/*
* create a random sequence from either dna or protein input sequence
* add sequence to sequence manager
*/
int ScrambleSeq(Tcl_Interp *interp,
int seq_num)
{
char *seq1 = GetSeqSequence(seq_num);
int length = GetSeqLength(seq_num);
int seq_id = GetSeqId(seq_num);
char *seq2;
char *name;
time_t tim;
int seed;
char *parental_name, *child_name;
int new_seq_num, start, end;
static int num = 0;
if (NULL == (seq2 = (char *)xmalloc((length+1) * sizeof(char))))
return -1;
memcpy(seq2, seq1, length);
tim = time(NULL);
seed = (int) tim;
scramble_seq(seq2, length, seed);
seq2[length] = '\0';
parental_name = GetParentalSeqName(seq_num);
child_name = GetSeqName(seq_num);
if (NULL == (name = (char *)xmalloc((strlen(parental_name)+13) *
sizeof(char))))
return -1;
sprintf(name, "%s_x%d", parental_name, num);
if (-1 == (new_seq_num = AddSequence(interp, -1, GetSeqLibrary(seq_num),
name, seq2, GetSeqStructure(seq_num),
GetSeqType(seq_num), NULL , " ")))
return -1;
xfree(name);
if (strcmp(parental_name, child_name) != 0) {
/* sub-sequence */
/*
* need to get seq num from seq_id instead of using seq_num incase
* AddSequence has deleted duplicate names
*/
start = GetSubSeqStart(GetSeqNum(seq_id));
end = GetSubSeqEnd(GetSeqNum(seq_id));
if (NULL == (name = (char *)xmalloc((strlen(child_name)+13) *
sizeof(char))))
return -1;
sprintf(name, "%s_x%d", child_name, num);
if (-1 == (AddSubSequence(interp, GetSeqId(new_seq_num), start, end, name)))
return -1;
}
num++;
return 0;
}
/*
* complement sequence
* add new sequence name to sequence manager
*/
int ComplementSeq(Tcl_Interp *interp,
int seq_num)
{
char *seq1 = GetSeqSequence(seq_num);
char *seq2;
char *name;
int length = GetSeqLength(seq_num);
int seq_id = GetSeqId(seq_num);
int new_seq_num, start, end;
char *parental_name, *child_name;
if (NULL == (seq2 = (char *)xmalloc((length+1) * sizeof(char))))
return -1;
memcpy(seq2, seq1, length);
(void) complement_seq(seq2, length);
seq2[length] = '\0';
parental_name = GetParentalSeqName(seq_num);
child_name = GetSeqName(seq_num);
if (NULL == (name = (char *)xmalloc((strlen(parental_name)+3) *
sizeof(char))))
return -1;
sprintf(name, "%s_c", parental_name);
if (-1 == (new_seq_num = AddSequence(interp, -1, GetSeqLibrary(seq_num),
name, seq2, GetSeqStructure(seq_num),
GetSeqType(seq_num), NULL, " ")))
return -1;
xfree(name);
if (strcmp(parental_name, child_name) != 0) {
/* sub-sequence */
/*
* need to get seq num from seq_id instead of using seq_num incase
* AddSequence has deleted duplicate names
*/
start = GetSubSeqStart(GetSeqNum(seq_id));
end = GetSubSeqEnd(GetSeqNum(seq_id));
if (NULL == (name = (char *)xmalloc((strlen(child_name)+3) *
sizeof(char))))
return -1;
sprintf(name, "%s_c", child_name);
if (-1 == (AddSubSequence(interp, GetSeqId(new_seq_num),
length - end + 1,
length - start + 1, name)))
return -1;
}
return 0;
}
/*
* add new sequence to sequence manager, but keep as dna but with an extension
* of _rf123 which signifies to the comparison functions that the sequence
* is to translated into it's 3 reading frames, each of which will be used
* in the comparison routine
*/
int TranslateTogether(Tcl_Interp *interp,
int seq_num)
{
char *name;
char *dna_seq;
char *prot_seq;
int seq_id = GetSeqId(seq_num);
int new_seq_num;
char *parental_name, *child_name;
int start, end;
#ifdef DEBUG
printf("START translate together \n");
#endif
dna_seq = GetSeqSequence(seq_num);
if (NULL == (prot_seq = strdup(dna_seq)))
return -1;
parental_name = GetParentalSeqName(seq_num);
child_name = GetSeqName(seq_num);
if (NULL == (name = (char *)xmalloc((strlen(parental_name)+7) *
sizeof(char))))
return -1;
sprintf(name, "%s_rf123", parental_name);
if (-1 == (new_seq_num = AddSequence(interp, -1, GetSeqLibrary(seq_num),
name, prot_seq, LINEAR, PROTEIN, NULL, " ")))
return -1;
xfree(name);
if (strcmp(parental_name, child_name) != 0) {
/* sub-sequence */
/*
* need to get seq num from seq_id instead of using seq_num incase
* AddSequence has deleted duplicate names
*/
start = GetSubSeqStart(GetSeqNum(seq_id));
end = GetSubSeqEnd(GetSeqNum(seq_id));
if (NULL == (name = (char *)xmalloc((strlen(child_name)+7) *
sizeof(char))))
return -1;
sprintf(name, "%s_rf123", child_name);
new_seq_num = AddSubSequence(interp, GetSeqId(new_seq_num), start, end,
name);
}
return new_seq_num;
}
int store_sim2(int seq1_num,
int seq2_num,
int start_h,
int end_h,
int start_v,
int end_v,
in_sim *input,
d_plot *data,
int n_pts)
{
seq_result *result;
int id;
if (NULL == (result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
/* realloc p_array to be the actual number of lines */
if (NULL == (data->p_array = (pt_score *)realloc(data->p_array, (n_pts+1)*
sizeof(pt_score))))
return -1;
id = get_reg_id();
result->data = data;
data->n_pts = n_pts;
data->dim.x0 = start_h;
data->dim.x1 = end_h;
data->dim.y0 = start_v;
data->dim.y1 = end_v;
/* need to initialise this here */
result->output = NULL;
result->seq_id[HORIZONTAL] = GetSeqId( seq1_num);
result->seq_id[VERTICAL] = GetSeqId(seq2_num);
result->input = (void *)input;
result->id = id;
result->graph = SEQ_DOT;
result->pr_func = dot_plot_line_func;
result->op_func = sim_callback;
result->txt_func = sim_text_func;
seq_register(seq1_num, sim_callback, (void *)result, SEQ_PLOT_PERM, id);
seq_register(seq2_num, sim_callback, (void *)result, SEQ_PLOT_PERM, id);
return id;
}
string CurrentLocationAsString () const
{
return GetSeqId() + " | " +
NStr::IntToString(GetVersion()) + " | " +
NStr::UInt8ToString(GetGi()) + " | " +
NStr::IntToString(GetTimestamp());
}
/*
* add sequence to seqed widget
*/
int add_seq_seqed(Tcl_Interp *interp,
char *sequence,
char *seqed_win,
int seq_num,
int pos,
int container_id,
char *c_win,
int element_id)
{
Tcl_CmdInfo info;
tkSeqed *se;
char *seq_name;
int sequence_type;
int seqed_id;
Tcl_GetCommandInfo(interp, seqed_win, &info);
se = (tkSeqed*)info.clientData;
seq_name = GetSeqName(seq_num);
sequence_type = GetSeqStructure(seq_num);
seqed_add_sequence(se, strlen(sequence), sequence, seq_name,
sequence_type, GetSeqId(seq_num), 0, 0);
seqed_id = seqed_reg(interp, seqed_win, seq_num, se, pos, container_id,
c_win, element_id);
return seqed_id;
}
int seqed_reg(Tcl_Interp *interp,
char *seqed_win,
int seq_num,
tkSeqed *se)
{
int id;
SeqedResult *seqed_result;
char *colour;
seq_cursor_notify cn;
int line_width;
if (NULL == (seqed_result = (SeqedResult *)xmalloc(sizeof(SeqedResult))))
return -1;
seqed_result->op_func = seqed_callback;
seqed_result->seq_id = GetSeqId(seq_num);
strcpy(seqed_result->seqed_win, seqed_win);
seqed_result->interp = interp;
id = get_reg_id();
seqed_result->index = id;
line_width = get_default_int(interp, spin_defs,
w("SEQ.CURSOR.LINE_WIDTH"));
colour = get_raster_colour();
se->rid = id;
se->seq_id = GetSeqId(seq_num);
strcpy(se->cursorCol, colour);
se->cursor = create_cursor(seq_num, 1, NULL, line_width, 1, HORIZONTAL);
se->cursor_visible = 0;
se->prev_pos = se->cursor->abspos;
se->cursor->abspos = se->cursorPos;
seq_register(seq_num, seqed_callback, (void *)seqed_result, SEQ_SEQED,
id);
cn.job = SEQ_CURSOR_NOTIFY;
cn.cursor = se->cursor;
cn.cursor->job = CURSOR_MOVE;
seq_notify(seq_num, (seq_reg_data *)&cn);
return id;
}
ostream& Print( ostream& o ) const {
return o
<< GetSeqId() << "\t"
<< GetPos() << "\t"
<< GetProb(0) << "\t"
<< GetProb(1) << "\t"
<< GetProb(2) << "\t"
<< GetProb(3);
}
/*
* copy range of sequence
* add new sequence name to sequence manager
*/
int CopyRange(Tcl_Interp *interp,
int seq_id,
int start,
int end)
{
int seq_num = GetSeqNum(seq_id);
char *seq1 = GetSeqSequence(seq_num);
char *seq2;
char *name;
int length = end - start + 1;
int new_seq_num;
char *parental_name, *child_name;
static int count = 1;
if (NULL == (seq2 = (char *)xmalloc((length+2) * sizeof(char))))
return -1;
strncpy(seq2, &seq1[start-1], end - start + 1);
seq2[end - start + 1] = '\0';
parental_name = GetParentalSeqName(seq_num);
child_name = GetSeqName(seq_num);
if (NULL == (name = (char *)xmalloc((strlen(parental_name)+20) *
sizeof(char))))
return -1;
sprintf(name, "%s_n%d", parental_name, count++);
if (-1 == (new_seq_num = AddSequence(interp, -1, GetSeqLibrary(seq_num),
name, seq2, GetSeqStructure(seq_num),
GetSeqType(seq_num), NULL, " ")))
return -1;
xfree(name);
/* don't think I need to deal with subsequences in copying a sequence. */
#if 0
if (strcmp(parental_name, child_name) != 0) {
/* sub-sequence */
/*
* need to get seq num from seq_id instead of using seq_num incase
* AddSequence has deleted duplicate names
*/
start = GetSubSeqStart(GetSeqNum(seq_id));
end = GetSubSeqEnd(GetSeqNum(seq_id));
if (NULL == (name = (char *)xmalloc((strlen(child_name)+3) *
sizeof(char))))
return -1;
sprintf(name, "%s_n%d", child_name, count++);
if (-1 == (AddSubSequence(interp, GetSeqId(new_seq_num),
start, end, name)))
return -1;
}
#endif
return 0;
}
int store_emboss_dot(int seq_num_h,
int start_h,
int end_h,
int seq_num_v,
int start_v,
int end_v,
e_graph *data,
in_emboss *input,
text_emboss *text_data,
Tcl_Obj **graph_obj)
{
seq_result *s_result;
int id;
if (NULL == (s_result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
id = get_reg_id();
/* data assignment */
s_result->seq_id[HORIZONTAL] = GetSeqId(seq_num_h);
s_result->seq_id[VERTICAL] = GetSeqId(seq_num_v);
s_result->id = id;
s_result->input = (void *)input;
s_result->type = SEQ_TYPE_DOT_PLOT;
s_result->gr_type = SEQ_TYPE_DOT_PLOT;
s_result->frame = 0;
s_result->graph = GRAPH;
s_result->data = *graph_obj;
s_result->text_data = text_data;
s_result->e = NULL;
s_result->pr_func = seq_plot_graph_func;
s_result->op_func = emboss_graph_callback;
s_result->txt_func = emboss_graph_text_func;
seq_register(seq_num_h, emboss_graph_callback, (void *)s_result,
SEQ_PLOT_PERM, id);
seq_register(seq_num_v, emboss_graph_callback, (void *)s_result,
SEQ_PLOT_PERM, id);
return id;
}
Seq &SeqVect::GetSeqById(unsigned uId)
{
const unsigned uSeqCount = GetSeqCount();
for (unsigned i = 0; i < uSeqCount; ++i)
{
if (GetSeqId(i) == uId)
return GetSeq(i);
}
Quit("SeqVect::GetSeqIdByUd(%d): not found", uId);
return (Seq &) *((Seq *) 0);
}
unsigned SeqVect::GetSeqIdFromName(const char *Name) const
{
const unsigned uSeqCount = GetSeqCount();
for (unsigned i = 0; i < uSeqCount; ++i)
{
if (!strcmp(Name, GetSeqName(i)))
return GetSeqId(i);
}
Quit("SeqVect::GetSeqIdFromName(%s): not found", Name);
return 0;
}
const CBioseq_Handle& CAlnVec::GetBioseqHandle(TNumrow row) const
{
TBioseqHandleCache::iterator i = m_BioseqHandlesCache.find(row);
if (i != m_BioseqHandlesCache.end()) {
return i->second;
} else {
CBioseq_Handle bioseq_handle =
GetScope().GetBioseqHandle(GetSeqId(row));
if (bioseq_handle) {
return m_BioseqHandlesCache[row] = bioseq_handle;
} else {
string errstr = string("CAlnVec::GetBioseqHandle(): ")
+ "Seq-id cannot be resolved: "
+ GetSeqId(row).AsFastaString();
NCBI_THROW(CAlnException, eInvalidSeqId, errstr);
}
}
}
int CSeq_id_Handle::CompareOrdered(const CSeq_id_Handle& id) const
{
// small optimization to avoid creation of temporary CSeq_id objects
if ( int diff = Which() - id.Which() ) {
return diff;
}
if ( IsGi() && id.IsGi() ) {
return GetGi() - id.GetGi();
}
return GetSeqId()->CompareOrdered(*id.GetSeqId());
}
string CSeq_id_Handle::AsString() const
{
CNcbiOstrstream os;
if ( IsGi() ) {
os << "gi|" << m_Packed;
}
else if ( m_Info ) {
GetSeqId()->WriteAsFasta(os);
}
else {
os << "unknown";
}
return CNcbiOstrstreamToString(os);
}
int store_emboss_graph(int seq_num,
int start,
int end,
e_graph *data,
in_emboss *input,
text_emboss *text_data,
Tcl_Obj **graph_obj)
{
seq_result *s_result;
int id;
#ifdef DEBUG
for (i = 0; i < data->n_pts; i++) {
printf("i %d pos %d score %f\n", i, data->p_array[i].pos,
data->p_array[i].score);
}
#endif
if (NULL == (s_result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
id = get_reg_id();
s_result->seq_id[HORIZONTAL] = GetSeqId(seq_num);
s_result->seq_id[VERTICAL] = -1;
s_result->id = id;
s_result->input = (void *)input;
s_result->type = SEQ_TYPE_GRAPH_PLOT;
s_result->gr_type = SEQ_TYPE_GRAPH_PLOT;
s_result->frame = 0;
s_result->graph = GRAPH;
s_result->data = *graph_obj;
s_result->text_data = text_data;
s_result->e = NULL;
s_result->pr_func = seq_plot_graph_func;
s_result->op_func = emboss_graph_callback;
s_result->txt_func = emboss_graph_text_func;
seq_register(seq_num, emboss_graph_callback, (void *)s_result,
SEQ_PLOT_PERM, id);
return id;
}
int TranslateSeq(Tcl_Interp *interp,
int seq_num,
int rf,
int start,
int end)
{
int i;
char *name;
char *dna_seq;
char *prot_seq;
int cnt = 0;
int seq_id = GetSeqId(seq_num);
int new_seq_num;
char *ptr;
char *parental_name, *child_name;
char *new_name;
int length = end - start + 1;
static int num = 0;
#ifdef DEBUG
printf("START translate seq %d to %d\n", start, end);
#endif
dna_seq = GetSeqSequence(seq_num);
if (NULL == (prot_seq = (char *)xmalloc(((length/3)+3) * sizeof(char))))
return -1;
if (NULL == (new_name = (char *)xmalloc(strlen(GetSeqName(seq_num))
* sizeof(char))))
return -1;
for (i = rf+start-1; i < end-2; i+=3) {
prot_seq[cnt++] = codon_to_acid1(&dna_seq[i]);
}
prot_seq[cnt] = '\0';
#ifdef DEBUG
printf("%s\n", prot_seq);
#endif
/*
* special case: remove _rf123 from name before adding _rfx to end
*/
parental_name = GetParentalSeqName(seq_num);
child_name = GetSeqName(seq_num);
ptr = strstr(parental_name, "_rf123");
if (NULL == (name = (char *)xmalloc((strlen(parental_name)+28)
* sizeof(char))))
return -1;
if (ptr) {
strncpy(new_name, parental_name, (ptr - parental_name));
new_name[ptr - parental_name] = '\0';
strcat(new_name, ptr+6);
sprintf(name, "%s_rf%d_%d", new_name, rf+1, num);
} else {
sprintf(name, "%s_rf%d_%d", parental_name, rf+1, num);
}
/* proteins can only be LINEAR ! */
if (-1 == (new_seq_num = AddSequence(interp, -1, GetSeqLibrary(seq_num),
name, prot_seq, LINEAR, PROTEIN, NULL, " ")))
return -1;
xfree(name);
xfree(new_name);
if (strcmp(parental_name, child_name) != 0) {
/* sub-sequence */
/*
* need to get seq num from seq_id instead of using seq_num incase
* AddSequence has deleted duplicate names
*/
start = ceil((GetSubSeqStart(GetSeqNum(seq_id))-1)/3.0 + 1);
end = (GetSubSeqEnd(GetSeqNum(seq_id)) - rf) / 3;
if (NULL == (name = (char *)xmalloc((strlen(child_name)+15) *
sizeof(char))))
return -1;
if (NULL == (new_name = (char *)xmalloc(strlen(GetSeqName(seq_num))
* sizeof(char))))
return -1;
ptr = strstr(child_name, "_rf123");
if (ptr) {
strncpy(new_name, child_name, (ptr - child_name));
new_name[ptr - child_name] = '\0';
strcat(new_name, ptr+6);
sprintf(name, "%s_rf%d_%d", new_name, rf+1, num);
} else {
sprintf(name, "%s_rf%d_%d", child_name, rf+1, num);
}
/* sprintf(name, "%s_rf%d", child_name, rf+1); */
new_seq_num = AddSubSequence(interp, GetSeqId(new_seq_num), start, end,
name);
xfree(new_name);
}
num++;
return new_seq_num;
}
int store_string_search(int seq_num,
in_string_search *input,
int start,
int end,
int *pos,
int *score,
int n_matches,
int string_length)
{
seq_result *result;
int id;
int i;
stick *data;
if (NULL == (result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
if (NULL == (data = (stick *)xmalloc(sizeof(stick))))
return -1;
if (NULL == (data->ap_array = (a_score *)xmalloc(sizeof(a_score))))
return -1;
if (NULL == (data->ap_array[0].p_array = (p_score *)xmalloc(n_matches *
sizeof(p_score))))
return -1;
result->data = data;
data->n_pts = 1;
data->ap_array[0].n_pts = n_matches;
data->ap_array[0].dim.x0 = start;
data->ap_array[0].dim.x1 = end;
data->ap_array[0].dim.y0 = 0;
data->ap_array[0].dim.y1 = 100;
for (i = 0; i < n_matches; i++) {
data->ap_array[0].p_array[i].pos = pos[i] + start - 1;
data->ap_array[0].p_array[i].score = (double)score[i] / string_length * 100;
}
id = get_reg_id();
result->seq_id[HORIZONTAL] = GetSeqId(seq_num);
result->seq_id[VERTICAL] = -1;
result->id = id;
result->input = (void *)input;
result->output = NULL;
result->type = SEQ_TYPE_STRINGSEARCH;
result->frame = 0;
result->graph = SEQ_STICK;
result->pr_func = stick_plot_func;
result->op_func = nip_string_search_callback;
result->txt_func = nip_string_search_text_func;
seq_register(seq_num, nip_string_search_callback, (void *)result,
SEQ_PLOT_PERM, id);
return id;
}
int store_stop_codons(int seq_num,
in_s_codon *input,
int start,
int end,
int *stop_codon,
int num_stop_codons,
int frame,
int type,
Tcl_Obj **graph_obj)
{
seq_result *s_result;
Graph *graph;
int id, i;
if (NULL == (s_result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
if (NULL == (graph = (Graph *)xmalloc(sizeof(Graph))))
return -1;
Tcl_InitGraph(&graph);
if (NULL == (graph->d_arrays = (darray *)xmalloc(sizeof(darray))))
return -1;
if (NULL == (graph->d_arrays[0].d_array = (gd_line *)xmalloc(num_stop_codons * sizeof(gd_line))))
return -1;
graph->d_arrays[0].n_dlines = num_stop_codons;
graph->n_darrays = 1;
graph->d_arrays[0].type = G_LINES;
graph->dim.x0 = start;
graph->dim.x1 = end;
for (i = 0; i < num_stop_codons; i++) {
graph->d_arrays[0].d_array[i].x0 = stop_codon[i];
graph->d_arrays[0].d_array[i].x1 = stop_codon[i];
}
/* must sort the array on x0 */
qsort((void *) graph->d_arrays[0].d_array, graph->d_arrays[0].n_dlines,
sizeof(gd_line), compare_darray);
*graph_obj = Tcl_NewGraphObj(graph);
/* these are copied over in Tcl_NewGraphObj so don't need them anymore */
xfree(graph->d_arrays[0].d_array);
xfree(graph->d_arrays);
xfree(graph);
id = get_reg_id();
s_result->seq_id[HORIZONTAL] = GetSeqId(seq_num);
s_result->seq_id[VERTICAL] = -1;
s_result->id = id;
s_result->input = (void *)input;
s_result->frame = frame;
s_result->graph = GRAPH;
s_result->data = *graph_obj;
s_result->e = NULL; /* initialise */
s_result->pr_func = seq_plot_graph_func;
s_result->op_func = nip_stop_codons_callback;
s_result->txt_func = nip_stop_codons_text_func;
if (type == STOP_CODON) {
s_result->type = SEQ_TYPE_STOPCODON;
} else {
s_result->type = SEQ_TYPE_STARTCODON;
}
s_result->gr_type = SEQ_TYPE_GRAPH_PLOT;
seq_register(seq_num, nip_stop_codons_callback, (void *)s_result,
SEQ_PLOT_PERM, id);
xfree(stop_codon);
return id;
}
int StoreSpliceSearch(int seq_num,
WtmatrixRes *ied,
WtmatrixRes *eia,
in_splice *input,
int start,
int end,
int frame)
{
seq_result *result;
stick *data;
int id, i;
text_wtmatrix **text_data;
if (NULL == (result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
if (NULL == (data = (stick *)xmalloc(sizeof(stick))))
return -1;
if (NULL == (data->ap_array = (a_score *)xmalloc(2 * sizeof(a_score))))
return -1;
if (NULL == (data->ap_array[0].p_array = (p_score *)xmalloc(ied->number_of_res *
sizeof(p_score))))
return -1;
if (NULL == (data->ap_array[1].p_array = (p_score *)xmalloc(eia->number_of_res *
sizeof(p_score))))
return -1;
if (NULL == (text_data = (text_wtmatrix **)xmalloc(2*sizeof(text_wtmatrix*))))
return -1;
if (NULL == (text_data[0] = (text_wtmatrix *)xmalloc(sizeof(text_wtmatrix))))
return -1;
if (NULL == (text_data[1] = (text_wtmatrix *)xmalloc(sizeof(text_wtmatrix))))
return -1;
result->data = data;
data->n_pts = 2;
data->ap_array[0].n_pts = ied->number_of_res;
data->ap_array[1].n_pts = eia->number_of_res;
data->ap_array[0].dim.x0 = start;
data->ap_array[0].dim.x1 = end;
data->ap_array[0].dim.y0 = ied->min;
data->ap_array[0].dim.y1 = 2*ied->max;
data->ap_array[1].dim.x0 = start;
data->ap_array[1].dim.x1 = end;
data->ap_array[1].dim.y0 = eia->min;
data->ap_array[1].dim.y1 = 2*eia->max;
#ifdef DEBUG
printf("ied %f %f eia %f %f\n", ied->min, ied->max, eia->min, eia->max);
#endif
id = get_reg_id();
for (i = 0; i < ied->number_of_res; i++) {
data->ap_array[0].p_array[i].pos = ied->match[i]->pos + 1;
data->ap_array[0].p_array[i].score = (double)ied->match[i]->score;
}
for (i = 0; i < eia->number_of_res; i++) {
data->ap_array[1].p_array[i].pos = eia->match[i]->pos + 1;
data->ap_array[1].p_array[i].score = (double)eia->match[i]->score;
}
result->text_data = text_data;
text_data[0]->length = ied->length;
text_data[0]->mark_pos = ied->mark_pos;
text_data[1]->length = eia->length;
text_data[1]->mark_pos = eia->mark_pos;
result->seq_id[HORIZONTAL] = GetSeqId(seq_num);
result->seq_id[VERTICAL] = -1;
result->id = id;
result->input = (void *)input;
result->output = NULL;
result->type = SEQ_TYPE_SPLICE;
result->frame = frame;
result->graph = SEQ_STICK;
result->pr_func = stick_pair_plot_func;
result->op_func = splice_search_callback;
result->txt_func = splice_search_text_func;
seq_register(seq_num, splice_search_callback, (void *)result,
SEQ_PLOT_PERM, id);
if (ied) free_WtmatrixRes (ied);
if (eia) free_WtmatrixRes (eia);
return id;
}
int store_sip_similar_spans(int seq1_num,
int seq2_num,
int window_length,
int min_score,
int start_h,
int end_h,
int start_v,
int end_v,
int *seq1_match,
int *seq2_match,
int *match_score,
int num_elements,
in_comp_spans *input)
{
seq_result *sip_result;
d_plot *data;
text_sim_spans *text_data;
int i, id;
if (NULL == (sip_result = (seq_result *)xmalloc(sizeof(seq_result))))
return -1;
if (NULL == (data = (d_plot *)xmalloc(sizeof(d_plot))))
return -1;
if (NULL == (data->p_array = (pt_score *)xmalloc(sizeof(pt_score) *
num_elements)))
return -1;
if (NULL == (text_data = (text_sim_spans *)xmalloc(sizeof(text_sim_spans))))
return -1;
id = get_reg_id();
sip_result->data = data;
/* data assignment */
for (i = 0; i < num_elements; i++) {
data->p_array[i].x = seq1_match[i];
data->p_array[i].y = seq2_match[i];
data->p_array[i].score = match_score[i];
}
data->win_len = window_length;
data->n_pts = num_elements;
data->dim.x0 = start_h;
data->dim.x1 = end_h;
data->dim.y0 = start_v;
data->dim.y1 = end_v;
sip_result->text_data = text_data;
text_data->min_score = min_score;
/* need to initialise this here */
sip_result->output = NULL;
/* save global sip_seq into sip_result structure */
sip_result->seq_id[HORIZONTAL] = GetSeqId(seq1_num);
sip_result->seq_id[VERTICAL] = GetSeqId(seq2_num);
sip_result->input = (void *)input;
sip_result->id = id;
sip_result->graph = SEQ_DOT;
sip_result->pr_func = dot_plot_middot_func;
sip_result->op_func = similar_spans_callback;
sip_result->txt_func = similar_spans_text_func;
seq_register(seq1_num, similar_spans_callback, (void *)sip_result,
SEQ_PLOT_PERM, id);
seq_register(seq2_num, similar_spans_callback, (void *)sip_result,
SEQ_PLOT_PERM, id);
return id;
}
int seqed_reg(Tcl_Interp *interp,
char *seqed_win,
int seq_num,
tkSeqed *se,
int pos,
int container_id,
char *c_win,
int element_id)
{
int id;
SeqedResult *seqed_result;
char *colour;
seq_cursor_notify cn;
int line_width;
element *e;
plot_data *result;
if (NULL == (seqed_result = (SeqedResult *)xmalloc(sizeof(SeqedResult))))
return -1;
if (NULL == (result = (plot_data *)xmalloc(sizeof(plot_data))))
return -1;
seqed_result->op_func = seqed_callback;
seqed_result->seq_id = GetSeqId(seq_num);
strcpy(seqed_result->seqed_win, seqed_win);
seqed_result->interp = interp;
id = get_reg_id();
seqed_result->index = id;
line_width = get_default_int(interp, spin_defs,
w("SEQ.CURSOR.LINE_WIDTH"));
se->rid = id;
se->seq_id = GetSeqId(seq_num);
colour = get_cursor_colour(se->rid);
strcpy(se->cursorCol, colour);
se->cursor = create_cursor(seq_num, 1, NULL, line_width, 1, HORIZONTAL, pos);
se->cursor_visible = 0;
se->prev_pos = se->cursor->abspos;
se->cursor->abspos = se->cursorPos;
if (NULL == (e = (get_element(element_id)))) {
e = create_element(interp, container_id, element_id, seqed_win, HORIZONTAL, -1);
}
seqed_result->e = e;
result->result_id = id;
result->amp_ruler = 0;
result->len_ruler = 0;
result->n_configure = 0;
result->sf_m = 1.0;
result->sf_c = 0.0;
result->scale = 0;
result->hidden = 0;
result->colour = NULL;
result->cursor = NULL;
set_seq_element_funcs(e);
add_seq_id_to_element(e, GetSeqId(seq_num), HORIZONTAL);
add_result_to_element(e, result, DBL_MAX, DBL_MAX, -DBL_MAX, -DBL_MAX, HORIZONTAL, SEQ_EDITOR);
add_element_to_container(interp, container_id, c_win, e,
INT_MAX, INT_MIN, INT_MAX, INT_MIN);
seq_register(seq_num, seqed_callback, (void *)seqed_result, SEQ_SEQED,
id);
seq_element_reg(interp, e);
cn.job = SEQ_CURSOR_NOTIFY;
cn.cursor = se->cursor;
cn.cursor->job = CURSOR_MOVE;
cn.show_all = 0;
seq_notify(seq_num, (seq_reg_data *)&cn);
return id;
}