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/dports/math/gap/gap-4.11.0/pkg/ExamplesForHomalg-2019.09.02/examples/
H A DHom(Hom(-,Z128),Z16)_On_Seq.g52 ## at homology degree: 2
61 ## at homology degree: 1
70 ## at homology degree: 0
93 ## at homology degree: 14
138 ## at homology degree: 9
147 ## at homology degree: 8
156 ## at homology degree: 7
165 ## at homology degree: 6
174 ## at homology degree: 5
183 ## at homology degree: 4
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H A DH0H1.g12 ## the 0-th homology of L:
14 ## the 1-st homology of L:
22 ## the 0-th homology of S:
24 ## the 1-st homology of S:
/dports/cad/gmsh/gmsh-4.9.2-source/Plugin/
H A DHomologyComputation.cpp125 Homology *homology = new Homology(m, domain, subdomain, imdomain, true, in execute() local
127 homology->setFileName(fileName); in execute()
129 if(hom != 0) homology->findHomologyBasis(dimsave); in execute()
130 if(coh != 0) homology->findCohomologyBasis(dimsave); in execute()
135 homology->addChainsToModel(dim, pviews, hompg); in execute()
136 if(hompg != -1) hompg += homology->betti(dim); in execute()
142 homology->addCochainsToModel(dim, pviews, cohpg); in execute()
143 if(cohpg != -1) cohpg += homology->betti(dim); in execute()
147 delete homology; in execute()
/dports/math/gap/gap-4.11.0/pkg/homalg-2019.09.01/examples/
H A DHom(Hom(-,Z128),Z16)_On_Seq.g62 ## at homology degree: 2
71 ## at homology degree: 1
80 ## at homology degree: 0
148 ## at homology degree: 9
157 ## at homology degree: 8
166 ## at homology degree: 7
175 ## at homology degree: 6
184 ## at homology degree: 5
193 ## at homology degree: 4
202 ## at homology degree: 3
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H A DLTensorProduct_Z.g42 ## at homology degree: 2
49 ## at homology degree: 1
57 ## at homology degree: 0
70 ## at homology degree: 5
77 ## at homology degree: 4
85 ## at homology degree: 3
93 ## at homology degree: 2
100 ## at homology degree: 1
108 ## at homology degree: 0
/dports/math/gap/gap-4.11.0/pkg/Modules-2019.09.02/examples/
H A DHom(Hom(-,Z128),Z16)_On_Seq.g62 ## at homology degree: 2
71 ## at homology degree: 1
80 ## at homology degree: 0
148 ## at homology degree: 9
157 ## at homology degree: 8
166 ## at homology degree: 7
175 ## at homology degree: 6
184 ## at homology degree: 5
193 ## at homology degree: 4
202 ## at homology degree: 3
[all …]
H A DLTensorProduct_Z.g42 ## at homology degree: 2
49 ## at homology degree: 1
57 ## at homology degree: 0
70 ## at homology degree: 5
77 ## at homology degree: 4
85 ## at homology degree: 3
93 ## at homology degree: 2
100 ## at homology degree: 1
108 ## at homology degree: 0
H A DH0H1.g10 ## the 0-th homology of L:
12 ## the 1-st homology of L:
20 ## the 0-th homology of S:
22 ## the 1-st homology of S:
/dports/math/gap/gap-4.11.0/pkg/GaussForHomalg-2019.09.02/examples/
H A DHom(Hom(-,Z128),Z16)_On_Seq.g59 ## at homology degree: 2
66 ## at homology degree: 1
73 ## at homology degree: 0
131 ## at homology degree: 9
138 ## at homology degree: 8
145 ## at homology degree: 7
152 ## at homology degree: 6
159 ## at homology degree: 5
166 ## at homology degree: 4
173 ## at homology degree: 3
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/dports/math/gap/gap-4.11.0/pkg/simpcomp/lib/
H A Dhomology.gd3 ## simpcomp / homology.gd
11 ## <#GAPDoc Label="homology">
14 ## for its homology computations. However, some additional (co-)homology related functionality cann…
15 ## For this, <Package>simpcomp</Package> contains an additional (co-)homology algorithm (cf. <Ref F…
17 …r possible <Package>simpcomp</Package> makes use of the &GAP; package ''homology'' <Cite Key="Duma…
18 ## homology groups (cf. <Ref Func="SCHomologyClassic" />) which sometimes is much faster than the b…
23 …rices or the simplicial homology of a given complex, <Package>simpcomp</Package> is also able to c…
H A Dpkghomalg.gi208 ## This function computes the ranks of the homology groups of
211 ## <M>\mathbb{Q}</M>-homology, a value of <C>1</C> computes the
213 ## prime power, computes the <M>\mathbb{F}_q</M>-homology ranks.<P/>
230 #homology: ker(M[i])/im(M[i+1])
243 rnam,"-homology ranks...");
271 ## <M>\mathbb{Q}</M>-homology, a value of <C>1</C> computes the
273 ## power, computes the <M>\mathbb{F}_q</M>-homology groups.<P/>
275 ## <C>hk:=CertainObject(homology,k);</C>, where <C>homology</C> is the
295 #homology: ker(M[i])/im(M[i+1])
318 "-homology groups.");
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H A Dpkghom.gi5 ## Loaded when `homology' package is available
12 #setup homology package settings
46 Info(InfoSimpcomp,1,"SCHomologyClassic: computing homology failed.");
/dports/biology/py-orange3-bioinformatics/Orange3-Bioinformatics-4.3.1/orangecontrib/bioinformatics/tests/ncbi/
H A Dtest_homologene.py9 self.homology = HomoloGene()
10 self.assertEqual(basename(normpath(self.homology.file_path)), 'homologene.tab')
13 self.assertEqual(self.homology.find_homolog('920', '9913'), '407098')
14 self.assertEqual(self.homology.find_homolog('920', '10090'), '12504')
15 self.assertEqual(self.homology.find_homolog('920', '10116'), '24932')
/dports/math/gap/gap-4.11.0/pkg/ModulePresentationsForCAP-2019.01.16/examples/
H A DKoszul.g79 homology := CokernelObject( boundaries_in_cyles );;
81 homology := ApplyFunctor( LessGenFunctor, homology );;
83 homology := ApplyFunctor( StdBasisFunctor, homology );;
84 Display( homology );
/dports/math/polymake/polymake-4.5/demo/
H A Dchain_complex_homology.ipynb9 …homology of simplicial complexes (see this [tutorial](apps_topaz.ipynb) for an introduction), `pol…
53 …aults to `SparseMatrix<Integer>`, as this allows computation of integer homology. The second param…
94 "### Computing integer homology\n",
96 …"There is a user function to compute integer homology of your complex. You can access the document…
120 "print homology($cc,0);"
127 …s of your homology modules, containing the torsion coefficients in curly brackets, and the betti n…
129 "There is an extra function for computing the generators of the homology modules as well.\n",
168 …"The output pairs the homology module representation with a representation of the cycles generatin…
172 …"If your complex' differentials do not have `Integer` coefficients, computing integer homology is …
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/
H A DAssemblyBasedSVDiscoveryTestDataProviderForBreakEndVariants.java145 String homology = StringUtil.bytesToString(Arrays.copyOfRange(contigSequence, 119, 201)); in forIntraChromosomeRefOrderSwapWithHomology() local
152 …plications = new BreakpointComplications.IntraChrRefOrderSwapBreakpointComplications(homology, ""); in forIntraChromosomeRefOrderSwapWithHomology()
160 …ele.create("A", true), "", "", true, false, true), contigName, 60, 119, homology, "", "BND_chr20_2… in forIntraChromosomeRefOrderSwapWithHomology()
217 String homology = StringUtil.bytesToString(Arrays.copyOfRange(contigSequence, 166, 322)); in forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner() local
223 …ntComplications = new BreakpointComplications.InterChromosomeBreakpointComplications(homology, ""); in forInterChromosomeNoStrandSwitchAndUpstreamLocIsFirstInPartner()
256 String homology = ""; in forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner() local
263 …mplications = new BreakpointComplications.InterChromosomeBreakpointComplications(homology, insSeq); in forInterChromosomeNoStrandSwitchAndUpstreamLocIsSecondInPartner()
291 String homology = ""; in forInterChromosomeStrandSwitch55() local
298 …mplications = new BreakpointComplications.InterChromosomeBreakpointComplications(homology, insSeq); in forInterChromosomeStrandSwitch55()
327 …String homology = SequenceUtil.reverseComplement(StringUtil.bytesToString(Arrays.copyOfRange(conti… in forInterChromosomeStrandSwitch33() local
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/dports/math/fricas/fricas-1.3.7/src/input/
H A Dbugs2016.input148 testcase "homology"
162 hsd1 := homology(sd1)
169 hsd2 := homology(sd2)
176 htd2 := homology(td2)
185 htd3 := homology(td3)
193 hrd3 := homology(rd3)
202 hps3 := homology(ps3)
209 hps4 := homology(ps4)
217 hs3 := homology(s3)
224 hp2 := homology(p2)
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/dports/biology/emboss/EMBOSS-6.6.0/test/pir/
H A Dpir1.ref36 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
56 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
74 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
90 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
118 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
150 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
167 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
398 A;Note: peptides were positioned by homology
865 A;Note: some peptides were positioned by homology
902 A;Note: some peptides were positioned by homology
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H A Dpir2.ref24 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
26 F;11-105/Domain: cytochrome c homology F;21,24/Binding site: heme (Cys) (covalent) #status predicted
43 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
45 F;11-105/Domain: cytochrome c homology F;21,24/Binding site: heme (Cys) (covalent) #status predicted
60 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
62 F;4-100/Domain: cytochrome c homology F;13,16/Binding site: heme (Cys) (covalent) #status predicted
76 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
78 F;4-107/Domain: cytochrome c homology F;13,16/Binding site: heme (Cys) (covalent) #status predicted
95 C;Superfamily: cytochrome c/cytochrome c2; cytochrome c homology
97 F;13-88/Domain: cytochrome c homology (fragment) F;70/Binding site: heme iron (Met) (axial ligand) …
/dports/cad/gmsh/gmsh-4.9.2-source/tutorial/
H A Dt14.geo10 // (co)homology space bases using a mesh of a model. The representative basis
38 // (co)homology computation and the subdomain of the relative (co)homology
58 // Find bases for relative homology spaces of the domain modulo the four
62 // Find homology space bases isomorphic to the previous bases: homology spaces
/dports/math/gap/gap-4.11.0/pkg/LocalizeRingForHomalg-2019.09.02/examples/
H A DResidueClass.g26 ## at homology degree: 2
33 ## at homology degree: 1
41 ## at homology degree: 0
70 ## at homology degree: 2
77 ## at homology degree: 1
88 ## at homology degree: 0
113 ## at homology degree: 2
120 ## at homology degree: 1
131 ## at homology degree: 0
/dports/math/gap/gap-4.11.0/pkg/simpcomp/
H A Dinit.g34 ReadPackage("simpcomp","lib/homology.gd");
44 # checks if package 'homology' is present and working
47 success:=IsPackageMarkedForLoading("homology", ">=1.4.2");
48 …ogy_gap","smithform_gap"], file -> Filename(DirectoriesPackagePrograms("homology"), file) = fail) …
78 …e(PACKAGE_ERROR,"package `homology' not installed or its binaries are not available, falling back …
/dports/cad/gmsh/gmsh-4.9.2-source/demos/simple_geo/
H A Dhomology.geo10 // (relative) (co)homology space bases using a mesh of a model.
116 // homology computation and the subdomain of the relative homology
132 // Find bases for relative homology spaces of
136 // Find homology space bases isomorphic to the previous bases:
137 // homology spaces modulo the non-terminal domain surface,
/dports/math/gap/gap-4.11.0/pkg/hap-1.25/lib/SimplicialGroups/
H A Dhomology.gi5 ## Output: The integral homology H_n(XC,Z)
22 ## Output: The integral homology H_n(C,Z)
38 ## Output: The integral homology H_n(G,Z)
/dports/math/gap/gap-4.11.0/pkg/SCO-2019.09.02/examples/orbifolds/
H A Dp6m.g66 #homology over Z:
68 #at homology degree: 0
71 #at homology degree: 1
74 #at homology degree: 2

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