/**
* Determines the name of a reaction process.
*
* @param r the reaction to name
* @return the name of the process
*/
protected String getReactionName(Reaction r) {
if (r.get(REACTION_TYPE).as(String.class).equals(MONO_REACTION)) {
// reaction1 is assumed to be a degredation reaction
String reactantId = r.get(REACTANT).as(String.class);
return reactantId + "_deg";
} else if (r.get(REACTION_TYPE).as(String.class).equals(BI_REACTION)) {
String r1Id = r.get(CATALYST).as(String.class);
String r2Id = r.get(REACTANT).as(String.class);
return r1Id
+ "_"
+ r2Id
+ "_r_"
+ ((r.get(INCREMENT).as(Integer.class) >= 0) ? "up" : "down");
} else {
return null;
}
}
protected void appendModel(StringBuilder out, Model m) {
out.append("<?xml version='1.0' encoding='utf-8'?>");
out.append(newLine);
out.append(
"<!DOCTYPE nta PUBLIC '-//Uppaal Team//DTD Flat System 1.1//EN' 'http://www.it.uu.se/research/group/darts/uppaal/flat-1_1.dtd'>");
out.append(newLine);
out.append("<nta>");
out.append(newLine);
out.append("<declaration>");
out.append(newLine);
// output global declarations
out.append("// Place global declarations here.");
out.append(newLine);
out.append("clock globalTime;");
out.append(newLine);
out.append("const int INFINITE_TIME = " + INFINITE_TIME + ";");
out.append(newLine);
// out.append("const int MAX_LEVELS = " + m.getProperties().get("levels").as(Integer.class) +
// ";");
// out.append(newLine);
int countReactions = 0;
for (Reaction r : m.getReactionCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
countReactions++;
}
}
out.append("const int N_REACTIONS = " + countReactions + ";");
out.append(newLine);
out.append("broadcast chan update;");
out.append(newLine);
out.append("chan reaction_happening[N_REACTIONS];");
out.append(newLine);
out.append("chan update_done[N_REACTIONS];");
out.append(newLine);
// out.append("chan priority update < reaction_happening;");
out.append("chan priority update");
for (int i = 0; i < countReactions; i++) {
out.append(" < reaction_happening[" + i + "]");
}
for (int i = 0; i < countReactions; i++) {
out.append(" < update_done[" + i + "]");
}
out.append(";");
out.append(newLine);
out.append(newLine);
for (Reactant r : m.getReactantCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
this.appendReactantVariables(out, r);
}
}
out.append("</declaration>");
out.append(newLine);
out.append(newLine);
// output templates
this.appendTemplates(out, m);
out.append(newLine);
out.append("<system>");
out.append(newLine);
out.append("Coord = Coordinator(reaction_happening, update, update_done);");
out.append(newLine);
out.append(newLine);
// output the process instantiation for each reactant and reaction
for (Reactant r : m.getReactantCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
if (r.get(GROUP) == null
|| r.get(GROUP).isNull()
|| r.get(GROUP).as(String.class).length() < 1) {
this.appendReactantProcesses(out, r);
}
}
}
for (String group : groups.keySet()) {
this.appendReactantGroupProcess(out, group);
}
out.append(newLine);
int reactionIndex = 0;
for (Reaction r : m.getReactionCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
this.appendReactionProcesses(out, m, r, reactionIndex);
reactionIndex++;
}
}
out.append(newLine);
out.append(newLine);
/*out.append("Crono = crono();");
out.append(newLine);
out.append(newLine);*/
// compose the system
out.append("system ");
for (Reactant r : m.getReactantCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
if (r.get(GROUP) == null
|| r.get(GROUP).isNull()
|| r.get(GROUP).as(String.class).length() < 1) {
out.append(r.getId() + "_reactant, ");
}
}
}
for (String group : groups.keySet()) {
out.append(group + "_group, ");
}
for (Reaction r : m.getReactionCollection()) {
if (r.get(ENABLED).as(Boolean.class)) {
out.append(getReactionName(r) + ", ");
}
}
// out.append("Coord, Crono;");
out.append("Coord;");
out.append(newLine);
out.append(newLine);
out.append("</system>");
out.append(newLine);
out.append("</nta>");
}
protected void appendTemplates(StringBuilder out, Model m) {
try {
StringWriter outString;
DocumentBuilder documentBuilder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
Document document;
Transformer tra = TransformerFactory.newInstance().newTransformer();
tra.setOutputProperty(OutputKeys.INDENT, "yes");
tra.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
tra.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
// This should have been a "Chronometer" process to force the update of globalTime for each
// simulation step, but it also curiously forces the UPPAAL engine to always choose the
// shortest simulation traces possible, thus voiding all the time intervals for reactions
/*outString = new StringWriter();
document = documentBuilder.parse(new ByteArrayInputStream(("<template><name>crono</name><declaration>int[0, 1073741821] metro := 0;</declaration><location id=\"id0\" x=\"0\" y=\"0\"><label kind=\"invariant\" x=\"-176\" y=\"-24\">globalTime<=metro+1</label></location><init ref=\"id0\"/><transition><source ref=\"id0\"/><target ref=\"id0\"/><label kind=\"guard\" x=\"56\" y=\"-24\">globalTime>=metro</label><label kind=\"assignment\" x=\"56\" y=\"0\">metro:=metro+1</label><nail x=\"56\" y=\"-48\"/><nail x=\"56\" y=\"48\"/></transition></template>").getBytes()));
tra.transform(new DOMSource(document), new StreamResult(outString));
out.append(outString.toString());
out.append(newLine);
out.append(newLine);*/
for (Reaction r : m.getReactionCollection()) {
if (!r.get(ENABLED).as(Boolean.class)) continue;
outString = new StringWriter();
if (r.get(REACTION_TYPE).as(String.class).equals(BI_REACTION)) {
document =
documentBuilder.parse(
new ByteArrayInputStream(
("<template><name x=\"5\" y=\"5\">Reaction2_"
+ r.get(CATALYST).as(String.class)
+ "_"
+ r.get(REACTANT).as(String.class)
+ "</name><parameter>int[0,"
+ m.getReactant(r.get(CATALYST).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "] &reactant1, int &reactant1_nonofficial, int[0,"
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "] &reactant2, int &reactant2_nonofficial, const int timeL["
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1]["
+ m.getReactant(r.get(CATALYST).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1], const int timeU["
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1]["
+ m.getReactant(r.get(CATALYST).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1], const int delta, broadcast chan &update, chan &inform_reacting, chan &inform_updated</parameter><declaration>clock c;</declaration><location id=\"id0\" x=\"-1816\" y=\"-736\"></location><location id=\"id1\" x=\"-1816\" y=\"-1128\"></location><location id=\"id2\" x=\"-1552\" y=\"-976\"><committed/></location><location id=\"id3\" x=\"-1816\" y=\"-872\"><label kind=\"invariant\" x=\"-2152\" y=\"-896\">timeU[reactant2][reactant1] == INFINITE_TIME\n|| c<=timeU[reactant2][reactant1]</label></location><location id=\"id4\" x=\"-1816\" y=\"-1016\"><committed/></location><init ref=\"id4\"/><transition><source ref=\"id3\"/><target ref=\"id3\"/><label kind=\"guard\" x=\"-2096\" y=\"-832\">reactant1 == reactant1_nonofficial\n&& reactant2 == reactant2_nonofficial</label><label kind=\"synchronisation\" x=\"-1976\" y=\"-800\">update?</label><nail x=\"-1856\" y=\"-832\"/><nail x=\"-1920\" y=\"-832\"/><nail x=\"-1920\" y=\"-776\"/><nail x=\"-1856\" y=\"-776\"/></transition><transition><source ref=\"id1\"/><target ref=\"id1\"/><label kind=\"guard\" x=\"-1928\" y=\"-1248\">reactant1 == reactant1_nonofficial\n&& reactant2 == reactant2_nonofficial</label><label kind=\"synchronisation\" x=\"-1840\" y=\"-1224\">update?</label><nail x=\"-1776\" y=\"-1208\"/><nail x=\"-1864\" y=\"-1208\"/></transition><transition><source ref=\"id1\"/><target ref=\"id4\"/><label kind=\"guard\" x=\"-2088\" y=\"-1160\">reactant1 != reactant1_nonofficial\n|| reactant2 != reactant2_nonofficial</label><label kind=\"synchronisation\" x=\"-2032\" y=\"-1128\">update?</label><nail x=\"-1968\" y=\"-1128\"/><nail x=\"-1968\" y=\"-1016\"/></transition><transition><source ref=\"id3\"/><target ref=\"id2\"/><label kind=\"guard\" x=\"-1736\" y=\"-960\">reactant1 != reactant1_nonofficial\n|| reactant2 != reactant2_nonofficial</label><label kind=\"synchronisation\" x=\"-1728\" y=\"-936\">update?</label><nail x=\"-1728\" y=\"-920\"/><nail x=\"-1624\" y=\"-920\"/></transition><transition><source ref=\"id0\"/><target ref=\"id2\"/><label kind=\"synchronisation\" x=\"-1776\" y=\"-752\">update?</label><nail x=\"-1424\" y=\"-736\"/><nail x=\"-1424\" y=\"-896\"/></transition><transition><source ref=\"id2\"/><target ref=\"id1\"/><label kind=\"guard\" x=\"-1792\" y=\"-1144\">timeL[reactant2][reactant1] == INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1792\" y=\"-1160\">inform_updated?</label><nail x=\"-1464\" y=\"-976\"/><nail x=\"-1464\" y=\"-1128\"/></transition><transition><source ref=\"id4\"/><target ref=\"id1\"/><label kind=\"guard\" x=\"-1952\" y=\"-1080\">timeL[reactant2][reactant1]== INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1872\" y=\"-1096\">inform_updated?</label></transition><transition><source ref=\"id2\"/><target ref=\"id3\"/><label kind=\"guard\" x=\"-1784\" y=\"-1032\">timeU[reactant2][reactant1] != INFINITE_TIME\n&& c>timeU[reactant2][reactant1]</label><label kind=\"synchronisation\" x=\"-1784\" y=\"-1008\">inform_updated?</label><label kind=\"assignment\" x=\"-1784\" y=\"-992\">c:=timeU[reactant2][reactant1]</label><nail x=\"-1736\" y=\"-976\"/></transition><transition><source ref=\"id2\"/><target ref=\"id3\"/><label kind=\"guard\" x=\"-1760\" y=\"-912\">(timeU[reactant2][reactant1] == INFINITE_TIME && timeL[reactant2][reactant1] != INFINITE_TIME)\n|| (timeU[reactant2][reactant1] != INFINITE_TIME && c<=timeU[reactant2][reactant1])</label><label kind=\"synchronisation\" x=\"-1760\" y=\"-888\">inform_updated?</label><nail x=\"-1552\" y=\"-872\"/></transition><transition><source ref=\"id3\"/><target ref=\"id0\"/><label kind=\"guard\" x=\"-1808\" y=\"-840\">c>=timeL[reactant2][reactant1]</label><label kind=\"synchronisation\" x=\"-1808\" y=\"-824\">inform_reacting!</label><label kind=\"assignment\" x=\"-1808\" y=\"-808\">reactant2_nonofficial := reactant2_nonofficial + delta,\nc:=0</label></transition><transition><source ref=\"id4\"/><target ref=\"id3\"/><label kind=\"guard\" x=\"-1968\" y=\"-976\">timeL[reactant2][reactant1]\n!= INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1968\" y=\"-952\">inform_updated?</label><label kind=\"assignment\" x=\"-1968\" y=\"-936\">c:=0</label></transition></template>")
.getBytes()));
} else {
document =
documentBuilder.parse(
new ByteArrayInputStream(
("<template><name x=\"5\" y=\"5\">Reaction_"
+ r.get(REACTANT).as(String.class)
+ "</name><parameter>int[0,"
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "] &reactant, int &reactant_nonofficial, const int timeL["
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1], const int timeU["
+ m.getReactant(r.get(REACTANT).as(String.class))
.get(NUMBER_OF_LEVELS)
.as(Integer.class)
+ "+1], const int delta, broadcast chan &update, chan &inform_reacting, chan &inform_updated</parameter><declaration>clock c;</declaration><location id=\"id5\" x=\"-1320\" y=\"-480\"></location><location id=\"id6\" x=\"-1320\" y=\"-920\"></location><location id=\"id7\" x=\"-1128\" y=\"-712\"><committed/></location><location id=\"id8\" x=\"-1320\" y=\"-624\"><label kind=\"invariant\" x=\"-1568\" y=\"-648\">timeU[reactant] == INFINITE_TIME\n|| c<=timeU[reactant]</label></location><location id=\"id9\" x=\"-1320\" y=\"-816\"><committed/></location><init ref=\"id9\"/><transition><source ref=\"id8\"/><target ref=\"id8\"/><label kind=\"guard\" x=\"-1552\" y=\"-560\">reactant == reactant_nonofficial</label><label kind=\"synchronisation\" x=\"-1496\" y=\"-544\">update?</label><nail x=\"-1376\" y=\"-560\"/><nail x=\"-1440\" y=\"-560\"/><nail x=\"-1440\" y=\"-504\"/><nail x=\"-1360\" y=\"-504\"/></transition><transition><source ref=\"id6\"/><target ref=\"id6\"/><label kind=\"guard\" x=\"-1424\" y=\"-1016\">reactant == reactant_nonofficial</label><label kind=\"synchronisation\" x=\"-1352\" y=\"-1000\">update?</label><nail x=\"-1288\" y=\"-984\"/><nail x=\"-1360\" y=\"-984\"/></transition><transition><source ref=\"id6\"/><target ref=\"id9\"/><label kind=\"guard\" x=\"-1600\" y=\"-936\">reactant != reactant_nonofficial</label><label kind=\"synchronisation\" x=\"-1544\" y=\"-920\">update?</label><nail x=\"-1480\" y=\"-920\"/><nail x=\"-1480\" y=\"-816\"/></transition><transition><source ref=\"id8\"/><target ref=\"id7\"/><label kind=\"guard\" x=\"-1264\" y=\"-696\">reactant != reactant_nonofficial</label><label kind=\"synchronisation\" x=\"-1264\" y=\"-688\">update?</label><nail x=\"-1264\" y=\"-672\"/><nail x=\"-1168\" y=\"-672\"/></transition><transition><source ref=\"id5\"/><target ref=\"id7\"/><label kind=\"synchronisation\" x=\"-1256\" y=\"-496\">update?</label><nail x=\"-944\" y=\"-480\"/><nail x=\"-944\" y=\"-656\"/></transition><transition><source ref=\"id7\"/><target ref=\"id6\"/><label kind=\"guard\" x=\"-1288\" y=\"-936\">timeL[reactant] == INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1288\" y=\"-952\">inform_updated?</label><nail x=\"-1040\" y=\"-712\"/><nail x=\"-1040\" y=\"-920\"/></transition><transition><source ref=\"id9\"/><target ref=\"id6\"/><label kind=\"guard\" x=\"-1440\" y=\"-864\">timeL[reactant] == INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1376\" y=\"-880\">inform_updated?</label></transition><transition><source ref=\"id7\"/><target ref=\"id8\"/><label kind=\"guard\" x=\"-1272\" y=\"-768\">timeU[reactant] != INFINITE_TIME\n&& c>timeU[reactant]</label><label kind=\"synchronisation\" x=\"-1272\" y=\"-744\">inform_updated?</label><label kind=\"assignment\" x=\"-1272\" y=\"-728\">c:=timeU[reactant]</label><nail x=\"-1264\" y=\"-712\"/></transition><transition><source ref=\"id7\"/><target ref=\"id8\"/><label kind=\"guard\" x=\"-1280\" y=\"-664\">(timeU[reactant] == INFINITE_TIME && timeL[reactant] != INFINITE_TIME)\n|| (timeU[reactant] != INFINITE_TIME && c<=timeU[reactant])</label><label kind=\"synchronisation\" x=\"-1280\" y=\"-640\">inform_updated?</label><nail x=\"-1128\" y=\"-624\"/></transition><transition><source ref=\"id8\"/><target ref=\"id5\"/><label kind=\"guard\" x=\"-1312\" y=\"-584\">c>=timeL[reactant]</label><label kind=\"synchronisation\" x=\"-1312\" y=\"-568\">inform_reacting!</label><label kind=\"assignment\" x=\"-1312\" y=\"-552\">reactant_nonofficial := reactant_nonofficial + delta,\nc:=0</label></transition><transition><source ref=\"id9\"/><target ref=\"id8\"/><label kind=\"guard\" x=\"-1424\" y=\"-792\">timeL[reactant] != INFINITE_TIME</label><label kind=\"synchronisation\" x=\"-1424\" y=\"-776\">inform_updated?</label><label kind=\"assignment\" x=\"-1424\" y=\"-760\">c:=0</label><nail x=\"-1320\" y=\"-656\"/></transition></template>")
.getBytes()));
}
tra.transform(new DOMSource(document), new StreamResult(outString));
out.append(outString.toString());
out.append(newLine);
out.append(newLine);
}
// This could possibly be removed.
// It is used to represent with a special template the "groups of reactants", which represent
// all the same molecule, with alternative, exclusive phosphorylation possibilities.
// The GROUP property for each node of the group needs to be set to the same value to
// represent this situation.
groups = new HashMap<String, Vector<Reactant>>();
for (Reactant r : m.getReactantCollection()) {
if (!r.get(ENABLED).as(Boolean.class)) continue;
if (r.get(GROUP) != null
&& !r.get(GROUP).isNull()
&& r.get(GROUP).as(String.class).length()
> 0) { // you simply have to set equal values for the GROUP property, and the
// Reactant will be output just for that group, as we see below
String group = r.get(GROUP).as(String.class);
if (groups.containsKey(group)) {
groups.get(group).add(r);
} else {
Vector<Reactant> v = new Vector<Reactant>();
v.add(r);
groups.put(group, v);
}
continue;
}
outString = new StringWriter();
document =
documentBuilder.parse(
new ByteArrayInputStream(
("<template><name>Reactant_"
+ r.getId()
+ "</name><parameter>int[0,"
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "] &official, int &nonofficial, broadcast chan &update</parameter><location id=\"id10\" x=\"-416\" y=\"-104\"></location><init ref=\"id10\"/><transition><source ref=\"id10\"/><target ref=\"id10\"/><label kind=\"guard\" x=\"-536\" y=\"-248\">nonofficial>"
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "</label><label kind=\"synchronisation\" x=\"-536\" y=\"-232\">update?</label><label kind=\"assignment\" x=\"-536\" y=\"-216\">official := "
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ ", nonofficial := "
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "</label><nail x=\"-168\" y=\"-200\"/><nail x=\"-168\" y=\"-256\"/><nail x=\"-544\" y=\"-256\"/><nail x=\"-544\" y=\"-192\"/><nail x=\"-416\" y=\"-192\"/></transition><transition><source ref=\"id10\"/><target ref=\"id10\"/><label kind=\"guard\" x=\"-496\" y=\"-48\">nonofficial<0</label><label kind=\"synchronisation\" x=\"-496\" y=\"-32\">update?</label><label kind=\"assignment\" x=\"-496\" y=\"-16\">official := 0, nonofficial := 0</label><nail x=\"-416\" y=\"-56\"/><nail x=\"-504\" y=\"-56\"/><nail x=\"-504\" y=\"8\"/><nail x=\"-288\" y=\"8\"/><nail x=\"-288\" y=\"-24\"/></transition><transition><source ref=\"id10\"/><target ref=\"id10\"/><label kind=\"guard\" x=\"-680\" y=\"-176\">nonofficial>=0\n&& nonofficial<="
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "</label><label kind=\"synchronisation\" x=\"-680\" y=\"-144\">update?</label><label kind=\"assignment\" x=\"-680\" y=\"-128\">official := nonofficial</label><nail x=\"-688\" y=\"-104\"/><nail x=\"-688\" y=\"-184\"/><nail x=\"-464\" y=\"-184\"/></transition></template>")
.getBytes()));
tra.transform(new DOMSource(document), new StreamResult(outString));
out.append(outString.toString());
out.append(newLine);
out.append(newLine);
}
if (!groups.isEmpty()) { // compose the Reactant for this group
for (String group : groups.keySet()) {
Vector<Reactant> v = groups.get(group);
outString = new StringWriter();
StringBuilder templateString = new StringBuilder();
templateString.append("<template><name>Reactant_group_" + group + "</name><parameter>");
for (int i = 0; i < v.size(); i++) {
Reactant r = v.elementAt(i);
templateString.append(
"int[0,"
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "] &official"
+ (i + 1)
+ ", int &unofficial"
+ (i + 1)
+ ", ");
}
templateString.append(
"broadcast chan &update</parameter><declaration>void updateAll(");
for (int i = 0; i < v.size() - 1; i++) {
Reactant r = v.elementAt(i);
templateString.append(
"int[0,"
+ r.get(NUMBER_OF_LEVELS).as(Integer.class)
+ "] &official"
+ (i + 1)
+ ", int &unofficial"
+ (i + 1)
+ ", ");
}
templateString.append(
"int[0,"
+ v.lastElement().get(NUMBER_OF_LEVELS).as(Integer.class)
+ "] &official"
+ v.size()
+ ", int &unofficial"
+ v.size()
+ ") {\n\tint i;\n\tint sum := 0;\n");
for (int i = 0; i < v.size(); i++) {
templateString.append(
"\tif (unofficial"
+ (i + 1)
+ " < 0) unofficial"
+ (i + 1)
+ " := 0;\n\tsum := sum + unofficial"
+ (i + 1)
+ ";\n");
}
// TODO: v.firstElement().get("levels").as(Integer.class) is the number of levels of the
// "grouped" reactant. So, we implicitly assume that all reactants in a group have the
// same NUMBER_OF_LEVELS
templateString.append(
"\n\twhile (sum > "
+ v.firstElement().get(NUMBER_OF_LEVELS).as(Integer.class)
+ ") {\n\t\tsum := 0;\n");
for (int i = 0; i < v.size(); i++) {
templateString.append(
"\t\tif (unofficial"
+ (i + 1)
+ " > 0) unofficial"
+ (i + 1)
+ "--;\n\t\tsum := sum + unofficial"
+ (i + 1)
+ ";\n");
}
templateString.append("\t}\n");
for (int i = 0; i < v.size(); i++) {
templateString.append("\tofficial" + (i + 1) + " := unofficial" + (i + 1) + ";\n");
}
templateString.append(
"}</declaration><location id=\"id5\" x=\"16\" y=\"88\"></location><init ref=\"id5\"/><transition><source ref=\"id5\"/><target ref=\"id5\"/><label kind=\"synchronisation\" x=\"-24\" y=\"-88\">update?</label><label kind=\"assignment\" x=\"-144\" y=\"-64\">updateAll(");
for (int i = 0; i < v.size() - 1; i++) {
templateString.append("official" + (i + 1) + ", unofficial" + (i + 1) + ", ");
}
templateString.append(
"official"
+ v.size()
+ ", unofficial"
+ v.size()
+ ")</label><nail x=\"72\" y=\"-40\"/><nail x=\"-48\" y=\"-40\"/></transition></template>");
document =
documentBuilder.parse(new ByteArrayInputStream(templateString.toString().getBytes()));
tra.transform(new DOMSource(document), new StreamResult(outString));
out.append(outString.toString());
out.append(newLine);
out.append(newLine);
}
}
outString = new StringWriter();
document =
documentBuilder.parse(
new ByteArrayInputStream(
"<template><name>Coordinator</name><parameter>chan &reaction_happening[N_REACTIONS], broadcast chan &update, chan &update_done[N_REACTIONS]</parameter><location id=\"id11\" x=\"-328\" y=\"-136\"><name x=\"-338\" y=\"-166\">updated</name></location><location id=\"id12\" x=\"-152\" y=\"-136\"><committed/></location><init ref=\"id11\"/><transition><source ref=\"id11\"/><target ref=\"id11\"/><label kind=\"select\" x=\"-552\" y=\"-152\">i : int[0,N_REACTIONS-1]</label><label kind=\"synchronisation\" x=\"-552\" y=\"-136\">update_done[i]!</label><nail x=\"-392\" y=\"-176\"/><nail x=\"-392\" y=\"-96\"/></transition><transition><source ref=\"id12\"/><target ref=\"id11\"/><label kind=\"synchronisation\" x=\"-312\" y=\"-80\">update!</label><nail x=\"-152\" y=\"-64\"/><nail x=\"-328\" y=\"-64\"/></transition><transition><source ref=\"id12\"/><target ref=\"id12\"/><label kind=\"select\" x=\"-80\" y=\"-160\">i : int[0,N_REACTIONS-1]</label><label kind=\"synchronisation\" x=\"-80\" y=\"-144\">reaction_happening[i]?</label><nail x=\"-88\" y=\"-176\"/><nail x=\"-88\" y=\"-104\"/></transition><transition><source ref=\"id11\"/><target ref=\"id12\"/><label kind=\"select\" x=\"-320\" y=\"-248\">i : int[0, N_REACTIONS-1]</label><label kind=\"synchronisation\" x=\"-320\" y=\"-232\">reaction_happening[i]?</label><nail x=\"-328\" y=\"-216\"/><nail x=\"-152\" y=\"-216\"/></transition></template>"
.getBytes()));
tra.transform(new DOMSource(document), new StreamResult(outString));
out.append(outString.toString());
out.append(newLine);
out.append(newLine);
} catch (Exception e) {
System.err.println("Error: " + e);
e.printStackTrace();
}
}
protected void appendReactionProcesses(StringBuilder out, Model m, Reaction r, int index) {
if (r.get(REACTION_TYPE).as(String.class).equals(MONO_REACTION)) {
String reactantId = r.get(REACTANT).as(String.class);
out.append(
"//Mono-reaction on "
+ reactantId
+ " ("
+ m.getReactant(reactantId).get(ALIAS).as(String.class)
+ ")");
out.append(newLine);
Table timesL, timesU;
Property property = r.get(TIMES_LOWER);
if (property != null) {
timesL = property.as(Table.class);
} else {
timesL = r.get(TIMES).as(Table.class);
}
property = r.get(TIMES_UPPER);
if (property != null) {
timesU = property.as(Table.class);
} else {
timesU = r.get(TIMES).as(Table.class);
}
assert timesL.getColumnCount() == 1 : "Table LowerBound is (larger than one)-dimensional.";
assert timesU.getColumnCount() == 1 : "Table UpperBound is (larger than one)-dimensional.";
assert timesL.getRowCount()
== m.getReactant(reactantId).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of rows in 'timesLower' table of '" + r + "'";
assert timesU.getRowCount()
== m.getReactant(reactantId).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of rows in 'timesUpper' table of '" + r + "'";
// output times table constants for this reaction (lower bound)
out.append(
"const int "
+ reactantId
+ "_tLower["
+ m.getReactant(reactantId).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1] := {");
for (int i = 0; i < timesL.getRowCount() - 1; i++) {
out.append(formatTime(timesL.get(i, 0)) + ", ");
}
out.append(formatTime(timesL.get(timesL.getRowCount() - 1, 0)) + "};");
out.append(newLine);
// output times table constants for this reaction (upper bound)
out.append(
"const int "
+ reactantId
+ "_tUpper["
+ m.getReactant(reactantId).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1] := {");
for (int i = 0; i < timesU.getRowCount() - 1; i++) {
out.append(formatTime(timesU.get(i, 0)) + ", ");
}
out.append(formatTime(timesU.get(timesU.getRowCount() - 1, 0)) + "};");
out.append(newLine);
// output reaction instantiation
final String name = getReactionName(r);
out.append(
name
+ " = Reaction_"
+ reactantId
+ "("
+ reactantId
+ ", "
+ reactantId
+ "_nonofficial, "
+ reactantId
+ "_tLower, "
+ reactantId
+ "_tUpper, "
+ r.get(INCREMENT).as(Integer.class)
+ ", update, reaction_happening["
+ index
+ "], update_done["
+ index
+ "]);");
out.append(newLine);
out.append(newLine);
} else if (r.get(REACTION_TYPE).as(String.class).equals(BI_REACTION)) {
String r1Id = r.get(CATALYST).as(String.class);
String r2Id = r.get(REACTANT).as(String.class);
out.append(
"//Reaction "
+ r1Id
+ " ("
+ m.getReactant(r1Id).get(ALIAS).as(String.class)
+ ") "
+ (r.get(INCREMENT).as(Integer.class) > 0 ? "-->" : "--|")
+ " "
+ r2Id
+ " ("
+ m.getReactant(r2Id).get(ALIAS).as(String.class)
+ ")");
out.append(newLine);
Table timesL, timesU;
Property property = r.get(TIMES_LOWER);
if (property != null) {
timesL = property.as(Table.class);
} else {
timesL = r.get(TIMES).as(Table.class);
}
property = r.get(TIMES_UPPER);
if (property != null) {
timesU = property.as(Table.class);
} else {
timesU = r.get(TIMES).as(Table.class);
}
assert timesL.getRowCount() == m.getReactant(r2Id).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of rows in 'times lower' table of '" + r + "'.";
assert timesU.getRowCount() == m.getReactant(r2Id).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of rows in 'times upper' table of '" + r + "'.";
assert timesL.getColumnCount()
== m.getReactant(r1Id).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of columns in 'times lower' table of '" + r + "'.";
assert timesU.getColumnCount()
== m.getReactant(r1Id).get(NUMBER_OF_LEVELS).as(Integer.class) + 1
: "Incorrect number of columns in 'times upper' table of '" + r + "'.";
// output times table constant for this reaction
out.append(
"const int "
+ r1Id
+ "_"
+ r2Id
+ "_r_tLower["
+ m.getReactant(r2Id).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1]["
+ m.getReactant(r1Id).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1] := {");
out.append(newLine);
// for each row
for (int row = 0; row < timesL.getRowCount(); row++) {
out.append("\t\t{");
// for each column
for (int col = 0; col < timesL.getColumnCount(); col++) {
out.append(formatTime(timesL.get(row, col)));
// seperate value with a comma if it is not the last one
if (col < timesL.getColumnCount() - 1) {
out.append(", ");
}
}
out.append("}");
// end row line with a comma if it is not the last one
if (row < timesL.getRowCount() - 1) {
out.append(",");
}
out.append(newLine);
}
out.append("};");
out.append(newLine);
// output times table constant for this reaction
out.append(
"const int "
+ r1Id
+ "_"
+ r2Id
+ "_r_tUpper["
+ m.getReactant(r2Id).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1]["
+ m.getReactant(r1Id).get(NUMBER_OF_LEVELS).as(Integer.class)
+ "+1] := {");
out.append(newLine);
// for each row
for (int row = 0; row < timesU.getRowCount(); row++) {
out.append("\t\t{");
// for each column
for (int col = 0; col < timesU.getColumnCount(); col++) {
out.append(formatTime(timesU.get(row, col)));
// seperate value with a comma if it is not the last one
if (col < timesU.getColumnCount() - 1) {
out.append(", ");
}
}
out.append("}");
// end row line with a comma if it is not the last one
if (row < timesU.getRowCount() - 1) {
out.append(",");
}
out.append(newLine);
}
out.append("};");
out.append(newLine);
out.append(newLine);
// output process instantiation
final String name = getReactionName(r);
out.append(
name
+ " = Reaction2_"
+ r1Id
+ "_"
+ r2Id
+ "("
+ r1Id
+ ", "
+ r1Id
+ "_nonofficial, "
+ r2Id
+ ", "
+ r2Id
+ "_nonofficial, "
+ r1Id
+ "_"
+ r2Id
+ "_r_tLower, "
+ r1Id
+ "_"
+ r2Id
+ "_r_tUpper, "
+ r.get(INCREMENT).as(Integer.class)
+ ", update, reaction_happening["
+ index
+ "], update_done["
+ index
+ "]);");
out.append(newLine);
out.append(newLine);
}
}