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debian/changelog
View file @ 9d9e693e
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@debian.org> Tue, 04 Dec 2018 19:10:38 +0100
libncl (2.1.21+git20171002.4becff7-2) unstable; urgency=medium
* Team upload
......
debian/control
View file @ 9d9e693e
......@@ -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
View file @ 9d9e693e
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@users.sourceforge.net>
Source: https://github.com/mtholder/ncl
......
debian/libncl2.symbols.amd64
View file @ 9d9e693e
......@@ -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@Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EEaSERKSB_@Base 2.1.18
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE11equal_rangeERS7_@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_@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_@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_@Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE4findERS7_@Base 2.1.21+git20171002.4becff7
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE5eraseERS7_@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_@Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E@Base 2.1.18
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_16NxsIntStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EEaSERKSF_@Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE11equal_rangeERS7_@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_@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_@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_@Base 2.1.21+git20171002.4becff7
(optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE4findERS7_@Base 2.1.21+git20171002.4becff7
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_17NxsRealStepMatrixESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE5eraseERS7_@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_@Base 2.1.18
......
example/normalizer/normalizer.cpp
View file @ 9d9e693e
......@@ -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
View file @ 9d9e693e
......@@ -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
View file @ 9d9e693e
......@@ -505,11 +505,14 @@ void writeAsNexml(PublicNexusReader & nexusReader, ostream & os, TranslatingConv
const NxsTaxaBlock * tb = nexusReader.GetTaxaBlock(t);
std::vector<const NxsAssumptionsBlock *> assumps;
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);
if (!transConv.emitTreesAndTaxaOnly)
{
const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(tb);
for (unsigned i = 0; i < nCharBlocks; ++i)
{
......@@ -521,16 +524,18 @@ void writeAsNexml(PublicNexusReader & nexusReader, ostream & os, TranslatingConv
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();
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);
}
}
......