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/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/genefinding/rnaz/herpes/x/
H A Drnaz.out14 Structure conservation index: 0.49
46 Structure conservation index: 0.58
76 Structure conservation index: 0.73
105 Structure conservation index: 0.84
134 Structure conservation index: 0.79
163 Structure conservation index: 0.82
192 Structure conservation index: 0.85
221 Structure conservation index: 0.68
250 Structure conservation index: 0.69
279 Structure conservation index: 0.82
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H A Drnaz_random.out14 Structure conservation index: 0.65
43 Structure conservation index: 0.85
72 Structure conservation index: 0.87
101 Structure conservation index: 0.83
130 Structure conservation index: 0.87
159 Structure conservation index: 0.74
188 Structure conservation index: 0.85
217 Structure conservation index: 0.90
246 Structure conservation index: 0.88
275 Structure conservation index: 0.92
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/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/rnaz/herpes/x/
H A Drnaz.out14 Structure conservation index: 0.49
46 Structure conservation index: 0.58
76 Structure conservation index: 0.73
105 Structure conservation index: 0.84
134 Structure conservation index: 0.79
163 Structure conservation index: 0.82
192 Structure conservation index: 0.85
221 Structure conservation index: 0.68
250 Structure conservation index: 0.69
279 Structure conservation index: 0.82
[all …]
H A Drnaz_random.out14 Structure conservation index: 0.65
43 Structure conservation index: 0.85
72 Structure conservation index: 0.87
101 Structure conservation index: 0.83
130 Structure conservation index: 0.87
159 Structure conservation index: 0.74
188 Structure conservation index: 0.85
217 Structure conservation index: 0.90
246 Structure conservation index: 0.88
275 Structure conservation index: 0.92
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/dports/biology/jalview/jalview/src/jalview/datamodel/
H A DSequenceGroup.java615 if ((conservation != null) in recalcConservation()
622 if (conservation != null) in recalcConservation()
656 if (conservation == null) in _updateConservationRow()
1167 if (conservation == null) in setConservationRow()
1169 conservation = aan; in setConservationRow()
1180 if (conservation == null) in getConservationRow()
1186 conservation.hasText = true; in getConservationRow()
1188 conservation.groupRef = this; in getConservationRow()
1192 return conservation; in getConservationRow()
1330 if (conservation != null) in getAlignmentAnnotation()
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/dports/biology/jalview/jalview/src/jalview/renderer/
H A DResidueShader.java75 private char[] conservation; field in ResidueShader
126 this.conservation = rs.conservation; in ResidueShader()
169 conservation = null; in setConservation()
174 conservation = cons.getConsSequence().getSequenceAsString() in setConservation()
364 if (conservation == null || conservation.length <= column) in applyConservation()
368 char conservationScore = conservation[column]; in applyConservation()
/dports/biology/jalview/jalview/src/jalview/workers/
H A DConservationThread.java47 AlignmentAnnotation conservation, quality; field in ConservationThread
80 conservation = alignViewport.getAlignmentConservationAnnotation(); in run()
82 ourAnnot.add(conservation); in run()
134 && conservation != null && quality != null) in updateResultAnnotation()
137 cons.completeAnnotations(conservation, quality, 0, alWidth); in updateResultAnnotation()
/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/genefinding/rnaz/human/x/
H A Drnaz.out14 Structure conservation index: 0.39
55 Structure conservation index: 0.65
96 Structure conservation index: 0.71
137 Structure conservation index: 0.69
178 Structure conservation index: 0.70
219 Structure conservation index: 0.69
260 Structure conservation index: 0.85
301 Structure conservation index: 0.76
342 Structure conservation index: 0.68
383 Structure conservation index: 0.68
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/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/rnaz/human/x/
H A Drnaz.out14 Structure conservation index: 0.39
55 Structure conservation index: 0.65
96 Structure conservation index: 0.71
137 Structure conservation index: 0.69
178 Structure conservation index: 0.70
219 Structure conservation index: 0.69
260 Structure conservation index: 0.85
301 Structure conservation index: 0.76
342 Structure conservation index: 0.68
383 Structure conservation index: 0.68
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/
H A Daln_utils.i158 std::vector<double> conservation; variable
164 conservation.push_back((double)c[i]);
169 return conservation;
181 std::vector<double> conservation; variable
187 conservation.push_back((double)c[i]);
192 return conservation;
/dports/graphics/R-cran-ggplot2/ggplot2/man/
H A Dlabeller.Rd78 p2 + facet_grid(vore ~ conservation, labeller = labeller(vore = capitalize))
91 p2 + facet_grid(vore ~ conservation, labeller = labeller(
93 conservation = conservation_status
98 idx <- match(msleep$conservation, names(conservation_status))
113 conservation = conservation_status,
118 p2 + facet_grid(vore ~ conservation, labeller = global_labeller)
H A Dmsleep.Rd14 \item{conservation}{the conservation status of the animal}
34 Additional variables order, conservation status and vore were added from
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/alnreader_test_cases/
H A Drw-865e.errors4 …conservation line. Each Clustal data block must end with a line that can contain a mix of *.: char…
/dports/math/reduce/Reduce-svn5758-src/packages/crack/
H A Dconlaw.tex18 try to find conservation laws
42 completed, if possible, to conservation laws by computing $P^i$ from
106 conservation laws exist,\\
113 \> \> zero for the conservation
118 The procedures {\tt CONLAWi} return a list of conservation laws
121 Each $C_i$ representing a conservation law
124 An ansatz for a conservation law can be formulated by specifying one
181 non-trivial conservation laws.
184 is that when seeking all conservation laws up to some order
321 determination of parameters, such that conservation laws exist:
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H A Dconlaw.tst32 The following example calculates all conservation laws of the KdV-
43 PDE-system. In this example all conservation laws of the wave
50 so the t-derivatives will be substituted in the conservation-law-
72 For the Burgers equation the following example finds all conservation
85 In this example all conservation laws of the Ito system are calculated
87 This is a further example of non-polynomial conservation laws;
98 investigated concerning conservation laws of order 0 and 1 in the
100 such that conservation laws exist. This complicates the problem by
H A Dconlaw.rlg6 This is CONLAW4 - a program for calculating conservation laws of DEs
16 Currently conservation laws with characteristic
77 Currently conservation laws with characteristic
81 There is no conservation law of this order.
84 Currently conservation laws with characteristic
117 This is CONLAW2 - a program for calculating conservation laws of DEs
171 Currently conservation laws with a conserved density
228 Currently conservation laws with a conserved density
293 Currently conservation laws with a conserved density
410 Currently conservation laws with a conserved density
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/dports/math/reduce/Reduce-svn5758-src/xmpl/
H A Dconlaw.tst32 The following example calculates all conservation laws of the KdV-
43 PDE-system. In this example all conservation laws of the wave
50 so the t-derivatives will be substituted in the conservation-law-
72 For the Burgers equation the following example finds all conservation
85 In this example all conservation laws of the Ito system are calculated
87 This is a further example of non-polynomial conservation laws;
98 investigated concerning conservation laws of order 0 and 1 in the
100 such that conservation laws exist. This complicates the problem by
H A Dconlaw.rlg6 This is CONLAW4 - a program for calculating conservation laws of DEs
16 Currently conservation laws with characteristic
77 Currently conservation laws with characteristic
81 There is no conservation law of this order.
84 Currently conservation laws with characteristic
117 This is CONLAW2 - a program for calculating conservation laws of DEs
171 Currently conservation laws with a conserved density
228 Currently conservation laws with a conserved density
293 Currently conservation laws with a conserved density
410 Currently conservation laws with a conserved density
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/dports/biology/jalview/jalview/src/jalview/analysis/
H A DConservation.java736 public void completeAnnotations(AlignmentAnnotation conservation, in completeAnnotations() argument
756 if (conservation != null && conservation.annotations != null in completeAnnotations()
757 && conservation.annotations.length != alWidth) in completeAnnotations()
759 conservation.annotations = new Annotation[alWidth]; in completeAnnotations()
793 if (conservation != null) in completeAnnotations()
800 conservation.annotations[i] = new Annotation(String.valueOf(c), in completeAnnotations()
/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/
H A Dmsa_utils.c425 float *conservation = NULL; in vrna_aln_conservation_struct() local
452 conservation = (float *)vrna_alloc(sizeof(float) * (n + 1)); in vrna_aln_conservation_struct()
461 conservation[i] += 1.; in vrna_aln_conservation_struct()
462 conservation[j] += 1.; in vrna_aln_conservation_struct()
465 conservation[i] /= (float)n_seq; in vrna_aln_conservation_struct()
466 conservation[j] /= (float)n_seq; in vrna_aln_conservation_struct()
476 return conservation; in vrna_aln_conservation_struct()
486 float *conservation = NULL; in vrna_aln_conservation_col() local
510 conservation = (float *)vrna_alloc(sizeof(float) * (n + 1)); in vrna_aln_conservation_col()
535 conservation[i] = (float)(-sum); in vrna_aln_conservation_col()
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/dports/math/reduce/Reduce-svn5758-src/packages/cde/examples/
H A Dkdv_nlcl1.red1 % KdV equation: non-local conservation laws on the cotangent covering
59 % We would like to find three conservation laws
65 % one could prove that one component of such conservation laws
78 % for the first conservation law solutions are found by hand
/dports/math/reduce/Reduce-svn5758-src/packages/cde/examples_book/
H A Dkdv_nlcl1.red1 % KdV equation: non-local conservation laws on the cotangent covering
59 % We would like to find three conservation laws
65 % one could prove that one component of such conservation laws
78 % for the first conservation law solutions are found by hand
/dports/biology/emboss/EMBOSS-6.6.0/emboss/acd/
H A Dplotcon.acd2 documentation: "Plot conservation of a sequence alignment"
6 (conservation)"
/dports/biology/viennarna/ViennaRNA-2.4.18/src/Utils/
H A Dcoloraln.pl386 my @conservation=(); # each column one score
394 push @conservation, 0;
405 push @conservation,$score;
458 my $score=shift @conservation;
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/tests/
H A Dtest_tabular_msa.py3069 cons = msa.conservation()
3184 self.assertRaises(ValueError, msa.conservation,
3190 self.assertRaises(ValueError, msa.conservation,
3197 self.assertRaises(ValueError, msa.conservation,
3221 self.assertRaises(ValueError, msa.conservation,
3322 msa.conservation(metric='xyz')
3326 msa.conservation(metric='xyz')
3332 msa.conservation(gap_mode='xyz')
3336 msa.conservation(gap_mode='xyz')
3342 msa.conservation(degenerate_mode='xyz')
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