| /dports/biology/treepuzzle/tree-puzzle-5.2/src/ |
| H A D | split.c | 27 int *trueID) in inittree_split() argument
64 (tmpedge[0].split)[0] = trueID[0]; /* leaf 0 above this edge */ in inittree_split()
66 (tmpedge[0].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ in inittree_split()
67 (tmpedge[0].split)[Maxspc-2] = trueID[2]; /* leaf 0 below this edge */ in inittree_split()
99 tmpedge[0].taxon = trueID[0]; in inittree_split()
100 tmpedge[1].taxon = trueID[1]; in inittree_split()
101 tmpedge[2].taxon = trueID[2]; in inittree_split()
104 tmpedgeofleaf[trueID[0]] = 0; in inittree_split()
105 tmpedgeofleaf[trueID[1]] = 1; in inittree_split()
106 tmpedgeofleaf[trueID[2]] = 2; in inittree_split()
[all …]
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| H A D | mrca.c | 69 *rootleaf = trueID[0]; in inittree_mrca()
91 mrcamatrix[trueID[1]][trueID[2]] = 0; in inittree_mrca()
92 mrcamatrix[trueID[2]][trueID[1]] = 0; in inittree_mrca()
95 mrcamatrix[trueID[1]][trueID[1]] = -8; in inittree_mrca()
96 mrcamatrix[trueID[2]][trueID[2]] = -8; in inittree_mrca()
112 tmpedge[0].taxon = trueID[0]; in inittree_mrca()
113 tmpedge[1].taxon = trueID[1]; in inittree_mrca()
114 tmpedge[2].taxon = trueID[2]; in inittree_mrca()
117 tmpedgeofleaf[trueID[0]] = 0; in inittree_mrca()
118 tmpedgeofleaf[trueID[1]] = 1; in inittree_mrca()
[all …]
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| H A D | pstep-deglob.c | 293 int *trueID) /* species permutation */ in writeOTU_orig() argument
302 *column += fputid(outfp, trueID[i]); in writeOTU_orig()
312 …eOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
321 …OTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
333 int *trueID) /* species permutation */ in writetree_orig() argument
337 column_orig += fputid(outfp, trueID[0]) + 3; in writetree_orig()
339 …edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column_orig, trueID); in writetree_orig()
343 …dge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column_orig, trueID); in writetree_orig()
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| H A D | recur-old.c | 27 int *trueID) in inittree_recur() argument
67 (tmpedge[0].split)[0] = trueID[0]; /* leaf 0 above this edge */ in inittree_recur()
69 (tmpedge[0].split)[Maxspc-1] = trueID[1]; /* leaf 0 below this edge */ in inittree_recur()
70 (tmpedge[0].split)[Maxspc-2] = trueID[2]; /* leaf 0 below this edge */ in inittree_recur()
103 tmpedge[0].taxon = trueID[0]; in inittree_recur()
104 tmpedge[1].taxon = trueID[1]; in inittree_recur()
105 tmpedge[2].taxon = trueID[2]; in inittree_recur()
108 tmpedgeofleaf[trueID[0]] = 0; in inittree_recur()
109 tmpedgeofleaf[trueID[1]] = 1; in inittree_recur()
110 tmpedgeofleaf[trueID[2]] = 2; in inittree_recur()
[all …]
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| H A D | recur.c | 27 int *trueID) in inittree_recur() argument
64 (tmpedge[0].cluster)[0] = trueID[1]; /* leaf 1 in edge cluster */ in inittree_recur()
65 (tmpedge[0].cluster)[1] = trueID[2]; /* leaf 2 in edge cluster */ in inittree_recur()
69 (tmpedge[1].cluster)[0] = trueID[1]; /* leaf 0 in edge cluster */ in inittree_recur()
90 tmpedge[0].taxon = trueID[0]; in inittree_recur()
91 tmpedge[1].taxon = trueID[1]; in inittree_recur()
92 tmpedge[2].taxon = trueID[2]; in inittree_recur()
95 tmpedgeofleaf[trueID[0]] = 0; in inittree_recur()
96 tmpedgeofleaf[trueID[1]] = 1; in inittree_recur()
97 tmpedgeofleaf[trueID[2]] = 2; in inittree_recur()
[all …]
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| H A D | pstep-mrca.c | 297 int *trueID) /* species permutation */ in writeOTU_orig() argument
305 *column += fputid(outfp, trueID[i]); in writeOTU_orig()
314 …eOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
322 …OTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
334 int *trueID) /* species permutation */ in writetree_orig() argument
340 column += fputid(outfp, trueID[0]) + 3; in writetree_orig()
342 …tfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
346 …fp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
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| H A D | pstep-recursive.c | 297 int *trueID) /* species permutation */ in writeOTU_orig() argument
305 *column += fputid(outfp, trueID[i]); in writeOTU_orig()
314 …eOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
322 …OTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
334 int *trueID) /* species permutation */ in writetree_orig() argument
340 column += fputid(outfp, trueID[0]) + 3; in writetree_orig()
342 …tfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
346 …fp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
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| H A D | pstep-trueID.c | 302 int *trueID) /* species permutation */ in writeOTU_orig() argument
310 *column += fputid(outfp, trueID[i]); in writeOTU_orig()
320 …eOTU_orig(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
329 …OTU_orig(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_orig()
342 int *trueID) /* species permutation */ in writetree_orig() argument
348 column += fputid(outfp, trueID[0]) + 3; in writetree_orig()
351 …tfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
356 …fp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_orig()
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| H A D | pstep-split.c | 432 int *trueID) /* species permutation */ in writeOTU_split() argument
440 *column += fputid(outfp, trueID[i]); in writeOTU_split()
449 …OTU_split(outfp, edge[ed].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_split()
457 …TU_split(outfp, edge[ed].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, column, trueID); in writeOTU_split()
470 int *trueID) /* species permutation */ in writetree_split() argument
476 column += fputid(outfp, trueID[0]) + 3; in writetree_split()
478 …tfp, edge[edgeofleaf[0]].downleft->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_split()
482 …fp, edge[edgeofleaf[0]].downright->numedge, edge, edgeofleaf, nextedge, nextleaf, &column, trueID); in writetree_split()
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| H A D | pstep.c | 233 int *trueID) in inittree_orig() argument
296 tmpedge[0].taxon = trueID[0]; in inittree_orig()
297 tmpedge[1].taxon = trueID[1]; in inittree_orig()
298 tmpedge[2].taxon = trueID[2]; in inittree_orig()
301 tmpedgeofleaf[trueID[0]] = 0; in inittree_orig()
302 tmpedgeofleaf[trueID[1]] = 1; in inittree_orig()
303 tmpedgeofleaf[trueID[2]] = 2; in inittree_orig()
306 *rootleaf = trueID[0]; in inittree_orig()
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| H A D | treesort.c | 169 int *trueID) /* in: permutation vector */
181 ctree[ct_sortkeyaddr(nextcurredge)] = trueID[i];
196 edge, edgeofleaf, numleaves, trueID);
201 edge, edgeofleaf, numleaves, trueID);
210 int *trueID, /* in: permutation vector */
226 ctree[ct_sortkeyaddr(0)] = trueID[0];
234 edgeset, edgeofleaf, numleaves, trueID);
239 edgeset, edgeofleaf, numleaves, trueID);
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| H A D | pstep-mrca.h | 110 int *trueID); /* species permutation */
118 int *trueID); /* species permutation */
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| H A D | pstep-recursive.h | 110 int *trueID); /* species permutation */
118 int *trueID); /* species permutation */
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| H A D | pstep-trueID.h | 110 int *trueID); /* species permutation */
118 int *trueID); /* species permutation */
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| H A D | pstep-deglob.h | 128 int *trueID); /* species permutation */
136 int *trueID); /* species permutation */
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| H A D | pstep-split.h | 136 int *trueID); /* species permutation */
144 int *trueID); /* species permutation */
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| H A D | treesort.h | 105 int *trueID); /* in: permutation vector */
111 int *trueID, /* in: permutation vector */
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| H A D | pstep.h | 278 int *trueID);
331 int *trueID);
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| H A D | pstep-orig.h | 58 ivector trueID; variable
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| H A D | puzzle.h | 533 int *trueID, /* in: permutation vector */
578 int *trueID, /* in: permutation list */
586 int *trueID, /* in: permutation list */
649 int *trueID, /* permutation array */
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| H A D | pstep-orig.c | 252 column += fputid(outfp, trueID[i]); in writeOTU()
279 column += fputid(outfp, trueID[0]) + 3; in writetree()
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| H A D | consensus.h | 76 int *trueID, /* in: permutation list */
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| /dports/biology/bbmap/bbmap/current/sketch/ |
| H A D | SketchIndex.java | 136 final int trueID=id-1;//Minimum id is 1, indicating sketch 0. in getSketchesList() local
137 idList.add(trueID);//Minimum id is 1, indicating sketch 0. in getSketchesList()
139 if(taxSet!=null){addToTaxSet(trueID, taxSet, contamLevel);} in getSketchesList()
248 final int trueID=id-1;//Minimum id is 1, indicating sketch 0. in getSketchesMap() local
249 idMap.increment(trueID); in getSketchesMap()
251 if(taxSet!=null){addToTaxSet(trueID, taxSet, contamLevel);} in getSketchesMap()
252 if(refHitCounts!=null && trueID!=a.sketchID){refHitCounts[i]++;} in getSketchesMap()
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| H A D | BlacklistMaker2.java | 434 final int trueID=sid-1;//Minimum id is 1, indicating sketch 0. in processKey()
437 addToMap(key, trueID); in processKey()
440 Sketch sk=searcher.refSketches.get(trueID); in processKey()
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| /dports/science/dakota/dakota-6.13.0-release-public.src-UI/packages/external/trilinos/packages/teuchos/parameterlist/src/ |
| H A D | Teuchos_StandardDependencyXMLConverters.cpp | 355 ParameterEntryValidator::ValidatorID trueID = in convertSpecialValidatorAttributes() local
360 validatorIDsMap.find(trueID) in convertSpecialValidatorAttributes()
365 "with ID " << trueID << in convertSpecialValidatorAttributes()
369 validatorIDsMap.find(trueID)->second; in convertSpecialValidatorAttributes()
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