1 | #include <stdio.h> |
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2 | |
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3 | #include <arbdbt.h> |
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4 | #include <TreeWrite.h> |
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5 | |
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6 | /* Input Tree_name argv[1] |
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7 | * Output(stdout) one line tree |
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8 | * */ |
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9 | |
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10 | |
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11 | int main(int argc, char **argv){ |
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12 | int exitcode = EXIT_SUCCESS; |
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13 | |
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14 | if (argc < 2) { |
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15 | fprintf(stderr, "\narb_export_tree - exports tree from running ARB to stdout\n" |
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16 | "syntax: arb_export_tree [--bifurcated] TREE_NAME\n" |
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17 | " --bifurcated write a bifurcated tree (default is a trifurcated tree)\n" |
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18 | " --nobranchlens do not write branchlengths\n" |
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19 | " --doublequotes use doublequotes (default is singlequotes)\n" |
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20 | "\n" |
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21 | "Note: If TREE_NAME is '\?\?\?\?' or '' an empty tree is written."); |
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22 | exitcode = EXIT_FAILURE; |
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23 | } |
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24 | else { |
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25 | GB_ERROR error = 0; |
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26 | GBDATA *gb_main = GBT_open(":","r",0); |
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27 | |
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28 | if (!gb_main){ |
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29 | error = GB_await_error(); |
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30 | exitcode = EXIT_FAILURE; |
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31 | } |
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32 | else { |
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33 | bool trifurcated = true; |
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34 | bool branchlens = true; |
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35 | bool doublequotes = false; |
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36 | const char *tree_name = 0; |
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37 | |
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38 | for (int a = 1; a < argc; a++) { |
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39 | if (strcmp(argv[a], "--bifurcated") == 0) trifurcated = false; |
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40 | else if (strcmp(argv[a], "--nobranchlens") == 0) branchlens = false; |
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41 | else if (strcmp(argv[a], "--doublequotes") == 0) doublequotes = true; |
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42 | else tree_name = argv[a]; |
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43 | } |
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44 | |
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45 | if (!tree_name) error = "Missing argument TREE_NAME"; |
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46 | else { |
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47 | GB_transaction dummy(gb_main); |
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48 | GBT_TREE *tree = GBT_read_tree(gb_main,tree_name, - sizeof(GBT_TREE)); |
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49 | if (tree) { |
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50 | error = TREE_export_tree(gb_main, stdout, tree, trifurcated, branchlens, doublequotes); |
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51 | } |
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52 | else { |
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53 | if (tree_name[0] && strcmp(tree_name, "????") != 0) // ignore tree names '????' and '' (no error, just export empty tree) |
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54 | { |
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55 | char *err = GBS_global_string_copy("arb_export_tree: Tree '%s' does not exist in DB\n", tree_name); |
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56 | GBT_message(gb_main, err); |
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57 | free(err); |
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58 | } |
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59 | else { |
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60 | error = GB_await_error(); |
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61 | } |
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62 | } |
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63 | printf(";\n"); // aka empty tree |
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64 | } |
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65 | GB_close(gb_main); |
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66 | } |
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67 | |
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68 | if (error) { |
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69 | fprintf(stderr, "\narb_export_tree: Error: %s\n", error); |
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70 | } |
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71 | } |
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72 | return exitcode; |
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73 | } |
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74 | |
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