TestResult* allocateNewStringTestTemplate(char* x, int xLength, char* expected,
char* testName) {
char* actual = allocateNewString(x, xLength);
TestResult* r = malloc(sizeof(TestResult));
r -> testName = testName;
r -> passed = areStringsEqual(actual, expected);
free(actual);
return r;
}
struct bufferedString * nameByID (long taxID)
{
static struct storedNameTag queryTag;
struct storedNameTag * res;
struct bufferedString * resStr = NULL;
queryTag.taxID = taxID;
res = (struct storedNameTag *)avl_find(nameTagAVL, &queryTag);
if (res)
{
resStr = allocateNewString();
appendRangeToString(resStr,globalNameBuffer,res->startIndex,res->startIndex+res->length-1);
}
return resStr;
}
int main (int argc, const char * argv[])
{
FILE *inFile,
*mapFile;
struct bufferedString **currentBuffers;
struct storedNameTag *aTag,
*aTag2;
char automatonState = 0,
currentField = 0,
currentChar = 0,
line_buffer [MAX_LINE_BUFFER];
long currentLineID = 1,
expectedFields = 2,
mappedID ,
indexer;
size_t current_buffer_index = 0L,
current_buffer_size = 0L;
globalNameBuffer = allocateNewString();
globalTagBuffer = allocateNewBufferedTag();
currentBuffers = (struct bufferedString**)malloc (expectedFields*sizeof (struct bufferedString*));
nameTagAVL = avl_create (compare_tags, NULL, NULL);
for (indexer = 0; indexer < expectedFields; indexer++)
currentBuffers[indexer] = allocateNewString();
if (argc != 3)
{
fprintf (stderr,"%s\n", UsageString);
return 1;
}
inFile = fopen (argv[1], "rb");
if (!inFile)
{
fprintf (stderr,"Failed to open input file: %s\n", argv[1]);
return 1;
}
mapFile = fopen (argv[2], "rb");
if (!mapFile)
{
fprintf (stderr,"Failed to open gid-taxid map file: %s\n", argv[2]);
return 1;
}
for (indexer = 0; indexer < 256; indexer ++) {
digits [indexer] = 0;
}
for (indexer = (long)'0'; indexer <= (long)'9'; indexer ++) {
digits [indexer] = 1;
}
for (;;) {
if (current_buffer_index >= current_buffer_size) {
current_buffer_size = fread (line_buffer, 1L, MAX_LINE_BUFFER, inFile);
if (current_buffer_size == 0L) {
break;
}
current_buffer_index = 1L;
currentChar = line_buffer[0];
} else {
currentChar = line_buffer[current_buffer_index++];
}
switch (automatonState)
{
case 0: /* start of the line; expecting numbers */
if (digits[currentChar])
{
automatonState = 1; /* reading sequence ID */
appendCharacterToString(currentBuffers[currentField],currentChar);
}
else
if (!(currentChar == '\n' || currentChar == '\r'))
reportErrorLine ("Could not find a valid sequence ID to start the line",currentLineID);
break;
case 1: /* reading file ID */
if (currentChar >= '0' && currentChar <='9')
appendCharacterToString(currentBuffers[currentField],currentChar);
else
if (currentChar == '\t')
{
currentField ++;
automatonState = 2;
/* reading file ID */
}
else
reportErrorLine ("Expected a tab following the gi ID",currentLineID);
break;
case 2: /* read a field */
if (isalnum(currentChar) || currentChar == '/' || currentChar == '.' || currentChar == '_' || currentChar == '-')
appendCharacterToString(currentBuffers[currentField],currentChar);
else
if (currentChar == '\n' || currentChar == '\r')
{
automatonState = 0;
currentLineID ++;
currentField = 0;
aTag = allocateNameTag();
aTag->taxID = atoi(currentBuffers[0]->sData);
aTag->startIndex = globalNameBuffer->sLength;
aTag->length = appendRangeToString(globalNameBuffer,currentBuffers[1],0,currentBuffers[1]->sLength-1);
appendTagToBuffer (globalTagBuffer, aTag->taxID, aTag->startIndex, aTag->length);
if (aTag->length <= 0)
reportErrorLine ("Empty name tag",currentLineID);
if (*avl_probe(nameTagAVL,aTag) != aTag)
{
free (aTag);
//reportErrorLine ("Duplicate name tag",currentLineID);
}
for (indexer = 0; indexer < expectedFields; indexer++)
clear_buffered_string(currentBuffers[indexer]);
}
else
reportErrorLine ("Unexpected character",currentLineID);
break;
}
}
fclose (inFile);
aTag = allocateNameTag();
fprintf (stderr, "Reading gid-taxid mapping file...\n");
currentLineID = 0;
current_buffer_index = current_buffer_size = 0L;
for (;;) {
if (current_buffer_index >= current_buffer_size) {
current_buffer_size = fread (line_buffer, 1L, MAX_LINE_BUFFER, mapFile);
if (current_buffer_size == 0L) {
break;
}
current_buffer_index = 1L;
currentChar = line_buffer[0];
} else {
currentChar = line_buffer[current_buffer_index++];
}
if (currentLineID > 1 && currentLineID % 5000000 == 0 && automatonState == 0) {
fprintf (stderr, "Read %ld lines\n", currentLineID);
}
switch (automatonState)
{
case 0: /* start of the line; expecting numbers */
if (currentChar >= '0' && currentChar <='9')
{
automatonState = 1; /* reading sequence ID */
appendCharacterToString(currentBuffers[currentField],currentChar);
}
else
if (!(currentChar == '\n' || currentChar == '\r'))
reportErrorLine ("Could not find a valid sequence ID to start the line",currentLineID);
break;
case 1: /* reading file ID */
if (digits[currentChar])
appendCharacterToString(currentBuffers[currentField],currentChar);
else
if (currentChar == '\t')
{
currentField ++;
automatonState = 2;
/* reading file ID */
}
else
reportErrorLine ("Expected a tab following the tax ID",currentLineID);
break;
case 2: /* read a field */
if (digits[currentChar])
appendCharacterToString(currentBuffers[currentField],currentChar);
else
if (currentChar == '\n' || currentChar == '\r')
{
automatonState = 0;
currentLineID ++;
currentField = 0;
aTag->taxID = atoi(currentBuffers[0]->sData);
mappedID = atoi(currentBuffers[1]->sData);
aTag2 = avl_find(nameTagAVL,aTag);
if (aTag2)
aTag2->mappedTag = mappedID;
for (indexer = 0; indexer < expectedFields; indexer++)
clear_buffered_string(currentBuffers[indexer]);
}
else
reportErrorLine ("Unexpected character",currentLineID);
break;
}
}
fclose (mapFile);
for (indexer = 0L; indexer < expectedFields; indexer++)
destroy_string(currentBuffers[indexer]);
free(currentBuffers);
for (indexer = 0L; indexer < globalTagBuffer->sLength; indexer++) {
aTag->taxID = globalTagBuffer->gID[indexer];
aTag2 = avl_find(nameTagAVL,aTag);
if (aTag2) {
printf ("%ld\t%ld\t", aTag->taxID,aTag2->mappedTag);
}
else {
printf ("%ld\t-1\t", aTag->taxID);
}
for (expectedFields = globalTagBuffer->startTag[indexer];
expectedFields < globalTagBuffer->startTag[indexer] + globalTagBuffer->lengthTag[indexer];
expectedFields ++)
{
printf ("%c",globalNameBuffer->sData[expectedFields]);
}
printf ("\n");
}
//printf ("-1,NULL");
free (aTag);
return 0;
}
char* convertIntToJsonBool(int x) {
if (x) {
return allocateNewString("true", 4);
}
return allocateNewString("false", 5);
}
