void look_door() {
if(query_open("door 2")) message("my_action", "It is open.", this_player());
else message("my_action", "It has been closed.", this_player());
}
static pllAlignmentData *
pllParseFASTA (const char * filename)
{
int i,j;
int status;
pllAlignmentData * alignmentData;
if (!query_open(filename))
{
errno = PLL_ERROR_FILE_OPEN;
return NULL;
}
alignmentData = (pllAlignmentData *) malloc(sizeof(pllAlignmentData));
alignmentData->sequenceData = NULL;
alignmentData->sequenceLabels = NULL;
int prev_qseqlen = -1;
while(1)
{
char * qhead;
int query_head_len;
char *qseq;
int qseqlen;
// int query_no = -1;
if ((status = query_getnext(&qhead, &query_head_len,
&qseq, &qseqlen, &query_no)) > 0)
{
alignmentData->sequenceData = (unsigned char **)realloc(alignmentData->sequenceData,
(query_no + 2)*sizeof(unsigned char *));
alignmentData->sequenceLabels = (char **)realloc(alignmentData->sequenceLabels,
(query_no + 2)*sizeof(char *));
/* remove trailing whitespace from sequence names */
j = query_head_len-1;
while(j>0 && (qhead[j] == ' ' || qhead[j] == '\t'))
{
qhead[j] = 0;
}
alignmentData->sequenceData[query_no+1] = (unsigned char *)strdup(qseq);
alignmentData->sequenceLabels[query_no+1] = strdup(qhead);
if (prev_qseqlen != -1)
{
/* fasta sequences not aligned, free everything except last read
which will be freed by query_close() */
if (qseqlen != prev_qseqlen)
{
errno = PLL_ERROR_FASTA_SYNTAX;
_pll_free_temp_alignment(alignmentData, query_no+1);
query_close();
return NULL;
}
}
else
{
alignmentData->sequenceLength = qseqlen;
alignmentData->originalSeqLength = qseqlen;
prev_qseqlen = qseqlen;
}
}
else if (status == -1)
{
errno = PLL_ERROR_FASTA_SYNTAX;
_pll_free_temp_alignment(alignmentData, query_no+1);
query_close();
return NULL;
}
else break;
}
alignmentData->sequenceCount = query_no+1;
query_close();
alignmentData->siteWeights = (int *) rax_malloc (alignmentData->sequenceLength * sizeof (int));
for (i = 0; i < alignmentData->sequenceLength; ++ i)
alignmentData->siteWeights[i] = 1;
/* ugly hack to turn it to one contiguous block of memory. This should be redesigned */
void * mem = malloc((alignmentData->sequenceCount)*(alignmentData->sequenceLength+1)*sizeof(unsigned char));
for (i = 1; i <= alignmentData->sequenceCount; ++i)
{
void * tmp = alignmentData->sequenceData[i];
alignmentData->sequenceData[i] = (unsigned char *) (mem + (i - 1) * (alignmentData->sequenceLength + 1) * sizeof (unsigned char));
memcpy(alignmentData->sequenceData[i], tmp, alignmentData->sequenceLength);
alignmentData->sequenceData[i][alignmentData->sequenceLength] = 0;
free(tmp);
}
alignmentData->sequenceData[0] = NULL;
return (alignmentData);
}
