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#ifndef __VOCABULARY_FILE_H__
#define __VOCABULARY_FILE_H__
/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET 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.
*
* CARET 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 CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "AbstractFile.h"
#include "CellStudyInfo.h"
#include "StudyMetaDataLinkSet.h"
class QDomNode;
class XmlGenericWriter;
/// class for storing vocabulary information
class VocabularyFile : public AbstractFile {
public:
/// stores vocabulary data entry
class VocabularyEntry {
public:
// constructor
VocabularyEntry();
// constructor
VocabularyEntry(const QString& abbreviationIn,
const QString& fullNameIn = "",
const QString& classNameIn = "",
const QString& vocabularyIDIn = "",
const QString& descriptionIn = "",
const QString& ontologySourceIn = "",
const QString& termIDIn = "",
const int studyNumberIn = -1);
// copy constructor
VocabularyEntry(const VocabularyEntry& ve);
// assignment operator
VocabularyEntry& operator=(const VocabularyEntry& ve);
// destructor
~VocabularyEntry();
// get full description of all fields for display to user
//QString getFullDescriptionForDisplayToUser(const bool useHTML) const;
/// get the abbreviation
QString getAbbreviation() const { return abbreviation; }
// set the abbreviation
void setAbbreviation(const QString& a);
/// get the full name
QString getFullName() const { return fullName; }
// set the full name
void setFullName(const QString& n);
/// get the description
QString getDescription() const { return description; }
// set the description
void setDescription(const QString& d);
/// get the class name
QString getClassName() const { return className; }
// set the class name
void setClassName(const QString& s);
/// get the ontology source
QString getOntologySource() const { return ontologySource; }
/// set the ontology source
void setOntologySource(const QString& s);
// get ontology source values
static void getOntologySourceValues(std::vector<QString>& ontologySourceValues);
/// get the term id
QString getTermID() const { return termID; }
/// set the term id
void setTermID(const QString& s);
/// get the vocabulary ID
QString getVocabularyID() const { return vocabularyID; }
// set the vocabulary ID
void setVocabularyID(const QString& s);
/// get the study number
int getStudyNumber() const { return studyNumber; }
// set the study number
void setStudyNumber(const int sn);
/// get the study metadata link set
StudyMetaDataLinkSet getStudyMetaDataLinkSet() const { return studyMetaDataLinkSet; }
/// set the study metadata link set
void setStudyMetaDataLinkSet(const StudyMetaDataLinkSet smdls);
/// write the data into a StringTable
static void writeDataIntoStringTable(const std::vector<VocabularyEntry>& data,
StringTable& table);
/// read the data from a StringTable
static void readDataFromStringTable(std::vector<VocabularyEntry>& data,
const StringTable& table) throw (FileException);
protected:
// copy helper
void copyHelper(const VocabularyEntry& ve);
// clear this item
void clear();
// set this item modified
void setModified();
// called to read from an XML structure.
void readXML(QDomNode& nodeIn) throw (FileException);
// called to write to an XML structure.
void writeXML(QDomDocument& xmlDoc,
QDomElement& parentElement) const;
// called to write XML
void writeXML(XmlGenericWriter& xmlWriter) const throw (FileException);
/// VocabularyFile entry with which this is association
VocabularyFile* vocabularyFile;
/// the abbreviated name
QString abbreviation;
/// the full name
QString fullName;
/// the class name
QString className;
/// ontology source
QString ontologySource;
/// term id
QString termID;
/// the vocabulary ID
QString vocabularyID;
/// the description
QString description;
/// the study number
int studyNumber;
/// the study metadata link
StudyMetaDataLinkSet studyMetaDataLinkSet;
// ***** IF ADDITIONAL MEMBERS ADDED, UPDATE copyHelper() **********
friend class VocabularyFile;
};
// constructor
VocabularyFile();
// destructor
~VocabularyFile();
// add a vocabulary entry (returns its index)
int addVocabularyEntry(const VocabularyEntry& ve);
// delete a vocabulary entry
void deleteVocabularyEntry(const int indx);
// append a vocabulary file to "this" vocabulary file
void append(const VocabularyFile& vf);
// Clears current file data in memory. Deriving classes must override this method and
// call AbstractFile::clearAbstractFile() from its clear method.
void clear();
// returns true if the file is isEmpty (contains no data)
bool empty() const;
/// get the number of vocabulary entries
int getNumberOfVocabularyEntries() const { return vocabularyEntries.size(); }
// a vocabulary entry using its index
VocabularyEntry* getVocabularyEntry(const int indx);
// a vocabulary entry using its index (const method)
const VocabularyEntry* getVocabularyEntry(const int indx) const;
// get the index of a vocabulary entry from its abbreviation (-1 if not found)
int getVocabularyEntryIndexFromName(const QString& abbreviationIn) const;
// get a vocabulary entry from its abbreviation (NULL if not found)
VocabularyEntry* getVocabularyEntryByName(const QString& abbreviationIn);
// get a vocabulary entry from its abbreviation (const method)
const VocabularyEntry* getVocabularyEntryByName(const QString& abbreviationIn) const;
// get the best matching vocabulary entry (abbreviationIn begins with entry name)
VocabularyEntry* getBestMatchingVocabularyEntry(const QString abbreviationIn,
const bool caseSensitive = true);
// get the best matching vocabulary entry (abbreviationIn begins with entry name)
const VocabularyEntry* getBestMatchingVocabularyEntry(const QString abbreviationIn,
const bool caseSensitive = true) const;
/// find out if comma separated file conversion supported
void getCommaSeparatedFileSupport(bool& readFromCSV,
bool& writeToCSV) const;
/// write the file's data into a comma separated values file (throws exception if not supported)
void writeDataIntoCommaSeparatedValueFile(CommaSeparatedValueFile& csv) throw (FileException);
/// read the file's data from a comma separated values file (throws exception if not supported)
void readDataFromCommaSeparatedValuesTable(const CommaSeparatedValueFile& csv) throw (FileException);
/// get a pointer to the study info
std::vector<CellStudyInfo>* getPointerToStudyInfo() { return &studyInfo; }
/// get number of study info
int getNumberOfStudyInfo() const { return studyInfo.size(); }
/// get the study info index from the study info's value
int getStudyInfoFromValue(const CellStudyInfo& studyInfo) const;
/// get a study info (const method)
const CellStudyInfo* getStudyInfo(const int index) const;
/// get a study info
CellStudyInfo* getStudyInfo(const int index);
/// add a study info
int addStudyInfo(const CellStudyInfo& studyInfo);
/// delete all study info
void deleteAllStudyInfo();
/// delete study info
void deleteStudyInfo(const int indx);
/// set a study info
void setStudyInfo(const int index, const CellStudyInfo& csi);
/// get PubMedID's of all linked studies
void getPubMedIDsOfAllLinkedStudyMetaData(std::vector<QString>& studyPMIDs) const;
/// write the file's memory in caret6 format to the specified name
virtual QString writeFileInCaret6Format(const QString& filenameIn, Structure structure,const ColorFile* colorFileIn, const bool useCaret6ExtensionFlag) throw (FileException);
protected:
// Read the contents of the file (header has already been read)
void readFileData(QFile& file,
QTextStream& stream,
QDataStream& binStream,
QDomElement& rootElement) throw (FileException);
// Write the file's data (header has already been written)
void writeFileData(QTextStream& stream,
QDataStream& binStream,
QDomDocument& xmlDoc,
QDomElement& rootElement) throw (FileException);
/// the vocabulary entries
std::vector<VocabularyEntry> vocabularyEntries;
/// the study info
std::vector<CellStudyInfo> studyInfo;
};
#endif // __VOCABULARY_FILE_H__
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