import exceptions and reference track permanence

src/harvest/HarvestIO.cpp

@@ -47,6 +47,11 @@ bool HarvestIO::loadHarvest(const char * file)
 {
 	int fd = open(file, O_RDONLY);
 
+	if ( fd < 0 )
+	{
+		return false;
+	}
+
 	FileInputStream raw_input(fd);
 	GzipInputStream gz(&raw_input);
 	CodedInputStream coded_input(&gz);
@@ -100,6 +105,11 @@ void HarvestIO::loadMFA(const char * file, bool findVariants)
 
 void HarvestIO::loadNewick(const char * file)
 {
+	if ( lcbList.getLcbCount() == 0 )
+	{
+		trackList.clear();
+	}
+
 	phylogenyTree.initFromNewick(file, &trackList);
 }
 

src/harvest/LcbList.cpp

@@ -32,14 +32,18 @@ void LcbList::initFromMfa(const char * file, ReferenceList * referenceList, Trac
 	ifstream in(file);
 	char line[1 << 20];
 	vector<string> seqs;
-	bool oldTags = trackList->getTrackCount();
+	const bool oldTags = phylogenyTree->getRoot();
 	string refTag;
 	int * trackIndecesNew;
 
 	if ( oldTags )
 	{
 		trackIndecesNew = new int[trackList->getTrackCount()];
 	}
+	else
+	{
+		trackList->clear();
+	}
 
 	while ( ! in.eof() )
 	{
@@ -64,7 +68,17 @@ void LcbList::initFromMfa(const char * file, ReferenceList * referenceList, Trac
 			if ( oldTags )
 			{
 				track = &trackList->getTrackMutable(seqs.size());
-				trackIndecesNew[trackList->getTrackIndexByFile(tag.c_str())] = seqs.size();
+
+				try
+				{
+					trackIndecesNew[trackList->getTrackIndexByFile(tag.c_str())] = seqs.size();
+				}
+				catch ( const TrackList::TrackNotFoundException & e )
+				{
+					delete [] trackIndecesNew;
+					throw;
+					return;
+				}
 			}
 			else
 			{
@@ -141,7 +155,7 @@ void LcbList::initFromXmfa(const char * file, ReferenceList * referenceList, Tra
 	char line[1 << 20];
 	int trackIndex = 0;
 	vector<string> seqs;
-	bool oldTags = trackList->getTrackCount();
+	const bool oldTags = phylogenyTree->getRoot();
 	int * trackIndecesNew;
 	bool mauve = false;
 	string ref;
@@ -156,6 +170,10 @@ void LcbList::initFromXmfa(const char * file, ReferenceList * referenceList, Tra
 	{
 		trackIndecesNew = new int[trackList->getTrackCount()];
 	}
+	else
+	{
+		trackList->clear();
+	}
 
 	LcbList::Lcb * lcb = 0;
 
@@ -191,7 +209,17 @@ void LcbList::initFromXmfa(const char * file, ReferenceList * referenceList, Tra
 					if ( oldTags )
 					{
 						track = &trackList->getTrackMutable(trackIndex);
-						trackIndecesNew[trackList->getTrackIndexByFile(suffix)] = trackIndex;
+
+						try
+						{
+							trackIndecesNew[trackList->getTrackIndexByFile(suffix)] = trackIndex;
+						}
+						catch ( const TrackList::TrackNotFoundException & e )
+						{
+							delete [] trackIndecesNew;
+							throw;
+							return;
+						}
 					}
 					else
 					{
@@ -217,7 +245,17 @@ void LcbList::initFromXmfa(const char * file, ReferenceList * referenceList, Tra
 				if ( oldTags )
 				{
 					track = &trackList->getTrackMutable(trackIndex);
-					trackIndecesNew[trackList->getTrackIndexByFile(suffix)] = trackIndex;
+
+					try
+					{
+						trackIndecesNew[trackList->getTrackIndexByFile(suffix)] = trackIndex;
+					}
+					catch ( const TrackList::TrackNotFoundException & e )
+					{
+						delete [] trackIndecesNew;
+						throw;
+						return;
+					}
 				}
 				else
 				{

src/harvest/PhylogenyTree.cpp

@@ -59,7 +59,16 @@ void PhylogenyTree::initFromNewick(const char * file, TrackList * trackList)
 	while ( in.getline(line, (1 << 20) - 1) )
 	{
 		char * token = line;
-		root = new PhylogenyTreeNode(token, trackList, useNames);
+
+		try
+		{
+			root = new PhylogenyTreeNode(token, trackList, useNames);
+		}
+		catch ( const TrackList::TrackNotFoundException & e )
+		{
+			root = 0;
+			throw;
+		}
 	}
 
 	in.close();

src/harvest/ReferenceList.cpp

@@ -55,6 +55,8 @@ int ReferenceList::getReferenceSequenceFromGi(long int gi) const
 		}
 	}
 
+	throw GiNotFoundException(std::to_string(gi));
+
 	return undef;
 }
 

src/harvest/ReferenceList.h

@@ -20,6 +20,20 @@ class ReferenceList
 {
 public:
 
+	class GiNotFoundException : public std::exception
+	{
+	public:
+
+		GiNotFoundException(const std::string & giNew)
+		{
+			gi = giNew;
+		}
+
+		virtual ~GiNotFoundException() throw() {}
+
+		std::string gi;
+	};
+
 	void addReference(std::string name, std::string sequence);
 	void clear();
 	int getPositionFromConcatenated(int sequence, long int position) const;

src/harvest/TrackList.cpp

@@ -2,6 +2,11 @@
 
 using namespace::std;
 
+TrackList::TrackList()
+{
+	trackReference = 0;
+}
+
 int TrackList::addTrack(const char * file, int size, const char * name, TrackType type)
 {
 	tracks.resize(tracks.size() + 1);
@@ -20,11 +25,20 @@ void TrackList::clear()
 {
 	tracks.clear();
 	tracksByFile.clear();
+	trackReference = 0;
 }
 
 int TrackList::getTrackIndexByFile(const char * file) const
 {
-	return tracksByFile.at(file);
+	try
+	{
+		return tracksByFile.at(file);
+	}
+	catch ( const out_of_range & e )
+	{
+		throw TrackNotFoundException(file);
+		return -1;
+	}
 }
 
 void TrackList::initFromProtocolBuffer(const Harvest::TrackList & msg)
@@ -55,6 +69,11 @@ void TrackList::initFromProtocolBuffer(const Harvest::TrackList & msg)
 	}
 
 	setTracksByFile();
+
+	if ( msg.has_variantreference() )
+	{
+		trackReference = msg.variantreference();
+	}
 }
 
 void TrackList::setTracksByFile()
@@ -93,4 +112,6 @@ void TrackList::writeToProtocolBuffer(Harvest * msg)
 			msgTrack->set_type((Harvest::TrackList::Track::Type)track.type);
 		}
 	}
+
+	msg->mutable_tracks()->set_variantreference(trackReference);
 }

src/harvest/TrackList.h

@@ -35,13 +35,31 @@ class TrackList
 		TrackType type;
 	};
 
+	class TrackNotFoundException : public std::exception
+	{
+	public:
+
+		TrackNotFoundException(const std::string & nameNew)
+		{
+			name = nameNew;
+		}
+
+		virtual ~TrackNotFoundException() throw() {}
+
+		std::string name;
+	};
+
+	TrackList();
+
 	int addTrack(const char * file, int size = 0, const char * name = "", TrackType type = NONE);
 	void clear();
 	const Track & getTrack(int index) const;
-	Track & getTrackMutable(int index);
-	int getTrackIndexByFile(const char * file) const;
 	int getTrackCount() const;
+	int getTrackIndexByFile(const char * file) const;
+	Track & getTrackMutable(int index);
+	int getTrackReference() const;
 	void initFromProtocolBuffer(const Harvest::TrackList & msg);
+	void setTrackReference(int trackReferenceNew);
 	void setTracksByFile();
 	void writeToProtocolBuffer(Harvest * msg);
 
@@ -53,6 +71,8 @@ class TrackList
 };
 
 inline const TrackList::Track & TrackList::getTrack(int index) const { return tracks[index]; }
-inline TrackList::Track & TrackList::getTrackMutable(int index) { return tracks[index]; }
 inline int TrackList::getTrackCount() const { return tracks.size(); }
+inline TrackList::Track & TrackList::getTrackMutable(int index) { return tracks[index]; }
+inline int TrackList::getTrackReference() const { return trackReference; }
+inline void TrackList::setTrackReference(int trackReferenceNew) { trackReference = trackReferenceNew; }
 #endif

src/harvest/VariantList.cpp

@@ -366,7 +366,18 @@ void VariantList::initFromVcf(const char * file, const ReferenceList & reference
 					if ( oldTags )
 					{
 						track = &trackList->getTrackMutable(n); // TODO: clear track
-						trackIndecesNew[trackList->getTrackIndexByFile(token)] = n;
+
+						try
+						{
+							trackIndecesNew[trackList->getTrackIndexByFile(token)] = n;
+						}
+						catch ( const TrackList::TrackNotFoundException & e )
+						{
+							delete [] trackIndecesNew;
+							throw;
+							return;
+						}
+
 						n++;
 					}
 					else

src/harvest/pb/harvest.proto

@@ -31,6 +31,7 @@ message Harvest
 		}
 
 		repeated Track tracks = 1;
+		optional uint32 variantReference = 2;
 	}
 
 	message Tree