Mon Mar 29 22:42:29 CEST 2010

Author: francois
Date: 2010-03-29 22:42:27 +0200 (Mon, 29 Mar 2010)
New Revision: 767

Added:
   libncl/2.1.11/
Modified:
   libncl/2.1.11/AUTHORS
   libncl/2.1.11/ChangeLog
   libncl/2.1.11/INSTALL
   libncl/2.1.11/Makefile.am
   libncl/2.1.11/Makefile.in
   libncl/2.1.11/NEWS
   libncl/2.1.11/README
   libncl/2.1.11/config/ax_cxx_flags.m4
   libncl/2.1.11/config/install-sh
   libncl/2.1.11/config/libtool.m4
   libncl/2.1.11/config/lt~obsolete.m4
   libncl/2.1.11/configure
   libncl/2.1.11/configure.ac
   libncl/2.1.11/data/unaligned.nex
   libncl/2.1.11/example/Makefile.am
   libncl/2.1.11/example/Makefile.in
   libncl/2.1.11/example/basiccmdline/basiccmdline.cpp
   libncl/2.1.11/example/basiccmdline/basiccmdline.h
   libncl/2.1.11/example/gapcode/gapcode.cpp
   libncl/2.1.11/example/nclsimplest/nclsimplest.cpp
   libncl/2.1.11/example/ncltest/ncltest.cpp
   libncl/2.1.11/example/ncltest/ncltest.h
   libncl/2.1.11/example/normalizer/converter.cpp
   libncl/2.1.11/example/normalizer/normalizer.cpp
   libncl/2.1.11/example/normalizer/us2ml.cpp
   libncl/2.1.11/example/patristic/patristic.cpp
   libncl/2.1.11/example/splitsinfile/Makefile.am
   libncl/2.1.11/example/splitsinfile/Makefile.in
   libncl/2.1.11/example/splitsinfile/splitsinfile.cpp
   libncl/2.1.11/example/translate/translateNuc.cpp
   libncl/2.1.11/html/BASICCMDLINE.html
   libncl/2.1.11/html/MyAssumptionsBlock.html
   libncl/2.1.11/html/MyCharactersBlock.html
   libncl/2.1.11/html/MyDataBlock.html
   libncl/2.1.11/html/MyNexusFileReader.html
   libncl/2.1.11/html/MyNexusToken.html
   libncl/2.1.11/html/MyToken.html
   libncl/2.1.11/html/NStrCaseInsensitiveEquals.html
   libncl/2.1.11/html/NStrCaseSensitiveEquals.html
   libncl/2.1.11/html/NxsAssumptionsBlock.html
   libncl/2.1.11/html/NxsBlock.html
   libncl/2.1.11/html/NxsCharactersBlock.html
   libncl/2.1.11/html/NxsDataBlock.html
   libncl/2.1.11/html/NxsDiscreteDatum.html
   libncl/2.1.11/html/NxsDiscreteMatrix.html
   libncl/2.1.11/html/NxsDistanceDatum.html
   libncl/2.1.11/html/NxsDistancesBlock.html
   libncl/2.1.11/html/NxsEmptyBlock.html
   libncl/2.1.11/html/NxsException.html
   libncl/2.1.11/html/NxsReader.html
   libncl/2.1.11/html/NxsSetReader.html
   libncl/2.1.11/html/NxsString.html
   libncl/2.1.11/html/NxsStringEqual.html
   libncl/2.1.11/html/NxsTaxaBlock.html
   libncl/2.1.11/html/NxsToken.html
   libncl/2.1.11/html/NxsTreesBlock.html
   libncl/2.1.11/html/classes.html
   libncl/2.1.11/html/contents.html
   libncl/2.1.11/html/functions.html
   libncl/2.1.11/html/index.html
   libncl/2.1.11/ncl/Makefile.am
   libncl/2.1.11/ncl/Makefile.in
   libncl/2.1.11/ncl/ncl.h
   libncl/2.1.11/ncl/nxsallocatematrix.h
   libncl/2.1.11/ncl/nxsassumptionsblock.cpp
   libncl/2.1.11/ncl/nxsassumptionsblock.h
   libncl/2.1.11/ncl/nxsblock.cpp
   libncl/2.1.11/ncl/nxsblock.h
   libncl/2.1.11/ncl/nxscdiscretematrix.h
   libncl/2.1.11/ncl/nxscharactersblock.cpp
   libncl/2.1.11/ncl/nxscharactersblock.h
   libncl/2.1.11/ncl/nxscxxdiscretematrix.cpp
   libncl/2.1.11/ncl/nxscxxdiscretematrix.h
   libncl/2.1.11/ncl/nxsdatablock.cpp
   libncl/2.1.11/ncl/nxsdatablock.h
   libncl/2.1.11/ncl/nxsdefs.h
   libncl/2.1.11/ncl/nxsdiscretedatum.h
   libncl/2.1.11/ncl/nxsdistancedatum.h
   libncl/2.1.11/ncl/nxsdistancesblock.cpp
   libncl/2.1.11/ncl/nxsdistancesblock.h
   libncl/2.1.11/ncl/nxsexception.cpp
   libncl/2.1.11/ncl/nxsexception.h
   libncl/2.1.11/ncl/nxsmultiformat.cpp
   libncl/2.1.11/ncl/nxsmultiformat.h
   libncl/2.1.11/ncl/nxspublicblocks.cpp
   libncl/2.1.11/ncl/nxspublicblocks.h
   libncl/2.1.11/ncl/nxsreader.cpp
   libncl/2.1.11/ncl/nxsreader.h
   libncl/2.1.11/ncl/nxssetreader.cpp
   libncl/2.1.11/ncl/nxssetreader.h
   libncl/2.1.11/ncl/nxsstring.cpp
   libncl/2.1.11/ncl/nxsstring.h
   libncl/2.1.11/ncl/nxstaxablock.cpp
   libncl/2.1.11/ncl/nxstaxablock.h
   libncl/2.1.11/ncl/nxstoken.cpp
   libncl/2.1.11/ncl/nxstoken.h
   libncl/2.1.11/ncl/nxstreesblock.cpp
   libncl/2.1.11/ncl/nxstreesblock.h
   libncl/2.1.11/ncl/nxsunalignedblock.cpp
   libncl/2.1.11/ncl/nxsunalignedblock.h
   libncl/2.1.11/ncl/nxsutilcopy.h
   libncl/2.1.11/swig/ncl.i
   libncl/2.1.11/test/Makefile
   libncl/2.1.11/test/Makefile.am
   libncl/2.1.11/test/Makefile.in
   libncl/2.1.11/test/NTSValidIn/avian_ovomucoids.nex
   libncl/2.1.11/test/roundTripNCLTest.py
   libncl/current/AUTHORS
   libncl/current/ChangeLog
   libncl/current/INSTALL
   libncl/current/Makefile.am
   libncl/current/Makefile.in
   libncl/current/NEWS
   libncl/current/README
   libncl/current/config/ax_cxx_flags.m4
   libncl/current/config/install-sh
   libncl/current/config/libtool.m4
   libncl/current/config/lt~obsolete.m4
   libncl/current/configure
   libncl/current/configure.ac
   libncl/current/data/unaligned.nex
   libncl/current/example/Makefile.am
   libncl/current/example/Makefile.in
   libncl/current/example/basiccmdline/basiccmdline.cpp
   libncl/current/example/basiccmdline/basiccmdline.h
   libncl/current/example/gapcode/gapcode.cpp
   libncl/current/example/nclsimplest/nclsimplest.cpp
   libncl/current/example/ncltest/ncltest.cpp
   libncl/current/example/ncltest/ncltest.h
   libncl/current/example/normalizer/converter.cpp
   libncl/current/example/normalizer/normalizer.cpp
   libncl/current/example/normalizer/us2ml.cpp
   libncl/current/example/patristic/patristic.cpp
   libncl/current/example/splitsinfile/Makefile.am
   libncl/current/example/splitsinfile/Makefile.in
   libncl/current/example/splitsinfile/splitsinfile.cpp
   libncl/current/example/translate/translateNuc.cpp
   libncl/current/html/BASICCMDLINE.html
   libncl/current/html/MyAssumptionsBlock.html
   libncl/current/html/MyCharactersBlock.html
   libncl/current/html/MyDataBlock.html
   libncl/current/html/MyNexusFileReader.html
   libncl/current/html/MyNexusToken.html
   libncl/current/html/MyToken.html
   libncl/current/html/NStrCaseInsensitiveEquals.html
   libncl/current/html/NStrCaseSensitiveEquals.html
   libncl/current/html/NxsAssumptionsBlock.html
   libncl/current/html/NxsBlock.html
   libncl/current/html/NxsCharactersBlock.html
   libncl/current/html/NxsDataBlock.html
   libncl/current/html/NxsDiscreteDatum.html
   libncl/current/html/NxsDiscreteMatrix.html
   libncl/current/html/NxsDistanceDatum.html
   libncl/current/html/NxsDistancesBlock.html
   libncl/current/html/NxsEmptyBlock.html
   libncl/current/html/NxsException.html
   libncl/current/html/NxsReader.html
   libncl/current/html/NxsSetReader.html
   libncl/current/html/NxsString.html
   libncl/current/html/NxsStringEqual.html
   libncl/current/html/NxsTaxaBlock.html
   libncl/current/html/NxsToken.html
   libncl/current/html/NxsTreesBlock.html
   libncl/current/html/classes.html
   libncl/current/html/contents.html
   libncl/current/html/functions.html
   libncl/current/html/index.html
   libncl/current/ncl/Makefile.am
   libncl/current/ncl/Makefile.in
   libncl/current/ncl/ncl.h
   libncl/current/ncl/nxsallocatematrix.h
   libncl/current/ncl/nxsassumptionsblock.cpp
   libncl/current/ncl/nxsassumptionsblock.h
   libncl/current/ncl/nxsblock.cpp
   libncl/current/ncl/nxsblock.h
   libncl/current/ncl/nxscdiscretematrix.h
   libncl/current/ncl/nxscharactersblock.cpp
   libncl/current/ncl/nxscharactersblock.h
   libncl/current/ncl/nxscxxdiscretematrix.cpp
   libncl/current/ncl/nxscxxdiscretematrix.h
   libncl/current/ncl/nxsdatablock.cpp
   libncl/current/ncl/nxsdatablock.h
   libncl/current/ncl/nxsdefs.h
   libncl/current/ncl/nxsdiscretedatum.h
   libncl/current/ncl/nxsdistancedatum.h
   libncl/current/ncl/nxsdistancesblock.cpp
   libncl/current/ncl/nxsdistancesblock.h
   libncl/current/ncl/nxsexception.cpp
   libncl/current/ncl/nxsexception.h
   libncl/current/ncl/nxsmultiformat.cpp
   libncl/current/ncl/nxsmultiformat.h
   libncl/current/ncl/nxspublicblocks.cpp
   libncl/current/ncl/nxspublicblocks.h
   libncl/current/ncl/nxsreader.cpp
   libncl/current/ncl/nxsreader.h
   libncl/current/ncl/nxssetreader.cpp
   libncl/current/ncl/nxssetreader.h
   libncl/current/ncl/nxsstring.cpp
   libncl/current/ncl/nxsstring.h
   libncl/current/ncl/nxstaxablock.cpp
   libncl/current/ncl/nxstaxablock.h
   libncl/current/ncl/nxstoken.cpp
   libncl/current/ncl/nxstoken.h
   libncl/current/ncl/nxstreesblock.cpp
   libncl/current/ncl/nxstreesblock.h
   libncl/current/ncl/nxsunalignedblock.cpp
   libncl/current/ncl/nxsunalignedblock.h
   libncl/current/ncl/nxsutilcopy.h
   libncl/current/swig/ncl.i
   libncl/current/test/Makefile
   libncl/current/test/Makefile.am
   libncl/current/test/Makefile.in
   libncl/current/test/NTSValidIn/avian_ovomucoids.nex
   libncl/current/test/roundTripNCLTest.py
Log:
updating ncl to 2.1.11 in libncl directory

Copied: libncl/2.1.11 (from rev 766, libncl/current)

Modified: libncl/2.1.11/AUTHORS
===================================================================

--- libncl/current/AUTHORS	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/AUTHORS	2010-03-29 20:42:27 UTC (rev 767)
@@ -18,4 +18,7 @@
   Derrick Zwickl
   Brian O'Meara
   Brandom Chisham
-  
+
+The code in examples/phylobase... was written by Brian O'Meara and Derrick Zwickl
+for phylobase.
+

Modified: libncl/2.1.11/ChangeLog
===================================================================
--- libncl/current/ChangeLog	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/ChangeLog	2010-03-29 20:42:27 UTC (rev 767)
@@ -18,15 +18,15 @@
 	- updated nexml writing to deal with changes in the schema
 	- fixed bug causing mis-indexing of taxa in trees if there is no taxa block
 		but a translate command.  This involves support for illegal nexus files.
-		I believe that the bug would have showed diagnosable pathologies if it 
+		I believe that the bug would have showed diagnosable pathologies if it
 		had affected any analysis (the highest number in the tree would have been
 		1 too high resulting in exceptions when the taxa block was queried).
 	- bug fix when trees are followed by labels that contain tokens that have to
 		be quoted
-	- fixed behavior of GetNamedStateSetOfColumn and GetObsStates so that they 
+	- fixed behavior of GetNamedStateSetOfColumn and GetObsStates so that they
 		are sensitive to the current gapmode for the char block
 	- explicit inclusion of cstdlib where needed
-	
+
 Library enhancements:
 	- Signal handling (via NxsReader::setNCLCatchesSignals ) commit r449
 	- Lots of external format extensions and bug fixes:
@@ -48,12 +48,12 @@
 	- Characters blocks now reject files in which the datatype is DNA, RNA, or protein
 		if SYMBOLS are added.
 
-	
+
 bug fixes API:
 	- Fixed setting of NXS_HAS_ALL_TAXA_BIT
-	- no longer duplicating blocks when the same reader is used to read more 
+	- no longer duplicating blocks when the same reader is used to read more
 		than one file
-	- allowing PublicNexusReader::Add to be called 
+	- allowing PublicNexusReader::Add to be called
 	- Some Windows-specific modifications to avoid warnings and errors compiling
 		under Visual Studio 2008 (VC9)
 	- characters block now generates an exception if there is no matrix
@@ -61,43 +61,43 @@
 	- better cleaning up in the multiformat reader when there is an error in the
 		reading of a file
 	- another accessor added for NxsSimpleTree
-	- PublicNexusReader GetXXXBlock functions changed to return 0L rather than 
+	- PublicNexusReader GetXXXBlock functions changed to return 0L rather than
 		raising an exception if you request a block that is out of range
 	- NCL_CONST_FUNCS macro added
-		
+
 API additions:
 	- improvements to phylip reading -- matchchar now accepted (multiformat
 		reader only).
 	- reading a single bare newick tree (as "phyliptree" or "relaxedphyliptree"
 		in multiformat reader stuff).
-	- added cullIdenticalTaxaBlocks() function to nexusreader.  You should call 
-		this before reading a file if you want all repeated taxa blocks to be 
+	- added cullIdenticalTaxaBlocks() function to nexusreader.  You should call
+		this before reading a file if you want all repeated taxa blocks to be
 		destroyed rather than saved
 	- support for genetic codes and translation to amino acids added
 	- GetEscapedDouble and GetEscapedInt added
 	- GetDatatypeMapForMixedType added
-	- added functionality to delete identical taxa blocks even if they are 
-		implied blocks.  This only will be triggered if the client code has 
-		called NxsReader::cullIdenticalTaxaBlocks(true).  This corrects an 
+	- added functionality to delete identical taxa blocks even if they are
+		implied blocks.  This only will be triggered if the client code has
+		called NxsReader::cullIdenticalTaxaBlocks(true).  This corrects an
 		issue DZ was seeing with reading multiple DATA blocks
 	- aliasing of block titles for culled blocks
 	- changed the handling of  the + character when a nxstoken instance has been
 		altered by a call to indictate hyphenNotPunctuation is in effecet (this
 		is done via the SetLabileFlagBit function). In almost all case this
-		function is called so that a number (particularly one writtend in 
-		scientific notation will be read as a single token, rather than as many 
-		as 4 tokens).  In rare cases, the + is used before the exponent or even 
-		in front of the entire number.  So that client code does not have to 
-		deal with these cases, the default behavior has been changed to using 
-		the hyphenNotPunctuation to indicate that in the reading of the next 
-		token neither - nor + should be treated as punctuation.  Client code 
-		that wishes to use the old behavior can compile NCL with the 
+		function is called so that a number (particularly one writtend in
+		scientific notation will be read as a single token, rather than as many
+		as 4 tokens).  In rare cases, the + is used before the exponent or even
+		in front of the entire number.  So that client code does not have to
+		deal with these cases, the default behavior has been changed to using
+		the hyphenNotPunctuation to indicate that in the reading of the next
+		token neither - nor + should be treated as punctuation.  Client code
+		that wishes to use the old behavior can compile NCL with the
 		NCL_VERSION_2_STYLE_HYPHEN macro defined to 1
 
 ================================================================================
 2.1.05 (relative to 2.1.04)
 ================================================================================
-Added include <cstdlib> at top of nxsdistancesblock.cpp and nxstoken.cpp to 
+Added include <cstdlib> at top of nxsdistancesblock.cpp and nxstoken.cpp to
 avoid compilation errors on Fedora 9 systems.
 
 ================================================================================
@@ -113,13 +113,13 @@
 ================================================================================
 2.1.02 (relative to 2.1.00)
 ================================================================================
-minor bug fixes and const correctness 
+minor bug fixes and const correctness
 
 ================================================================================
 Since 2.1-specific changes.
 ================================================================================
 Support for multiple instances of the same block type
-	* NxsBlockFactory mechanism API - see the examples/normalizer for an 
+	* NxsBlockFactory mechanism API - see the examples/normalizer for an
 		example of usage. Full adoption of these API's is not required, but may
 		make your life easier.
 	* Reader now stores "implied blocks" -- e.g. makes a DATA block look to the
@@ -131,27 +131,27 @@
 		the same as {AG}.  Such files are not legal, but are common.
 	* handling for TITLE and BLOCKID commands added to NxsBlock
 	* optimizations (tokenizing and data structures in taxa block) -- now 50
-		fold faster than 2.0 on the 11361 Taxon, 1360 Character file in the 
+		fold faster than 2.0 on the 11361 Taxon, 1360 Character file in the
 		CIPRES test files.
 	* TaxPartition and TreePartition read
 	* SETS and CODONS blocks now read. Actually read as a big, fat ASSUMPTIONS
-		block that spawns implied blocks (to deal with common practice of mixing 
+		block that spawns implied blocks (to deal with common practice of mixing
 		the commands in these blocks).
 	* WtSet, UserType, and TypeSet command
 	* now tolerating DATATYPE not being first in FORMAT command (to deal with
 		Clustal exports)
 	* tokenizer now skipping embedded comments (note that this changes the
-		behavior of command comment storing -- they are only returned if they 
+		behavior of command comment storing -- they are only returned if they
 		precede token)
 	* support for DATATYPE=MIXED added in CHARACTERS block
 	* trees block can now validates trees as they are read to improve error
 		reporting  -- this feature not used unless TreesBlock::
-		SetProcessAllTreesDuringParse(true) is called on the trees block 
+		SetProcessAllTreesDuringParse(true) is called on the trees block
 		instance.
 	* some support for NHX parsing -- in the TreesDescription.
 	* support for LINK command (as introduced by Mesquite)
 	* support Mesquite-style CharSet/TaxSet syntax.
- 	* NCL_MAJOR_VERSION and  NCL_MINOR_VERSION defines added. You can wrap any 
+ 	* NCL_MAJOR_VERSION and  NCL_MINOR_VERSION defines added. You can wrap any
  		ncl-2.1 specific code (you shouldn't need much) as follows:
 
 ================================================================================
@@ -170,7 +170,7 @@
 		generate errors for VECTOR)
 	* fixes to the Distances block if the input order is not identical to the
 		taxa block order
-	* Some CharSet reading 
+	* Some CharSet reading
 	* Lots more that I forgot to document.
 
 Behavior changes (could be called features or bugs depending on your POV):
@@ -185,10 +185,10 @@
 12 Dec 2007 Mark Holder (mholder at users.sourceforge.net)
 	* Version 2.0.04 (https://svn.sourceforge.net/svnroot/ncl/branches/v2-stable
 revision 75)
-	* new features: Basic handling of Continuous datatype (ITEMS now 
-		supported).  Brian O'Meara contribute code and suggestions to this 
+	* new features: Basic handling of Continuous datatype (ITEMS now
+		supported).  Brian O'Meara contribute code and suggestions to this
 		new feature.
-	* bug fixes: taxa information after a treedef (root taxa info) is now 
+	* bug fixes: taxa information after a treedef (root taxa info) is now
 		accepted
 
 30 Nov 2007 Mark Holder (mholder at users.sourceforge.net)

Modified: libncl/2.1.11/INSTALL
===================================================================
--- libncl/current/INSTALL	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/INSTALL	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,7 +1,7 @@
 Copyright (c) 2004 by Paul O. Lewis
 
 ================================================================================
-Building from svn checkout 
+Building from svn checkout
 ================================================================================
 In the instructions, the $ represents your shell's prompt (you don't type the in
 
@@ -19,9 +19,9 @@
 	$ make installcheck
 
 ================================================================================
-Building from svn checkout 
+Building from svn checkout
 ================================================================================
-After you unpack the archive follow the instructions above (in the 
+After you unpack the archive follow the instructions above (in the
 "Building from svn checkout" section), except that you can skip the first step.
 
 
@@ -34,7 +34,7 @@
 For instance invoking:
 	$ ../v2.1/configure --prefix=`pwd`/installed
 will make the install products go inside an installed subdirectory
-of your build directory. This is paricularly helpful if you 
+of your build directory. This is paricularly helpful if you
 build several different variants (you can have builddebug and buildrelease
 directories built from the same source tree).
 

Modified: libncl/2.1.11/Makefile.am
===================================================================
--- libncl/current/Makefile.am	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/Makefile.am	2010-03-29 20:42:27 UTC (rev 767)
@@ -9,8 +9,8 @@
 
 
 dist-hook:
-	find "$(distdir)/data" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/html" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/test" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/swig" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
+	find "$(distdir)/data" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/html" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/test" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/swig" -depth -name .svn -and -type d -and -exec rm -rf {} \;
 

Modified: libncl/2.1.11/Makefile.in
===================================================================
--- libncl/current/Makefile.in	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/Makefile.in	2010-03-29 20:42:27 UTC (rev 767)
@@ -687,10 +687,10 @@
 
 
 dist-hook:
-	find "$(distdir)/data" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/html" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/test" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
-	find "$(distdir)/swig" -depth -name .svn -and -type d -and -exec rm -rf {} \; 
+	find "$(distdir)/data" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/html" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/test" -depth -name .svn -and -type d -and -exec rm -rf {} \;
+	find "$(distdir)/swig" -depth -name .svn -and -type d -and -exec rm -rf {} \;
 # 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:

Modified: libncl/2.1.11/NEWS
===================================================================
--- libncl/current/NEWS	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/NEWS	2010-03-29 20:42:27 UTC (rev 767)
@@ -8,14 +8,14 @@
 
 Version 2.0
 -----------
-This version significant upgrade to NCL in terms of ease of use for programmers 
-and the coverage of variants of NEXUS files.  This version naturally supports 
-multiple instances of blocks (common in files from Mesquite) and the Mixed 
+This version significant upgrade to NCL in terms of ease of use for programmers
+and the coverage of variants of NEXUS files.  This version naturally supports
+multiple instances of blocks (common in files from Mesquite) and the Mixed
 datatype used by MrBayes. Support for the UNALIGNED and ASSUMPTIONS block has
-been dramatically improved. The SETS and CODONS blocks are now handled 
-(they are treated as special forms of the ASSUMPTIONS block to tolerate the 
-inclusion of many of the same commands in different block types). Almost all of 
-the changes in this version were made by Mark Holder, so please direct bug 
+been dramatically improved. The SETS and CODONS blocks are now handled
+(they are treated as special forms of the ASSUMPTIONS block to tolerate the
+inclusion of many of the same commands in different block types). Almost all of
+the changes in this version were made by Mark Holder, so please direct bug
 reports, questions, and feature requests to him (though the sourceforge page
 is the best place to report these).
 
@@ -24,12 +24,12 @@
 -----------
 Although this is the second version of the library, it is really the
 first official release. My container classes used in the first version
-have been replaced by their STL equivalents, and the source code 
+have been replaced by their STL equivalents, and the source code
 documentation is now much more thorough. This version is being pubicized
 in the form of an application note in the journal Bioinformatics.
 
 Version 1.0
 -----------
 This first version did not make use of the standard template library,
-instead using container classes of my own design. This version was 
+instead using container classes of my own design. This version was
 distributed from my web site, but never publicized.

Modified: libncl/2.1.11/README
===================================================================
--- libncl/current/README	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/README	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,6 +1,6 @@
 NCL README -- the NEXUS Class Library (NCL) README file
 
-Most documentation for this C++ class library is in the form of HTML 
+Most documentation for this C++ class library is in the form of HTML
 files in the html directory. Please begin by viewing the html/index.html
 file in your web browser.
 
@@ -13,8 +13,8 @@
 http://www.molevol.org/camel/projects/nexus/ for more information), the Mesquite
 package, and from TreeBase (thanks, to Bill Piel!).
 
-	The SWIG bindings for version 2.1 were inspired by the work of David Suarez 
-Pascal in the 2007 Google Summer of Code.  They were simplified using new 
+	The SWIG bindings for version 2.1 were inspired by the work of David Suarez
+Pascal in the 2007 Google Summer of Code.  They were simplified using new
 features of NCL 2.1.  Thanks to David for blazing the way on the old version,
 Google for funding, and NESCent (in particular Hilmar Lapp) for getting the
 NESCent GSoC program going.

Modified: libncl/2.1.11/config/ax_cxx_flags.m4
===================================================================
--- libncl/current/config/ax_cxx_flags.m4	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/config/ax_cxx_flags.m4	2010-03-29 20:42:27 UTC (rev 767)
@@ -4,15 +4,15 @@
 dnl @license AllPermissive
 AC_DEFUN([AX_CXXFLAGS],
 [
-	
+
 	dnl Check for debugging mode.
 	AC_ARG_ENABLE(
 		debugging,
 		AC_HELP_STRING(
 			[--enable-debugging],
 			[build for debugging]
-			), 
-		, 
+			),
+		,
 		[enable_debugging=no]
 		)
 	AC_ARG_ENABLE(
@@ -20,8 +20,8 @@
 		AC_HELP_STRING(
 			[--enable-asserts],
 			[build with asserts turned on even if not debugging]
-			), 
-		, 
+			),
+		,
 		[enable_asserts=yes]
 		)
 	if test "$enable_debugging" = yes
@@ -35,7 +35,7 @@
 		fi
 	fi
 
-	
+
 	if test "$enable_debugging" = yes; then
 		CXXFLAGS_OPTIM_SPEED="-O0"
 		CXXFLAGS="$CXXFLAGS -g"
@@ -52,7 +52,7 @@
 		case "$build_os" in
 			darwin*) CXXFLAGS="$CXXFLAGS -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 ";;
 			*);;
-		esac	
+		esac
 	elif test "$CC" = "ccc"; then
 			#	Compaq C compiler for Linux
 		if test "x$arch" = "x"; then
@@ -77,7 +77,7 @@
 				#   development, but these warnings should also not trip for release builds)
 			CXXFLAGS_WARNINGS="$CXXFLAGS_WARNINGS -Wall -Wimplicit -Wreturn-type -Wunused -Wredundant-decls -Wcast-align -Wcomment -Wextra"
 		else
-				#	Just suppress warnings about possibly uninitialized variables	
+				#	Just suppress warnings about possibly uninitialized variables
 			CXXFLAGS_WARNINGS="$CXXFLAGS_WARNINGS"
 			CXXFLAGS_OPTIM_SPEED="-O3 -ffast-math"
 			CXXFLAGS_OPTIM_SIZE="-Os -ffast-math"
@@ -85,13 +85,13 @@
 		case "$build_os" in
 			darwin*) CXXFLAGS_WARNINGS="$CXXFLAGS_WARNINGS";;
 			*);;
-		esac	
+		esac
 	fi
 	if test "x$CXXFLAGS_OPTIM_SIZE" = "x"; then
 		CXXFLAGS_OPTIM_SIZE=$CXXFLAGS_OPTIM_SPEED
 	fi
 
-	
+
 	CXXFLAGS="$CXXFLAGS $CXXFLAGS_OPTIM_SPEED $CXXFLAGS_WARNINGS"
 
 ])

Modified: libncl/2.1.11/config/install-sh
===================================================================
--- libncl/current/config/install-sh	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/config/install-sh	2010-03-29 20:42:27 UTC (rev 767)
@@ -115,7 +115,7 @@
 if [ x"$dir_arg" != x ]; then
 	dst=$src
 	src=""
-	
+
 	if [ -d $dst ]; then
 		instcmd=:
 		chmodcmd=""
@@ -125,7 +125,7 @@
 else
 
 # Waiting for this to be detected by the "$instcmd $src $dsttmp" command
-# might cause directories to be created, which would be especially bad 
+# might cause directories to be created, which would be especially bad
 # if $src (and thus $dsttmp) contains '*'.
 
 	if [ -f "$src" ] || [ -d "$src" ]
@@ -135,7 +135,7 @@
 		echo "install:  $src does not exist"
 		exit 1
 	fi
-	
+
 	if [ x"$dst" = x ]
 	then
 		echo "install:	no destination specified"
@@ -202,17 +202,17 @@
 
 # If we're going to rename the final executable, determine the name now.
 
-	if [ x"$transformarg" = x ] 
+	if [ x"$transformarg" = x ]
 	then
 		dstfile=`basename $dst`
 	else
-		dstfile=`basename $dst $transformbasename | 
+		dstfile=`basename $dst $transformbasename |
 			sed $transformarg`$transformbasename
 	fi
 
 # don't allow the sed command to completely eliminate the filename
 
-	if [ x"$dstfile" = x ] 
+	if [ x"$dstfile" = x ]
 	then
 		dstfile=`basename $dst`
 	else
@@ -243,7 +243,7 @@
 # Now rename the file to the real destination.
 
 	$doit $rmcmd -f $dstdir/$dstfile &&
-	$doit $mvcmd $dsttmp $dstdir/$dstfile 
+	$doit $mvcmd $dsttmp $dstdir/$dstfile
 
 fi &&
 

Modified: libncl/2.1.11/config/libtool.m4
===================================================================
--- libncl/current/config/libtool.m4	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/config/libtool.m4	2010-03-29 20:42:27 UTC (rev 767)
@@ -945,10 +945,10 @@
       _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
     darwin1.*)
       _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
-    darwin*) # darwin 5.x on 
+    darwin*) # darwin 5.x on
       # if running on 10.5 or later, the deployment target defaults
       # to the OS version, if on x86, and 10.4, the deployment
-      # target defaults to 10.4. Don't you love it? 
+      # target defaults to 10.4. Don't you love it?
       case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
 	10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
 	  _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
@@ -2679,7 +2679,7 @@
 if test "$GCC" = yes; then
   variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
 fi
- 
+
 if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
   sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
 fi

Modified: libncl/2.1.11/config/lt~obsolete.m4
===================================================================
--- libncl/current/config/lt~obsolete.m4	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/config/lt~obsolete.m4	2010-03-29 20:42:27 UTC (rev 767)
@@ -25,7 +25,7 @@
 # included after everything else.  This provides aclocal with the
 # AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
 # because those macros already exist, or will be overwritten later.
-# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6. 
+# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
 #
 # Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
 # Yes, that means every name once taken will need to remain here until

Modified: libncl/2.1.11/configure
===================================================================
--- libncl/current/configure	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/configure	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.61 for NCL 2.1.09.
+# Generated by GNU Autoconf 2.61 for NCL 2.1.11.
 #
 # Report bugs to <paul.lewis at uconn.edu>.
 #
@@ -723,8 +723,8 @@
 # Identity of this package.
 PACKAGE_NAME='NCL'
 PACKAGE_TARNAME='ncl'
-PACKAGE_VERSION='2.1.09'
-PACKAGE_STRING='NCL 2.1.09'
+PACKAGE_VERSION='2.1.11'
+PACKAGE_STRING='NCL 2.1.11'
 PACKAGE_BUGREPORT='paul.lewis at uconn.edu'
 
 ac_unique_file="ChangeLog"
@@ -1397,7 +1397,7 @@
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures NCL 2.1.09 to adapt to many kinds of systems.
+\`configure' configures NCL 2.1.11 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1467,7 +1467,7 @@
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of NCL 2.1.09:";;
+     short | recursive ) echo "Configuration of NCL 2.1.11:";;
    esac
   cat <<\_ACEOF
 
@@ -1570,7 +1570,7 @@
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-NCL configure 2.1.09
+NCL configure 2.1.11
 generated by GNU Autoconf 2.61
 
 Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1584,7 +1584,7 @@
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by NCL $as_me 2.1.09, which was
+It was created by NCL $as_me 2.1.11, which was
 generated by GNU Autoconf 2.61.  Invocation command line was
 
   $ $0 $@
@@ -2290,7 +2290,7 @@
 
 # Define the identity of the package.
  PACKAGE='ncl'
- VERSION='2.1.09'
+ VERSION='2.1.11'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -17077,7 +17077,7 @@
 fi
 
 
-ac_config_files="$ac_config_files Makefile example/Makefile example/basiccmdline/Makefile example/basicfactory/Makefile example/gapcode/Makefile example/nclsimplest/Makefile example/ncltest/Makefile example/normalizer/Makefile example/patristic/Makefile example/splitsinfile/Makefile example/translate/Makefile ncl/Makefile test/Makefile nclv2.1.pc"
+ac_config_files="$ac_config_files Makefile example/Makefile example/basiccmdline/Makefile example/gapcode/Makefile example/nclsimplest/Makefile example/ncltest/Makefile example/normalizer/Makefile example/patristic/Makefile example/phylobaseinterface/Makefile example/splitsinfile/Makefile example/translate/Makefile ncl/Makefile test/Makefile nclv2.1.pc"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -17503,7 +17503,7 @@
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by NCL $as_me 2.1.09, which was
+This file was extended by NCL $as_me 2.1.11, which was
 generated by GNU Autoconf 2.61.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -17556,7 +17556,7 @@
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF
 ac_cs_version="\\
-NCL config.status 2.1.09
+NCL config.status 2.1.11
 configured by $0, generated by GNU Autoconf 2.61,
   with options \\"`echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
 
@@ -18025,12 +18025,12 @@
     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
     "example/Makefile") CONFIG_FILES="$CONFIG_FILES example/Makefile" ;;
     "example/basiccmdline/Makefile") CONFIG_FILES="$CONFIG_FILES example/basiccmdline/Makefile" ;;
-    "example/basicfactory/Makefile") CONFIG_FILES="$CONFIG_FILES example/basicfactory/Makefile" ;;
     "example/gapcode/Makefile") CONFIG_FILES="$CONFIG_FILES example/gapcode/Makefile" ;;
     "example/nclsimplest/Makefile") CONFIG_FILES="$CONFIG_FILES example/nclsimplest/Makefile" ;;
     "example/ncltest/Makefile") CONFIG_FILES="$CONFIG_FILES example/ncltest/Makefile" ;;
     "example/normalizer/Makefile") CONFIG_FILES="$CONFIG_FILES example/normalizer/Makefile" ;;
     "example/patristic/Makefile") CONFIG_FILES="$CONFIG_FILES example/patristic/Makefile" ;;
+    "example/phylobaseinterface/Makefile") CONFIG_FILES="$CONFIG_FILES example/phylobaseinterface/Makefile" ;;
     "example/splitsinfile/Makefile") CONFIG_FILES="$CONFIG_FILES example/splitsinfile/Makefile" ;;
     "example/translate/Makefile") CONFIG_FILES="$CONFIG_FILES example/translate/Makefile" ;;
     "ncl/Makefile") CONFIG_FILES="$CONFIG_FILES ncl/Makefile" ;;

Modified: libncl/2.1.11/configure.ac
===================================================================
--- libncl/current/configure.ac	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/configure.ac	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,7 +1,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 
-AC_INIT(NCL, 2.1.09, paul.lewis at uconn.edu)
+AC_INIT(NCL, 2.1.11, paul.lewis at uconn.edu)
 AC_CONFIG_HEADERS([config.h])
 
 AC_PREREQ(2.57)
@@ -25,8 +25,8 @@
 AC_PROG_LIBTOOL
 
 ################################################################################
-# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the 
-#	the AX_CXXFLAGS macro below.   
+# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
+#	the AX_CXXFLAGS macro below.
 # So we cache the argument to configure
 #	here in ARG_CXX_FLAGS (so that our macro does not override them)
 ARG_CXX_FLAGS="$CXXFLAGS"
@@ -125,7 +125,7 @@
 # these tests should not cause failure of configure if python is not found.
 ################################################################################
 AC_PATH_PROG([PYTHON], [python], [], [$PATH])
-AC_PYTHON_MODULE([subprocess], [], [])  
+AC_PYTHON_MODULE([subprocess], [], [])
 AC_SUBST(PYTHON)
 
 if test -z "$PYTHON"
@@ -161,12 +161,12 @@
 	Makefile 						\
 	example/Makefile				\
 	example/basiccmdline/Makefile	\
-	example/basicfactory/Makefile	\
 	example/gapcode/Makefile		\
 	example/nclsimplest/Makefile	\
 	example/ncltest/Makefile		\
 	example/normalizer/Makefile		\
 	example/patristic/Makefile		\
+	example/phylobaseinterface/Makefile		\
 	example/splitsinfile/Makefile	\
 	example/translate/Makefile   	\
 	ncl/Makefile					\

Modified: libncl/2.1.11/data/unaligned.nex
===================================================================
--- libncl/current/data/unaligned.nex	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/data/unaligned.nex	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,6 +1,6 @@
 #nexus
 
-begin taxa; 
+begin taxa;
   dimensions ntax=10;
   taxlabels
     taxon_1

Modified: libncl/2.1.11/example/Makefile.am
===================================================================
--- libncl/current/example/Makefile.am	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/example/Makefile.am	2010-03-29 20:42:27 UTC (rev 767)
@@ -1,2 +1,2 @@
-SUBDIRS = nclsimplest ncltest basiccmdline normalizer basicfactory patristic gapcode splitsinfile translate
+SUBDIRS = nclsimplest ncltest basiccmdline normalizer patristic gapcode splitsinfile translate phylobaseinterface
 

Modified: libncl/2.1.11/example/Makefile.in
===================================================================
--- libncl/current/example/Makefile.in	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/example/Makefile.in	2010-03-29 20:42:27 UTC (rev 767)
@@ -178,7 +178,7 @@
 target_alias = @target_alias@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-SUBDIRS = nclsimplest ncltest basiccmdline normalizer basicfactory patristic gapcode splitsinfile translate
+SUBDIRS = nclsimplest ncltest basiccmdline normalizer patristic gapcode splitsinfile translate phylobaseinterface
 all: all-recursive
 
 .SUFFIXES:

Modified: libncl/2.1.11/example/basiccmdline/basiccmdline.cpp
===================================================================
--- libncl/current/example/basiccmdline/basiccmdline.cpp	2010-03-29 18:44:30 UTC (rev 766)
+++ libncl/2.1.11/example/basiccmdline/basiccmdline.cpp	2010-03-29 20:42:27 UTC (rev 767)
@@ -13,7 +13,7 @@
 //	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., 
+//	along with NCL; if not, write to the Free Software Foundation, Inc.,
 //	59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 //
 
@@ -21,8 +21,9 @@
 #include "basiccmdline.h"
 #include <sstream>
 #include <cassert>
+using namespace std;
 /*----------------------------------------------------------------------------------------------------------------------
-|	The constructor simply passes along `i' to the base class constructor. Nothing else needs to be done.
+	The constructor simply passes along `i' to the base class constructor. Nothing else needs to be done.
 */
 MyNexusToken::MyNexusToken(
   istream & i)	/* is the input file stream attached to the NEXUS file to be read */
@@ -31,9 +32,9 @@
 	}
 
 /*----------------------------------------------------------------------------------------------------------------------
-|	Overrides the NxsToken::OutputComment virtual function (which does nothing) to display output comments [!comments
-|	like this one beginning with an exclamation point]. The output comment contained in `msg' is simply sent to the
-|	standard output stream cout.
+	Overrides the NxsToken::OutputComment virtual function (which does nothing) to display output comments [!comments
+	like this one beginning with an exclamation point]. The output comment contained in `msg' is simply sent to the
+	standard output stream cout.
 */
 void MyNexusToken::OutputComment(
   const NxsString & msg)	/* is the output comment to be displayed */
@@ -42,9 +43,9 @@
 	}
 
 /*----------------------------------------------------------------------------------------------------------------------
-|	Initializes the `id' data member to "BASICCMDLINE" and calls the FactoryDefaults member function to perform the 
-|	remaining initializations. The data member `next_command' is set to NULL so that memory will be allocated for it in
-|	FactoryDefaults.
+	Initializes the `id' data member to "BASICCMDLINE" and calls the FactoryDefaults member function to perform the
+	remaining initializations. The data member `next_command' is set to NULL so that memory will be allocated for it in
+	FactoryDefaults.
 */
 BASICCMDLINE::BASICCMDLINE()
 	{
@@ -66,7 +67,7 @@
 	}
 
 /*----------------------------------------------------------------------------------------------------------------------
-|	Closes `logf' if it is open and deletes memory allocated to `next_command'.
+	Closes `logf' if it is open and deletes memory allocated to `next_command'.
 */
 BASICCMDLINE::~BASICCMDLINE()
 	{
@@ -78,12 +79,12 @@
 	}
 
 /*----------------------------------------------------------------------------------------------------------------------
-|	The code here is identical to the base class version (simply returns 0), so the code here should either be 
-|	modified or this derived version eliminated altogether. Under what circumstances would you need to modify the 
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/phylobase -r 767
