int process(const char *fileName){
// Reading file
char *buffer;
unsigned int fileSize = 0;
int result = readFile(fileName, &buffer, fileSize);
if(result != 0)
return result; // If there was a problem, return its error code
// First Byte must be a StartOfHeader SOH character
if(buffer[0] != 1)
return 2; // File is not compressed in huff format
// Got number of padding bytes
char paddingBits = buffer[1];
unsigned int pos(2);
TreeNode *root = generateTree(buffer, pos);
// XXX TESTING
printTreeElements(root);
// Creating bitstring
std::string bitString;
for(unsigned int i = pos+2; i < fileSize; i++){
bitString += bits_in_byte(buffer[i]).to_string();
}
std::string decodedString;
decode(bitString, root, decodedString);
char pops = (char) paddingBits / calculateShortestDistance(root);
for(char i = 0; i < pops; i++){
decodedString.pop_back();
}
std::string outputFileName(fileName);
for(char i = 0; i < 4; i++){
outputFileName.pop_back();
}
std::ofstream out(outputFileName);
out << decodedString;
out.close();
/*
*/
return 0;
}
int main (int argc, char *argv[])
{
FILE *input, *output;
Alignment Aln;
Alignment *AlnPtr;
int i;
char fileName[200];
if (argc != 5) {
/*printf("Error in number of arguments. \n");*/
printf("The command line should be of the format: \n");
printf(">./Evolution <alignmentFile> <networkFilesList> <pdbFilesList> <output> \n");
printf(" where:\n");
printf(" alignmentFile is file with alignment.\n");
printf(" networkFilesList is the file with names of files for the networks for different molecules in the same order as the molecules are in the alignment\n");
printf(" pdbFilesList is the file with names of files for the pdb files for different molecules in the same order as the molecules in the alignment\n");
printf(" output is the name for output directory (directory should exist)\n");
exit(1);
}
//Reading Alignment
if ( (input=fopen(argv[1], "r")) == NULL ) {
printf("Alignment file does not exist.\n");
exit(1);
}
AlnPtr = &Aln;
readSequenceAlignment(AlnPtr, input);
mappingSequenceAlignment(AlnPtr);
fclose(input);
//Reading networks
if ((input=fopen(argv[2], "r")) == NULL) {
printf("File for list of network files does not exist. \n");
exit(1);
}
readNetworkFiles(AlnPtr, input);
fclose(input);
//Reading pdb file names
if ( (input=fopen(argv[3], "r")) == NULL ) {
printf("File for list of pdb files does not exist.\n");
exit(1);
}
readPdbFileNames(AlnPtr, input);
fclose(input);
//Creating and opening output files for each sequence
for (i=0; i<AlnPtr->Nseq; i++) {
AlnPtr->Sequence[i]->fileName[0] = '\0';
strcat(AlnPtr->Sequence[i]->fileName, argv[4]);
strcat(AlnPtr->Sequence[i]->fileName, "/");
strcat(AlnPtr->Sequence[i]->fileName, AlnPtr->Sequence[i]->name);
strcat(AlnPtr->Sequence[i]->fileName, ".out");
//printf("fileName is %s\n",fileName);
output=fopen(AlnPtr->Sequence[i]->fileName, "w");
fprintf(output, "Name %s\n", AlnPtr->Sequence[i]->name);
fprintf(output, "PDB file %s", AlnPtr->Sequence[i]->pdbName);
fprintf(output, "Network file %s\n", AlnPtr->Sequence[i]->networkName);
fclose(output);
}
//Creating Alignment Edges
AlnPtr->Nedges = numberEdgesAlignment(AlnPtr);
createAlnEdges(AlnPtr);
//Calculating conservation of nodes and edges in the alignment
nodeConservation(AlnPtr);
edgeConservation(AlnPtr);
numberEdgeMatches(AlnPtr);
fileName[0] = '\0';
strcat(fileName, argv[4]);
strcat(fileName, "/");
strcat(fileName, "edgeIdentity.dis");
output=fopen(fileName, "w");
calculateEdgeIdentity(AlnPtr,output);
fclose(output);
calculateShortestDistance(AlnPtr);
fileName[0] = '\0';
strcat(fileName, argv[4]);
strcat(fileName, "/");
strcat(fileName, "shortestDistance.dis");
output=fopen(fileName, "w");
diffShortestDistanceAligned(AlnPtr,output);
fclose(output);
deleteAlignment(AlnPtr);
return 0;
}
