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Author: Andreas Tille <tille@debian.org>
Last-Update: 2017-03-17
Description: Enable linking against libhmmer.a as packaged
in hmmer2 source package
--- a/algorithm-hmm/hmm-binding.cpp
+++ b/algorithm-hmm/hmm-binding.cpp
@@ -71,7 +71,7 @@ int HMM::load(char *filename) {
if(strlen(filename) == 0) return -1;
// Load the model from the specified file.
- if((hmmfp = HMMFileOpen(filename, "HMMERDB")) == NULL) return -1;
+ if((hmmfp = HMMFileOpen(filename, (char *)"HMMERDB")) == NULL) return -1;
if(! HMMFileRead(hmmfp, &tmp_model)) {
HMMFileClose(hmmfp);
@@ -95,25 +95,26 @@ int HMM::load(char *filename) {
HMMReport *HMM::search(char *seq) {
struct tophit_s *ghit, *dhit;
+ struct dpmatrix_s *mx;
struct p7trace_s *trace;
double pvalue, evalue;
int numhits;
HMMReport *hmmrep;
float score;
int seqlen;
- char *dseq;
+ unsigned char *dseq;
// Ensure we have a valid model and sequence.
if((model == NULL) ||(seq == NULL) || (!(seqlen = strlen(seq)))) return NULL;
// Convert the sequence to the format the HMMER library expects.
- dseq = DigitizeSequence(seq, seqlen);
+ dseq = DigitizeSequence((char *)seq, seqlen);
// Calculate the raw scores for the sequence.
if (P7ViterbiSize(seqlen, model->M) <= RAMLIMIT)
- score = P7Viterbi(dseq, seqlen, model, &trace);
+ score = P7Viterbi(dseq, seqlen, model, mx, &trace);
else
- score = P7SmallViterbi(dseq, seqlen, model, &trace);
+ score = P7SmallViterbi(dseq, seqlen, model, mx, &trace);
// Calculate the score using the forward algorithm if we need.
@@ -241,7 +242,7 @@ void HMM::init(char *filename, int df, i
thresh.globT = -FLT_MAX;
thresh.domT = -FLT_MAX;
thresh.domE = FLT_MAX;
- thresh.autocut = CUT_NONE;
+ thresh.autocut = threshold_s::CUT_NONE;
thresh.Z = 1;
doForward = df;
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