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