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
|
// 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
//
#ifndef NCL_BASICCMDLINE_H
#define NCL_BASICCMDLINE_H
#include <iostream>
#define COMMAND_MAXLEN 255
/*----------------------------------------------------------------------------------------------------------------------
| BASICCMDLINE provides a template for creating a program that reads NEXUS data files and provides a basic command
| line. After compiling BASICCMDLINE, you will already have a program that understands the following commands, either
| typed in at the console or provided in a BASICCMDLINE block in a NEXUS data file (exception is the execute command,
| which can only be entered at the console). Keywords in the descriptions below are given in uppercase, however the
| commands themselves are case-insensitive. Lower-case indicates a parameter supplied by the user (e.g., "filename"
| would be replaced by the actual name of the file). Square brackets indicate optional keywords or subcommands.
|>
| EXECUTE filename;
|
| LOG [options];
|
| Option Action
| ------------------------------------------------------
| FILE=filename specifies name of log file to start
| START indicates logging is to be started
| STOP indicates logging is to be stopped
| APPEND append to log file if it already exists
| REPLACE replace log file without asking
|
| QUIT;
|>
| See the Read function for details and to add other commands.
|
| To change the name of the program (which is also the prompt name and the name of the program's private NEXUS
| block), replace all occurrences of BASICCMDLINE with the name of your program (also search for the string
| "basiccmdline" and replace with an appropriate string at each occurrence).
|
| This class handles reading and storage for the NxsReader block BASICCMDLINE. It also serves as the main class for
| the program BASICCMDLINE, acting as both a NxsReader object (in order to be capable of parsing data files) as well
| as a NxsBlock object (in order to be able to process commands in a BASICCMDLINE block).
|
| Acting as a NxsBlock, it overrides the member functions Read and Reset, which are virtual functions in the base
| class NxsBlock. Acting as a NxsReader object, it overrides the member functions EnteringBlock, SkippingBlock, and
| NexusError.
|
| Adding a new data member? Don't forget to:
|~
| o Describe it in the class header comment at the top of "basiccmdline.h"
| o Initialize it (unless it is self-initializing) in the constructor and reinitialize it in the Reset function
| o Describe the initial state in the constructor documentation
| o Delete memory allocated to it in both the destructor and Reset function
| o Report it in some way in the Report function
|~
*/
class BASICCMDLINE
: public NxsBlock,
public NxsReader
{
public:
enum UserQueryEnum /* enumeration used with UserQuery member function to specify which choices to provide the user */
{
uq_cancel = 0x01, /* provide opportunity to cancel */
uq_ok = 0x02, /* provide opportunity to answer ok */
uq_yes = 0x04, /* provide opportunity to answer yes */
uq_no = 0x08 /* provide opportunity to answer no */
};
BASICCMDLINE();
virtual ~BASICCMDLINE();
bool EnteringBlock(NxsString blockName);
void ExitingBlock(NxsString blockName);
void ExecuteStarting();
void ExecuteStopping();
void OutputComment(const NxsString &msg);
void HandleNextCommand();
void NexusError(NxsString msg, file_pos pos, long line, long col);
void PreprocessNextCommand();
void PrintMessage(bool linefeed = true) const ;
virtual void Report(std::ostream & out) NCL_COULD_BE_CONST ;
void Run(char *infile_name);
void SkippingBlock(NxsString blockName);
void SkippingCommand(NxsString commandName);
void SkippingDisabledBlock(NxsString blockName);
virtual bool UserQuery(NxsString mb_message, NxsString mb_title, BASICCMDLINE::UserQueryEnum mb_choices = BASICCMDLINE::uq_ok);
virtual unsigned CharLabelToNumber(NxsString s) NCL_COULD_BE_CONST;
protected:
bool inf_open; /* true if `inf' is currently open */
bool logf_open; /* true if `logf' is currently open */
bool quit_now; /* set to false at beginning of Run and turns true only when QUIT command processed */
mutable std::ofstream logf; /* the log file output stream */
mutable NxsString message; /* workspace for composing output strings */
NxsTreesBlock * trees; /* pointer to NxsTreesBlock object */
NxsTaxaBlock * taxa; /* pointer to NxsTaxaBlock object */
NxsAssumptionsBlock * assumptions; /* pointer to NxsAssumptionsBlock object */
NxsDistancesBlock * distances; /* pointer to NxsDistancesBlock object */
NxsCharactersBlock * characters; /* pointer to NxsCharactersBlock object */
NxsDataBlock * data; /* pointer to NxsDataBlock object */
NxsUnalignedBlock * unaligned; /* pointer to NxsUnalignedBlock object */
char * next_command; /* workspace for processing next command entered interactively by user */
bool FileExists(const char* fn);
NxsString GetFileName(NxsToken& token);
void FactoryDefaults();
void HandleEndblock(NxsToken& token);
void HandleShow(NxsToken& token);
void HandleHelp(NxsToken& token);
void HandleLog(NxsToken& token);
void HandleExecute(NxsToken& token);
void PurgeBlocks();
virtual void Read(NxsToken& token);
virtual void Reset();
unsigned TaxonLabelToNumber(NxsString s) const;
};
/*----------------------------------------------------------------------------------------------------------------------
| The MyNexusToken class provides a NxsToken-derived object that can display output comments as it encounters them.
| The virtual function NxsToken::OutputComment is overridden in this class for this purpose.
*/
class MyNexusToken
: public NxsToken
{
public:
MyNexusToken(std::istream &i);
void OutputComment(const NxsString &msg);
};
/*----------------------------------------------------------------------------------------------------------------------
| Will be called by NxsReader::Execute after the initial "#NEXUS" keyword is found in a NEXUS file but before other
| tokens are read. Add code here if you need to do any initializations prior to encountering any NEXUS blocks in a
| NEXUS data file.
*/
inline void BASICCMDLINE::ExecuteStarting()
{
}
/*----------------------------------------------------------------------------------------------------------------------
| Will be called by NxsReader::Execute just before it exits after reading to the end of a NEXUS data file (or until
| encountering a LEAVE command between NEXUS blocks. Add code here if you need to clean up any memory allocated in
| ExecuteStarting.
*/
inline void BASICCMDLINE::ExecuteStopping()
{
}
/*----------------------------------------------------------------------------------------------------------------------
| Called if an "output comment" is encountered in a NEXUS data file. An output comment is a comment [text enclosed in
| square brackets] that begins with an exclamation point. [!This is an example of a NEXUS output comment]. Output
| comments are supposed to be displayed when encountered. Modify this function's body to display output comments,
| which are made available as they are encountered via the `msg' argument.
*/
inline void BASICCMDLINE::OutputComment(const NxsString &)
{
}
#endif
|
