[Phylobase-commits] r768 - in libncl: 2.1.11/example 2.1.11/example/phylobaseinterface 2.1.11/example/splitsinfile 2.1.11/html 2.1.11/html/v2.1 2.1.11/html/v2.1/funcdocs 2.1.11/html/v2.1/funcdocs/search 2.1.11/html/v2.1/funcdocs/simpleNCLClient current/example current/example/phylobaseinterface current/example/splitsinfile current/html current/html/v2.1 current/html/v2.1/funcdocs current/html/v2.1/funcdocs/search current/html/v2.1/funcdocs/simpleNCLClient

[noreply at r-forge.r-project.org]

Author: francois
Date: 2010-03-29 22:49:59 +0200 (Mon, 29 Mar 2010)
New Revision: 768

Added:
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Log:
adding some missing files

Added: libncl/2.1.11/example/phylobaseinterface/Makefile.am
===================================================================
--- libncl/2.1.11/example/phylobaseinterface/Makefile.am	                        (rev 0)
+++ libncl/2.1.11/example/phylobaseinterface/Makefile.am	2010-03-29 20:49:59 UTC (rev 768)
@@ -0,0 +1,6 @@
+LDADD       = @top_builddir@/ncl/libncl.la
+AM_CPPFLAGS = -I at top_srcdir@/ncl
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+
+
+PhylobaseNCLInterfaceExample_SOURCES = NCLInterface.cpp NCLInterface.h

Added: libncl/2.1.11/example/phylobaseinterface/Makefile.in
===================================================================
--- libncl/2.1.11/example/phylobaseinterface/Makefile.in	                        (rev 0)
+++ libncl/2.1.11/example/phylobaseinterface/Makefile.in	2010-03-29 20:49:59 UTC (rev 768)
@@ -0,0 +1,487 @@
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+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+	clean-generic clean-libtool ctags distclean distclean-compile \
+	distclean-generic distclean-libtool distclean-tags distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-binPROGRAMS install-data install-data-am install-dvi \
+	install-dvi-am install-exec install-exec-am install-html \
+	install-html-am install-info install-info-am install-man \
+	install-pdf install-pdf-am install-ps install-ps-am \
+	install-strip installcheck installcheck-am installdirs \
+	maintainer-clean maintainer-clean-generic mostlyclean \
+	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
+	pdf pdf-am ps ps-am tags uninstall uninstall-am \
+	uninstall-binPROGRAMS
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

Added: libncl/2.1.11/example/phylobaseinterface/NCLInterface.cpp
===================================================================
--- libncl/2.1.11/example/phylobaseinterface/NCLInterface.cpp	                        (rev 0)
+++ libncl/2.1.11/example/phylobaseinterface/NCLInterface.cpp	2010-03-29 20:49:59 UTC (rev 768)
@@ -0,0 +1,2220 @@
+//  Copyright (C) 2007-2008 Brian O'Meara & Derrick Zwickl
+//  A modification of the BasicCommandLine file of the NCL (see below)
+//  to use for loading trees and data from Nexus into R. Licensing as below.
+
+//	Copyright (C) 1999-2002 Paul O. Lewis
+//
+//	This file is part of NCL (Nexus Class Library).
+//
+//	NCL is free software; you can redistribute it and/or modify
+//	it under the terms of the GNU General Public License as published by
+//	the Free Software Foundation; either version 2 of the License, or
+//	(at your option) any later version.
+//
+//	NCL is distributed in the hope that it will be useful,
+//	but WITHOUT ANY WARRANTY; without even the implied warranty of
+//	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+//	GNU General Public License for more details.
+//
+//	You should have received a copy of the GNU General Public License
+//	along with NCL; if not, write to the Free Software Foundation, Inc.,
+//	59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+//
+
+#include <ncl/ncl.h>
+#include "NCLInterface.h"
+
+#include <iostream>
+#include <sstream>
+#include <cassert>
+
+
+
+std::string BASICCMDLINE::TestRunning() {
+	string output="The NCL has been loaded";
+	return output;
+}
+
+#if defined(NEW_NCL_INTERFACE)
+
+MultiFormatReader * instantiateReader(int gStrictLevel);
+
+
+
+void BASICCMDLINE::AppendRContent(
+  NxsString & nexuscharacters,
+  NxsCharactersBlock &characters,
+  bool allchar,
+  bool polymorphictomissing,
+  bool levelsall) const
+{
+
+	int nchartoreturn = 0;
+	NxsTaxaBlockAPI * taxa = characters.GetTaxaBlockPtr();
+	if (!taxa)
+		return;
+	int ntax = taxa->GetNumTaxonLabels();
+
+	if (!characters.IsEmpty())
+		{
+		//characters.Report(cerr);
+		if (1==characters.GetDataType()) { //standard datatype
+		//if((characters.GetDatatypeName())=="standard") {
+			//nexuscharacters=characters.GetDatatypeName();
+			nexuscharacters+="data.frame(";
+
+			if (allchar) {
+				nchartoreturn=characters.GetNCharTotal();
+			}
+			else {
+				nchartoreturn=characters.GetNChar();
+			}
+			for (int character=0; character<nchartoreturn; character++) { //We only pass the non-eliminated chars
+				NxsString charlabel=characters.GetCharLabel(character);
+				if (character>0) {
+					nexuscharacters+=", ";
+				}
+				if (charlabel.length()>1) {
+					nexuscharacters+="'";
+					nexuscharacters+=charlabel;
+					nexuscharacters+="'";
+				}
+				else {
+					nexuscharacters+="standard_char_";
+					nexuscharacters+=character+1;
+				}
+				nexuscharacters+=" = ";
+
+				nexuscharacters+="factor(c(";
+				for (int taxon=0;taxon<ntax;taxon++) {
+					int statenumber=characters.GetInternalRepresentation(taxon,character,0);
+
+					if(characters.IsMissingState(taxon,character)) {
+						nexuscharacters+="NA";
+					}
+					else if (characters.GetNumStates(taxon,character)>1) {
+						if(polymorphictomissing) {
+							nexuscharacters+="NA";
+						}
+						else {
+							nexuscharacters+='{';
+							for (unsigned int k=0;k<characters.GetNumStates(taxon,character);k++) {
+								nexuscharacters+=characters.GetInternalRepresentation(taxon,character,0);
+								if (k+1<characters.GetNumStates(taxon,character)) {
+									nexuscharacters+=',';
+								}
+							}
+							nexuscharacters+='}';
+						}
+					}
+					else {
+						nexuscharacters+=statenumber;
+					}
+					if (taxon+1<ntax) {
+						nexuscharacters+=',';
+					}
+				}
+				nexuscharacters+=')';
+				if (levelsall) {
+					nexuscharacters+=", levels=c(";
+					for (unsigned int l=0;l<characters.GetMaxObsNumStates(); l++) {
+						nexuscharacters+=l;
+						if (l+1<characters.GetMaxObsNumStates()) {
+							nexuscharacters+=',';
+						}
+					}
+					nexuscharacters+=')';
+				}
+				else {
+
+					NxsString levels=", levels=c(";
+					NxsString labels=", labels=c(";
+					unsigned int totallabellength=0;
+					for (unsigned int l=0;l<characters.GetObsNumStates(character); l++) {
+						labels+='"';
+						labels+= characters.GetStateLabel(character,l);
+						totallabellength+=(characters.GetStateLabel(character,l)).length();
+						labels+='"';
+						levels+= l;
+						if (l+1<characters.GetObsNumStates(character)) {
+							labels+=',';
+							levels+=',';
+						}
+					}
+					levels+=')';
+					labels+=')';
+					//cout<<"labels.length="<<labels.length()<<endl<<"levels.length="<<levels.length()<<endl<<"total label length="<<totallabellength<<endl;
+					if (totallabellength>characters.GetObsNumStates(character)) {
+						nexuscharacters+=levels;
+						nexuscharacters+=labels;
+					}
+				}
+				nexuscharacters+=")\n";
+			}
+			nexuscharacters+=", row.names=c(";
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				nexuscharacters+=RemoveUnderscoresAndSpaces(characters.GetTaxonLabel(taxon));
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+			nexuscharacters+="))";
+		}
+		else if (2==characters.GetDataType() || 3==characters.GetDataType() || 4==characters.GetDataType()) { //dna, rna, nucleotide
+	//	if((characters.GetDatatypeName())=="dna") {
+
+			nexuscharacters+="data.frame(";
+			if (2==characters.GetDataType()) {
+				nexuscharacters+="dna_alignment_1=c(";
+			}
+			else if (3==characters.GetDataType()) {
+				nexuscharacters+="rna_alignment_1=c(";
+			}
+			else {
+				nexuscharacters+="nucleotide_alignment_1=c(";
+			}
+
+			if (allchar) {
+				nchartoreturn=characters.GetNCharTotal();
+			}
+			else {
+				nchartoreturn=characters.GetNChar();
+			}
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				for (int character=0; character<nchartoreturn; character++) {
+					int numstates=characters.GetNumStates(taxon,character);
+					if (characters.IsGapState(taxon,character)) {
+						nexuscharacters+="-";
+					}
+					else if (characters.IsMissingState(taxon,character)) {
+						nexuscharacters+="?";
+					}
+					else if ( numstates == 1) {
+						nexuscharacters+=characters.GetState(taxon,character,0);
+					}
+					else {
+						bool hasA=false;
+						bool hasT=false;
+						bool hasG=false;
+						bool hasC=false;
+						for (int i=0;i<numstates;i++) {
+							unsigned currentstate=characters.GetState(taxon,character,i);
+							if (currentstate=='A') {
+								hasA=true;
+							}
+							else if (currentstate=='T') {
+								hasT=true;
+							}
+							else if (currentstate=='G') {
+								hasG=true;
+							}
+							else if (currentstate=='C') {
+								hasC=true;
+							}
+							else {
+								cout<<"Error: currentstate "<<currentstate<<" does not match ATGC"<<endl;
+							}
+						}
+						if (hasA && hasG && !hasT && !hasC) {
+							nexuscharacters+="R";
+						}
+						else if (!hasA && !hasG && hasC && hasT) {
+							nexuscharacters+="Y";
+						}
+						else if (hasA && !hasG && hasC && !hasT) {
+							nexuscharacters+="M";
+						}
+						else if (!hasA && hasG && !hasC && hasT) {
+							nexuscharacters+="K";
+						}
+						else if (!hasA && hasG && hasC && !hasT) {
+							nexuscharacters+="S";
+						}
+						else if (hasA && !hasG && !hasC && hasT) {
+							nexuscharacters+="W";
+						}
+						else if (hasA && !hasG && hasC && hasT) {
+							nexuscharacters+="H";
+						}
+						else if (!hasA && hasG && hasC && hasT) {
+							nexuscharacters+="B";
+						}
+						else if (hasA && hasG && hasC && !hasT) {
+							nexuscharacters+="V";
+						}
+						else if (hasA && hasG && !hasC && hasT) {
+							nexuscharacters+="D";
+						}
+						else if (hasA && hasG && hasC && hasT) {
+							nexuscharacters+="N";
+						}
+						else {
+							nexuscharacters+="N";
+						}
+					}
+				}
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+
+			nexuscharacters+="), row.names=c(";
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				nexuscharacters+=RemoveUnderscoresAndSpaces(characters.GetTaxonLabel(taxon));
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+			nexuscharacters+="), stringsAsFactors=FALSE)";
+
+		}
+		else if (5==characters.GetDataType()) { //protein
+			nexuscharacters+="data.frame(";
+			nexuscharacters+="aa_alignment_1=c(";
+
+
+			if (allchar) {
+				nchartoreturn=characters.GetNCharTotal();
+			}
+			else {
+				nchartoreturn=characters.GetNChar();
+			}
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				for (int character=0; character<nchartoreturn; character++) {
+					int numstates=characters.GetNumStates(taxon,character);
+					if (characters.IsGapState(taxon,character)) {
+						nexuscharacters+="-";
+					}
+					else if (characters.IsMissingState(taxon,character)) {
+						nexuscharacters+="?";
+					}
+					else if ( numstates == 1) {
+						nexuscharacters+=characters.GetState(taxon,character,0);
+					}
+					else {
+						nexuscharacters+="X";
+					}
+				}
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+
+			nexuscharacters+="), row.names=c(";
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				nexuscharacters+=RemoveUnderscoresAndSpaces(characters.GetTaxonLabel(taxon));
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+			nexuscharacters+="), stringsAsFactors=FALSE)";
+		}
+		else if (6==characters.GetDataType()) { //continuousnexuscharacters+="data.frame(";
+			nexuscharacters+="data.frame(";
+
+			if (allchar) {
+				nchartoreturn=characters.GetNCharTotal();
+			}
+			else {
+				nchartoreturn=characters.GetNChar();
+			}
+			for (int character=0; character<nchartoreturn; character++) { //We only pass the non-eliminated chars
+				NxsString charlabel=characters.GetCharLabel(character);
+				if (character>0) {
+					nexuscharacters+=", ";
+				}
+				if (charlabel.length()>1) {
+					nexuscharacters+="'";
+					nexuscharacters+=charlabel;
+					nexuscharacters+="'";
+				}
+				else {
+					nexuscharacters+="continuous_char_";
+					nexuscharacters+=character+1;
+				}
+				nexuscharacters+=" = ";
+
+				nexuscharacters+="c(";
+				for (int taxon=0;taxon<ntax;taxon++) {
+					double state=characters.GetSimpleContinuousValue(taxon,character);
+					//cout<<"State at "<<taxon+1<<" char "<<character+1<<" = "<<state<<endl;
+					if (state==DBL_MAX) {
+							nexuscharacters+="NA";
+					}
+					else {
+						nexuscharacters+=state;
+					}
+
+					if (taxon+1<ntax) {
+						nexuscharacters+=',';
+					}
+				}
+				nexuscharacters+=")";
+			}
+			nexuscharacters+=", row.names=c(";
+			for (int taxon=0;taxon<ntax;taxon++) {
+				nexuscharacters+='"';
+				nexuscharacters+=RemoveUnderscoresAndSpaces(characters.GetTaxonLabel(taxon));
+				nexuscharacters+='"';
+				if (taxon+1<ntax) {
+					nexuscharacters+=',';
+				}
+			}
+			nexuscharacters+="))";
+			//message="Warning: Continuous characters do not work";
+			//PrintMessage();
+		}
+		else {
+			std::string message="Error: character matrix loaded, but does not match any category (dna, standard, etc.)";
+			errorMessage(message);
+		}
+		nexuscharacters=RemoveUnderscoresAndSpaces(nexuscharacters);
+	}
+
+}
+
+void BASICCMDLINE::AppendRContent(
+  NxsString & nexustrees,
+  NxsTreesBlock &treesB) const
+{
+	NxsTaxaBlockAPI * taxa = treesB.GetTaxaBlockPtr();
+	if (!taxa)
+		return;
+	if (!treesB.IsEmpty())
+	{
+
+		nexustrees+= "\nBEGIN TREES;\n";
+		for (unsigned k = 0; k < treesB.GetNumTrees(); k++)
+		{
+			NxsString s = treesB.GetTreeName(k);
+			s.BlanksToUnderscores();
+			nexustrees+="\tTREE ";
+			nexustrees+=s;
+			nexustrees+=" = ";
+			if (treesB.IsRootedTree(k))
+				nexustrees+="[&R]";
+			else
+				nexustrees+="[&U]";
+			nexustrees+=treesB.GetTranslatedTreeDescription(k);
+			nexustrees+=";\n";
+		}
+		nexustrees+="END;\n";
+	}
+}
+
+void BASICCMDLINE::AppendRContent(
+  NxsString & nexusdistances,
+  NxsDistancesBlock &distancesB) const
+{
+	NxsTaxaBlockAPI * taxa = distancesB.GetTaxaBlockPtr();
+	if (!taxa)
+		return;
+	int ntax = taxa->GetNumTaxonLabels();
+
+	if (!distancesB.IsEmpty())
+	{ //fill cols first, first col has taxon 1, first row has taxon 2 (no diags)
+		nexusdistances+="\ndistances <- structure(c(";
+		vector<double> distancevector;
+		for (int col=0;col<ntax-1;col++) {
+			for (int row=col+1;row<ntax;row++) {
+				distancevector.push_back(distancesB.GetDistance(row,col));
+			}
+		}
+		for (unsigned int i=0;i<distancevector.size();i++) {
+			nexusdistances+=distancevector.at(i);
+			if (i+1<distancevector.size()) {
+				nexusdistances+=',';
+			}
+		}
+		nexusdistances+="), Size = ";
+		nexusdistances+=ntax;
+		nexusdistances+="L, Labels = c(";
+		for (int taxon=0; taxon<ntax;taxon++) {
+			nexusdistances+='"';
+			nexusdistances+=RemoveUnderscoresAndSpaces(taxa->GetTaxonLabel(taxon));
+			nexusdistances+='"';
+			if (taxon+1<ntax) {
+				nexusdistances+=", ";
+			}
+		}
+		nexusdistances+="), Upper = FALSE, Diag = FALSE, class = \"dist\")\n";
+	}
+}
+
+
+void BASICCMDLINE::RReturnCharacters(NxsString & outputstring, bool allchar, bool polymorphictomissing, bool levelsall)
+{
+	if (!nexusReader)
+		return;
+	const unsigned nTaxaBlocks = nexusReader->GetNumTaxaBlocks();
+	for (unsigned t = 0; t < nTaxaBlocks; ++t) {
+		const NxsTaxaBlock * tb = nexusReader->GetTaxaBlock(t);
+		const unsigned nCharBlocks = nexusReader->GetNumCharactersBlocks(tb);
+		if (nCharBlocks == 0)
+			continue;
+		for (unsigned i = 0; i < nCharBlocks; ++i) {
+			NxsCharactersBlock * cb = nexusReader->GetCharactersBlock(tb, i);
+			if (cb) {
+				AppendRContent(outputstring, *cb, allchar, polymorphictomissing, levelsall);
+			}
+		}
+	}
+}
+
+
+void BASICCMDLINE::RReturnTrees(NxsString & outputstring)
+{
+	if (!nexusReader)
+		return;
+	const unsigned nTaxaBlocks = nexusReader->GetNumTaxaBlocks();
+	for (unsigned t = 0; t < nTaxaBlocks; ++t) {
+		const NxsTaxaBlock * tb = nexusReader->GetTaxaBlock(t);
+		const unsigned nTreesBlocks = nexusReader->GetNumTreesBlocks(tb);
+		if (nTreesBlocks == 0)
+			continue;
+		for (unsigned i = 0; i < nTreesBlocks; ++i) {
+			NxsTreesBlock * treesb = nexusReader->GetTreesBlock(tb, i);
+			if (treesb) {
+				AppendRContent(outputstring, *treesb);
+			}
+		}
+	}
+}
+
+void BASICCMDLINE::RReturnDistances(NxsString & outputstring)
+{
+	if (!nexusReader)
+		return;
+	const unsigned nTaxaBlocks = nexusReader->GetNumTaxaBlocks();
+	for (unsigned t = 0; t < nTaxaBlocks; ++t) {
+		const NxsTaxaBlock * tb = nexusReader->GetTaxaBlock(t);
+		const unsigned nDistancesBlocks = nexusReader->GetNumDistancesBlocks(tb);
+		if (nDistancesBlocks == 0)
+			continue;
+		for (unsigned i = 0; i < nDistancesBlocks; ++i) {
+			NxsDistancesBlock * distancesb = nexusReader->GetDistancesBlock(tb, i);
+			if (distancesb) {
+				AppendRContent(outputstring, *distancesb);
+			}
+		}
+	}
+}
+
+
+
+void BASICCMDLINE::writeMessage(MessageLevel level, const std::string & m)  const {
+	if (level >= int(this->verboseLevel)) {
+		std::cerr << m << std::endl;
+	}
+}
+
+
+MultiFormatReader * instantiateReader(int gStrictLevel)
+{
+	MultiFormatReader * nexusReader = new MultiFormatReader(-1, NxsReader::WARNINGS_TO_STDERR);
+
+
+	if (gStrictLevel != 2)
+		nexusReader->SetWarningToErrorThreshold((int)NxsReader::FATAL_WARNING + 1 - (int) gStrictLevel);
+	NxsCharactersBlock * charsB = nexusReader->GetCharactersBlockTemplate();
+	NxsDataBlock * dataB = nexusReader->GetDataBlockTemplate();
+	charsB->SetAllowAugmentingOfSequenceSymbols(true);
+	dataB->SetAllowAugmentingOfSequenceSymbols(true);
+
+	NxsTreesBlock * treesB = nexusReader->GetTreesBlockTemplate();
+	assert(treesB);
+	if (gStrictLevel < 2)
+		treesB->SetAllowImplicitNames(true);
+	if (gStrictLevel < 2)
+		{
+		NxsStoreTokensBlockReader *storerB =  nexusReader->GetUnknownBlockTemplate();
+		assert(storerB);
+		storerB->SetTolerateEOFInBlock(true);
+		}
+	nexusReader->conversionOutputRecord.addNumbersToDisambiguateNames = true;
+	return nexusReader;
+}
+
+
+void BASICCMDLINE::Clear()
+{
+	if (nexusReader) {
+		MultiFormatReader * nr = nexusReader;
+		nexusReader = 0L;
+		try {
+			nr->DeleteBlocksFromFactories();
+		}
+		catch (...) {
+			delete nr;
+			throw;
+		}
+		delete nr;
+	}
+
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+// Creates a NxsReader, and tries to read the file `filename`.  If the
+//	read succeeds, then processContent will be called.
+////////////////////////////////////////////////////////////////////////////////
+void BASICCMDLINE::processFilepath(const char * filename) // enum indicating the file format to expect.
+{
+	if (! (this->nexusReader)) {
+		nexusReader = instantiateReader(this->gStrictLevel);
+	}
+
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 768