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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "config.h" |
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#include <algorithm> |
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#include <stdlib.h> |
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#include <cctype> |
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#include <cstdlib> |
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#include <string> |
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|
#include "utils/StringUtils.hpp" |
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|
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< |
using namespace std; |
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using namespace oopse; |
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#ifdef _MSC_VER |
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#define strcasecmp _stricmp |
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#define strdup _strdup |
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#define strtoull _strtoui64 |
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#endif |
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|
|
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string UpperCase(const string& S) { |
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string uc = S; |
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unsigned int n = uc.size(); |
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for (unsigned int j = 0; j < n; j++) { |
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char sj = uc[j]; |
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if (sj >= 'a' && sj <= 'z') uc[j] = (char)(sj - ('a' - 'A')); |
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> |
|
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> |
namespace OpenMD { |
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std::string UpperCase(const std::string& S) { |
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std::string uc = S; |
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unsigned int n = uc.size(); |
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for (unsigned int j = 0; j < n; j++) { |
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char sj = uc[j]; |
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if (sj >= 'a' && sj <= 'z') uc[j] = (char)(sj - ('a' - 'A')); |
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} |
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return uc; |
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} |
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return uc; |
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} |
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|
|
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< |
string LowerCase(const string& S) { |
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< |
string lc = S; |
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< |
unsigned int n = lc.size(); |
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< |
for (unsigned int j = 0; j < n; j++) { |
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< |
char sj = lc[j]; |
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< |
if (sj >= 'A' && sj <= 'Z') lc[j] = (char)(sj + ('a' - 'A')); |
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> |
std::string LowerCase(const std::string& S) { |
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std::string lc = S; |
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> |
unsigned int n = lc.size(); |
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for (unsigned int j = 0; j < n; j++) { |
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char sj = lc[j]; |
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if (sj >= 'A' && sj <= 'Z') lc[j] = (char)(sj + ('a' - 'A')); |
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} |
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return lc; |
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} |
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return lc; |
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} |
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|
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< |
int findBegin(istream theStream, char* startText ){ |
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< |
const int MAXLEN = 1024; |
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< |
char readLine[MAXLEN]; |
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< |
int foundText = 0; |
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< |
int lineNum; |
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char* the_token; |
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char* eof_test; |
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char* trimSpaces(char *str) { |
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size_t len; |
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char *right, *left; |
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|
|
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< |
// rewind the stream |
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theStream.seekg (0, ios::beg); |
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lineNum = 0; |
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> |
if (strlen(str) == 0) return(str); |
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|
|
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< |
if (!theStream.eof()) { |
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< |
theStream.getline(readLine, MAXLEN); |
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< |
lineNum++; |
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< |
} else { |
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< |
printf( "Error fast forwarding stream: stream is empty.\n"); |
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< |
return -1; |
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> |
/* Trim whitespace from left side */ |
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for (left = str; isspace(*left); left++); |
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|
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/* Trim whitespace from right side */ |
89 |
> |
if ((len = strlen(left))) |
90 |
> |
{ |
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> |
right = left + (len - 1); |
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> |
|
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> |
while (isspace(*right)) |
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{ |
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> |
*right = '\0'; |
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> |
right--; |
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> |
} |
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> |
} |
99 |
> |
|
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> |
/* Only do the str copy if there were spaces to the left */ |
101 |
> |
if (left != str) |
102 |
> |
strcpy(str, left); |
103 |
> |
|
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> |
return (str); |
105 |
|
} |
106 |
+ |
|
107 |
+ |
int findBegin(std::istream &theStream, const char* startText ){ |
108 |
+ |
const int MAXLEN = 1024; |
109 |
+ |
char readLine[MAXLEN]; |
110 |
+ |
int foundText = 0; |
111 |
+ |
int lineNum; |
112 |
+ |
char* the_token; |
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|
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// rewind the stream |
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theStream.seekg (0, std::ios::beg); |
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lineNum = 0; |
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|
|
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< |
while ( !foundText ) { |
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< |
|
120 |
< |
if (theStream.eof()) { |
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< |
printf("Error fast forwarding stream at line %d: " |
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< |
"stream ended unexpectedly.\n", lineNum); |
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> |
if (!theStream.eof()) { |
119 |
> |
theStream.getline(readLine, MAXLEN); |
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> |
lineNum++; |
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> |
} else { |
122 |
> |
printf( "Error fast forwarding stream: stream is empty.\n"); |
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|
return -1; |
124 |
|
} |
125 |
< |
|
126 |
< |
the_token = strtok( readLine, " ,;\t" ); |
127 |
< |
|
128 |
< |
if (!strcasecmp("begin", the_token)) { |
129 |
< |
the_token = TrimSpaces(strtok( NULL, " ,;\t" )); |
130 |
< |
foundText = !strcasecmp( startText, the_token ); |
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< |
} |
60 |
< |
|
61 |
< |
if (!foundText) { |
62 |
< |
if (!theStream.eof()) { |
63 |
< |
theStream.getline(readLine, MAXLEN); |
64 |
< |
lineNum++; |
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< |
} else { |
66 |
< |
printf( "Error fast forwarding stream at line %d: " |
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< |
"stream ended unexpectedly.\n", lineNum); |
125 |
> |
|
126 |
> |
while ( !foundText ) { |
127 |
> |
|
128 |
> |
if (theStream.eof()) { |
129 |
> |
printf("Error fast forwarding stream at line %d: " |
130 |
> |
"stream ended unexpectedly.\n", lineNum); |
131 |
|
return -1; |
132 |
|
} |
133 |
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|
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the_token = strtok( readLine, " ,;\t" ); |
135 |
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if ( the_token != NULL) |
136 |
+ |
if (!strcasecmp("begin", the_token)) { |
137 |
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the_token = strtok( NULL, " ,;\t" ); |
138 |
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if ( the_token != NULL){ |
139 |
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foundText = !strcasecmp( startText, the_token ); |
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+ |
} |
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} |
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|
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if (!foundText) { |
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+ |
if (!theStream.eof()) { |
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theStream.getline(readLine, MAXLEN); |
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+ |
lineNum++; |
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} else { |
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+ |
printf( "Error fast forwarding stream at line %d: " |
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+ |
"stream ended unexpectedly.\n", lineNum); |
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+ |
return -1; |
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} |
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+ |
} |
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|
} |
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+ |
return lineNum; |
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|
} |
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– |
return lineNum; |
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– |
} |
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|
|
157 |
< |
int countTokens(char *line, char *delimiters) { |
158 |
< |
/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
157 |
> |
int countTokens(char *line, char *delimiters) { |
158 |
> |
/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
159 |
|
|
160 |
< |
char *working_line; /* WORKING COPY OF LINE. */ |
161 |
< |
int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
162 |
< |
char *strtok_ptr; /* POINTER FOR STRTOK. */ |
160 |
> |
char *working_line; /* WORKING COPY OF LINE. */ |
161 |
> |
int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
162 |
> |
char *strtok_ptr; /* POINTER FOR STRTOK. */ |
163 |
|
|
164 |
< |
strtok_ptr= working_line= strdup(line); |
164 |
> |
strtok_ptr= working_line= strdup(line); |
165 |
|
|
166 |
< |
ntokens=0; |
167 |
< |
while (strtok(strtok_ptr,delimiters)!=NULL) |
168 |
< |
{ |
169 |
< |
ntokens++; |
170 |
< |
strtok_ptr=NULL; |
171 |
< |
} |
166 |
> |
ntokens=0; |
167 |
> |
while (strtok(strtok_ptr,delimiters)!=NULL) |
168 |
> |
{ |
169 |
> |
ntokens++; |
170 |
> |
strtok_ptr=NULL; |
171 |
> |
} |
172 |
|
|
173 |
< |
free(working_line); |
174 |
< |
return(ntokens); |
175 |
< |
} |
173 |
> |
free(working_line); |
174 |
> |
return(ntokens); |
175 |
> |
} |
176 |
|
|
177 |
< |
char* TrimSpaces(char *str) { |
178 |
< |
size_t len; |
179 |
< |
char *right, *left; |
177 |
> |
int isEndLine(char *line) { |
178 |
> |
char *working_line; |
179 |
> |
char *foo; |
180 |
|
|
181 |
< |
if (strlen(str) == 0) return(str); |
181 |
> |
working_line = strdup(line); |
182 |
|
|
183 |
< |
/* Trim whitespace from left side */ |
184 |
< |
for (left = str; isspace(*left); left++); |
183 |
> |
foo = strtok(working_line, " ,;\t"); |
184 |
> |
|
185 |
> |
if (foo != NULL) { |
186 |
> |
|
187 |
> |
if (!strcasecmp(foo, "end")) return 1; |
188 |
> |
|
189 |
> |
} |
190 |
> |
|
191 |
> |
return 0; |
192 |
> |
} |
193 |
|
|
194 |
< |
/* Trim whitespace from right side */ |
195 |
< |
if ((len = strlen(left))) |
196 |
< |
{ |
197 |
< |
right = left + (len - 1); |
198 |
< |
|
199 |
< |
while (isspace(*right)) |
110 |
< |
{ |
111 |
< |
*right = '\0'; |
112 |
< |
right--; |
113 |
< |
} |
194 |
> |
std::string OpenMD_itoa(int value, unsigned int base) { |
195 |
> |
const char digitMap[] = "0123456789abcdef"; |
196 |
> |
std::string buf; |
197 |
> |
|
198 |
> |
if (base == 0 || base > 16) { |
199 |
> |
return buf; |
200 |
|
} |
201 |
+ |
|
202 |
+ |
if (value == 0) { |
203 |
+ |
buf = "0"; |
204 |
+ |
return buf; |
205 |
+ |
} |
206 |
+ |
|
207 |
+ |
// Take care negative int: |
208 |
+ |
|
209 |
+ |
std::string sign; |
210 |
+ |
int _value = value; |
211 |
+ |
if (value < 0) { |
212 |
+ |
_value = -value; |
213 |
+ |
sign = "-"; |
214 |
+ |
} |
215 |
+ |
|
216 |
+ |
// Translating number to string with base: |
217 |
+ |
for (int i = 30; _value && i ; --i) { |
218 |
+ |
buf = digitMap[ _value % base ] + buf; |
219 |
+ |
_value /= base; |
220 |
+ |
} |
221 |
+ |
return sign.append(buf); |
222 |
+ |
} |
223 |
+ |
|
224 |
+ |
|
225 |
+ |
std::string getPrefix(const std::string& str) { |
226 |
+ |
return str.substr(0, str.rfind('.')); |
227 |
+ |
} |
228 |
+ |
|
229 |
+ |
std::string getSuffix(const std::string& str) { |
230 |
+ |
return str.substr(0, str.find('.')); |
231 |
+ |
} |
232 |
|
|
233 |
< |
/* Only do the str copy if their was spaces to the left */ |
234 |
< |
if (left != str) |
235 |
< |
strcpy(str, left); |
236 |
< |
|
237 |
< |
return (str); |
238 |
< |
} |
233 |
> |
bool isInteger(const std::string& str) { |
234 |
> |
|
235 |
> |
bool result = false; |
236 |
> |
|
237 |
> |
std::string::const_iterator i = str.begin(); |
238 |
> |
if (i != str.end() && (*i == '+' || *i == '-' || std::isdigit(*i) )) { |
239 |
> |
++i; |
240 |
> |
while (i != str.end() && std::isdigit(*i)) |
241 |
> |
++i; |
242 |
> |
if (i == str.end()) |
243 |
> |
result = true; |
244 |
> |
} |
245 |
> |
|
246 |
> |
return result; |
247 |
> |
} |
248 |
|
|
249 |
< |
int isEndLine(char *line) { |
250 |
< |
char *working_line; |
251 |
< |
char *foo; |
249 |
> |
bool CaseInsensitiveEquals(const char ch1, const char ch2) { |
250 |
> |
return std::toupper((unsigned char)ch1) == std::toupper((unsigned char)ch2); |
251 |
> |
} |
252 |
|
|
253 |
< |
working_line = strdup(line); |
253 |
> |
size_t CaseInsensitiveFind(const std::string& str1, const std::string& str2) { |
254 |
> |
std::string::const_iterator pos = std::search(str1.begin(), str1.end(), str2.begin(), str2.end(), CaseInsensitiveEquals); |
255 |
> |
if (pos == str1.end()) |
256 |
> |
return std::string::npos; |
257 |
> |
else |
258 |
> |
return pos - str1.begin(); |
259 |
> |
} |
260 |
|
|
261 |
< |
foo = strtok(working_line, " ,;\t"); |
262 |
< |
|
263 |
< |
if (!strcasecmp(foo, "end")) return 1; |
264 |
< |
|
265 |
< |
return 0; |
261 |
> |
/** |
262 |
> |
* memparse - parse a string with mem suffixes into a number |
263 |
> |
* @param ptr: Where parse begins |
264 |
> |
* @param retptr: (output) Pointer to next char after parse completes |
265 |
> |
* |
266 |
> |
* Parses a string into a number. The number stored at @param ptr is |
267 |
> |
* potentially suffixed with %K (for kilobytes, or 1024 bytes), |
268 |
> |
* %M (for megabytes, or 1048576 bytes), or %G (for gigabytes, or |
269 |
> |
* 1073741824). If the number is suffixed with K, M, or G, then |
270 |
> |
* the return value is the number multiplied by one kilobyte, one |
271 |
> |
* megabyte, or one gigabyte, respectively. |
272 |
> |
*/ |
273 |
> |
unsigned long long memparse (char *ptr, char **retptr) { |
274 |
> |
unsigned long long ret = strtoull (ptr, retptr, 0); |
275 |
> |
|
276 |
> |
switch (**retptr) { |
277 |
> |
case 'G': |
278 |
> |
case 'g': |
279 |
> |
ret <<= 10; |
280 |
> |
case 'M': |
281 |
> |
case 'm': |
282 |
> |
ret <<= 10; |
283 |
> |
case 'K': |
284 |
> |
case 'k': |
285 |
> |
ret <<= 10; |
286 |
> |
(*retptr)++; |
287 |
> |
default: |
288 |
> |
break; |
289 |
> |
} |
290 |
> |
return ret; |
291 |
> |
} |
292 |
> |
|
293 |
|
} |