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/*
© Copyright 2008 Randal A. Koene <randalk@netmorph.org>
With design assistance from J. van Pelt & A. van Ooyen, and support
from the Netherlands Organization for Scientific Research (NWO)
Program Computational Life Sciences grant CLS2003 (635.100.005) and
from the EC Marie Curie Research and Training Network (RTN)
NEURoVERS-it 019247.
This file is part of NETMORPH.
NETMORPH is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
NETMORPH is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with NETMORPH. If not, see <http://www.gnu.org/licenses/>.
*/
// synapse.cc
// Randal A. Koene, 20041118
// [Update AC 20110322:] Added include fibre_structure.hh and APICAL/BASAL flag write to .synapses file
#include "synapse.hh"
#include "synapse_structure.hh"
#include "connection.hh"
#include "Color_Table.hh"
#include "global.hh"
#include "fibre_structure.hh"
synaptogenesis_data * SynaptoGenesis_Data = NULL;
bool figattr_receptor[syntype_candidate] = {
true,
true,
true,
};
const char synapse_type_name[syntype_IDs][10] = {
"AMPAR",
"NMDAR",
"GABAR",
"candidate",
"GluR",
"iGluR",
"mGluR",
};
#ifdef SYNAPTOGENESIS_AND_LOSS_INVENTORY
long unsigned int synapse_inventory[syntype_IDs][2] = {
{ 0, 0},
{ 0, 0},
{ 0, 0},
{ 0, 0},
{ 0, 0},
{ 0, 0},
{ 0, 0}
};
long unsigned int candidates_conversion_attempted = 0;
#endif
synapse::synapse(connection & conn, synapse_type id, synapse_structure * synstruc): type_id(id), c(&conn), s(synstruc) {
// Here the synapse is added to a connection and depending on its derived
// type synapse building functions may create details such as neuroanatomy
// and neurophysiology, including morphology and arborization for a
// axon-dendritic or axon-somatic synapse.
c->Synapses()->link_before(this);
if (s) s->require();
#ifdef SYNAPTOGENESIS_AND_LOSS_INVENTORY
synapse_inventory[type_id][SYNGENESIS]++;
#endif
}
synapse::~synapse() {
if (s) s->release();
#ifdef SYNAPTOGENESIS_AND_LOSS_INVENTORY
synapse_inventory[type_id][SYNLOSS]++;
#endif
//cout << "DS" << String((long) this) << '\n'; cout.flush();
}
neuron * synapse::Presynaptic_Neuron() {
return c->PreSynaptic();
}
neuron * synapse::Postsynaptic_Neuron() {
return c->PostSynaptic();
}
void synapse::move_add(spatial & addvec) {
if (s) s->move_add(addvec);
}
void synapse::fanin_rot() {
if (s) s->fanin_rot();
}
Fig_Object * synapse::net_Fig() {
synapse_type stype = this->type_ID();
if (stype<syntype_candidate) {
if (!figattr_receptor[stype]) return 0;
_figvar_connection_color=colortable->colnum(static_cast<color_table_name>(CT_AMPAR+stype));
}
Fig_Circle * fc = 0;
if (s) return s->net_Fig();
return fc;
// [***INCOMPLETE] I may wish to add the following:
// a) radio button selection of _show_synapse_structure and _show_synapse_dot
// b) derived type net_Fig() that call this net_Fig() first, thereby setting
// up the color, which can then draw a dot of a size that relates to some
// parameter value (e.g. strength)
}
Txt_Object * synapse::net_Txt() {
/* Output format:
1. [integer] synapse index (incremental)
2. [string] synapse type name
3. [real] presynaptic location X
4. [real] presynaptic location Y
5. [real] presynaptic location Z
6. [real] postsynaptic location X
7. [real] postsynaptic location Y
8. [real] postsynaptic location Z
9. [integer] ID of presynaptic axon fiber segment piece
10. [integer] ID of postsynaptic dendrite fiber segment piece
11. [integer] ID of presynaptic neuron
12. [integer] ID of postsynaptic neuron
13. (conditionally) [real] time of synaptogenesis
*/
(*Txt_synapselist) += String(Txt_synapseindex);
(*Txt_synapselist) += ',';
(*Txt_synapselist) += synapse_type_name[type_id];
///(*Txt_synapselist) += ','+String((long) this);
///(*Txt_synapselist) += ','+String((long) s);
double x=0.0, y=0.0, z=0.0;
(s->P0).get_all(x,y,z);
(*Txt_synapselist) += String(x,",%f");
(*Txt_synapselist) += String(y,",%f");
(*Txt_synapselist) += String(z,",%f");
(s->P1).get_all(x,y,z);
(*Txt_synapselist) += String(x,",%f");
(*Txt_synapselist) += String(y,",%f");
(*Txt_synapselist) += String(z,",%f,");
(*Txt_synapselist) += String((long) (s->AxonSegment())) + ',';
(*Txt_synapselist) += String((long) (s->DendriteSegment())) + ',';
(*Txt_synapselist) += String((long) Presynaptic_Neuron());
(*Txt_synapselist) += ',';
(*Txt_synapselist) += String((long) Postsynaptic_Neuron());
if (SynaptoGenesis_Data) (*Txt_synapselist) += String(SynaptoGenesis_Data->find_t_genesis(this),",%f");
if(s->DendriteSegment()->APICAL == 6)
{
(*Txt_synapselist) += String(",APICAL\n");
}
else
{
(*Txt_synapselist) += String(",BASAL\n");
}
Txt_synapseindex++;
return NULL;
}
void synaptogenesis_data::add(synapse * s, double t) {
if (dataidx>=datalen) {
unsigned int newdatalen = datalen + 10240;
synapseptr * sptr = new synapseptr[newdatalen];
double * d = new double[newdatalen];
for (unsigned int i = 0; i<dataidx; i++) {
sptr[i] = synlist[i];
d[i] = data[i];
}
datalen = newdatalen;
delete[] synlist;
delete[] data;
synlist = sptr;
data = d;
}
synlist[dataidx] = s;
data[dataidx] = t;
dataidx++;
}
double synaptogenesis_data::find_t_genesis(synapse * s) {
for (unsigned int i = 0; i<dataidx; i++) if (synlist[i] == s) return data[i];
return -1.0;
}
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