should the quick prefix table be? */ |
|---|
| 23 | #define MAXQPREFIXLOOKUPSIZE 7 |
|---|
| 24 | |
|---|
| 25 | /* ratio between bignodes and small nodes, based on experimental values -- |
|---|
| 26 | if you ever run out of nodes buffer, increase this value. If you see |
|---|
| 27 | messages about lots of memory wasted, decrease these values. */ |
|---|
| 28 | #define SMALLNODESPERCENT 105 |
|---|
| 29 | #define BIGNODESPERCENT 10 |
|---|
| 30 | |
|---|
| 31 | /* short edge maximum length (maximum length of edge stored implicitely |
|---|
| 32 | and not in the dictionary) */ |
|---|
| 33 | #define SHORTEDGEMAX 6 |
|---|
| 34 | |
|---|
| 35 | /* double delta leaf compression */ |
|---|
| 36 | //#define DOUBLEDELTALEAVES |
|---|
| 37 | //#define DOUBLEDELTAOPTIONAL |
|---|
| 38 | |
|---|
| 39 | /* size of hash table for duplicates detection during query */ |
|---|
| 40 | #define QUERYHITSHASHSIZE 12800009 |
|---|
| 41 | |
|---|
| 42 | /* size of the hash table for species lookup by name */ |
|---|
| 43 | #define SPECIESNAMEHASHSIZE 10000 |
|---|
| 44 | |
|---|
| 45 | /* minimum length of probe for searching */ |
|---|
| 46 | #define MIN_PROBE_LENGTH 8 |
|---|
| 47 | |
|---|
| 48 | /* error decrease for mismatches in probe design */ |
|---|
| 49 | #define PROBE_MISM_DEC 0.2 |
|---|
| 50 | |
|---|
| 51 | |
|---|
| 52 | // Allow dots in match. When building the tree, up to MAXDOTSINMATCH dots |
|---|
| 53 | // in succession will be converted to SEQCODE_N. In ps_SeqDataCompressed, |
|---|
| 54 | // they will be saved as dots. One replaced dot will add the same mismatch |
|---|
| 55 | // as a replaced N. (So 0.1 at the moment) |
|---|
| 56 | // This feature is not well testet, yet! |
|---|
| 57 | //#define ALLOWDOTSINMATCH |
|---|
| 58 | |
|---|
| 59 | // Number of allowed dots in succession |
|---|
| 60 | #define MAXDOTSINMATCH 5 |
|---|
| 61 | |
|---|
| 62 | |
|---|
| 63 | // Allowed error when comparing floats |
|---|
| 64 | #define EPSILON 0.000001 |
|---|
| 65 | |
|---|
| 66 | |
|---|
| 67 | |
|---|
| 68 | |
|---|
| 69 | #endif /* GLOBALPREFS_H */ |
|---|
