From b6822b60279b42f36e5f5123ed6091f6504af209 Mon Sep 17 00:00:00 2001 From: Eric Nawrocki Date: Wed, 22 Jun 2016 12:11:04 -0400 Subject: [PATCH] Silences a bunch of warnings reported with --Wall with gcc 4.8.1 related to set but unused variables. Doesn't silence them all. I left several where I decided the variables are helpful for understanding the code. --- rmark/rmark-create.c | 5 +---- src/bandcyk-truncation-test.c | 3 --- src/cm_alidisplay.c | 2 -- src/cm_dpalign.c | 19 ++++--------------- src/cm_dpalign_trunc.c | 8 ++------ src/cm_dpsearch.c | 6 ------ src/cm_dpsearch_trunc.c | 4 ---- src/cm_modelmaker.c | 6 +++--- src/cm_mx.c | 8 -------- src/cm_p7_modelmaker.c | 3 --- src/cm_parsetree.c | 5 ++--- src/cm_pipeline.c | 2 -- src/cm_submodel.c | 10 ---------- src/cm_tophits.c | 4 ++-- src/cmalign.c | 6 ++---- src/cmbuild.c | 8 ++------ src/cmcalibrate.c | 2 -- src/cmscan.c | 4 ---- src/cmsearch.c | 5 ----- src/cp9_modelmaker.c | 9 +-------- src/cp9_trace.c | 6 +++--- src/hmmband.c | 19 +++---------------- src/impl_sse/sse_cm_dpsearch.c | 8 +++----- src/impl_sse/sse_cm_dpsmall.c | 14 +++++++------- src/impl_sse/sse_cmcons_hitmx.c | 6 +++--- src/trcyk.c | 2 -- 26 files changed, 38 insertions(+), 136 deletions(-) diff --git a/rmark/rmark-create.c b/rmark/rmark-create.c index 71942c0b..793b59a3 100644 --- a/rmark/rmark-create.c +++ b/rmark/rmark-create.c @@ -530,7 +530,6 @@ remove_fragments(struct cfg_s *cfg, ESL_MSA *msa, ESL_MSA **ret_filteredmsa, int int *useme = NULL; double len = 0.0; int i; - int nfrags; int status; /* min length is cfg->fragfrac * average length */ @@ -539,7 +538,7 @@ remove_fragments(struct cfg_s *cfg, ESL_MSA *msa, ESL_MSA **ret_filteredmsa, int len *= cfg->fragfrac / (double) msa->nseq; ESL_ALLOC(useme, sizeof(int) * msa->nseq); - for (nfrags = 0, i = 0; i < msa->nseq; i++) + for (i = 0; i < msa->nseq; i++) useme[i] = (esl_abc_dsqrlen(msa->abc, msa->ax[i]) < len) ? 0 : 1; if ((status = esl_msa_SequenceSubset(msa, useme, ret_filteredmsa)) != eslOK) goto ERROR; @@ -580,7 +579,6 @@ separate_sets(struct cfg_s *cfg, ESL_MSA *msa, int **ret_i_am_train, int **ret_i int nc = 0; int c; int ctrain; /* index of the cluster that becomes the training alignment */ - int ntrain; /* number of seqs in the training alignment */ int nskip; int i, i2; int status; @@ -591,7 +589,6 @@ separate_sets(struct cfg_s *cfg, ESL_MSA *msa, int **ret_i_am_train, int **ret_i if ((status = esl_msacluster_SingleLinkage(msa, cfg->idthresh1, &assignment, &nin, &nc)) != eslOK) goto ERROR; ctrain = esl_vec_IArgMax(nin, nc); - ntrain = esl_vec_IMax(nin, nc); for (i = 0; i < msa->nseq; i++) i_am_train[i] = (assignment[i] == ctrain) ? 1 : 0; if ((status = esl_msa_SequenceSubset(msa, i_am_train, &trainmsa)) != eslOK) goto ERROR; diff --git a/src/bandcyk-truncation-test.c b/src/bandcyk-truncation-test.c index dd034835..7345249b 100644 --- a/src/bandcyk-truncation-test.c +++ b/src/bandcyk-truncation-test.c @@ -53,7 +53,6 @@ static ESL_OPTIONS options[] = { { "--betaW", eslARG_REAL, "1E-5", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for W calculation to ", 0 }, { "--beta1", eslARG_REAL, "1E-5", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for dmin1/dmax1 to ", 0 }, { "--beta2", eslARG_REAL, "1E-6", NULL, "x>0.",NULL, NULL, NULL, "set tail probability thresh for dmin2/dmax2 to ", 0 }, - { "--verbose", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL, "show output (default: silently return 0 on success)", 0 }, { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }, }; static char usage[] = "[-options] where width Z1 < Z2."; @@ -80,7 +79,6 @@ main(int argc, char **argv) double gbeta1; /* geometric decay constant, truncation error calc */ double gbeta2; /* geometric decay constant, truncation error calc */ double g; /* log of an estimated gamma[n] */ - int be_verbose; ESL_ALPHABET *abc = NULL; char errbuf[eslERRBUFSIZE]; /* for error messages */ CM_QDBINFO *qdbinfo1 = NULL; /* holds dmin1/dmax1 and dmin2/dmax2 for first choice of Z */ @@ -95,7 +93,6 @@ main(int argc, char **argv) betaW = esl_opt_GetReal (go, "--betaW"); beta1 = esl_opt_GetReal (go, "--beta1"); beta2 = esl_opt_GetReal (go, "--beta2"); - be_verbose = esl_opt_GetBoolean(go, "--verbose"); if (Z1 >= Z2) cm_Fail("Please set a width Z1 < width Z2, else the check won't work right."); diff --git a/src/cm_alidisplay.c b/src/cm_alidisplay.c index eca937da..07e67f2f 100644 --- a/src/cm_alidisplay.c +++ b/src/cm_alidisplay.c @@ -76,7 +76,6 @@ cm_alidisplay_Create(CM_t *cm, char *errbuf, CM_ALNDATA *adata, const ESL_SQ *sq int pos; /* position in growing ali */ int lc, rc; /* indices for left, right pos in consensus */ int symi, symj; - int d; char mode; int lrf, rrf; /* chars in annotation line; left, right */ int lstr, rstr; /* chars in structure line; left, right */ @@ -416,7 +415,6 @@ cm_alidisplay_Create(CM_t *cm, char *errbuf, CM_ALNDATA *adata, const ESL_SQ *sq lpost = '.'; /* init to gap, if it corresponds to a residue, we'll reset it below */ rpost = '.'; /* init to gap, if it corresponds to a residue, we'll reset it below */ } - d = tr->emitr[ti] - tr->emitl[ti] + 1; mode = tr->mode[ti]; /* Calculate four of the six lines: rfline, csline, model, and aseq. diff --git a/src/cm_dpalign.c b/src/cm_dpalign.c index ea402391..7d7ed88c 100644 --- a/src/cm_dpalign.c +++ b/src/cm_dpalign.c @@ -270,7 +270,7 @@ cm_alignT_hb(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, int ESL_STACK *pda; /* stack that tracks bifurc parent of a right start */ int v,j,d,i; /* indices for state, j, subseq len */ int k; /* subseq len for bifurcs */ - int z; /* state index */ + /*int z;*/ /* state index */ int y, yoffset; /* child state y, it's offset */ int bifparent; /* B_st parent */ int b; /* local begin state */ @@ -340,7 +340,7 @@ cm_alignT_hb(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, int if (cm->sttype[v] == B_st) { k = shmx->kshadow[v][jp_v][dp_v]; /* k = offset len of right fragment */ - z = cm->cnum[v]; + /*z = cm->cnum[v];*/ /* Store info about the right fragment that we'll retrieve later: */ @@ -2201,7 +2201,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM int sdr; /* StateRightDelta(cm->sttype[v] */ int j_sdr; /* j - sdr */ int d_sd; /* d - sd */ - float tsc; /* a transition score */ int have_el; /* TRUE if CM has local ends on, otherwise FALSE */ /* the DP matrices */ @@ -2244,7 +2243,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM /* Main recursion */ for (v = cm->M-1; v >= 0; v--) { - float const *tsc_v = cm->tsc[v]; /* transition scores for state v */ sd = StateDelta(cm->sttype[v]); sdr = StateRightDelta(cm->sttype[v]); @@ -2321,7 +2319,6 @@ cm_OptAccAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, CM */ for (y = cm->cfirst[v]; y < (cm->cfirst[v] + cm->cnum[v]); y++) { yoffset = y - cm->cfirst[v]; - tsc = tsc_v[yoffset]; j_sdr = 0; for (j = sdr; j <= L; j++, j_sdr++) { d_sd = 0; @@ -3001,7 +2998,6 @@ cm_CYKOutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit float **esc_vAA; /* ptr to cm->oesc, optimized emission scores */ float escore; /* an emission score, tmp variable */ int voffset; /* index of v in t_v(y) transition scores */ - int emitmode; /* EMITLEFT, EMITRIGHT, EMITPAIR, EMITNONE, for state y */ int sd; /* StateDelta(cm->sttype[y]) */ int sdr; /* StateRightDelta(cm->sttype[y] */ @@ -3111,7 +3107,6 @@ cm_CYKOutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit if ((cm->flags & CMH_LOCAL_END) && NOT_IMPOSSIBLE(cm->endsc[v])) { sdr = StateRightDelta(cm->sttype[v]); /* note sdr is for state v */ sd = StateDelta(cm->sttype[v]); /* note sd is for state v */ - emitmode = Emitmode(cm->sttype[v]); /* note emitmode is for state v */ for (j = 0; j <= L; j++) { for (d = 0; d <= j; d++) { @@ -4023,7 +4018,6 @@ cm_OutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, i float **esc_vAA; /* ptr to cm->oesc, optimized emission scores */ float escore; /* an emission score, tmp variable */ int voffset; /* index of v in t_v(y) transition scores */ - int emitmode; /* EMITLEFT, EMITRIGHT, EMITPAIR, EMITNONE, for state y */ int sd; /* StateDelta(cm->sttype[y]) */ int sdr; /* StateRightDelta(cm->sttype[y] */ @@ -4128,7 +4122,6 @@ cm_OutsideAlign(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, float size_limit, i if ((cm->flags & CMH_LOCAL_END) && NOT_IMPOSSIBLE(cm->endsc[v])) { sdr = StateRightDelta(cm->sttype[v]); /* note sdr is for state v */ sd = StateDelta(cm->sttype[v]); /* note sd is for state v */ - emitmode = Emitmode(cm->sttype[v]); /* note emitmode is for state v */ for (j = 0; j <= L; j++) { for (d = 0; d <= j; d++) { @@ -5196,7 +5189,6 @@ cm_EmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, CM_HB_MX int status; int v, j, d; /* state, position, subseq length */ int i; /* sequence position */ - int sd; /* StateDelta(v) */ int ip_v; /* offset i in banded matrix */ int ip_v2; /* another offset i in banded matrix */ int jp_v; /* offset j in banded matrix */ @@ -5225,7 +5217,6 @@ cm_EmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, CM_HB_MX * leftwise (l_pp) or rightwise (r_pp). */ for(v = 0; v < cm->M; v++) { - sd = StateDelta(cm->sttype[v]); if(cm->sttype[v] == MP_st || cm->sttype[v] == ML_st || cm->sttype[v] == IL_st) { for(j = jmin[v]; j <= jmax[v]; j++) { jp_v = j - jmin[v]; @@ -5450,7 +5441,7 @@ int cm_PostCode(CM_t *cm, char *errbuf, int L, CM_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp) { int status; - int x, v, i, j, d, r; /* counters */ + int x, v, i, j, r; /* counters */ char *ppstr; /* the PP string, created here */ float p; /* a probability */ float sum_logp; /* log of summed probability of all residues emitted thus far */ @@ -5464,7 +5455,6 @@ cm_PostCode(CM_t *cm, char *errbuf, int L, CM_EMIT_MX *emit_mx, Parsetree_t *tr, v = tr->state[x]; i = tr->emitl[x]; j = tr->emitr[x]; - d = j-i+1; /* Only P, L, R, and EL states have emissions. */ if(cm->sttype[v] == EL_st) { /* EL state, we have to handle this guy special */ @@ -5510,7 +5500,7 @@ int cm_PostCodeHB(CM_t *cm, char *errbuf, int L, CM_HB_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp) { int status; - int x, v, i, j, d, r; /* counters */ + int x, v, i, j, r; /* counters */ char *ppstr; /* the PP string, created here */ float p; /* a probability */ float sum_logp; /* log of summed probability of all residues emitted thus far */ @@ -5533,7 +5523,6 @@ cm_PostCodeHB(CM_t *cm, char *errbuf, int L, CM_HB_EMIT_MX *emit_mx, Parsetree_t v = tr->state[x]; i = tr->emitl[x]; j = tr->emitr[x]; - d = j-i+1; /* Only P, L, R, and EL states have emissions. */ if(cm->sttype[v] == EL_st) { /* EL state, we have to handle this guy special */ diff --git a/src/cm_dpalign_trunc.c b/src/cm_dpalign_trunc.c index 41746efd..e3a69a1a 100644 --- a/src/cm_dpalign_trunc.c +++ b/src/cm_dpalign_trunc.c @@ -9217,7 +9217,6 @@ cm_TrEmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, char pr int status; int v, j, d; /* state, position, subseq length */ int i; /* sequence position */ - int sd; /* StateDelta(v) */ int fill_L, fill_R; /* do we need to fill Ll_pp/Rr_pp matrices? */ int jp_v; /* j-jmin[v] for current j, and current v */ int jp_v2; /* another offset j in banded matrix */ @@ -9253,7 +9252,6 @@ cm_TrEmitterPosteriorHB(CM_t *cm, char *errbuf, int L, float size_limit, char pr * leftwise (*l_pp) or rightwise (*r_pp). */ for(v = 0; v < cm->M; v++) { - sd = StateDelta(cm->sttype[v]); if(cm->sttype[v] == MP_st || cm->sttype[v] == ML_st || cm->sttype[v] == IL_st) { if(cm->cp9b->Jvalid[v]) { for(j = jmin[v]; j <= jmax[v]; j++) { @@ -9588,7 +9586,7 @@ int cm_TrPostCode(CM_t *cm, char *errbuf, int L, CM_TR_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp) { int status; - int x, v, i, j, d, r; /* counters */ + int x, v, i, j, r; /* counters */ char *ppstr; /* the PP string, created here */ float p; /* a probability */ float sum_logp; /* log of summed probability of all residues emitted thus far */ @@ -9606,7 +9604,6 @@ cm_TrPostCode(CM_t *cm, char *errbuf, int L, CM_TR_EMIT_MX *emit_mx, Parsetree_t v = tr->state[x]; i = tr->emitl[x]; j = tr->emitr[x]; - d = j-i+1; mode = tr->mode[x]; /* Only P, L, R, and EL states have emissions. */ @@ -9694,7 +9691,7 @@ int cm_TrPostCodeHB(CM_t *cm, char *errbuf, int L, CM_TR_HB_EMIT_MX *emit_mx, Parsetree_t *tr, char **ret_ppstr, float *ret_avgp) { int status; - int x, v, i, j, d, r; /* counters */ + int x, v, i, j, r; /* counters */ char *ppstr; /* the PP string, created here */ float p; /* a probability */ float sum_logp; /* log of summed probability of all residues emitted thus far */ @@ -9721,7 +9718,6 @@ cm_TrPostCodeHB(CM_t *cm, char *errbuf, int L, CM_TR_HB_EMIT_MX *emit_mx, Parset v = tr->state[x]; i = tr->emitl[x]; j = tr->emitr[x]; - d = j-i+1; mode = tr->mode[x]; /* Only P, L, R, and EL states have emissions. */ diff --git a/src/cm_dpsearch.c b/src/cm_dpsearch.c index d7fb7c60..04f0c3ee 100644 --- a/src/cm_dpsearch.c +++ b/src/cm_dpsearch.c @@ -745,7 +745,6 @@ RefCYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq, in int dn_w, dx_w; /* minimum/maximum valid d for state w */ int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */ int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */ - int cnum; /* number of children for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -869,7 +868,6 @@ RefCYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq, in jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur; jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; dn = dnA[v]; dx = dxA[v]; /* if we emit right, precalc score of emitting res j from state v */ @@ -2388,7 +2386,6 @@ RefIInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq int dn_w, dx_w; /* minimum/maximum valid d for state w */ int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */ int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */ - int cnum; /* number of children for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ int **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -2512,7 +2509,6 @@ RefIInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur; jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; dn = dnA[v]; dx = dxA[v]; /* if we emit right, precalc score of emitting res j from state v */ @@ -2768,7 +2764,6 @@ RefFInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq int dn_w, dx_w; /* minimum/maximum valid d for state w */ int *dmin; /* [0..v..cm->M-1] minimum d allowed for this state */ int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */ - int cnum; /* number of children for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -2891,7 +2886,6 @@ RefFInsideScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, int qdbidx, ESL_DSQ *dsq jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur; jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; dn = dnA[v]; dx = dxA[v]; /* if we emit right, precalc score of emitting res j from state v */ diff --git a/src/cm_dpsearch_trunc.c b/src/cm_dpsearch_trunc.c index e220092d..2c5631f7 100644 --- a/src/cm_dpsearch_trunc.c +++ b/src/cm_dpsearch_trunc.c @@ -111,7 +111,6 @@ RefTrCYKScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int pass_ int dx_w; /* maximum valid d for state w */ int kn, kx; /* minimum/maximum valid k for current d in B_st recursion */ int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */ - int cnum; /* number of children for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -260,7 +259,6 @@ RefTrCYKScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int pass_ jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; jq_y = (StateRightDelta(cm->sttype[v]) > 0) ? cur : prv; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; /* if we emit right, precalc score of emitting res j from state v */ float esc_j = IMPOSSIBLE; float rmesc_j = IMPOSSIBLE; @@ -768,7 +766,6 @@ RefITrInsideScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int p int dx_y; /* maximum valid d for state y */ int dx_w; /* maximum valid d for state w */ int *dmax; /* [0..v..cm->M-1] maximum d allowed for this state */ - int cnum; /* number of children for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ int **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -917,7 +914,6 @@ RefITrInsideScan(CM_t *cm, char *errbuf, CM_TR_SCAN_MX *trsmx, int qdbidx, int p jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; jq_y = (StateRightDelta(cm->sttype[v]) > 0) ? cur : prv; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; /* if we emit right, precalc score of emitting res j from state v */ int esc_j = -INFTY; int rmesc_j = -INFTY; diff --git a/src/cm_modelmaker.c b/src/cm_modelmaker.c index ed7f0df1..6b339f40 100644 --- a/src/cm_modelmaker.c +++ b/src/cm_modelmaker.c @@ -1831,7 +1831,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2) int ret_val; int i, yoffset; int to_detach; - int to_keep; + /*int to_keep;*/ float diff; ret_val = FALSE; @@ -1843,7 +1843,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2) { ret_val = TRUE; to_detach = insert1; - to_keep = insert2; + /*to_keep = insert2;*/ } if(cm->sttype[insert2+1] == E_st) { @@ -1851,7 +1851,7 @@ cm_check_before_detaching(CM_t *cm, int insert1, int insert2) cm_Fail("ERROR: in cm_check_before_detaching() insert1: %d and insert2: %d both map to END_E-1 states.\n", insert1, insert2); ret_val = TRUE; to_detach = insert2; - to_keep = insert1; + /*to_keep = insert1;*/ } /* check to make sure we have 0.0 counts in to_detach */ diff --git a/src/cm_mx.c b/src/cm_mx.c index 8c872db6..037b79d0 100644 --- a/src/cm_mx.c +++ b/src/cm_mx.c @@ -2162,11 +2162,9 @@ cm_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_ny_cells, in int64_t y_ncells; int64_t k_ncells; float Mb_needed; - int nbifs; y_ncells = 0; k_ncells = 0; - nbifs = CMCountStatetype(cm, B_st); Mb_needed = (float) (sizeof(CM_SHADOW_MX) + ((cm->M) * sizeof(char **)) + /* mx->yshadow[] ptrs */ @@ -2776,7 +2774,6 @@ cm_tr_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_Jny_cells int64_t Rk_ncells; int64_t Tk_ncells; float Mb_needed; - int nbifs; Jy_ncells = 0; Ly_ncells = 0; @@ -2785,7 +2782,6 @@ cm_tr_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, int L, int64_t *ret_Jny_cells Lk_ncells = 0; Rk_ncells = 0; Tk_ncells = 0; - nbifs = CMCountStatetype(cm, B_st); Mb_needed = (float) (sizeof(CM_TR_SHADOW_MX) + (3 * (cm->M) * sizeof(char **)) + /* mx->{J,L,R}yshadow[] ptrs */ @@ -3195,13 +3191,11 @@ cm_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t *re int64_t y_ncells, k_ncells; int jbw; float Mb_needed; - int nbifs; /* contract check */ if(cp9b == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "cm_hb_shadow_mx_SizeNeeded() entered with cp9b == NULL.\n"); y_ncells = k_ncells = 0; - nbifs = CMCountStatetype(cm, B_st); Mb_needed = (float) (sizeof(CM_HB_SHADOW_MX) + @@ -3992,7 +3986,6 @@ cm_tr_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t int64_t Tk_ncells; int jbw; float Mb_needed; - int nbifs; /* contract check */ if(cp9b == NULL) ESL_FAIL(eslEINCOMPAT, errbuf, "cm_tr_hb_shadow_mx_SizeNeeded() entered with cp9b == NULL.\n"); @@ -4004,7 +3997,6 @@ cm_tr_hb_shadow_mx_SizeNeeded(CM_t *cm, char *errbuf, CP9Bands_t *cp9b, int64_t Lk_ncells = 0; Rk_ncells = 0; Tk_ncells = 0; - nbifs = CMCountStatetype(cm, B_st); Mb_needed = (float) (sizeof(CM_TR_HB_SHADOW_MX) + (3 * (cp9b->cm_M) * sizeof(char **)) + /* mx->{J,L,R}yshadow[] ptrs */ diff --git a/src/cm_p7_modelmaker.c b/src/cm_p7_modelmaker.c index bae5c498..769dc661 100644 --- a/src/cm_p7_modelmaker.c +++ b/src/cm_p7_modelmaker.c @@ -351,7 +351,6 @@ cm_p7_Tau(ESL_RANDOMNESS *r, char *errbuf, P7_OPROFILE *om, P7_PROFILE *gm, P7_B double gmu, glam; int status; int i; - int M; int do_generic; if(om == NULL && gm == NULL) { status = eslEINVAL; goto ERROR; } @@ -361,12 +360,10 @@ cm_p7_Tau(ESL_RANDOMNESS *r, char *errbuf, P7_OPROFILE *om, P7_PROFILE *gm, P7_B if(do_generic) { gx = p7_gmx_Create(gm->M, L); /* DP matrix: for ForwardParser, L rows */ if (gx == NULL) { status = eslEMEM; goto ERROR; } - M = gm->M; } else { ox = p7_omx_Create(om->M, 0, L); /* DP matrix: for ForwardParser, L rows */ if (ox == NULL) { status = eslEMEM; goto ERROR; } - M = om->M; } ESL_ALLOC(xv, sizeof(double) * N); diff --git a/src/cm_parsetree.c b/src/cm_parsetree.c index fda3c081..df6e9360 100644 --- a/src/cm_parsetree.c +++ b/src/cm_parsetree.c @@ -2621,7 +2621,7 @@ cm_StochasticParsetree(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_MX *mx, E int el_is_possible; /* TRUE if we can jump to EL from current state (and we're in local mode) FALSE if not */ float fsc = 0.; /* score of the parsetree we're sampling */ int choice; /* index represeting sampled choice */ - int sd, sdl, sdr; /* state delta, state left delta, state right delta */ + int sd, sdr; /* state delta, state right delta */ /* the DP matrix, filled by prior call to cm_InsideAlign() */ float ***alpha = mx->dp; /* pointer to the alpha DP matrix */ @@ -2703,7 +2703,6 @@ cm_StochasticParsetree(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_MX *mx, E /* add in emission score (or 0.0 if we're a non-emitter) */ fsc += get_femission_score(cm, dsq, v, i, j); sd = StateDelta(cm->sttype[v]); - sdl = StateLeftDelta(cm->sttype[v]); sdr = StateRightDelta(cm->sttype[v]); /* set pA[] as (float-ized) log odds scores for each child we can transit to, @@ -2860,7 +2859,7 @@ cm_StochasticParsetreeHB(CM_t *cm, char *errbuf, ESL_DSQ *dsq, int L, CM_HB_MX * int jp_z, kp_z; /* j - jmin[z], d - hdmin[z][jp_z] */ int jp_y_sdr; /* j - jmin[y] - vms_sdr */ int dp_y_sd; /* hdmin[y][jp_y_vms_sdr] - vms_sd */ - int jp_0; /* L offset in ROOT_S's (v==0) j band */ + int jp_0; /* j offset in ROOT_S's (v==0) j band */ int Lp_0; /* L offset in ROOT_S's (v==0) d band */ int kmin, kmax; /* min/max k */ diff --git a/src/cm_pipeline.c b/src/cm_pipeline.c index ab9e16c7..cc96e7e8 100644 --- a/src/cm_pipeline.c +++ b/src/cm_pipeline.c @@ -2436,7 +2436,6 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P int64_t *new_we = NULL; /* used when copying/modifying we */ float *new_wb = NULL; /* used when copying/modifying wb */ int nsurv_fwd; /* number of windows that survive fwd filter */ - int new_nsurv_fwd; /* used when merging fwd survivors */ ESL_DSQ *subdsq; /* a ptr to the first position of a window */ int have_rest; /* do we have the full read in? */ P7_HMM_WINDOWLIST wlist; /* list of windows, structure taken by p7_MSVFilter_longtarget() */ @@ -2763,7 +2762,6 @@ pli_p7_filter(CM_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, float *p7_evparam, P } } /* we could have overlapping windows, merge those that do overlap */ - new_nsurv_fwd = 0; ESL_ALLOC(useme, sizeof(int) * nsurv_fwd); esl_vec_ISet(useme, nsurv_fwd, FALSE); i2 = 0; diff --git a/src/cm_submodel.c b/src/cm_submodel.c index a5c744cf..bc623698 100644 --- a/src/cm_submodel.c +++ b/src/cm_submodel.c @@ -423,7 +423,6 @@ map_orig2sub_cm_helper(CM_t *orig_cm, CM_t *sub_cm, CMSubMap_t *submap, int orig { int sub_nd; int orig_nd; - int is_insert; /*printf("\nin helper: orig_v: %d sub_v: %d\n", orig_v, sub_v);*/ @@ -437,10 +436,8 @@ map_orig2sub_cm_helper(CM_t *orig_cm, CM_t *sub_cm, CMSubMap_t *submap, int orig orig_nd = orig_cm->ndidx[orig_v]; sub_nd = sub_cm->ndidx[sub_v]; - is_insert = FALSE; if(sub_cm->sttype[sub_v] == IL_st || sub_cm->sttype[sub_v] == IR_st) { - is_insert = TRUE; /* Make sure that neither orig_v nor sub_v is a detached insert state, * if either is, we return b/c it's irrelevant, and we don't store that info in the maps */ if(orig_cm->sttype[(orig_v+1)] == E_st || sub_cm->sttype[(sub_v+1)] == E_st) @@ -861,9 +858,7 @@ CP9NodeForPosn(CP9_t *hmm, int i0, int j0, int x, CP9_MX *post, '1' for insert */ int max_sc; /* score (log probability) from post matrix for max_k node max_type state type */ int k; /* counter over nodes */ - int reached_mass; /* TRUE if we've reached our pmass */ - reached_mass = FALSE; if(!is_start) pmass = 1. - pmass; /* we move left to right */ /*printf("in CP9NodeForPosn is_start: %d pmass: %f\n", is_start, pmass);*/ @@ -2046,9 +2041,6 @@ check_sub_cm_by_sampling(CM_t *orig_cm, CM_t *sub_cm, char *errbuf, ESL_RANDOMNE CP9_t *sub_hmm; /* constructed CP9 HMM from the sub_cm */ CP9Map_t *orig_cp9map; /* maps the orig_cm to the orig_hmm and vice versa */ CP9Map_t *sub_cp9map; /* maps the sub_cm to the sub_hmm and vice versa */ - int debug_level; - - debug_level = 0; /* Build two CP9 HMMs, one for the orig_cm and one for the sub_cm */ if((status = build_cp9_hmm(orig_cm, errbuf, FALSE, 0.0001, print_flag, &orig_hmm, &orig_cp9map)) != eslOK) return status; @@ -3329,7 +3321,6 @@ sub_cm2cm_parsetree(CM_t *orig_cm, CM_t *sub_cm, Parsetree_t **ret_orig_tr, Pars int orig_v2; int orig_nd1; int orig_nd2; - int nodes_used; int cm_nd; int i; int parent_tr_nd; @@ -3594,7 +3585,6 @@ sub_cm2cm_parsetree(CM_t *orig_cm, CM_t *sub_cm, Parsetree_t **ret_orig_tr, Pars } orig_tr = CreateParsetree(100); - nodes_used = 0; for(cm_nd = 0; cm_nd < orig_cm->nodes; cm_nd++) { emitl_flag = 0; diff --git a/src/cm_tophits.c b/src/cm_tophits.c index 741d7897..1723fe05 100644 --- a/src/cm_tophits.c +++ b/src/cm_tophits.c @@ -1770,7 +1770,7 @@ cm_tophits_HitAlignmentStatistics(FILE *ofp, CM_TOPHITS *th, int used_hb, int us int is_reported; int is_included; int is_removed_duplicate; - int is_marked_duplicate; + /*int is_marked_duplicate;*/ /* not used, currently */ /* variables for alignments for all hits */ int64_t all_naln = 0; /* total number alignments */ @@ -1836,7 +1836,7 @@ cm_tophits_HitAlignmentStatistics(FILE *ofp, CM_TOPHITS *th, int used_hb, int us is_reported = (th->unsrt[h].flags & CM_HIT_IS_REPORTED) ? TRUE : FALSE; is_included = (th->unsrt[h].flags & CM_HIT_IS_INCLUDED) ? TRUE : FALSE; is_removed_duplicate = (th->unsrt[h].flags & CM_HIT_IS_REMOVED_DUPLICATE) ? TRUE : FALSE; - is_marked_duplicate = (th->unsrt[h].flags & CM_HIT_IS_MARKED_OVERLAP) ? TRUE : FALSE; + /*is_marked_duplicate = (th->unsrt[h].flags & CM_HIT_IS_MARKED_OVERLAP) ? TRUE : FALSE;*/ if(th->unsrt[h].ad != NULL) { all_naln++; all_tot_matrix_Mb += th->unsrt[h].ad->matrix_Mb; diff --git a/src/cmalign.c b/src/cmalign.c index 06947f8f..fee98f3f 100644 --- a/src/cmalign.c +++ b/src/cmalign.c @@ -2081,7 +2081,7 @@ create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char int cur_clen; /* consensus length (non-gap #=GC RF length) of current alignment */ int apos; /* alignment position */ ESL_MSA *fmsa = NULL; /* the merged alignment created by merging all alignments in msaA */ - int alen_fmsa; /* number of columns in merged MSA */ + /*int alen_fmsa;*/ /* number of columns in merged MSA */ int *ngap_insA = NULL; /* [0..alen] number of insert gap columns to add after each alignment column when merging */ int *ngap_elA = NULL; /* [0..alen] number of missing data ('~') gap columns to add after each alignment column when merging */ int *ngap_eitherA = NULL; /* [0..apos..alen] = ngap_insA[apos] + ngap_elA[apos] */ @@ -2165,7 +2165,7 @@ create_and_output_final_msa(const ESL_GETOPTS *go, const struct cfg_s *cfg, char * final (3rd) pass we'll output aligned data. */ fmsa = esl_msa_Create(nseq_tot, -1); - alen_fmsa = cm->clen + esl_vec_ISum(maxins, (cm->clen+1)); + /*alen_fmsa = cm->clen + esl_vec_ISum(maxins, (cm->clen+1));*/ /* if there was any GS annotation in any of the individual alignments, * do second pass through alignment files, outputting GS annotation as we go. */ @@ -2483,7 +2483,6 @@ inflate_gc_with_gaps_and_els(FILE *ofp, ESL_MSA *msa, int *ngap_insA, int *ngap_ int apos = 0; int apos2print = 0; int i; - int prv_cpos = -1; int alen2print = 0; char *rf2print; char *ss_cons2print; @@ -2509,7 +2508,6 @@ inflate_gc_with_gaps_and_els(FILE *ofp, ESL_MSA *msa, int *ngap_insA, int *ngap_ if(apos < msa->alen) { rf2print[apos2print] = msa->rf[apos]; ss_cons2print[apos2print++] = msa->ss_cons[apos]; - if(! esl_abc_CIsGap(msa->abc, msa->rf[apos])) prv_cpos = apos; } } diff --git a/src/cmbuild.c b/src/cmbuild.c index b5628acd..12f814a5 100644 --- a/src/cmbuild.c +++ b/src/cmbuild.c @@ -1611,21 +1611,17 @@ static P7_PRIOR * cm_p7_prior_CreateNucleic(void); static int set_model_cutoffs(const ESL_GETOPTS *go, const struct cfg_s *cfg, char *errbuf, ESL_MSA *msa, CM_t *cm) { - int cutoff_was_set = FALSE; if(msa->cutset[eslMSA_TC1]) { cm->tc = msa->cutoff[eslMSA_TC1]; cm->flags |= CMH_TC; - cutoff_was_set = TRUE; } if(msa->cutset[eslMSA_GA1]) { cm->ga = msa->cutoff[eslMSA_GA1]; cm->flags |= CMH_GA; - cutoff_was_set = TRUE; } if(msa->cutset[eslMSA_NC1]) { cm->nc = msa->cutoff[eslMSA_NC1]; cm->flags |= CMH_NC; - cutoff_was_set = TRUE; } return eslOK; } @@ -2761,7 +2757,7 @@ find_mindiff(ESL_TREE *T, double *diff, int target_nc, int **ret_clust, int *ret float high = 1.0; float low = 0.0; int high_nc = 0; - int low_nc = 0; + /*int low_nc = 0;*/ float mindiff = 0.5; int curr_nc = -1; int curr_best = -1; @@ -2785,7 +2781,7 @@ find_mindiff(ESL_TREE *T, double *diff, int target_nc, int **ret_clust, int *ret } else {/* curr_nc >= target_nc */ low = mindiff; - low_nc = curr_nc; + /*low_nc = curr_nc;*/ mindiff += (high - mindiff) / 2.; if(fabs(high-low) < thresh) keep_going = FALSE; /* stop, high and low have converged */ /*printf("GREATER nc: %d mindiff: %f low: %f high: %f\n", curr_nc, mindiff, low, high);*/ diff --git a/src/cmcalibrate.c b/src/cmcalibrate.c index 58db9be6..f2d291fc 100644 --- a/src/cmcalibrate.c +++ b/src/cmcalibrate.c @@ -441,7 +441,6 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg) int cmi; /* CM index, which model we're working on */ char time_buf[128]; /* string for printing elapsed time (safely holds up to 10^14 years) */ int exp_mode; /* ctr over exp tail modes */ - double asec; /* actual number of seconds for calibrating current CM */ double psec; /* predicted number of seconds for calibrating current CM */ double total_psec = 0.; /* predicted number of seconds for calibrating all CMs */ double total_asec = 0.; /* actual number of seconds for calibrating all CMs */ @@ -628,7 +627,6 @@ serial_master(ESL_GETOPTS *go, struct cfg_s *cfg) FormatTimeString(time_buf, cfg->w->elapsed, FALSE); printf("] %12s\n", time_buf); fflush(stdout); - asec = cfg->w->elapsed; total_asec += cfg->w->elapsed; } /* end of if(! esl_opt_IsUsed(go, "--forecast")) */ diff --git a/src/cmscan.c b/src/cmscan.c index ea168788..d3f529bf 100644 --- a/src/cmscan.c +++ b/src/cmscan.c @@ -946,8 +946,6 @@ thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, READER_INFO *rinfo, CM_FILE /* variables related to --clanin */ int have_clans; /* set to TRUE if we have information on clans, else FALSE */ - int clan_idx = -1; /* clan index, -1 if current family is not part of a clan */ - int clan_fam_idx = -1; /* index of current family in clan_fam_kh, if it exists, else -1 */ /* do we have clan info? */ have_clans = (rinfo->clan_fam_kh != NULL && rinfo->clan_mapA != NULL) ? TRUE : FALSE; @@ -980,8 +978,6 @@ thread_loop(ESL_THREADS *obj, ESL_WORK_QUEUE *queue, READER_INFO *rinfo, CM_FILE rinfo->msvdataA[cm_idx] = block->msvdataA[i]; /* figure out clan_idx and set it in the block and rinfo */ - clan_idx = -1; - clan_fam_idx = -1; if(have_clans) { block->clan_idxA[i] = determine_clan_index(rinfo->omA[cm_idx]->name, rinfo->clan_fam_kh, rinfo->clan_mapA); } else { block->clan_idxA[i] = -1; } rinfo->clan_idxA[cm_idx] = block->clan_idxA[i]; diff --git a/src/cmsearch.c b/src/cmsearch.c index 70743516..87f14337 100644 --- a/src/cmsearch.c +++ b/src/cmsearch.c @@ -780,7 +780,6 @@ serial_loop(WORKER_INFO *info, ESL_SQFILE *dbfp, int64_t *srcL) int status; int wstatus; int prv_pli_ntophits; /* number of top hits before each cm_Pipeline() */ - int prv_seq_ntophits; /* number of top hits before each target sequence */ int64_t seq_idx = 0; ESL_SQ *dbsq = esl_sq_CreateDigital(info->cm->abc); @@ -800,7 +799,6 @@ serial_loop(WORKER_INFO *info, ESL_SQFILE *dbfp, int64_t *srcL) if(dbsq->start == 1) dbsq->L = srcL[seq_idx-1]; cm_pli_NewSeq(info->pli, dbsq, seq_idx-1); - prv_seq_ntophits = info->th->N; if (info->pli->do_top) { prv_pli_ntophits = info->th->N; @@ -962,8 +960,6 @@ pipeline_thread(void *arg) ESL_SQ_BLOCK *block = NULL; void *newBlock; int prv_pli_ntophits; /* number of top hits before each cm_Pipeline() */ - int prv_seq_ntophits; /* number of top hits before each target sequence */ - #ifdef HAVE_FLUSH_ZERO_MODE /* In order to avoid the performance penalty dealing with sub-normal @@ -991,7 +987,6 @@ pipeline_thread(void *arg) ESL_SQ *dbsq = block->list + i; cm_pli_NewSeq(info->pli, dbsq, block->first_seqidx + i); - prv_seq_ntophits = info->th->N; if (info->pli->do_top) { prv_pli_ntophits = info->th->N; diff --git a/src/cp9_modelmaker.c b/src/cp9_modelmaker.c index 1ffbcf71..1b760fd1 100644 --- a/src/cp9_modelmaker.c +++ b/src/cp9_modelmaker.c @@ -1199,7 +1199,6 @@ cm2hmm_trans_probs_cp9(CM_t *cm, CP9_t *hmm, CP9Map_t *cp9map, int k, double *ps int *bp; /* CM states b' that map to HMM state b, * bp[1] is -1 if only 1 CM state maps to b*/ - int n; /* CM node that maps to HMM node k */ int k_state; /*either HMMMATCH, HMMINSERT, or HMMDELETE*/ int hmm_trans_idx; /*0-8; CTMM, CTMI, CTMD, CTIM, CTII, CTID, CTDM, CTDI, or CTDD*/ @@ -1209,7 +1208,7 @@ cm2hmm_trans_probs_cp9(CM_t *cm, CP9_t *hmm, CP9Map_t *cp9map, int k, double *ps ESL_ALLOC(ap, sizeof (int) * 2); ESL_ALLOC(bp, sizeof (int) * 2); - n = cp9map->pos2nd[k]; + /* Fill all 9 transitions with virtual counts, later normalize these into * probabilities. * @@ -1599,8 +1598,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap int k, double *psi) { int status; - int s_n; /* CM node that maps to HMM node with start state */ - int e_n; /* CM node that maps to HMM node with end state */ int v; /* state index in CM */ double *sub_psi; /*sub_psi[v] is the expected number of times state v is @@ -1612,7 +1609,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap int y; int x; char tmap_val; - int n_v; /* CM node containing state v*/ int is_insert; /* 1 if v is insert, 0 if not */ float insert_to_start; /* is start is not an insert and the insert state of * HMM node k < start, this is the @@ -1654,8 +1650,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap return cm->t[start][0]; } to_return = 0.; - s_n = cm->ndidx[start]; - e_n = cm->ndidx[end]; ESL_ALLOC(sub_psi, sizeof(double) * (end - start + 1)); /* Initialize sub_psi[0]. Need to check if we need to ignore the probability @@ -1686,7 +1680,6 @@ cm_sum_subpaths_cp9(CM_t *cm, CP9Map_t *cp9map, int start, int end, char ***tmap { /*printf("\t\t\tv: %d\n", v);*/ sub_psi[v-start] = 0.; - n_v = cm->ndidx[v]; if(cm->sttype[v] == IL_st || cm->sttype[v] == IR_st) is_insert = 1; else diff --git a/src/cp9_trace.c b/src/cp9_trace.c index bd5ac2ab..f444c2cf 100644 --- a/src/cp9_trace.c +++ b/src/cp9_trace.c @@ -100,16 +100,16 @@ CP9_fake_tracebacks(ESL_MSA *msa, int *matassign, CP9trace_t ***ret_tr) int apos; /* position in alignment columns */ int tpos; /* position in traceback */ int first_match; /* first match column */ - int last_match; /* last match column */ + /*int last_match;*/ /* last match column, not used */ ESL_ALLOC(tr, sizeof(CP9trace_t *) * msa->nseq); first_match = -1; - last_match = -1; + /*last_match = -1;*/ for (apos = 0; apos < msa->alen; apos++) { if(matassign[apos+1] && first_match == -1) first_match = apos; - if(matassign[apos+1]) last_match = apos; + /*if(matassign[apos+1]) last_match = apos;*/ } for (idx = 0; idx < msa->nseq; idx++) diff --git a/src/hmmband.c b/src/hmmband.c index 9e59d063..7fcd662b 100644 --- a/src/hmmband.c +++ b/src/hmmband.c @@ -1533,12 +1533,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t * int v; /* ptrs to cp9b data, for convenience */ - int *pn_min_m; /* pn_min_m[k] = first position in HMM band for match state of HMM node k */ - int *pn_max_m; /* pn_max_m[k] = last position in HMM band for match state of HMM node k */ - int *pn_min_i; /* pn_min_i[k] = first position in HMM band for insert state of HMM node k */ - int *pn_max_i; /* pn_max_i[k] = last position in HMM band for insert state of HMM node k */ - int *pn_min_d; /* pn_min_d[k] = first position in HMM band for delete state of HMM node k */ - int *pn_max_d; /* pn_max_d[k] = last position in HMM band for delete state of HMM node k */ int *imin; /* imin[v] = first position in band on i for state v to be filled in this function. [1..M] */ int *imax; /* imax[v] = last position in band on i for state v to be filled in this function. [1..M] */ int *jmin; /* jmin[v] = first position in band on j for state v to be filled in this function. [1..M] */ @@ -1552,7 +1546,7 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t * int on_right; /* TRUE if we're on the right for current node during our CM traversal */ int w; /* a state index */ int lpos, rpos; /* left/right border of subtree for current node */ - int k; /* counter of HMM nodes */ + /*int k;*/ /* counter of HMM nodes, for debugging print statements, currently not used */ int hmm_is_localized; /* TRUE if HMM has local begins, ends or ELs on */ int cm_is_fully_localized; /* TRUE if CM has local begins and ends on */ @@ -1590,12 +1584,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t * cm_is_fully_localized = ((cm->flags & CMH_LOCAL_BEGIN) && (cm->flags & CMH_LOCAL_END)) ? TRUE : FALSE; /* ptrs to cp9b arrays, for convenience */ - pn_min_m = cp9b->pn_min_m; - pn_max_m = cp9b->pn_max_m; - pn_min_i = cp9b->pn_min_i; - pn_max_i = cp9b->pn_max_i; - pn_min_d = cp9b->pn_min_d; - pn_max_d = cp9b->pn_max_d; imin = cp9b->imin; imax = cp9b->imax; jmin = cp9b->jmin; @@ -1642,7 +1630,6 @@ cp9_HMM2ijBands(CM_t *cm, char *errbuf, CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t * if(!hmm_is_localized) assert(r_mx[hmm_M] == j0 || r_ix[hmm_M] == j0 || r_dx[hmm_M] == j0); } nd = 0; - k = 0; lpos = 0; rpos = 0; @@ -2287,7 +2274,7 @@ HMMBandsEnforceValidParse(CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *cp9map, char * int c; /* counter */ int sd; /* state delta, number of emissions for each state */ int local_begins_ends_on; /* TRUE if HMM has local begins (M_0(B) -> M_k for k = 1..M and local ends (M_k -> E) for k = 1..M-1 */ - int j0_is_reachable = FALSE; /* TRUE if we can reach j0 for some node */ + /*int j0_is_reachable = FALSE; */ /* TRUE if we can reach j0 for some node */ /* ptrs to cp9b data, for convenience */ int *pn_min_m; /* pn_min_m[k] = first position in HMM band for match state of HMM node k */ int *pn_max_m; /* pn_max_m[k] = final position in HMM band for match state of HMM node k */ @@ -2758,7 +2745,7 @@ HMMBandsEnforceValidParse(CP9_t *cp9, CP9Bands_t *cp9b, CP9Map_t *cp9map, char * */ k -= 1; } - else if(r_nx_hmm[k] == j0) j0_is_reachable = TRUE; + /*else if(r_nx_hmm[k] == j0) j0_is_reachable = TRUE;*/ } /* final check, if we're doing alignment, the first residue i0, must be first emitted * residue, and the final residue, j0 must be final emittable residue. Enforce it. diff --git a/src/impl_sse/sse_cm_dpsearch.c b/src/impl_sse/sse_cm_dpsearch.c index f0904887..c6d935e2 100644 --- a/src/impl_sse/sse_cm_dpsearch.c +++ b/src/impl_sse/sse_cm_dpsearch.c @@ -80,8 +80,7 @@ SSE_CYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, ESL_DSQ *dsq, int i0, int j int W; /* max d; max size of a hit, this is min(L, smx->W) */ int sd; /* StateDelta(cm->sttype[v]), # emissions from v */ int *dnA, *dxA; /* tmp ptr to 1 row of dnAA, dxAA */ - int dn, dx; /* minimum/maximum valid d for current state */ - int cnum; /* number of children for current state */ + /*int dn, dx; */ /* minimum/maximum valid d for current state */ int *jp_wA; /* rolling pointer index for B states, gets precalc'ed */ float **init_scAA; /* [0..v..cm->M-1][0..d..W] initial score for each v, d for all j */ double **act; /* [0..j..W-1][0..a..abc->K-1], alphabet count, count of residue a in dsq from 1..jp where j = jp%(W+1) */ @@ -387,9 +386,8 @@ SSE_CYKScan(CM_t *cm, char *errbuf, CM_SCAN_MX *smx, ESL_DSQ *dsq, int i0, int j jp_v = (cm->stid[v] == BEGL_S) ? (j % (W+1)) : cur; jp_y = (StateRightDelta(cm->sttype[v]) > 0) ? prv : cur; sd = StateDelta(cm->sttype[v]); - cnum = cm->cnum[v]; - dn = dnA[v]; - dx = dxA[v]; + /*dn = dnA[v];*/ + /*dx = dxA[v];*/ if(cm->sttype[v] == B_st) { float *vec_access; diff --git a/src/impl_sse/sse_cm_dpsmall.c b/src/impl_sse/sse_cm_dpsmall.c index 4ea19980..35e0c881 100644 --- a/src/impl_sse/sse_cm_dpsmall.c +++ b/src/impl_sse/sse_cm_dpsmall.c @@ -388,7 +388,7 @@ SSE_CYKDemands(CM_t *cm, int L, int be_quiet) float bifcalcs; /* # of inner loops executed for bifurcation calculations */ float dpcalcs; /* # of inner loops executed for non-bif calculations */ int j; - float avg_Mb_per_banded_deck; /* average megabytes per deck in mem efficient big mode */ + /*float avg_Mb_per_banded_deck;*/ /* average megabytes per deck in mem efficient big mode */ const int vecwidth = 4; Mb_per_deck = sse_size_vjd_deck(L, 1, L, vecwidth); @@ -404,7 +404,7 @@ SSE_CYKDemands(CM_t *cm, int L, int be_quiet) dpcalcs = (float) (L+2)*(float)(L+1)*0.5*(float) (cm->M - bif_decks - nends +1); bigmemory = (float) (cm->M - nends +1) * Mb_per_deck; dpcells = (float) (L+2)*(float)(L+1)*0.5*(float) (cm->M - nends +1); - avg_Mb_per_banded_deck = 0.; /* irrelevant */ + /*avg_Mb_per_banded_deck = 0.; */ /* irrelevant */ if(!be_quiet) { @@ -3915,7 +3915,7 @@ SSE_CYKFilter_epi16(CM_OPTIMIZED *ocm, ESL_DSQ *dsq, int L, int vroot, int vend, int nends; /* counter that tracks when we can release end deck to the pool */ int *touch; /* keeps track of how many higher decks still need this deck */ int v,y,z; /* indices for states */ - int j,d,i,k; /* indices in sequence dimensions */ + int j,d,i,k; /* indices in sequence dimensions */ int16_t sc; /* a temporary variable holding a score */ int yoffset; /* y=base+offset -- counter in child states that v can transit to */ int W; /* subsequence length */ @@ -4950,11 +4950,11 @@ sse_insideT_size(CM_t *cm, int L, int r, int z, int i0, int j0, int x) { float Mb; int maxdecks; - int nends; - int nbif; + /*int nends;*/ + /*int nbif;*/ - nends = CMSegmentCountStatetype(cm, r, z, E_st); - nbif = CMSegmentCountStatetype(cm, r, z, B_st); + /*nends = CMSegmentCountStatetype(cm, r, z, E_st);*/ + /*nbif = CMSegmentCountStatetype(cm, r, z, B_st);*/ maxdecks = cyk_deck_count(cm, r, z); Mb = (float) (sizeof(sse_deck_t *) * cm->M) / 1000000.; /* the score matrix */ diff --git a/src/impl_sse/sse_cmcons_hitmx.c b/src/impl_sse/sse_cmcons_hitmx.c index 79f66411..f7570e43 100644 --- a/src/impl_sse/sse_cmcons_hitmx.c +++ b/src/impl_sse/sse_cmcons_hitmx.c @@ -127,7 +127,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i CM_TOPHITS *hitlist, int W, int sW) { int i, d; - int bestd; + /*int bestd;*/ int ip, jp; int do_report_hit; uint8_t hit_sc, bestd_sc; @@ -186,7 +186,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i hit->hmmonly = FALSE; } } - bestd = 0; + /*bestd = 0;*/ bestd_sc = hit_sc; /* Now, if current score is greater than maximum seen previous, report * it if >= cutoff and set new max */ @@ -210,7 +210,7 @@ UpdateGammaHitMx_epu8(CM_CONSENSUS *ccm, char *errbuf, GammaHitMx_epu8 *gamma, i hit->hmmonly = FALSE; } } - bestd = d; + /*bestd = d;*/ bestd_sc = hit_sc; } } diff --git a/src/trcyk.c b/src/trcyk.c index 9af50915..6aae8514 100644 --- a/src/trcyk.c +++ b/src/trcyk.c @@ -27,7 +27,6 @@ main(int argc, char **argv) Parsetree_t *tr; Fancyali_t *fali; Fancyali_t *rev_fali; - CMConsensus_t *cons; int do_local; @@ -48,7 +47,6 @@ main(int argc, char **argv) tr = NULL; fali = NULL; rev_fali = NULL; - cons = NULL; format = eslSQFILE_UNKNOWN; do_local = TRUE;