Changes for multi-DB intersection.

src/intersectFile/intersectFile.cpp

@@ -37,7 +37,7 @@ FileIntersect::~FileIntersect(void) {
 	delete _recordOutputMgr;
 }
 
-void FileIntersect::processHits(RecordKeyList &hits) {
+void FileIntersect::processHits(RecordKeyVector &hits) {
     _recordOutputMgr->printRecord(hits);
 }
 
@@ -58,11 +58,11 @@ bool FileIntersect::processSortedFiles()
     	return false;
     }
 
-    RecordKeyList hitSet;
+    RecordKeyVector hitSet;
     while (sweep.next(hitSet)) {
     	if (_context->getObeySplits()) {
-    		RecordKeyList keySet(hitSet.getKey());
-    		RecordKeyList resultSet(hitSet.getKey());
+    		RecordKeyVector keySet(hitSet.getKey());
+    		RecordKeyVector resultSet(hitSet.getKey());
     		_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
     		processHits(resultSet);
     	} else {
@@ -85,11 +85,11 @@ bool FileIntersect::processUnsortedFiles()
 		if (queryRecord == NULL) {
 			continue;
 		}
-		RecordKeyList hitSet(queryRecord);
+		RecordKeyVector hitSet(queryRecord);
 		binTree->getHits(queryRecord, hitSet);
     	if (_context->getObeySplits()) {
-    		RecordKeyList keySet(hitSet.getKey());
-    		RecordKeyList resultSet;
+    		RecordKeyVector keySet(hitSet.getKey());
+    		RecordKeyVector resultSet;
     		_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
     		processHits(resultSet);
     	} else {

src/intersectFile/intersectFile.h

@@ -14,7 +14,7 @@
 
 using namespace std;
 
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
 
 using namespace std;
 
@@ -37,7 +37,7 @@ private:
 	BlockMgr *_blockMgr;
 	RecordOutputMgr *_recordOutputMgr;
 
-	void processHits(RecordKeyList &hits);
+	void processHits(RecordKeyVector &hits);
 	bool processSortedFiles();
 	bool processUnsortedFiles();
 

src/intersectFile/intersectMain.cpp

@@ -13,6 +13,7 @@ using namespace std;
 
 #include "intersectFile.h"
 #include "ContextIntersect.h"
+#include "CommonHelp.h"
 
 // define our program name
 #define PROGRAM_NAME "bedtools intersect"
@@ -46,6 +47,9 @@ void intersect_help(void) {
 
     cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
 
+    cerr << "\t\t"				<< "Note: -b may be followed with multiple databases and/or " << endl;
+    cerr << "\t\t"					"wildcard (*) character(s). " << endl;
+
     cerr << "Options: " << endl;
 
     cerr << "\t-abam\t"         << "The A input file is in BAM format.  Output will be BAM as well." << endl << endl;
@@ -119,6 +123,17 @@ void intersect_help(void) {
     cerr 						<<"\t\tother software tools and scripts that need to process one" << endl;
     cerr 						<<"\t\tline of bedtools output at a time." << endl << endl;
 
+    cerr << "\t-names\t"       << "When using multiple databases, provide an alias for each that" << endl;
+    cerr						<<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
+
+    cerr << "\t-filenames"       << "\tWhen using multiple databases, show each complete filename" << endl;
+    cerr						<<"\t\t\tinstead of a fileId when also printing the DB record." << endl << endl;
+
+    cerr << "\t-sortout\t"       << "When using multiple databases, sort the output DB hits" << endl;
+    cerr						<< "\t\t\tfor each record." << endl << endl;
+
+    CommonHelp();
+
     cerr << "Notes: " << endl;
     cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
     cerr << "\tand exlcuded if an overlap cannot be found.  If multiple overlaps exist, they are not" << endl;

src/jaccard/Jaccard.cpp

@@ -49,11 +49,11 @@ bool Jaccard::getIntersectionAndUnion() {
 	if (!sweep.init()) {
 		return false;
 	}
-	RecordKeyList hitSet;
+	RecordKeyVector hitSet;
 	while (sweep.next(hitSet)) {
 		if (_context->getObeySplits()) {
-			RecordKeyList keySet(hitSet.getKey());
-			RecordKeyList resultSet(hitSet.getKey());
+			RecordKeyVector keySet(hitSet.getKey());
+			RecordKeyVector resultSet(hitSet.getKey());
 			_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
 			_intersectionVal += getTotalIntersection(&resultSet);
 		} else {
@@ -69,7 +69,7 @@ bool Jaccard::getIntersectionAndUnion() {
 	return true;
 }
 
-unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
+unsigned long Jaccard::getTotalIntersection(RecordKeyVector *recList)
 {
 	unsigned long intersection = 0;
 	const Record *key = recList->getKey();
@@ -77,8 +77,8 @@ unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
 	int keyEnd = key->getEndPos();
 
 	int hitIdx = 0;
-	for (RecordKeyList::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
-		const Record *currRec = iter->value();
+	for (RecordKeyVector::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
+		const Record *currRec = *iter;
 		int maxStart = max(currRec->getStartPos(), keyStart);
 		int minEnd = min(currRec->getEndPos(), keyEnd);
 		if (_context->getObeySplits()) {

src/jaccard/Jaccard.h

@@ -33,7 +33,7 @@ private:
     int _numIntersections;
 
     bool getIntersectionAndUnion();
-    unsigned long getTotalIntersection(RecordKeyList *hits);
+    unsigned long getTotalIntersection(RecordKeyVector *hits);
 };
 
 #endif /* JACCARD_H */

src/mapFile/mapFile.cpp

@@ -41,11 +41,11 @@ bool FileMap::mapFiles()
     if (!sweep.init()) {
       return false;
     }
-    RecordKeyList hitSet;
+    RecordKeyVector hitSet;
     while (sweep.next(hitSet)) {
     	if (_context->getObeySplits()) {
-			RecordKeyList keySet(hitSet.getKey());
-			RecordKeyList resultSet(hitSet.getKey());
+			RecordKeyVector keySet(hitSet.getKey());
+			RecordKeyVector resultSet(hitSet.getKey());
 			_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
 			_recordOutputMgr->printRecord(resultSet.getKey(), _context->getColumnOpsVal(resultSet));
     	} else {

src/mapFile/mapFile.h

@@ -17,7 +17,7 @@ using namespace std;
 #include <sstream>
 #include <iomanip>
 #include "VectorOps.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
 #include "ContextMap.h"
 
 using namespace std;

src/mergeFile/mergeFile.cpp

@@ -28,7 +28,7 @@ MergeFile::~MergeFile()
 
 bool MergeFile::merge()
 {
-    RecordKeyList hitSet;
+    RecordKeyVector hitSet;
     FileRecordMgr *frm = _context->getFile(0);
     while (!frm->eof()) {
     	Record *key = frm->getNextRecord(&hitSet);

src/utils/BinTree/BinTree.cpp

@@ -3,8 +3,7 @@
 
 
 BinTree::BinTree(ContextIntersect *context)
-: _databaseFile(NULL),
-  _context(context),
+:  _context(context),
   _binOffsetsExtended(NULL),
   _showBinMetrics(false),
   _maxBinNumFound(0)
@@ -36,7 +35,7 @@ BinTree::~BinTree() {
 				}
 				for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
 					const Record *record = listIter->value();
-					_databaseFile->deleteRecord(record);
+					_context->getFile(record->getFileIdx())->deleteRecord(record);
 				}
 				delete bin;
 				bin = NULL;
@@ -70,25 +69,27 @@ BinTree::~BinTree() {
 
 void BinTree::loadDB()
 {
-	_databaseFile = _context->getFile(_context->getDatabaseFileIdx());
-
-	Record *record = NULL;
-	while (!_databaseFile->eof()) {
-		record = _databaseFile->getNextRecord();
-		//In addition to NULL records, we also don't want to add unmapped reads.
-		if (record == NULL || record->isUnmapped()) {
-			continue;
-		}
+	for (int i=0; i < _context->getNumDatabaseFiles(); i++) {
+		FileRecordMgr *databaseFile = _context->getDatabaseFile(i);
+
+		Record *record = NULL;
+		while (!databaseFile->eof()) {
+			record = databaseFile->getNextRecord();
+			//In addition to NULL records, we also don't want to add unmapped reads.
+			if (record == NULL || record->isUnmapped()) {
+				continue;
+			}
 
-		if (!addRecordToTree(record)) {
-			fprintf(stderr, "ERROR: Unable to add record to tree.\n");
-			_databaseFile->close();
-			exit(1);
+			if (!addRecordToTree(record)) {
+				fprintf(stderr, "ERROR: Unable to add record to tree.\n");
+				databaseFile->close();
+				exit(1);
+			}
 		}
 	}
 }
 
-void BinTree::getHits(Record *record, RecordKeyList &hitSet)
+void BinTree::getHits(Record *record, RecordKeyVector &hitSet)
 {
 	if (_showBinMetrics) {
 		return; //don't care about query entries just yet.
@@ -149,6 +150,9 @@ void BinTree::getHits(Record *record, RecordKeyList &hitSet)
         startBin >>= _binNextShift;
         endBin >>= _binNextShift;
     }
+	if (_context->getSortOutput()) {
+		hitSet.sortVector();
+	}
 }
 
 bool BinTree::addRecordToTree(const Record *record)

src/utils/BinTree/BinTree.h

@@ -28,11 +28,10 @@ public:
 
 	~BinTree();
 	void loadDB();
-	void getHits(Record *record, RecordKeyList &hitSet);
+	void getHits(Record *record, RecordKeyVector &hitSet);
 
 private:
 
-	FileRecordMgr *_databaseFile;
 	ContextIntersect *_context;
 
     //
@@ -52,8 +51,8 @@ private:
 	static const uint32_t _binFirstShift = 14;       /* How much to shift to get to finest bin. */
 	static const uint32_t _binNextShift  = 3;        /* How much to shift to get to next larger bin. */
 
-	typedef BTlist<const Record *> innerListType;
-	typedef const BTlistNode<const Record *> * innerListIterType;
+	typedef RecordList innerListType;
+	typedef const RecordListNode * innerListIterType;
 	typedef innerListType * binType;
 	typedef binType * allBinsType;
 	typedef QuickString mainKeyType;

src/utils/Contexts/ContextBase.cpp

@@ -36,18 +36,17 @@ ContextBase::ContextBase()
   _reciprocal(false),
   _sameStrand(false),
   _diffStrand(false),
-   _sortedInput(false),
+  _sortedInput(false),
+  _sortOutput(false),
+  _reportDBnameTags(false),
+  _reportDBfileNames(false),
   _printHeader(false),
   _printable(true),
    _explicitBedOutput(false),
   _queryFileIdx(-1),
-  _databaseFileIdx(-1),
   _bamHeaderAndRefIdx(-1),
   _maxNumDatabaseFields(0),
   _useFullBamTags(false),
-  _reportCount(false),
-  _reportNames(false),
-  _reportScores(false),
   _numOutputRecords(0),
   _hasConstantSeed(false),
   _seed(0),
@@ -193,6 +192,9 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-delim") == 0) {
 			if (!handle_delim()) return false;
         }
+        else if (strcmp(_argv[_i], "-sortout") == 0) {
+			if (!handle_sortout()) return false;
+        }
 
 	}
 	return true;
@@ -210,7 +212,11 @@ bool ContextBase::isValidState()
 		return false;
 	}
 	if (hasColumnOpsMethods()) {
-		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+
+		//TBD: Adjust column ops for multiple databases.
+		//For now, use last file.
+//		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+		FileRecordMgr *dbFile = getFile(getNumInputFiles()-1);
 		_keyListOps->setDBfileType(dbFile->getFileType());
 		if (!_keyListOps->isValidColumnOps(dbFile)) {
 			return false;
@@ -251,7 +257,7 @@ bool ContextBase::openFiles() {
 	_files.resize(_fileNames.size());
 
 	for (int i = 0; i < (int)_fileNames.size(); i++) {
-		FileRecordMgr *frm = getNewFRM(_fileNames[i]);
+		FileRecordMgr *frm = getNewFRM(_fileNames[i], i);
 		if (hasGenomeFile()) {
 			frm->setGenomeFile(_genomeFile);
 		}
@@ -281,7 +287,7 @@ int ContextBase::getBamHeaderAndRefIdx() {
 		if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
 			_bamHeaderAndRefIdx = _queryFileIdx;
 		} else {
-			_bamHeaderAndRefIdx = _databaseFileIdx;
+			_bamHeaderAndRefIdx = _dbFileIdxs[0];
 		}
 		return _bamHeaderAndRefIdx;
 	}
@@ -492,6 +498,13 @@ bool ContextBase::handle_delim()
     return true;
 }
 
+bool ContextBase::handle_sortout()
+{
+	setSortOutput(true);
+	markUsed(_i - _skipFirstArgs);
+	return true;
+}
+
 void ContextBase::setColumnOpsMethods(bool val)
 {
 	if (val && !_hasColumnOpsMethods) {
@@ -501,20 +514,24 @@ void ContextBase::setColumnOpsMethods(bool val)
 	_hasColumnOpsMethods = val;
 }
 
-const QuickString &ContextBase::getColumnOpsVal(RecordKeyList &keyList) const {
+const QuickString &ContextBase::getColumnOpsVal(RecordKeyVector &keyList) const {
 	if (!hasColumnOpsMethods()) {
 		return _nullStr;
 	}
 	return _keyListOps->getOpVals(keyList);
 }
 
-FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename) {
-	if (!_useMergedIntervals) {
-		return new FileRecordMgr(filename);
-	} else {
+FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename, int fileIdx) {
+
+	if (_useMergedIntervals) {
 		FileRecordMergeMgr *frm = new FileRecordMergeMgr(filename);
 		frm->setStrandType(_desiredStrand);
 		frm->setMaxDistance(_maxDistance);
+		frm->setFileIdx(fileIdx);
+		return frm;
+	} else {
+		FileRecordMgr *frm = new FileRecordMgr(filename);
+		frm->setFileIdx(fileIdx);
 		return frm;
 	}
 }

src/utils/Contexts/ContextBase.h

@@ -98,6 +98,15 @@ public:
     virtual bool getSortedInput() const {return _sortedInput; }
     virtual void setSortedInput(bool val) { _sortedInput = val; }
 
+    virtual bool getSortOutput() const {return _sortOutput; }
+    virtual void setSortOutput(bool val) { _sortOutput = val; }
+
+    virtual bool getUseDBnameTags() const { return _reportDBnameTags; }
+    virtual void setUseDBnameTags(bool val) { _reportDBnameTags = val; }
+
+    virtual bool getUseDBfileNames() const { return _reportDBfileNames; }
+    virtual void setUseDBfileNames(bool val) { _reportDBfileNames = val; }
+
     virtual bool getPrintHeader() const {return _printHeader; }
     virtual void setPrintHeader(bool val) { _printHeader = val; }
 
@@ -107,24 +116,6 @@ public:
     virtual bool getUseFullBamTags() const { return _useFullBamTags; }
     virtual void setUseFullBamTags(bool val) { _useFullBamTags = val; }
 
-//	//
-//	// MERGE METHODS
-//	//
-//    virtual bool getReportCount() const { return _reportCount; }
-//    virtual void setReportCount(bool val) { _reportCount = val; }
-//
-//    virtual int getMaxDistance() const { return _maxDistance; }
-//    virtual void setMaxDistance(int distance) { _maxDistance = distance; }
-//
-//    virtual bool getReportNames() const { return _reportNames; }
-//    virtual void setReportNames(bool val) { _reportNames = val; }
-//
-//    virtual bool getReportScores() const { return _reportScores; }
-//    virtual void setReportScores(bool val) { _reportScores = val; }
-//
-//    virtual const QuickString &getScoreOp() const { return _scoreOp; }
-//    virtual void setScoreOp(const QuickString &op) { _scoreOp = op; }
-
 
 	// METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER
 	// OF OUTPUT RECORDS.
@@ -150,7 +141,7 @@ public:
     // are available.
     void setColumnOpsMethods(bool val);
     virtual bool hasColumnOpsMethods() const { return _hasColumnOpsMethods; }
-    const QuickString &getColumnOpsVal(RecordKeyList &keyList) const;
+    const QuickString &getColumnOpsVal(RecordKeyVector &keyList) const;
     //methods applicable only to column operations.
 
 protected:
@@ -192,18 +183,19 @@ protected:
     bool _sameStrand;
     bool _diffStrand;
     bool _sortedInput;
+    bool _sortOutput;
+    bool _reportDBnameTags;
+    bool _reportDBfileNames;
     bool _printHeader;
     bool _printable;
     bool _explicitBedOutput;
     int _queryFileIdx;
-    int _databaseFileIdx;
+    vector<int> _dbFileIdxs;
+    vector<QuickString> _dbNameTags;
+    map<int, int> _fileIdsToDbIdxs;
     int _bamHeaderAndRefIdx;
     int _maxNumDatabaseFields;
     bool _useFullBamTags;
-	bool _reportCount;
-	bool _reportNames;
-	bool _reportScores;
-	QuickString _scoreOp;
 
 	int _numOutputRecords;
 
@@ -227,7 +219,7 @@ protected:
 	bool isUsed(int i) const { return _argsProcessed[i]; }
 	bool cmdArgsValid();
 	bool openFiles();
-	virtual FileRecordMgr *getNewFRM(const QuickString &filename);
+	virtual FileRecordMgr *getNewFRM(const QuickString &filename, int fileIdx);
 
 	//set cmd line params and counter, i, as members so code
 	//is more readable (as opposed to passing all 3 everywhere).
@@ -256,6 +248,7 @@ protected:
 	virtual bool handle_o();
 	virtual bool handle_null();
 	virtual bool handle_delim();
+	virtual bool handle_sortout();
 
 	bool parseIoBufSize(QuickString bufStr);
 

src/utils/Contexts/ContextIntersect.cpp

@@ -44,6 +44,12 @@ bool ContextIntersect::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-b") == 0) {
 			if (!handle_b()) return false;
 		}
+        else if (strcmp(_argv[_i], "-names") == 0) {
+			if (!handle_names()) return false;
+		}
+        else if (strcmp(_argv[_i], "-filenames") == 0) {
+			if (!handle_filenames()) return false;
+		}
         else if (strcmp(_argv[_i], "-u") == 0) {
 			if (!handle_u()) return false;
         }
@@ -92,7 +98,7 @@ bool ContextIntersect::isValidState()
 		return false;
 	}
 
-	if (_queryFileIdx == -1 || _databaseFileIdx == -1) {
+	if (_queryFileIdx == -1 || _dbFileIdxs.size() == -0) {
 		_errorMsg = "\n***** ERROR: query and database files not specified. *****";
 		return false;
 	}
@@ -113,6 +119,11 @@ bool ContextIntersect::isValidState()
 			return false;
 		}
 	}
+	if (getUseDBnameTags() && _dbNameTags.size() != _dbFileIdxs.size()) {
+		_errorMsg = "\n***** ERROR: Number of database name tags given does not match number of databases. *****";
+		return false;
+
+	}
 	if (getWriteOverlap()) {
 
 		if (getWriteA()) {
@@ -149,7 +160,7 @@ bool ContextIntersect::isValidState()
 	if (getAnyHit() || getNoHit() || getWriteCount()) {
 		setPrintable(false);
 	}
-	if (_files.size() != 2 ) {
+	if (_files.size()  < 2 ) {
 		return false;
 	}
 	return true;
@@ -161,8 +172,8 @@ bool ContextIntersect::determineOutputType() {
 	}
 
 	//determine the maximum number of database fields.
-	for (int i=0; i < (int)_files.size(); i++) {
-		int numFields = _files[i]->getNumFields();
+	for (int i=0; i < getNumDatabaseFiles(); i++) {
+		int numFields = getDatabaseFile(i)->getNumFields();
 		if ( numFields > _maxNumDatabaseFields) {
 			_maxNumDatabaseFields = numFields;
 		}
@@ -211,19 +222,46 @@ bool ContextIntersect::handle_abam()
 bool ContextIntersect::handle_b()
 {
 	if (_argc <= _i+1) {
-		_errorMsg = "\n***** ERROR: -b option given, but no query file specified. *****";
+		_errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
 		return false;
 	}
 
-	addInputFile(_argv[_i+1]);
-	_databaseFileIdx = getNumInputFiles() -1;
-	markUsed(_i - _skipFirstArgs);
-	_i++;
-	markUsed(_i - _skipFirstArgs);
+	do {
+		addInputFile(_argv[_i+1]);
+		int fileId = getNumInputFiles() -1;
+		_dbFileIdxs.push_back(fileId);
+		_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
+		markUsed(_i - _skipFirstArgs);
+		_i++;
+		markUsed(_i - _skipFirstArgs);
+	} while (_argc > _i+1 && _argv[_i+1][0] != '-');
 	return true;
 }
 
 
+bool ContextIntersect::handle_names()
+{
+	if (_argc <= _i+1) {
+		_errorMsg = "\n***** ERROR: -b option given, but no database names specified. *****";
+		return false;
+	}
+
+	do {
+		addDatabaseNameTag(_argv[_i+1]);
+		markUsed(_i - _skipFirstArgs);
+		_i++;
+		markUsed(_i - _skipFirstArgs);
+	} while (_argc > _i+1 && _argv[_i+1][0] != '-');
+	setUseDBnameTags(true);
+	return true;
+}
+
+bool ContextIntersect::handle_filenames()
+{
+	markUsed(_i - _skipFirstArgs);
+	setUseDBfileNames(true);
+	return true;
+}
 
 bool ContextIntersect::handle_c()
 {

src/utils/Contexts/ContextIntersect.h

@@ -22,19 +22,22 @@ public:
 	//NOTE: Query and database files will only be marked as such by either the
 	//parseCmdArgs method, or by explicitly setting them.
 	FileRecordMgr *getQueryFile() { return getFile(_queryFileIdx); }
-	FileRecordMgr *getDatabaseFile() { return getFile(_databaseFileIdx); }
+	FileRecordMgr *getDatabaseFile(int idx) { return getFile(_dbFileIdxs[idx]); }
     int getQueryFileIdx() const { return _queryFileIdx; }
 	void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
-	int getDatabaseFileIdx() const { return _databaseFileIdx; }
-	void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
+	int getNumDatabaseFiles() { return (int)_dbFileIdxs.size(); }
+	const vector<int> &getDbFileIdxs() const { return _dbFileIdxs; }
 	const QuickString &getQueryFileName() const { return _files[_queryFileIdx]->getFileName(); }
-	const QuickString &getDatabaseFileName() const { return _files[_databaseFileIdx]->getFileName(); }
+	const QuickString &getDatabaseFileName(int idx) const { return _files[_dbFileIdxs[idx]]->getFileName(); }
 	ContextFileType getQueryFileType() const { return _files[_queryFileIdx]->getFileType(); }
-	ContextFileType getDatabaseFileType() const { return _files[_databaseFileIdx]->getFileType(); }
+	ContextFileType getDatabaseFileType(int idx) const { return _files[_dbFileIdxs[idx]]->getFileType(); }
 	ContextRecordType getQueryRecordType() const { return _files[_queryFileIdx]->getRecordType(); }
-	ContextRecordType getDatabaseRecordType() const { return _files[_databaseFileIdx]->getRecordType(); }
+	ContextRecordType getDatabaseRecordType(int idx) const { return _files[_dbFileIdxs[idx]]->getRecordType(); }
 	int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
 	void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
+	int getDbIdx(int fileId) { return _fileIdsToDbIdxs.find(fileId)->second; }
+	void addDatabaseNameTag(const QuickString &tag) { _dbNameTags.push_back(tag); }
+	const QuickString &getDatabaseNameTag(int dbIdx) const { return _dbNameTags[dbIdx]; }
 
 	bool getAnyHit() const {return _anyHit; }
 	void setAnyHit(bool val) { _anyHit = val; }
@@ -83,6 +86,9 @@ private:
 	virtual bool handle_a();
 	virtual bool handle_abam();
 	virtual bool handle_b();
+	virtual bool handle_names();
+	virtual bool handle_filenames();
+