1 | // ================================================================ // |
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2 | // // |
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3 | // File : awt_nei.hxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // ================================================================ // |
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10 | |
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11 | #ifndef AWT_NEI_HXX |
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12 | #define AWT_NEI_HXX |
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13 | |
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14 | #ifndef ARB_ASSERT_H |
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15 | #include <arb_assert.h> |
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16 | #endif |
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17 | |
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18 | #define ph_assert(cond) arb_assert(cond) |
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19 | |
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20 | class PH_NEIGHBOUR_DIST { |
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21 | public: |
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22 | PH_NEIGHBOUR_DIST(void); |
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23 | long i,j; |
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24 | AP_FLOAT val; |
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25 | PH_NEIGHBOUR_DIST *next, *previous; |
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26 | void remove(void) { |
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27 | ph_assert(previous); // already removed |
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28 | if (next) {next->previous = previous;} |
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29 | previous->next = next;previous = 0; |
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30 | }; |
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31 | |
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32 | void add(PH_NEIGHBOUR_DIST *root) { |
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33 | next = root->next; |
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34 | root->next = this; |
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35 | previous = root; |
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36 | if (next) next->previous = this; |
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37 | }; |
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38 | }; |
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39 | |
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40 | class PH_NEIGHBOURJOINING { |
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41 | PH_NEIGHBOUR_DIST **dist_matrix; |
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42 | PH_NEIGHBOUR_DIST *dist_list; // array of dist_list lists |
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43 | long dist_list_size; |
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44 | AP_FLOAT dist_list_corr; |
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45 | AP_FLOAT *net_divergence; |
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46 | |
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47 | long size; |
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48 | long *swap_tab; |
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49 | long swap_size; |
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50 | |
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51 | AP_FLOAT get_max_di(AP_FLOAT **m); |
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52 | void remove_taxa_from_dist_list(long i); |
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53 | void add_taxa_to_dist_list(long j); |
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54 | AP_FLOAT get_max_net_divergence(void); |
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55 | void remove_taxa_from_swap_tab(long i); |
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56 | |
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57 | public: |
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58 | |
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59 | PH_NEIGHBOURJOINING(AP_FLOAT **m, long size); |
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60 | ~PH_NEIGHBOURJOINING(void); |
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61 | |
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62 | void join_nodes(long i,long j,AP_FLOAT &leftl,AP_FLOAT& rightlen); |
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63 | void get_min_ij(long& i, long& j); |
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64 | void get_last_ij(long& i, long& j); |
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65 | AP_FLOAT get_dist(long i, long j); |
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66 | }; |
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67 | |
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68 | #else |
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69 | #error awt_nei.hxx included twice |
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70 | #endif // AWT_NEI_HXX |
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