[med-svn] [Git][med-team/libncl][master] 7 commits: Update symbols
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 4 18:17:07 GMT 2018
Andreas Tille pushed to branch master at Debian Med / libncl
Commits:
cdfeafce by Andreas Tille at 2018-12-04T18:10:12Z
Update symbols
- - - - -
e20e24f0 by Andreas Tille at 2018-12-04T18:10:33Z
New upstream version 2.1.21+git20180827.c71b264
- - - - -
ef6f74bb by Andreas Tille at 2018-12-04T18:10:35Z
Update upstream source from tag 'upstream/2.1.21+git20180827.c71b264'
Update to upstream version '2.1.21+git20180827.c71b264'
with Debian dir 886e52263bd022c5a500121b36fcbf7cadd2fde4
- - - - -
e81c29a9 by Andreas Tille at 2018-12-04T18:10:35Z
New upstream version
- - - - -
e1875041 by Andreas Tille at 2018-12-04T18:10:38Z
Standards-Version: 4.2.1
- - - - -
ab0fd753 by Andreas Tille at 2018-12-04T18:10:38Z
Secure URI in copyright format
- - - - -
9d9e693e by Andreas Tille at 2018-12-04T18:15:56Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/libncl2.symbols.amd64
- example/normalizer/normalizer.cpp
- example/normalizer/normalizer.h
- example/normalizer/us2ml.cpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+libncl (2.1.21+git20180827.c71b264-1) unstable; urgency=medium
+
+ * Update symbols
+ Closes: #913608
+ * New upstream version
+ * Standards-Version: 4.2.1
+ * Secure URI in copyright format
+
+ -- Andreas Tille <tille at debian.org> Tue, 04 Dec 2018 19:10:38 +0100
+
libncl (2.1.21+git20171002.4becff7-2) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
d-shlibs,
python
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/libncl
Vcs-Git: https://salsa.debian.org/med-team/libncl.git
Homepage: https://github.com/mtholder/ncl
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: NCL
Upstream-Contact: Mark T. Holder <mholder at users.sourceforge.net>
Source: https://github.com/mtholder/ncl
=====================================
debian/libncl2.symbols.amd64
=====================================
@@ -1122,14 +1122,16 @@ libncl.so.2 libncl2 #MINVER#
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EEaSERKSB_ at Base 2.1.18
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE11equal_rangeERS7_ at Base 2.1.21+git20171002.4becff7
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 2.1.18
+ (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 2.1.18
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE17_M_emplace_uniqueIJS6_IS5_S8_EEEES6_ISt17_Rb_tree_iteratorIS9_EbEDpOT_ at Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE4findERS7_ at Base 2.1.21+git20171002.4becff7
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE5eraseERS7_ at Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE7_M_copyINSF_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS9_EPKSJ_PSt18_Rb_tree_node_baseRT_ at Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E at Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EEaSERKSF_ at Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE11equal_rangeERS7_ at Base 2.1.21+git20171002.4becff7
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 2.1.18
+ (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 2.1.18
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE17_M_emplace_uniqueIJS6_IS5_S8_EEEES6_ISt17_Rb_tree_iteratorIS9_EbEDpOT_ at Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE4findERS7_ at Base 2.1.21+git20171002.4becff7
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE5eraseERS7_ at Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE7_M_copyINSF_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS9_EPKSJ_PSt18_Rb_tree_node_baseRT_ at Base 2.1.18
=====================================
example/normalizer/normalizer.cpp
=====================================
@@ -67,6 +67,7 @@ std::ostream * gCommonOstream = 0L;
RELAXED_PHYLIP_EXPORT_FORMAT,
FASTA_EXPORT_FORMAT,
NEXML_EXPORT_FORMAT,
+ TREE_NEXML_EXPORT_FORMAT,
UNSUPPORTED_EXPORT_FORMAT
};
ExportFormatEnum gExportFormat = NEXML_EXPORT_FORMAT;
@@ -81,9 +82,10 @@ std::ostream * gCommonOstream = 0L;
"phylip",
"relaxedphylip",
"fasta",
- "nexml"
+ "nexml",
+ "treenexml"
};
- const unsigned gNumExportFormats = 5;
+ const unsigned gNumExportFormats = 6;
NxsString l(s.c_str());
NxsString::to_lower(l);
@@ -274,8 +276,12 @@ void processContent(PublicNexusReader & nexusReader, ostream *os, ProcessActions
MultiFormatReader::DataFormatType f = MultiFormatReader::NEXUS_FORMAT;
if (gExportFormat == NEXUS_EXPORT_FORMAT)
exportData(nexusReader, MultiFormatReader::NEXUS_FORMAT, gInterleaveLen, gExportPrefix, gCommonOstream, gTranslatingConventions);
- else if (gExportFormat == NEXML_EXPORT_FORMAT)
+ else if (gExportFormat == NEXML_EXPORT_FORMAT || gExportFormat == TREE_NEXML_EXPORT_FORMAT ) {
+ if (gExportFormat == TREE_NEXML_EXPORT_FORMAT) {
+ gTranslatingConventions.emitTreesAndTaxaOnly = true;
+ }
exportData(nexusReader, MultiFormatReader::NEXML_FORMAT, gInterleaveLen, gExportPrefix, gCommonOstream, gTranslatingConventions);
+ }
else if (gExportFormat == PHYLIP_EXPORT_FORMAT) {
fullExportPrefix = gExportPrefix;
fullExportPrefix.append(".dna");
@@ -550,6 +556,7 @@ void printHelp(ostream & out)
out << " -ephylip Trees and character data in phylip (could result in multiple output files)\n";
out << " -erelaxedphylip Trees and character data in relaxed phylip (could result in multiple output files)\n";
out << " -enexml nexml output (this is also the default)\n";
+ out << " -etreenexml nexml output of trees and taxa only\n";
#endif
out << " -f<format> specifies the input file format expected:\n";
out << " -fnexus NEXUS (this is also the default)\n";
=====================================
example/normalizer/normalizer.h
=====================================
@@ -22,7 +22,8 @@ class TranslatingConventions {
currentTreeIndex(0),
currentNodeIndex(0),
currentEdgeIndex(0),
- treatNodeLabelsAsStrings(false) {
+ treatNodeLabelsAsStrings(false),
+ emitTreesAndTaxaOnly(false) {
}
std::string idPrefix;
bool globalIncrementingIDs;
@@ -38,6 +39,7 @@ class TranslatingConventions {
unsigned currentNodeIndex;
unsigned currentEdgeIndex;
bool treatNodeLabelsAsStrings;
+ bool emitTreesAndTaxaOnly;
};
#endif
\ No newline at end of file
=====================================
example/normalizer/us2ml.cpp
=====================================
@@ -505,32 +505,37 @@ void writeAsNexml(PublicNexusReader & nexusReader, ostream & os, TranslatingConv
const NxsTaxaBlock * tb = nexusReader.GetTaxaBlock(t);
std::vector<const NxsAssumptionsBlock *> assumps;
- for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(tb); ++j)
- assumps.push_back(nexusReader.GetAssumptionsBlock(tb, j));
-
+ if (!transConv.emitTreesAndTaxaOnly)
+ {
+ for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(tb); ++j)
+ assumps.push_back(nexusReader.GetAssumptionsBlock(tb, j));
+ }
writeOTUS(os, tb, assumps, memo, t);
-
- const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(tb);
- for (unsigned i = 0; i < nCharBlocks; ++i)
+ if (!transConv.emitTreesAndTaxaOnly)
{
- NxsCharactersBlock * cb = nexusReader.GetCharactersBlock(tb, i);
+ const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(tb);
+ for (unsigned i = 0; i < nCharBlocks; ++i)
+ {
+ NxsCharactersBlock * cb = nexusReader.GetCharactersBlock(tb, i);
- assumps.clear();
- for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(cb); ++j)
- assumps.push_back(nexusReader.GetAssumptionsBlock(cb, j));
+ assumps.clear();
+ for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(cb); ++j)
+ assumps.push_back(nexusReader.GetAssumptionsBlock(cb, j));
- writeCharacters(os, cb, assumps, memo, nCharBlocksRead++);
+ writeCharacters(os, cb, assumps, memo, nCharBlocksRead++);
+ }
}
-
const unsigned nTreesBlocks = nexusReader.GetNumTreesBlocks(tb);
for (unsigned i = 0; i < nTreesBlocks; ++i)
{
NxsTreesBlock * cb = nexusReader.GetTreesBlock(tb, i);
assumps.clear();
- for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(cb); ++j)
- assumps.push_back(nexusReader.GetAssumptionsBlock(cb, j));
-
+ if (!transConv.emitTreesAndTaxaOnly)
+ {
+ for (unsigned j= 0; j < nexusReader.GetNumAssumptionsBlocks(cb); ++j)
+ assumps.push_back(nexusReader.GetAssumptionsBlock(cb, j));
+ }
writeTrees(os, cb, assumps, memo, nTreeBlocksRead++, transConv.treatNodeLabelsAsStrings);
}
}
View it on GitLab: https://salsa.debian.org/med-team/libncl/compare/dceaf113f9c709df475556b9520ca097cd23aa9a...9d9e693ef32e604a43ac86cc81449580d716c6ac
--
View it on GitLab: https://salsa.debian.org/med-team/libncl/compare/dceaf113f9c709df475556b9520ca097cd23aa9a...9d9e693ef32e604a43ac86cc81449580d716c6ac
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