File: NexusClassLibrary.html

package info (click to toggle)
treeviewx 0.5.1%2Bgit20100823.7e4d0e9-3
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 2,664 kB
  • sloc: cpp: 14,362; xml: 82; makefile: 66
file content (956 lines) | stat: -rwxr-xr-x 38,360 bytes parent folder | download | duplicates (9)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
<html>
<body bgcolor=white>
<h1>NEXUS Class Library (NCL) Release 2</h1>
<dl><dd><b>Author: Paul O. Lewis</b>
<dd><b>Copyright &copy; 1999. All Rights Reserved.</b>
<dd>Last modified: <i>October 14, 1999</i>
</dl>

<hr>

<h2>Contents</h2>
<ul>
<li><a href="#introduction">What is the NCL?</a>
<li><a href="#download">Obtaining the NCL?</a>
<li><a href="#characterisitics">Characteristics of the NCL</a>
  <ul>
  <li><a href="#portability">Portability</a>
  <li><a href="#crossplatform">Cross-platform features</a>
  <li><a href="#extensibility">Extensibility</a>
  </ul>
<li><a href="#limitations">Current limitations</a>
<li><a href="#reader">Building a NEXUS File Reader</a>
  <ul>
  <li><a href="#readermain">The Main Function</a>
  <li><a href="#readernexus">Deriving From the NEXUS Class</a>
  <li><a href="#readertoken">Deriving From the NexusToken Class</a>
  <li><a href="#readerall">Putting It All Together</a>
  <li><a href="#readerdata">A Sample Data File</a>
  </ul>
<li><a href="#rollown">Creating Your Own NEXUS Block</a>
  <ul>
  <li><a href="#classheadercomment">Class header comment</a>
  <li><a href="#enumcomment">Enumeration comment</a>
  <li><a href="#constructorcomment">Constructor comment</a>
  <li><a href="#destructorcomment">Destructor comment</a>
  <li><a href="#noparamscomment">Method comment (no parameters)</a>
  <li><a href="#paramscomment">Method comment (with parameters)</a>
  <li><a href="#throwcomment">Method comment (throws exceptions)</a>
  <li><a href="#operatorcomment">Operator comment</a>
  <li><a href="#castcomment">Cast operator comment</a>
  <li><a href="#manipcomment">Manipulator comment</a>
  </ul>
<li><a href="#advice">General Advice</a>
<li><a href="#whatyoucando">What You Can Do For Me</a>
<li><a href="#future">Future Of The NCL Project</a>
<li><a href="#index">Index of NCL Classes</a>
</ul>

<a name="introduction">
<h2>What is the NCL?</h2>
</a>

The NEXUS Class Library (NCL) is an integrated collection of C++ classes designed to
provide a NEXUS data file reader that is both easy to implement and easily
extensible.

<p>A word about the intended audience is in order before we get too far along (no
need to waste your time if the NCL will not be helpful to you).
The intended audience for both this documentation and the
accompanying class library comprises <i>computer programmers</i> who wish to endow
their C++ programs with the ability to read NEXUS data files.  If you are not a
programmer and simply use NEXUS files as a means of inputting data to the programs
you use for analyzing your data, the NCL is not something that will be useful to you.
The NCL is also not for you if you are a programmer but do not use the C++ language, 
since the NCL depends heavily on the object oriented programming features built into C++.

<p>The NEXUS data file format was specified in the publication cited below.
Please read this paper for further information about the format specification
itself; the documentation for the NCL does not attempt to explain this.

<p>
<b>Maddison, D. R., D. L. Swofford, and Wayne P. Maddison.</b>
1997. NEXUS:  an extensible file format for systematic information.
<i>Systematic Biology</i> <b>46</b>(4): 590-621.

<p>
The basic goal of the NCL is to provide a relatively easy way to endow a C++
program with the ability to read NEXUS data files.  The steps
necessary to use the NCL to create a bare-bones program that can read a NEXUS
data file are simple and few (see below), and it is hoped that the availability
of this class library will encourage the use of the NEXUS format.  This will
in turn encourage consistency in how programs read NEXUS files and how programs
respond to errors in data files.

<p>
A further benefit can be seen by looking at the large number of special
data file formats that are out there.  This places an extra burden on the
end user, who must deal with an increasing number of file formats all differing
in a number of ways.  To port one's data to another file format often involves
manual manipulation of the data, an activity that is inherently dangerous and
probably has resulted in the corruption of many data files.  At the very least,
the large number of formats in existance has led to a proliferation of data
file variants.  With many copies of a given data file on a hard disk, each
formatted differently for various analysis programs, it becomes very easy to
change one (say, correct a datum found to be in error) and fail to correct the
other versions.  The NEXUS file format provides a means for keeping one master
copy of the data and using it with several programs without modification.  The
NCL provides a means for encouraging programmers to use the NEXUS file format
in future programs they write.

<a name="download">
<h2>Obtaining the NCL?</h2>
</a>
The current version of the NCL is available by anonymous ftp from 
<code>alleyn.eeb.uconn.edu</code> (137.99.27.148) in the directory <code>pub/ncl2</code>.
The NCL is available in two archive formats:  compressed tar archive or 
zip format.  Download the compressed tar archive if you plan to develop
only for the Unix platform; the zip file contains everything in the tar
file as well as project files for both the Borland and Metrowerks IDEs.

<p>The links below are provided to make the anonymous ftp access easier:
<p><strong><a href="ftp://137.99.27.148/pub/ncl/ncl.tar.Z">Compressed tar file</a></strong>
<br><strong><a href="ftp://137.99.27.148/pub/ncl/ncl.zip">Zip file</a></strong>
<br><strong><a href="ftp://137.99.27.148/pub/ncl/readme.txt">README file</a></strong>

<a name="characterisitics">
<h2>Characteristics of the NCL</h2>
</a>

<a name="portability">
<h3>Portability</h3>
</a>
The NCL has been designed to be as portable as possible for a C++ class library.
The NCL <i>does</i> make use of the ANSI Standard C++ Library, which may cause problems
if the compiler you are using is a couple of years old or older.  The standard 
library has been adopted by all modern compilers, including the most recent versions
of Metrowerks CodeWarrier Pro and Borland C++, as well as the EGCS compiler (a
free compiler available for most unix platforms).  Thus, if your compiler chokes
on the template-based container classes used in the NCL (such as vector, list, map, string, etc.)
then you will need to upgrade your compiler in order to use the NCL.  Assuming
you have a modern compiler, however, the NCL is fully portable across Mac, Windows, 
and most Unix platforms.

<a name="crossplatform">
<h3>Cross-platform features</h3>
</a>
I have attempted to create the NCL in such a way that one is not limited in the
type of platform targeted.  For example, NEXUS files can contain "output comments"
that are supposed to be displayed in the output of the program reading the NEXUS
file.  Such comments are handled automatically by the NCL, and are sent
to a virtual function that can be overridden by you in a derived class.
This provides a means for you to tailor the output of such comments to the platform
of your choice.  For example, if you are writing a standard Unix console application
(i.e., not a graphical X-Windows application), you might want such output comments
to simply be sent to standard output or to an ofstream object.  For a graphical
Windows, MacIntosh or X-Windows application, you might deem it more user-friendly to pop up
a message box with the output comment as the message.  This would ensure that the
user noticed the output comment.  You also have the option of having your program
completely ignore such comments in the data file.

<p>
The NCL provides similar hooks for noting the progress in reading the data file.
For example, a virtual function called EnteringBlock is called and provided with
the name of the block about to be read.  You can override EnteringBlock in your
derived class to allow, for example, a message to be displayed in a status bar
at the bottom of your program's main window (in a graphical application) indicating
which block is currently being read.  Other such virtual functions include
SkippingBlock (to allow users to be warned that your program is ignoring a block
in the data file), SkippingCommand (to allow users to be warned about particular
commands being skipped within a block), and NexusError, which is the function
called whenever anything unexpected happens when reading the file.

<a name="extensibility">
<h3>Extensibility</h3>
</a>
The basic tools provided in the NCL allow you to create your own NEXUS blocks
and use them in your program.  This makes it easy to define a private block
to contain commands that only your program recognizes, allowing your users to
run your program in batch mode (see the section below entitled <a href="#advice">
General Advice</a> for more information on this topic).

<a name="limitations">
<h2>Current limitations</h2>
</a>

The main current limitation is that the NCL is incomplete.  Some standard NEXUS
blocks have been provided with this distribution, but because the NEXUS format
is so extensive, I have not had the time to write code implementing even all of
the standard blocks described in the paper cited above (or even all of the standard
blocks I have included!). Here is a summary table showing what has been implemented
thus far:
<table width=600>
<tr>
<th align="left" valign="bottom">Block<br><hr>
<th align="left" valign="bottom">Current Limitations<br><hr>

<tr>
<td valign="top">ASSUMPTIONS
<td valign="top">Only TAXSETS, CHARSETS, and EXSETS have been implemented thus far.

<tr>
<td valign="top">ALLELES
<td valign="top">Cannot yet handle transposed MATRIX, and only DATAPOINT=STANDARD
is implemented (however, as far as I know, no other program in existance handles anything
but standard datapoints so this is not a great limitation at the moment).

<tr>
<td valign="top">CHARACTERS
<td valign="top">Only ITEMS=STATES and STATESFORMAT=STATESPRESENT has been implemented
thus far, and DATATYPE=CONTINUOUS has not been implemented.

<tr>
<td valign="top">DISTANCES
<td valign="top">No limitations, completely implemented

<tr>
<td valign="top">DATA
<td valign="top">Since the DATA block is essentially the same as a CHARACTERS block,
the same limitations apply.

<tr>
<td valign="top">TAXA
<td valign="top">No limitations, completely implemented

<tr>
<td valign="top">TREES
<td valign="top">No limitations, completely implemented

</table>

While the limitations for the CHARACTERS block may seem a bit extreme, this
block is nevertheless implemented to the point where almost all existing
morphological and molecular data sets can be read.  This is because most
existing programs (including MacClade and PAUP) are limited in the same
ways. In order to put my efforts where they are most needed, I have
delayed finishing the work on the CHARACTERS block until it becomes
apparent that someone wishes to write a program with the capability to
read data files having other ITEMS or STATESFORMAT options, or a data
file containing continuous data.  If you fall into this category, by all
means contact me and I will consider pushing ahead!

<p>
The NCL is written in C++ and designed for use in a C++ program.  It is not
available in a C version (or any other language for that matter), which will
represent a limitation if you are not a C++ programmer.  I do intend to produce
a Java version eventually (once the bugs are worked out of the C++ version).
I have written the NCL in a style that mimics Java (i.e., no operators are
defined, objects are passed by reference whenever possible, etc.) so that this
conversion, when it happens, will be as easy as possible.

<p>
The NCL has been designed to be portable, easy-to-use, and informative in the 
error messages produced.  It will be apparent to anyone who looks very closely
at the code that efficiency has been sacrificed to meet these goals.
You can expect the minimum size of an executable handling only the reading of
TAXA and TREES blocks to be at least 92 KB (94208 bytes).  Adding the ability
to read the CHARACTERS block pushes this up to 135 KB (138752 bytes).  These
figures are based on compiling a Win32 console program with Borland C++ 5.02
compiler with no optimizations. Speed has also been sacrificed, however I
think it can be argued that speed in reading a data file is not all that
important compared to the NCL's other benefits.

<a name="reader">
<h2>Building a NEXUS File Reader</h2>
</a>

This section illustrates how you could build a simple NEXUS file reader application
capable of reading in a TAXA and a TREES block.  Note that the application NCLTEST, 
for which you have the source code, is essentially an expanded version of this 
sample program that can read all of the NEXUS blocks incorporated to date into the
NCL.  To keep things simple, we will just write output to an ofstream object 
(nothing graphical here).

<p>
As you work through this example, feel free to look into the NCL classes in more
detail.  Each class has its own documentation in the form of a web page having a
name of the form NCLClassName.html, where NCLClassName is replaced by
the name of the class.  For example, the NexusBlock class is described in the file
NexusBlock.html.  An <a href="#index">index</a> to all classes in the NCL is 
provided at the end of this document for quick access to the full range of
class-specific web pages.

<a name="readermain">
<h3>The Main Function</h3>
</a>

<pre>
int main()
{
  taxa = new TaxaBlock();
  trees = new TreesBlock(*taxa);

  MyNexus nexus( "testfile.nex", "output.txt" );
  nexus.Add( taxa );
  nexus.Add( trees );

  MyToken token( nexus.inf, nexus.outf );
  nexus.Execute( token );

  taxa->Report( nexus.outf );
  trees->Report( nexus.outf );

  return 0;
}
</pre>

<p>
<b>Creating block objects.</b>
The first two lines of main involve the creation of objects corresponding to
the two types of NEXUS blocks we want our program to recognize.  TaxaBlock
is declared in the header file "taxablock.h" and defined in the source code
file "taxablock.cpp", whereas the TreesBlock class is declared in "treesblock.h"
and defined in "treesblock.cpp".  Note that the TreesBlock constructor requires
a reference to an object of type TaxaBlock.  This is because a TREES block in
a NEXUS data file requires the number of taxa and the taxon labels to have been
previously definined earlier in the data file.  In the NCL, any block that defines
taxon labels stores this information in the TaxaBlock object, and any block that
needs such information requires a reference to the TaxaBlock object in its
constructor.

<p>
<b>Adding the block objects to the NEXUS object.</b>
The next three lines involve creating a NEXUS object and adding our
two block objects to a linked list maintained by the NEXUS object.  The MyNexus
class is derived from the Nexus class, which is declared in "nexus.h" and
defined in "nexus.cpp".  Objects cannot be created from the Nexus class alone,
as it contains pure virtual functions that must be overridden in a derived class.
Examples of pure virtual functions in Nexus that must be overridden are:
EnteringBlock, SkippingBlock, and NexusError.  The reason the Nexus object must
maintain a list of block ojects is so that it can figure out who is responsible
for reading each block found in the data file.  The block objects taxa and trees
have each inherited an id variable of type char* that stores their block name
(i.e., "TAXA" for the TaxaBlock and "TREES" for the TreesBlock).  When the Nexus
object's Execute method encounters a block name, it searches its linked list of block
objects until it finds one whose id variable is identical to the name of the block
encountered.  It then calls the Read function of that block object to do the work
of reading the block from the data file and storing its contents.  It is possible
of course that a block name will appear in a data file for which there is no
corresponding block object.  In this case, the Nexus Execute method calls the
SkippingBlock method to report the fact that it is skipping over the contents of
the unknown block.

<p>
<b>Reading the data file.</b>
The next two lines create a token object (MyToken is derived from the NexusToken
class), and initiate the reading of the NEXUS data file using the Nexus Execute
function.  The input and output files are created within the MyNexus class.
While this is not required, it facilitates handling messages generated while
the data file is being read.  The NexusToken class has one virtual member
function - OutputComment - which enables you to control how output comments
are displayed.  The NexusToken version of OutputComment does nothing, so you
must derive your own token class from NexusToken and override the OutputComment
method in order for the output comments in the data file to be displayed.
The main function of the NexusToken class is to provide a means for grabbing
NEXUS tokens one by one from the data file.  Calling the GetNextToken function
reads and stores the next token found in the data file, correctly handling any
comments found along the way.  This greatly simplifies reading a NEXUS data file.

<p>
<b>Reporting on block objects' contents.</b>
The last two lines call the Report functions of each of the blocks.  This just
spits out a summary of any data contained in these objects that has been
read from the data file.

<a name="readernexus">
<h3>Deriving From the Nexus Class</h3>
</a>
Note that the ifstream is opened in binary mode.  You should always open your
input file in binary mode so that the file can be read properly regardless of
the platform on which it was created.  For example, suppose someone created a NEXUS
data file on a MacIntosh and wanted to read it with your program, which is
running on a Windows 95 machine.  Opening the file in binary mode allows the
NexusToken object you are using to recognize the newline character in the Mac
file as such, even though MacIntosh computers use a different symbol (ASCII 13)
to represent the newline character than computers running Windows (which use
the ASCII 13, ASCII 10 combination for newlines).

<p>Also, note the special version of one line in the NexusError method that is
necessary when using the Metrowerks CodeWarrior Professional (Release 4) compiler.
Metrowerks uses a class called streampos to keep track of the file position
rather than typedefing streampos to a simple long value.  You must call the
streampos object's offset() member function to obtain a value that you can
use (no automatic conversions from streampos to long).  If you are using 
CoeWarrior Pro Release 5, the special handling is not necessary (there was
apparently a bug in Release 4 that has since been fixed).

<pre>
class MyNexus : public Nexus
{
   public:
      ifstream inf;
      ofstream outf;

      MyNexus( char* infname, char* outfname ) : Nexus() {
         inf.open( infname, ios::binary );
         outf.open( outfname );
      }

      ~MyNexus() {
         inf.close();
         outf.close();
      }

      void EnteringBlock( char* blockName ) {
         cout << "Reading \"" << blockName << "\" block..." << endl;
         outf << "Reading \"" << blockName << "\" block..." << endl;
      }

      void SkippingBlock( char* blockName ) {
         cout << "Skipping unknown block (" << blockName << ")..." << endl;
         outf << "Skipping unknown block (" << blockName << ")..." << endl;
      }

      void OutputComment( char* msg ) {
         outf << msg;
      }

      void NexusError( char* msg, streampos pos, long line, long col ) {
         cerr << endl;
         cerr << "Error found at line " << line;
         cerr << ", column " << col;
#if defined( __MWERKS__ )
         // if using MetroWerks CodeWarrior Pro 5, use other (normal) version
         cerr << " (file position " << pos.offset() << "):" << endl;
#else
         cerr << " (file position " << pos << "):" << endl;
#endif
         cerr << msg << endl;

         outf << endl;
         outf << "Error found at line " << line;
         outf << ", column " << col;
#if defined( __MWERKS__ )
         // if using MetroWerks CodeWarrior Pro 5, use other (normal) version
         outf << " (file position " << pos.offset() << "):" << endl;
#else
         outf << " (file position " << pos << "):" << endl;
#endif
         outf << msg << endl;

         exit(0);
      }
};
</pre>

<a name="readertoken">
<h3>Deriving From the NexusToken Class</h3>
</a>
We derive our own token reader from the NexusToken class in order to display
the output comments present in the data file (if any).  The virtual function
OutputComment in the base class is overridden to accomplish this.
<pre>
class MyToken : public NexusToken
{
   ostream& out;

   public:
      MyToken( istream& is, ostream& os ) : out(os), NexusToken(is) {}
      void OutputComment( char* msg ) {
         cout << msg << endl;
         out << msg << endl;
      }
};
</pre>

<a name="readerall">
<h3>Putting It All Together</h3>
</a>
Here is the entire program.  Note that in order for this to link properly, you
will need to also compile the following files included with the NCL (and instruct
your linker to link them into your main executable):  nexustoken.cpp,
labellist.cpp, nexus.cpp, nexusblock.cpp, taxablock.cpp, and treesblock.cpp.
The documentation for individual classes within the NCL provides a "See also"
section for each class.  The classes listed in this "See also" section indicate
which other NCL classes the class being documented depends on.  Use the "See also"
lists to figure out which files you will need to compile for any particular project.
<pre>
#include &lt;stdlib.h&gt;
#include &lt;fstream.h&gt;

#include "nexustoken.h"
#include "labellist.h"
#include "nexus.h"
#include "taxablock.h"
#include "treesblock.h"

TaxaBlock* taxa;
TreesBlock* trees;

class MyToken : public NexusToken
{
   ostream& out;

   public:
      MyToken( istream& is, ostream& os ) : out(os), NexusToken(is) {}
      void OutputComment( char* msg ) {
         cout << msg << endl;
         out << msg << endl;
      }
};

class MyNexus : public Nexus
{
   public:
      ifstream inf;
      ofstream outf;

      MyNexus( char* infname, char* outfname ) : Nexus() {
         inf.open( infname, ios::binary );
         outf.open( outfname );
      }

      ~MyNexus() {
         inf.close();
         outf.close();
      }

      void EnteringBlock( char* blockName ) {
         cout << "Reading \"" << blockName << "\" block..." << endl;
         outf << "Reading \"" << blockName << "\" block..." << endl;
      }

      void SkippingBlock( char* blockName ) {
         cout << "Skipping unknown block (" << blockName << ")..." << endl;
         outf << "Skipping unknown block (" << blockName << ")..." << endl;
      }

      void OutputComment( char* msg ) {
         outf << msg;
      }

      void NexusError( char* msg, streampos pos, long line, long col ) {
         cerr << endl;
         cerr << "Error found at line " << line;
         cerr << ", column " << col;
#if defined( __MWERKS__ )
         cerr << " (file position " << pos.offset() << "):" << endl;
#else
         cerr << " (file position " << pos << "):" << endl;
#endif
         cerr << msg << endl;

         outf << endl;
         outf << "Error found at line " << line;
         outf << ", column " << col;
#if defined( __MWERKS__ )
         outf << " (file position " << pos.offset() << "):" << endl;
#else
         outf << " (file position " << pos << "):" << endl;
#endif
         outf << msg << endl;

         exit(0);
      }
};

int main()
{
  taxa = new TaxaBlock();
  trees = new TreesBlock(*taxa);

  MyNexus nexus( "testfile.nex", "output.txt" );
  nexus.Add( taxa );
  nexus.Add( trees );

  MyToken token( nexus.inf, nexus.outf );
  nexus.Execute( token );

  taxa->Report( nexus.outf );
  trees->Report( nexus.outf );

  return 0;
}
</pre>

<a name="readerdata">
<h3>A Sample Data File</h3>
</a>
Here is a sample data file that exercises a lot of the features of the
NEXUS file reader we have just created.  First, there are both output
and regular comments scattered around.  Some are between tokens, some
occur at the beginning of a token, and still others begin right after
a token.  Some comments even have nested within them words surrounded by
square brackets.  There are also blocks in this data file (i.e., the
gdadata block) that are not recognized by the NEXUS file reader we have
created. The NEXUS reader handles all of these situations without
needing any code from you!

<p>Feel free to introduce various sorts of errors (e.g., delete semicolons,
misspell keywords, etc.) into the the sample data file to get a feel for
what types of error messages the NEXUS file reader generates.

<pre>
#nexus

[!Output comment before first block]

begin gdadata; [this is an unknown block]
  dimensions npops=2 nloci=3;
end;

[!Let's see if we can deal with [nested] comments]

[!
What happens if we do this!
]

begin [comment at beginning of token]taxa;
  dimensions[comment at end of token] ntax=11;
  taxlabels  [comment between tokens]
      P._fimbriata
		'P. robusta'
		'P. americana'
		'P. myriophylla'
		'P. articulata'
		'P. parksii'
		'P. gracilis'
		'P. macrophylla'
		'P. polygama'
		'P. basiramia'
		'P. ciliata'
      [!output comment in TAXLABELS command]
  ;
end;

begin trees;
  translate
	1  P._fimbriata,
	2  P._robusta,
	3  P._americana,
	4  P._myriophylla,
	5  P._articulata,
	6  P._parksii,
	7  P._polygama,
	8  P._macrophylla,
	9  P._gracilis,
  10  P._basiramia,
  11  P._ciliata
  ;
  tree alpha = (1,2,((((3,4),5),6),((7,8),(9,(10,11)))));
  tree beta = (1,2,((((3,4),5),6),(7,(8,(9,(10,11))))));
end;
</pre>

<a name="rollown">
<h2>Creating Your Own NEXUS Block</h2>
</a>

Creating your own NEXUS block involves deriving a class from the NexusBlock
base class and overriding the three pure virtual functions Read, Reset, and
Report.  Use the files emptyblock.cpp and emptyblock.h as templates for your
own source code and header files.  While creating your own block class is
not a complicated endeavor, here are some things to nevertheless watch out for:
<ul>
<li> Be sure to document your class in the way I have done for the other blocks.
I have employed a system of documentation similar to that used for the Java
Development Kit.  The program makedoc was supplied with your copy of NCL.  This
program reads the special tags in the source code comments of the NCL source
files and creates HTML documentation automatically.  Because the documentation
is actually inside the source code files, this system makes it relatively
easy both to document your source code when you write it, and also keep it up
to date as you make changes later on.  Some examples of the special comment
style you must use to make this system work are given at the end of this section.
<li> Be sure to write the Reset function in such a way that all heap memory is
cleaned up (deleted).  This means whenever you use the "new" keyword to allocate
memory for an object that will potentially persist until the Reset method is
called, you need to put code in the Reset function to delete it.  Also, it is
important to delete such objects in the destructor for the class as well.
<li> When writing the Read function, put assert macros whereever you make an
assumption, however insignificant this assumption seems at the time of writing.
This tremendously speeds up the task of finding bugs when one of your assumptions
turns out to not always be true!
<li> When writing the Read function, put in lots of tests of the form:
<pre>
if( !token.Equals(";") ) {
	sprintf( errormsg, "Expecting ';' but found %s instead", token.GetToken() );
	throw XNexus(errormsg);
}
</pre>
Such checks will give your users some hope of finding where they have made a
mistake in constructing their data file.  We all know how frustrating it can
be to have a program exit with an uninformative error message.
<li> Don't forget to update your main class comment if you add variables to
your class's header file.  This is easy to forget, since the header file
does not contain any of the special documentation comments.
</ul>

To use makedoc, compile makedoc for your operating system and then simply type

<pre>
makedoc myblock.cpp
</pre>

at the system prompt to create a help file for the class defined in myblock.
Note that there can be only one class defined per source code file to use this
system, and all of the special comments must be in the same file for a particular
class.  Here are some examples of source code comments for use with the
makedoc program.  Feel free to look through the NCL source code files for other
examples.

<a name="classheadercomment">
<h3>Class header comment</h3>
</a>
<pre>
/**
 * @class      TaxaBlock
 * @file       taxablock.h
 * @file       taxablock.cpp
 * @author     Paul O. Lewis
 * @copyright  Copyright  1999. All Rights Reserved.
 * @variable   ntax [int:private] number of taxa (set from NTAX specification)
 * @variable   taxonLabels [LabelList:private] storage for list of taxon labels
 * @see        LabelList
 * @see        Nexus
 * @see        NexusBlock
 * @see        NexusToken
 * @see        XNexus
 *
 * This class handles reading and storage for the NEXUS block TAXA.
 * It overrides the member functions Read and Reset, which are abstract
 * virtual functions in the base class NexusBlock.  The taxon names are
 * stored in an array of strings (taxonLabels) that is accessible through
 * the member functions GetTaxonLabel, AddTaxonLabel, ChangeTaxonLabel,
 * and GetNumTaxonLabels.
 */
</pre>

<a name="enumcomment">
<h3>Enumeration comment</h3>
</a>
<pre>
/**
 * @enumeration
 * @enumitem  saveCommandComment [0x0001] if set, command comments expected and will be saved
 * @enumitem  parentheticalToken [0x0002] if set, parenthetical token expected
 *
 * For use with the variable labileFlags.
 */
</pre>

<a name="constructorcomment">
<h3>Constructor comment</h3>
</a>
<pre>
/**
 * @constructor
 *
 * Default constructor. Initializes id to "TAXA" and ntax to 0.
 */
</pre>

<a name="destructorcomment">
<h3>Destructor comment</h3>
</a>
<pre>
/**
 * @destructor
 *
 * Deletes the memory used by id and flushes taxonLabels.
 */
</pre>

<a name="noparamscomment">
<h3>Method comment (no parameters)</h3>
</a>
<pre>
/**
 * @method Reset [void:protected]
 *
 * Flushes taxonLabels and sets ntax to 0 in preparation for reading a
 * new TAXA block.
 */
</pre>

<a name="paramscomment">
<h3>Method comment (with parameters)</h3>
</a>
<pre>
/**
 * @method ChangeTaxonLabel [void:public]
 * @param i [int] the taxon label number to change
 * @param s [char*] the string used to replace label i
 *
 * Changes the label for taxon i to s.  Deletes the old
 * label and reallocates enough memory to store the new
 * label.
 */
</pre>

<a name="throwcomment">
<h3>Method comment (throws exceptions)</h3>
</a>
<pre>
/**
 * @method Read [void:protected]
 * @param token [NexusToken&] the token used to read from in
 * @param in [istream&] the input stream from which to read
 * @throws XNexus
 *
 * This function provides the ability to read everything following the block name
 * (which is read by the Nexus object) to the end or endblock statement.
 * Characters are read from the input stream in. Overrides the
 * abstract virtual function in the base class.
 */
</pre>

<a name="operatorcomment">
<h3>Operator comment</h3>
</a>
<pre>
/**
 * @operator = [NxsGDADataBlock&:public]
 * @param gdaData [const NxsGDADataBlock&] the NxsGDADataBlock to be copied
 *
 * Copies the information from gdaData to this object.
 */
</pre>

<a name="castcomment">
<h3>Cast operator comment</h3>
</a>
<pre>
/**
 * @castoperator () [double:public]
 *
 * Casts value of cell to a double.
 */
</pre>

<a name="manipcomment">
<h3>Manipulator comment</h3>
</a>
<pre>
/**
 * @manipulator setleft
 *
 * Specifies the left boundary of the Table body.
 * All columns added before this point are considered
 * row headers and will be repeated for each output
 * page.
 */
</pre>

<a name="advice">
<h2>General Advice</h2>
</a>

A typical program making use of this library might have the following two general characteristics:
<ul>
<li> Structured so that it can be compiled either as a command-line driven, Unix-style program
or as a graphical application (with a Windows, MacIntosh, or XWindows Graphical User Interface, or GUI)
<li> Handles a private NEXUS block that contains commands identical to those
that can be entered on the command line, enabling the program to be run in batch mode
</ul>

The program PAUP is perhaps the most well-known example of this type of program.

<p>After developing several programs like this, I have come up with the following strategy that 
make efficient use of the object-oriented nature of the NCL.  I will assume your non-graphical program will
be called simply "foo" and will read a private NEXUS block named "FOO". I will assume
that the GUI version will be targeted for the Windows platform, and will be colled "winfoo".
<ul>
<li> Create a class (call it <b>FooBase</b>) that encapsulates the kernel of the program.  
Be careful not to place any GUI code in this class.  This class should be derived (publicly) from
the <b>NexusBlock</b> class (this class will encapsulate your program's private NEXUS block).
<li> In class FooBase, override the NexusBlock virtual functions <b>Read</b>, <b>Reset</b>, <b>Report</b>, and <b>HandleEndblock</b>, 
and any other handler functions needed to process the commands in the private block.
<li> Now create a class <b>WinFoo</b> that handles the Windows GUI interface.  Derive this class from
both <b>Nexus</b> (so that it can serve as the Nexus reader) and from FooBase (so that it can also
serve as the private block object as well as handle all the core functionality).  In the WinFoo
constructor, create all the NEXUS block objects needed (i.e., a CharactersBlock object and TaxaBlock object)
and add these to the nexus reader using the Add function.  Don't forget to "Add(this)" too so that
your program can read the private block.  Note that "this" is both a Nexus object as well as a
NexusBlock object, so it is able to add itself to the list of blocks processed upon execution of
a NEXUS data file.
<li> In class WinFoo, override the Nexus virtual functions <b>EnteringBlock</b>, <b>SkippingBlock</b>, and
<b>NexusError</b>.  For instance, within NexusError, you might put up a MessageBox telling the
user about an error encountered in the data file.
<li> For the Unix, command-driven version, create a class <b>foo</b> that is derived from FooBase,
overrides the Nexus and NexusBlock virtual functions (like its GUI counterpart, WinFoo), and provides
a means for users to enter commands (you should create a mechanism in FooBase so that you can 
use the same macbinery to process commands typed in from the keyboard as you use to process
commands contained in a private block).
</ul>

<a name="whatyoucando">
<h2>What You Can Do For Me</h2>
</a>

I hope this library is useful to you, and it is offered free of charge so long
as you don't sell it or make it part of a commercial software package.  If you
include the NCL as part of a program that you sell, please contact me at the
address below to discuss license fees.
<p>
Although you are not obligated in any way to me as a result of using this
package to improve your programs, there are a few things that you can do to
help encourage me to continue improving this library.  Please make use of any
of the following means of support that you feel comfortable with:
<ul>
<li> Cite me!  If you publish an announcement of a program of yours that
includes the NCL, please acknowledge that your program includes the NCL.
<li> Advertise me!  If your program produces output either on the screen or
in the form of a file, mention that your program includes the NCL in your
program's output.
<li> Help me fix bugs. If you discover a bug in the NCL, please let me know
about it so that I can get it fixed.
<li> Give me suggestions.  I welcome suggestions for improving the library
and making it more convenient to use.
</ul>

<a name="future">
<h2>Future Of The NCL Project</h2>
</a>
The current capabilities of the NCL are best illustrated by taking a look at
some of the data files that it can successfully read.  
Most of these example NEXUS data files are from the 
<a href="http://ucjeps.herb.berkeley.edu/bryolab/greenplantpage.html">"Green 
Plant Phylogeny Research Coordination Group"</a> website; the two remaining
data files contain multiple DISTANCES blocks (distances.nex) or multiple
CHARACTERS blocks (characters.nex) to illustrate some of the formatting
options available with these two NEXUS block types.  These examples amply
demonstrate the capabilities of the NCL as it now stands, however the NCL
will continue to grow as code for recognizing more and more NEXUS
blocks are added.  I welcome both suggestions for improvement as well as
bug reports, of course.

<p>My current mail and email addresses as well as my phone and fax numbers
are given below:

<pre>
Paul O. Lewis, Assistant Professor
Department of Ecology and Evolutionary Biology
The University of Connecticut
U-43, 75 North Eagleville Road
Storrs, CT 06269-3043

Ph:    +1-860-486-2069
FAX:   +1-860-486-6364 (the departmental fax machine)
Email: <a href="mailto:plewis@uconnvm.uconn.edu">plewis@uconnvm.uconn.edu</a>
URL:   <a href="http://www.eeb.uconn.edu/faculty/plewis.htm">http://www.eeb.uconn.edu/faculty/plewis.htm</a>
</pre>

<a name="index">
<h2>Index To NCL Classes</h2>
</a>
<ul>
<li><a href="AllelesBlock.html"> AllelesBlock class </a>
<li><a href="AssumptionsBlock.html"> AssumptionsBlock class </a>
<li><a href="CharactersBlock.html"> CharactersBlock class </a>
<li><a href="DataBlock.html"> DataBlock class </a>
<li><a href="DiscreteDatum.html"> DiscreteDatum class </a>
<li><a href="DiscreteMatrix.html"> DiscreteMatrix class </a>
<li><a href="DistanceDatum.html"> DistanceDatum class </a>
<li><a href="DistancesBlock.html"> DistancesBlock class </a>
<li><a href="Nexus.html"> Nexus class </a>
<li><a href="NexusBlock.html"> NexusBlock class </a>
<li><a href="NexusToken.html"> NexusToken class </a>
<li><a href="SetReader.html"> SetReader class </a>
<li><a href="TaxaBlock.html"> TaxaBlock class </a>
<li><a href="TreesBlock.html"> TreesBlock class </a>
<li><a href="XNexus.html"> XNexus class </a>
</ul>

</body>
</html>