struct ntree_data* ntree_sub_alignment(struct ntree_data* ntree_data,int* tree,int num)
{
struct dp_matrix *dp = 0;
struct alignment* aln = 0;
int i,j,g,a,b,c;
int len_a;
int len_b;
float** local_profile = 0;
float* profa = 0;
float* profb = 0;
int** local_map = 0;
int* local_sl = 0;
int* local_nsip = 0;
int** local_sip = 0;
int* which_to_alloc = 0;
unsigned int numseq;
unsigned int numprofiles;
struct kalign_context *ctx = get_kalign_context();
numseq = ctx->numseq;
numprofiles = ctx->numprofiles;
aln = ntree_data->aln;
which_to_alloc = malloc(sizeof(int*)*numprofiles);
for ( i = 0;i< numprofiles;i++){
which_to_alloc[i] = 0;
}
local_profile = malloc(sizeof(float*)*numprofiles);
local_sl = malloc(sizeof(int)*numprofiles);
local_nsip = malloc(sizeof(int)*numprofiles);
local_sip = malloc(sizeof(int*)*numprofiles);
for (i = 0; i < num-1;i++){
a = tree[i*3+1];
if(!which_to_alloc[a]){
which_to_alloc[a] = 1;
}
b = tree[i*3+2];
if(!which_to_alloc[b]){
which_to_alloc[b] = 1;
}
c = tree[i*3+3];
if(!which_to_alloc[c]){
which_to_alloc[c] = 2;
}
}
//for ( i = 0;i< numprofiles;i++){
// k_printf("alloc?:%d %d\n",i,which_to_alloc[i]);
//}
// exit(0);
for ( i = 0;i< numprofiles;i++){
if(which_to_alloc[i] == 1){
local_profile[i] = ntree_data->profile[i];
local_sl[i] = aln->sl[i];
local_nsip[i] = aln->nsip[i];
local_sip[i] = malloc(sizeof(int*)*aln->nsip[i]);
for(j = 0;j < aln->nsip[i];j++){
local_sip[i][j] = aln->sip[i][j];
}
}else{
local_profile[i] = 0;
local_sl[i] = 0;
local_nsip[i] = 0;
local_sip[i] = 0;
}
}
/*
for ( i = 0;i< numprofiles;i++){
local_profile[i] = ntree_data->profile[i];
local_sl[i] = aln->sl[i];
local_nsip[i] = aln->nsip[i];
if(aln->sip[i]){
k_printf("Allocing..:%d\n",aln->nsip[i]);
local_sip[i] = malloc(sizeof(int*)*aln->nsip[i]);
for(j = 0;j < aln->nsip[i];j++){
local_sip[i][j] = aln->sip[i][j];
}
}else{
local_sip[i] = 0;
}
}*/
local_map = malloc(sizeof(int*)*numprofiles);
for ( i = 0;i < numprofiles;i++){
local_map[i] = 0;
}
dp = dp_matrix_alloc(dp,511,511);
c = numseq;
for (i = 0; i < num-1;i++){
a = tree[i*3+1];
b = tree[i*3+2];
c = tree[i*3+3];
// k_printf("Aligning:%d %d->%d\n",a,b,c);
len_a = local_sl[a];
len_b = local_sl[b];
dp = dp_matrix_realloc(dp,len_a,len_b);
local_map[c] = malloc(sizeof(int) * (len_a+len_b+2));
for (j = len_a+len_b+2;j--;){
local_map[c][j] = 0;
}
if (a < numseq){
local_profile[a] = make_profile(local_profile[a],aln->s[a],len_a,ntree_data->submatrix);
}
if (b < numseq){
local_profile[b] = make_profile(local_profile[b],aln->s[b],len_b,ntree_data->submatrix);
}
profa = local_profile[a];
profb = local_profile[b];
set_gap_penalties(profa,len_a,local_nsip[b],0,local_nsip[a]);
set_gap_penalties(profb,len_b,local_nsip[a],0,local_nsip[b]);
if(local_nsip[a] == 1){
if(local_nsip[b] == 1){
local_map[c] = ss_dyn(ntree_data->submatrix,local_map[c],dp,aln->s[a],aln->s[b],len_a,len_b);
}else{
local_map[c] = ps_dyn(local_map[c],dp,profb,aln->s[a],len_b,len_a,local_nsip[b]);
local_map[c] = mirror_path(local_map[c]);
}
}else{
if(local_nsip[b] == 1){
local_map[c] = ps_dyn(local_map[c],dp,profa,aln->s[b],len_a,len_b,local_nsip[a]);
}else{
if (len_a > len_b){
local_map[c] = pp_dyn(local_map[c],dp,profa,profb,len_a,len_b);
}else{
local_map[c] = pp_dyn(local_map[c],dp,profb,profa,len_b,len_a);
local_map[c] = mirror_path(local_map[c]);
}
}
}
local_profile[c] = malloc(sizeof(float)*64*(len_a+len_b+2));
local_profile[c] = update(profa,profb,local_profile[c],local_map[c],local_nsip[a],local_nsip[b]);
local_sl[c] = local_map[c][0];
local_nsip[c] = local_nsip[a] + local_nsip[b];
local_sip[c] = malloc(sizeof(int)*(local_nsip[a] + local_nsip[b]));
g =0;
for (j = local_nsip[a];j--;){
local_sip[c][g] = local_sip[a][j];
g++;
}
for (j = local_nsip[b];j--;){
local_sip[c][g] = local_sip[b][j];
g++;
}
// free(profa);
// free(profb);
}
if(ntree_data->profile[c]){
if(ntree_data->map[c][ntree_data->map[c][0]+2] < local_map[c][local_map[c][0]+2]){
k_printf("%d\n",local_map[c][local_map[c][0]+2]);
//remove old map,profile,etc..
for (i = 0; i < num-1;i++){
c = tree[i*3+3];
free(ntree_data->map[c]);
free(ntree_data->profile[c]);
free(aln->sip[c]);
ntree_data->map[c] = malloc(sizeof(int)*(local_map[c][0]+3));
for (j = 0; j < local_map[c][0]+3;j++){
ntree_data->map[c][j] = local_map[c][j];
}
aln->sip[c] = malloc(sizeof(int)*local_nsip[c]);
aln->nsip[c] = local_nsip[c];
for (j = 0; j < local_nsip[c];j++){
aln->sip[c][j] = local_sip[c][j];
}
aln->sl[c] = local_sl[c];
}
ntree_data->profile[c] = malloc(sizeof(int)*64*(aln->sl[c]+1));
for (i = 0; i < (64*(aln->sl[c]+1));i++){
ntree_data->profile[c][i] = local_profile[c][i];
}
ntree_data->tree[0] -= (tree[0]-1);
for (j = 1; j < tree[0];j++){
ntree_data->tree[ntree_data->tree[0]+j-1] = tree[j];
}
ntree_data->tree[0] += (tree[0]-1);
}else{
k_printf("no improvement\n");
}
}else{
k_printf("%d\n",local_map[c][local_map[c][0]+2]);
for (i = 0; i < num-1;i++){
c = tree[i*3+3];
ntree_data->map[c] = malloc(sizeof(int)*(local_map[c][0]+3));
for (j = 0; j < local_map[c][0]+3;j++){
ntree_data->map[c][j] = local_map[c][j];
}
aln->sip[c] = malloc(sizeof(int)*local_nsip[c]);
aln->nsip[c] = local_nsip[c];
for (j = 0; j < local_nsip[c];j++){
aln->sip[c][j] = local_sip[c][j];
}
aln->sl[c] = local_sl[c];
}
ntree_data->profile[c] = malloc(sizeof(int)*64*(aln->sl[c]+1));
for (i = 0; i < (64*(aln->sl[c]+1));i++){
ntree_data->profile[c][i] = local_profile[c][i];
}
for (j = 1; j < tree[0];j++){
ntree_data->tree[ntree_data->tree[0]+j-1] = tree[j];
}
ntree_data->tree[0] += tree[0]-1;
}
for ( i = 0;i< numprofiles;i++){
if(which_to_alloc[i] == 1){
free(local_sip[i]);
if(i < numseq){
free(local_profile[i]);
}
}
if(which_to_alloc[i] == 2){
free(local_profile[i]);
free(local_map[i]);
free(local_sip[i]);
}
}
free(which_to_alloc);
free(local_map);
free(local_sip);
free(local_nsip);
free(local_profile);
free(local_sl);
dp_matrix_free(dp);
return ntree_data;
}
void linphone_call_start_media_streams(LinphoneCall *call, bool_t all_inputs_muted, bool_t send_ringbacktone){
LinphoneCore *lc=call->core;
LinphoneAddress *me=linphone_core_get_primary_contact_parsed(lc);
const char *tool="linphone-" LINPHONE_VERSION;
char *cname;
int used_pt=-1;
#ifdef VIDEO_ENABLED
const SalStreamDescription *vstream=sal_media_description_find_stream(call->resultdesc,
SalProtoRtpAvp,SalVideo);
#endif
bool_t use_arc=linphone_core_adaptive_rate_control_enabled(lc);
if(call->audiostream == NULL)
{
ms_fatal("start_media_stream() called without prior init !");
return;
}
call->current_params = call->params;
/* adjust rtp jitter compensation. It must be at least the latency of the sound card */
int jitt_comp=MAX(lc->sound_conf.latency,lc->rtp_conf.audio_jitt_comp);
if (call->media_start_time==0) call->media_start_time=time(NULL);
cname=linphone_address_as_string_uri_only(me);
{
const SalStreamDescription *stream=sal_media_description_find_stream(call->resultdesc,
SalProtoRtpAvp,SalAudio);
if (stream && stream->dir!=SalStreamInactive && stream->port!=0){
MSSndCard *playcard=lc->sound_conf.lsd_card ?
lc->sound_conf.lsd_card : lc->sound_conf.play_sndcard;
MSSndCard *captcard=lc->sound_conf.capt_sndcard;
const char *playfile=lc->play_file;
const char *recfile=lc->rec_file;
call->audio_profile=make_profile(call,call->resultdesc,stream,&used_pt);
bool_t use_ec,use_arc_audio=use_arc;
if (used_pt!=-1){
if (playcard==NULL) {
ms_warning("No card defined for playback !");
}
if (captcard==NULL) {
ms_warning("No card defined for capture !");
}
/*Replace soundcard filters by inactive file players or recorders
when placed in recvonly or sendonly mode*/
if (stream->port==0 || stream->dir==SalStreamRecvOnly){
captcard=NULL;
playfile=NULL;
}else if (stream->dir==SalStreamSendOnly){
playcard=NULL;
captcard=NULL;
recfile=NULL;
/*And we will eventually play "playfile" if set by the user*/
/*playfile=NULL;*/
}
if (send_ringbacktone){
captcard=NULL;
playfile=NULL;/* it is setup later*/
}
/*if playfile are supplied don't use soundcards*/
if (lc->use_files) {
captcard=NULL;
playcard=NULL;
}
use_ec=captcard==NULL ? FALSE : linphone_core_echo_cancellation_enabled(lc);
#if defined(VIDEO_ENABLED)
if (vstream && vstream->dir!=SalStreamInactive && vstream->payloads!=NULL){
/*when video is used, do not make adaptive rate control on audio, it is stupid.*/
use_arc_audio=FALSE;
#if defined(ANDROID)
/*On android we have to disable the echo canceller to preserve CPU for video codecs */
use_ec=FALSE;
#endif
}
#endif
audio_stream_enable_adaptive_bitrate_control(call->audiostream,use_arc_audio);
audio_stream_start_full(
call->audiostream,
call->audio_profile,
stream->addr[0]!='\0' ? stream->addr : call->resultdesc->addr,
stream->port,
stream->port+1,
used_pt,
jitt_comp,
playfile,
recfile,
playcard,
captcard,
use_ec
);
post_configure_audio_streams(call);
if (all_inputs_muted && !send_ringbacktone){
audio_stream_set_mic_gain(call->audiostream,0);
}
if (stream->dir==SalStreamSendOnly && playfile!=NULL){
int pause_time=500;
ms_filter_call_method(call->audiostream->soundread,MS_FILE_PLAYER_LOOP,&pause_time);
}
if (send_ringbacktone){
setup_ring_player(lc,call);
}
audio_stream_set_rtcp_information(call->audiostream, cname, tool);
}else ms_warning("No audio stream accepted ?");
}
}
#ifdef VIDEO_ENABLED
{
used_pt=-1;
/* shutdown preview */
if (lc->previewstream!=NULL) {
video_preview_stop(lc->previewstream);
lc->previewstream=NULL;
}
call->current_params.has_video=FALSE;
if (vstream && vstream->dir!=SalStreamInactive && vstream->port!=0) {
const char *addr=vstream->addr[0]!='\0' ? vstream->addr : call->resultdesc->addr;
call->video_profile=make_profile(call,call->resultdesc,vstream,&used_pt);
if (used_pt!=-1){
VideoStreamDir dir=VideoStreamSendRecv;
MSWebCam *cam=lc->video_conf.device;
bool_t is_inactive=FALSE;
call->current_params.has_video=TRUE;
video_stream_set_sent_video_size(call->videostream,linphone_core_get_preferred_video_size(lc));
video_stream_enable_self_view(call->videostream,lc->video_conf.selfview);
if (lc->video_window_id!=0)
video_stream_set_native_window_id(call->videostream,lc->video_window_id);
if (lc->preview_window_id!=0)
video_stream_set_native_preview_window_id (call->videostream,lc->preview_window_id);
video_stream_use_preview_video_window (call->videostream,lc->use_preview_window);
if (vstream->dir==SalStreamSendOnly && lc->video_conf.capture ){
cam=get_nowebcam_device();
dir=VideoStreamSendOnly;
}else if (vstream->dir==SalStreamRecvOnly && lc->video_conf.display ){
dir=VideoStreamRecvOnly;
}else if (vstream->dir==SalStreamSendRecv){
if (lc->video_conf.display && lc->video_conf.capture)
dir=VideoStreamSendRecv;
else if (lc->video_conf.display)
dir=VideoStreamRecvOnly;
else
dir=VideoStreamSendOnly;
}else{
ms_warning("video stream is inactive.");
/*either inactive or incompatible with local capabilities*/
is_inactive=TRUE;
}
if (call->camera_active==FALSE || all_inputs_muted){
cam=get_nowebcam_device();
}
if (!is_inactive){
video_stream_set_direction (call->videostream, dir);
video_stream_start(call->videostream,
call->video_profile, addr, vstream->port,
vstream->port+1,
used_pt, jitt_comp, cam);
video_stream_set_rtcp_information(call->videostream, cname,tool);
}
}else ms_warning("No video stream accepted.");
}else{
ms_warning("No valid video stream defined.");
}
}
#endif
call->all_muted=all_inputs_muted;
call->playing_ringbacktone=send_ringbacktone;
call->up_bw=linphone_core_get_upload_bandwidth(lc);
if (ortp_zrtp_available()) {
OrtpZrtpParams params;
params.zid=get_hexa_zrtp_identifier(lc);
params.zid_file=lc->zrtp_secrets_cache;
audio_stream_enable_zrtp(call->audiostream,¶ms);
}
goto end;
end:
ms_free(cname);
linphone_address_destroy(me);
}
