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Copyright (c) 2010, Ali Tofigh
See the end of the file for license conditions

                                NHparser
                                ********

1. Introduction
===============

NHparser is a C library for parsing trees in the Newick or New Hampshire
format. NHparser was designed, written, and is being maintained by Ali
Tofigh <[email protected]>.


2. Installation
===============

The NHparser package uses the GNU autotools for building and
installation. Please see the file INSTALL for general instructions. For
the impatient try

$ ./configure && make && make install

This will install the header files and the library in standard system
locations (e.g., /usr/include and /usr/lib). If you do not have write
permissions to the system directories, you can install the program in a
local directory of your choice:

$ ./configure --prefix=/path/to/install/location && make && make install

Also, try

$ ./configure --help

for more information about setting environment and compiler flags.


3. Usage
========

The library functions and the exported data types are declared in
NHparser.h and NHtypes.h, respectively. The most useful functions are:

NHNode *
NH_read_tree (FILE *inFile, FILE *errorFile, const char *errorPrefix);

NHNode *
NH_read_tree_str (const char *str, FILE *errorFile, const char *errorPrefix);

To use the library functions in your code, simply

#include <NHparser/NHparser.h>

and call the appropriate function(s). The NHNode data structure is
pretty self-explanatory and anyone familiar with the New Hampshire tree
format should be able to understand what each field represents. Compile
your code and link with the NHparser library (usually giving the
-lNHparser flag).


4. Known Issues
===============

- There is no documentation beside this README file.
- Line and column numbers are not always reported correctly.
- Only one tree can be read from each file. Try using NH_read_tree_str
  if you need to process a file with multiple trees.


5. Reporting Bugs
=================

Any suggestions, requests for enhancements, or bug reports can be sent
directly to the author via electronic mail: <[email protected]>.


6. License
==========

NHparser is released under the terms of the license contained in the
file LICENSE.