/usr/include/relion-1.3/src/metadata_table.h is in librelion-dev-common 1.3+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | /***************************************************************************
*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program 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.
*
* This program 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.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
/***************************************************************************
*
* Authors: J.R. Bilbao-Castro (jrbcast@ace.ual.es)
*
* Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
*
* This program 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.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA
*
* All comments concerning this program package may be sent to the
* e-mail address 'xmipp@cnb.csic.es'
***************************************************************************/
#ifndef METADATA_TABLE_H
#define METADATA_TABLE_H
#include <map>
#include <vector>
#include <iostream>
#include <iterator>
#include <sstream>
#include <time.h>
#include <stdio.h>
#include <sstream>
#if !defined(__APPLE__)
#include <malloc.h>
#endif
#include "src/funcs.h"
#include "src/args.h"
#include "src/metadata_container.h"
/** For all objects.
@code
FOR_ALL_OBJECTS_IN_METADATA(metadata) {
double rot;
DF.getValue( EMDL_ANGLEROT, rot);
}
@endcode
*/
#define FOR_ALL_OBJECTS_IN_METADATA_TABLE(kkkk_metadata) \
for(long int current_object = (kkkk_metadata).firstObject(); \
current_object != MetaDataTable::NO_MORE_OBJECTS && current_object!= MetaDataTable::NO_OBJECTS_STORED; \
current_object=(kkkk_metadata).nextObject())
/** MetaDataTable Manager.
*
*/
class MetaDataTable
{
// Effectively stores all metadata
std::vector<MetaDataContainer *> objects;
// Current object id
long int current_objectID;
// Is this a 2D table or a 1D list?
bool isList;
// Name of the metadata table
std::string name;
// A comment for the metadata table
std::string comment;
public:
/** What labels have been read from a docfile/metadata file
* and/or will be stored on a new metadata file when "save" is
* called
**/
std::vector<EMDLabel> activeLabels;
/** When reading a column formated file, if a label is found that
* does not exists as a EMDLabel, it is ignored. For further
* file processing, such columns must be ignored and this structure
* allows to do that
**/
std::vector<unsigned int> ignoreLabels;
/** Empty Constructor.
*
* The MetaDataTable is created with no data stored on it.
*/
MetaDataTable();
/** Copy constructor
*
* Created a new MetaDataTable by copying all data from an existing MetaDataTable object.
*/
MetaDataTable(const MetaDataTable & c);
/** Assignment operator
* @ingroup MetaDataConstructors
*
* Copies MetaDataTable from an existing MetaDataTable object.
*/
MetaDataTable& operator =(const MetaDataTable &MD);
/** Destructor
* @ingroup MetaDataTableConstructors
*
* Frees all used memory and destroys object.
*/
~MetaDataTable();
/** Set to false if this is a MetaDataTable
* set to true if this is a simple list of parameters
*
*/
void setIsList(bool is_list);
// returns true of the metadatatable contains no objects
bool isEmpty() const;
// Returns the number of elements in the table
long int numberOfObjects() const;
// Removes all objects from the metadatatable
void clear();
/**Set Comment
*/
void setComment(const std::string Comment = "");
/**Get Comment
*/
std::string getComment() const;
/** Does this table contain a comment?
*/
bool containsComment() const;
/**Set Name
*/
void setName(const std::string Name = "");
/**Get Name
*/
std::string getName() const;
size_t size(void)
{
return objects.size();
}
/* Get value for any label.
* If the label does not exist, false is returned
* Otherwise, value is set correctly and true is returned
*/
template<class T>
bool getValue(EMDLabel name, T &value,
long int objectID = -1) const
{
if (isEmpty())
return false;
MetaDataContainer * aux = getObject(objectID);
// Inside getValue of the container there will be a check of the correct type
bool result = aux->getValue(name, value);
return result;
}
// Read/set a new pair/value for an specified object. If no objectID is given, that
// pointed by the class iterator is used
bool setValue(const std::string &name, const std::string &value,
long int objectID = -1);
template<class T>
bool setValue(EMDLabel name, const T &value, long int objectID=-1)
{
if (!isEmpty() && EMDL::isValidLabel(name))
{
long int auxID = (objectID == -1) ? current_objectID : objectID;
MetaDataContainer * aux = objects[auxID];
// Check whether label is correct (belongs to the enum in the metadata_container header
// and whether it is present in the activeLabels vector. If not, add it to all the other
// objects with default values
std::vector<EMDLabel>::iterator location;
std::map<long int, MetaDataContainer *>::iterator It;
location = std::find(activeLabels.begin(), activeLabels.end(), name);
if (location == activeLabels.end())
{
activeLabels.push_back(name);
// Add this label to the rest of the objects in this class
for (long int idx = 0; idx < objects.size(); idx++)
{
if (objects[idx] != aux)
{
objects[idx]->addValue(name, T());
}
}
}
aux->addValue(name, value);
return true;
}
else
{
std::cerr << " %%WARNING%%: unsuccessful setValue" << std::endl;
std::cerr << " isEmpty()= " << isEmpty() << std::endl;
std::cerr << " EMDL::isValidLabel(name)= " << EMDL::isValidLabel(name) << std::endl;
std::cerr << " name= " << EMDL::label2Str(name) << " value= " << value <<std::endl;
return false;
}
}
// Sort the order of the elements based on the values in the input label (only numbers, no strings/bools!)
// Have to pass dummy T parameter to get the template thing running?
void sort(EMDLabel name, bool do_reverse = false, bool only_set_index = false)
{
if ( !(EMDL::isInt(name) || EMDL::isLong(name) || EMDL::isDouble(name)) )
REPORT_ERROR("MetadataTable::sort%% ERROR: can only sorted numbers");
std::vector<std::pair<double,long int> > vp;
vp.reserve(objects.size());
long int i = 0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(*this)
{
double dval;
if (EMDL::isInt(name))
{
int val;
getValue(name, val);
dval = (double) val;
}
else if (EMDL::isLong(name))
{
long int val;
getValue(name, val);
dval = (double) val;
}
else
{
// EMDL::isDouble(name)
getValue(name, dval);
}
vp.push_back(std::make_pair(dval, i));
i++;
}
std::sort(vp.begin(), vp.end());
if (do_reverse)
std::reverse(vp.begin(), vp.end());
if (only_set_index)
{
// Add an extra column with the sorted position of each entry
for (long int j = 0; j < vp.size(); j++)
{
(*this).setValue(EMDL_SORTED_IDX, j, vp[j].second);
}
}
else
{
// Change the actual order in the MetaDataTable
MetaDataTable MDaux;
for (long int j = 0; j < vp.size(); j++)
{
MDaux.addObject();
MDaux.setObject((*this).getObject(vp[j].second));
}
*this = MDaux;
}
// return pointer to the beginning of the table
firstObject();
}
bool valueExists(EMDLabel name)
{
return (objects[current_objectID])->valueExists(name);
}
/** Check whether a label is contained in metadata.
*/
bool containsLabel(const EMDLabel label) const;
/** Deactivate a column from a table, so that it is no longer written out
*/
void deactivateLabel(EMDLabel label);
/** Append the app table to this one
*/
void append(MetaDataTable &app);
/** Add a new label to the metadata.
*/
bool addLabel(const EMDLabel label);
/** Adds a new object to the objects map.
* If objectID == -1 the new ID will be that for the last object inserted + 1, else
* the given objectID is used.
* If there is already an object whose objectID == input objectID, the old one will be replaced by the new one
* If data !=NULL, the object will be set to contain these data
**/
long int addObject(MetaDataContainer * data = NULL, long int objectID = -1);
/** Remove an object from the table. If objectID is not given, the current object will be removed
* This function resets the current pointer to the last entry and returns the lastObject in the table */
long int removeObject(long int objectID = -1);
/* Get metadatacontainer for objectID (is current_objectID when -1)
*/
MetaDataContainer * getObject(long int objectID = -1) const;
/* Set metadatacontainer for current metadata object
* This function assumes there already exists an object with objectID
* If objectID==-1,, then the (assumedly existing) currrent_objectID will be set
*
* Use addObject() to set an object that does not yet exist
*/
void setObject(MetaDataContainer * data, long int objectID = -1);
// Possible error codes for the map
enum errors
{
NO_OBJECTS_STORED = -1, // NOTE: Do not change this value (-1)
NO_MORE_OBJECTS = -2,
NO_OBJECT_FOUND = -3
};
long int firstObject();
long int nextObject();
long int lastObject();
long int goToObject(long int objectID);
/* Read a STAR loop structure
*/
void readStarLoop(std::ifstream& in, std::vector<EMDLabel> *labelsVector = NULL);
/* Read a STAR list
* The function returns true if the list is followed by a loop, false otherwise
*/
bool readStarList(std::ifstream& in, std::vector<EMDLabel> *labelsVector = NULL);
/* Read a MetaDataTable from a STAR-format data block
*
* If the data block contains a list and a table, the function will return 2,
* the first time it is called and the list is read into the MetaDataTable
* in that case the function needs to be called another time. The second time
* it will read the _loop structure into the MetaDataTable and 1 will be returned
*
* If the data block contains only a list or a table, it is read in the MetaDataTable and the function will return 1
*
* If no data block is found the function will return 0 and the MetaDataTable remains empty
*
*/
int readStar(std::ifstream& in, const std::string &name = "", std::vector<EMDLabel> *labelsVector = NULL);
// Read a MetaDataTable (get fileformat from extension)
int read(const FileName &filename, const std::string &name = "", std::vector<EMDLabel> *labelsVector = NULL);
// Write a MetaDataTable in STAR format
void write(std::ostream& out = std::cout);
// Write to a single file
void write(const FileName & fn_out);
void writeValueToString(std::string & result,
const std::string & inputLabel);
};
#endif
|