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1 | + | /* |
2 | + | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 | + | * |
4 | + | * The University of Notre Dame grants you ("Licensee") a |
5 | + | * non-exclusive, royalty free, license to use, modify and |
6 | + | * redistribute this software in source and binary code form, provided |
7 | + | * that the following conditions are met: |
8 | + | * |
9 | + | * 1. Redistributions of source code must retain the above copyright |
10 | + | * notice, this list of conditions and the following disclaimer. |
11 | + | * |
12 | + | * 2. Redistributions in binary form must reproduce the above copyright |
13 | + | * notice, this list of conditions and the following disclaimer in the |
14 | + | * documentation and/or other materials provided with the |
15 | + | * distribution. |
16 | + | * |
17 | + | * This software is provided "AS IS," without a warranty of any |
18 | + | * kind. All express or implied conditions, representations and |
19 | + | * warranties, including any implied warranty of merchantability, |
20 | + | * fitness for a particular purpose or non-infringement, are hereby |
21 | + | * excluded. The University of Notre Dame and its licensors shall not |
22 | + | * be liable for any damages suffered by licensee as a result of |
23 | + | * using, modifying or distributing the software or its |
24 | + | * derivatives. In no event will the University of Notre Dame or its |
25 | + | * licensors be liable for any lost revenue, profit or data, or for |
26 | + | * direct, indirect, special, consequential, incidental or punitive |
27 | + | * damages, however caused and regardless of the theory of liability, |
28 | + | * arising out of the use of or inability to use software, even if the |
29 | + | * University of Notre Dame has been advised of the possibility of |
30 | + | * such damages. |
31 | + | * |
32 | + | * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
33 | + | * research, please cite the appropriate papers when you publish your |
34 | + | * work. Good starting points are: |
35 | + | * |
36 | + | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
37 | + | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
38 | + | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
39 | + | * [4] Vardeman & Gezelter, in progress (2009). |
40 | + | */ |
41 | + | |
42 | + | #include <algorithm> |
43 | #include "utils/StringUtils.hpp" | |
44 | ||
45 | < | using namespace std; |
46 | < | using namespace oopse; |
47 | < | |
48 | < | string UpperCase(const string& S) { |
49 | < | string uc = S; |
50 | < | unsigned int n = uc.size(); |
51 | < | for (unsigned int j = 0; j < n; j++) { |
52 | < | char sj = uc[j]; |
53 | < | if (sj >= 'a' && sj <= 'z') uc[j] = (char)(sj - ('a' - 'A')); |
45 | > | namespace OpenMD { |
46 | > | std::string UpperCase(const std::string& S) { |
47 | > | std::string uc = S; |
48 | > | unsigned int n = uc.size(); |
49 | > | for (unsigned int j = 0; j < n; j++) { |
50 | > | char sj = uc[j]; |
51 | > | if (sj >= 'a' && sj <= 'z') uc[j] = (char)(sj - ('a' - 'A')); |
52 | > | } |
53 | > | return uc; |
54 | } | |
13 | – | return uc; |
14 | – | } |
55 | ||
56 | < | string LowerCase(const string& S) { |
57 | < | string lc = S; |
58 | < | unsigned int n = lc.size(); |
59 | < | for (unsigned int j = 0; j < n; j++) { |
60 | < | char sj = lc[j]; |
61 | < | if (sj >= 'A' && sj <= 'Z') lc[j] = (char)(sj + ('a' - 'A')); |
56 | > | std::string LowerCase(const std::string& S) { |
57 | > | std::string lc = S; |
58 | > | unsigned int n = lc.size(); |
59 | > | for (unsigned int j = 0; j < n; j++) { |
60 | > | char sj = lc[j]; |
61 | > | if (sj >= 'A' && sj <= 'Z') lc[j] = (char)(sj + ('a' - 'A')); |
62 | > | } |
63 | > | return lc; |
64 | } | |
23 | – | return lc; |
24 | – | } |
65 | ||
66 | < | int findBegin(istream theStream, char* startText ){ |
67 | < | const int MAXLEN = 1024; |
68 | < | char readLine[MAXLEN]; |
29 | < | int foundText = 0; |
30 | < | int lineNum; |
31 | < | char* the_token; |
32 | < | char* eof_test; |
66 | > | char* trimSpaces(char *str) { |
67 | > | size_t len; |
68 | > | char *right, *left; |
69 | ||
70 | < | // rewind the stream |
35 | < | theStream.seekg (0, ios::beg); |
36 | < | lineNum = 0; |
70 | > | if (strlen(str) == 0) return(str); |
71 | ||
72 | < | if (!theStream.eof()) { |
73 | < | theStream.getline(readLine, MAXLEN); |
74 | < | lineNum++; |
75 | < | } else { |
76 | < | printf( "Error fast forwarding stream: stream is empty.\n"); |
77 | < | return -1; |
72 | > | /* Trim whitespace from left side */ |
73 | > | for (left = str; isspace(*left); left++); |
74 | > | |
75 | > | /* Trim whitespace from right side */ |
76 | > | if ((len = strlen(left))) |
77 | > | { |
78 | > | right = left + (len - 1); |
79 | > | |
80 | > | while (isspace(*right)) |
81 | > | { |
82 | > | *right = '\0'; |
83 | > | right--; |
84 | > | } |
85 | > | } |
86 | > | |
87 | > | /* Only do the str copy if there were spaces to the left */ |
88 | > | if (left != str) |
89 | > | strcpy(str, left); |
90 | > | |
91 | > | return (str); |
92 | } | |
93 | + | |
94 | + | int findBegin(std::istream &theStream, const char* startText ){ |
95 | + | const int MAXLEN = 1024; |
96 | + | char readLine[MAXLEN]; |
97 | + | int foundText = 0; |
98 | + | int lineNum; |
99 | + | char* the_token; |
100 | + | char* eof_test; |
101 | + | |
102 | + | // rewind the stream |
103 | + | theStream.seekg (0, std::ios::beg); |
104 | + | lineNum = 0; |
105 | ||
106 | < | while ( !foundText ) { |
107 | < | |
108 | < | if (theStream.eof()) { |
109 | < | printf("Error fast forwarding stream at line %d: " |
110 | < | "stream ended unexpectedly.\n", lineNum); |
106 | > | if (!theStream.eof()) { |
107 | > | theStream.getline(readLine, MAXLEN); |
108 | > | lineNum++; |
109 | > | } else { |
110 | > | printf( "Error fast forwarding stream: stream is empty.\n"); |
111 | return -1; | |
112 | } | |
113 | < | |
114 | < | the_token = strtok( readLine, " ,;\t" ); |
115 | < | |
116 | < | if (!strcasecmp("begin", the_token)) { |
117 | < | the_token = TrimSpaces(strtok( NULL, " ,;\t" )); |
118 | < | foundText = !strcasecmp( startText, the_token ); |
59 | < | } |
60 | < | |
61 | < | if (!foundText) { |
62 | < | if (!theStream.eof()) { |
63 | < | theStream.getline(readLine, MAXLEN); |
64 | < | lineNum++; |
65 | < | } else { |
66 | < | printf( "Error fast forwarding stream at line %d: " |
67 | < | "stream ended unexpectedly.\n", lineNum); |
113 | > | |
114 | > | while ( !foundText ) { |
115 | > | |
116 | > | if (theStream.eof()) { |
117 | > | printf("Error fast forwarding stream at line %d: " |
118 | > | "stream ended unexpectedly.\n", lineNum); |
119 | return -1; | |
120 | } | |
121 | + | |
122 | + | the_token = strtok( readLine, " ,;\t" ); |
123 | + | if ( the_token != NULL) |
124 | + | if (!strcasecmp("begin", the_token)) { |
125 | + | the_token = strtok( NULL, " ,;\t" ); |
126 | + | if ( the_token != NULL){ |
127 | + | foundText = !strcasecmp( startText, the_token ); |
128 | + | } |
129 | + | } |
130 | + | |
131 | + | if (!foundText) { |
132 | + | if (!theStream.eof()) { |
133 | + | theStream.getline(readLine, MAXLEN); |
134 | + | lineNum++; |
135 | + | } else { |
136 | + | printf( "Error fast forwarding stream at line %d: " |
137 | + | "stream ended unexpectedly.\n", lineNum); |
138 | + | return -1; |
139 | + | } |
140 | + | } |
141 | } | |
142 | + | return lineNum; |
143 | } | |
72 | – | return lineNum; |
73 | – | } |
144 | ||
145 | < | int countTokens(char *line, char *delimiters) { |
146 | < | /* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
145 | > | int countTokens(char *line, char *delimiters) { |
146 | > | /* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
147 | ||
148 | < | char *working_line; /* WORKING COPY OF LINE. */ |
149 | < | int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
150 | < | char *strtok_ptr; /* POINTER FOR STRTOK. */ |
148 | > | char *working_line; /* WORKING COPY OF LINE. */ |
149 | > | int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
150 | > | char *strtok_ptr; /* POINTER FOR STRTOK. */ |
151 | ||
152 | < | strtok_ptr= working_line= strdup(line); |
152 | > | strtok_ptr= working_line= strdup(line); |
153 | ||
154 | < | ntokens=0; |
155 | < | while (strtok(strtok_ptr,delimiters)!=NULL) |
156 | < | { |
157 | < | ntokens++; |
158 | < | strtok_ptr=NULL; |
159 | < | } |
154 | > | ntokens=0; |
155 | > | while (strtok(strtok_ptr,delimiters)!=NULL) |
156 | > | { |
157 | > | ntokens++; |
158 | > | strtok_ptr=NULL; |
159 | > | } |
160 | ||
161 | < | free(working_line); |
162 | < | return(ntokens); |
163 | < | } |
161 | > | free(working_line); |
162 | > | return(ntokens); |
163 | > | } |
164 | ||
165 | < | char* TrimSpaces(char *str) { |
166 | < | size_t len; |
167 | < | char *right, *left; |
165 | > | int isEndLine(char *line) { |
166 | > | char *working_line; |
167 | > | char *foo; |
168 | ||
169 | < | if (strlen(str) == 0) return(str); |
169 | > | working_line = strdup(line); |
170 | ||
171 | < | /* Trim whitespace from left side */ |
172 | < | for (left = str; isspace(*left); left++); |
173 | < | |
174 | < | /* Trim whitespace from right side */ |
175 | < | if ((len = strlen(left))) |
176 | < | { |
107 | < | right = left + (len - 1); |
108 | < | |
109 | < | while (isspace(*right)) |
110 | < | { |
111 | < | *right = '\0'; |
112 | < | right--; |
113 | < | } |
171 | > | foo = strtok(working_line, " ,;\t"); |
172 | > | |
173 | > | if (foo != NULL) { |
174 | > | |
175 | > | if (!strcasecmp(foo, "end")) return 1; |
176 | > | |
177 | } | |
178 | + | |
179 | + | return 0; |
180 | + | } |
181 | ||
182 | < | /* Only do the str copy if their was spaces to the left */ |
183 | < | if (left != str) |
184 | < | strcpy(str, left); |
185 | < | |
186 | < | return (str); |
182 | > | std::string OpenMD_itoa(int value, unsigned int base) { |
183 | > | const char digitMap[] = "0123456789abcdef"; |
184 | > | std::string buf; |
185 | > | |
186 | > | if (base == 0 || base > 16) { |
187 | > | return buf; |
188 | > | } |
189 | > | |
190 | > | if (value == 0) { |
191 | > | buf = "0"; |
192 | > | return buf; |
193 | > | } |
194 | > | |
195 | > | // Take care negative int: |
196 | > | |
197 | > | std::string sign; |
198 | > | int _value = value; |
199 | > | if (value < 0) { |
200 | > | _value = -value; |
201 | > | sign = "-"; |
202 | > | } |
203 | > | |
204 | > | // Translating number to string with base: |
205 | > | for (int i = 30; _value && i ; --i) { |
206 | > | buf = digitMap[ _value % base ] + buf; |
207 | > | _value /= base; |
208 | > | } |
209 | > | return sign.append(buf); |
210 | > | } |
211 | > | |
212 | > | |
213 | > | std::string getPrefix(const std::string& str) { |
214 | > | return str.substr(0, str.rfind('.')); |
215 | > | } |
216 | > | |
217 | > | std::string getSuffix(const std::string& str) { |
218 | > | return str.substr(0, str.find('.')); |
219 | > | } |
220 | > | |
221 | > | bool isInteger(const std::string& str) { |
222 | > | |
223 | > | bool result = false; |
224 | > | |
225 | > | std::string::const_iterator i = str.begin(); |
226 | > | if (i != str.end() && (*i == '+' || *i == '-' || std::isdigit(*i) )) { |
227 | > | ++i; |
228 | > | while (i != str.end() && std::isdigit(*i)) |
229 | > | ++i; |
230 | > | if (i == str.end()) |
231 | > | result = true; |
232 | > | } |
233 | > | |
234 | > | return result; |
235 | } | |
236 | ||
237 | < | int isEndLine(char *line) { |
238 | < | char *working_line; |
239 | < | char *foo; |
126 | < | |
127 | < | working_line = strdup(line); |
128 | < | |
129 | < | foo = strtok(working_line, " ,;\t"); |
237 | > | bool CaseInsensitiveEquals(const char ch1, const char ch2) { |
238 | > | return std::toupper((unsigned char)ch1) == std::toupper((unsigned char)ch2); |
239 | > | } |
240 | ||
241 | < | if (!strcasecmp(foo, "end")) return 1; |
242 | < | |
243 | < | return 0; |
241 | > | size_t CaseInsensitiveFind(const std::string& str1, const std::string& str2) { |
242 | > | std::string::const_iterator pos = std::search(str1.begin(), str1.end(), str2.begin(), str2.end(), CaseInsensitiveEquals); |
243 | > | if (pos == str1.end()) |
244 | > | return std::string::npos; |
245 | > | else |
246 | > | return pos - str1.begin(); |
247 | } | |
248 | + | |
249 | + | } |
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