Beispiel #1
0
 /**
  * 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;
   }
 }
Beispiel #2
0
  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 &lt; reaction_happening;");
    out.append("chan priority update");
    for (int i = 0; i < countReactions; i++) {
      out.append(" &lt; reaction_happening[" + i + "]");
    }
    for (int i = 0; i < countReactions; i++) {
      out.append(" &lt; 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>");
  }
Beispiel #3
0
  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&lt;=metro+1</label></location><init ref=\"id0\"/><transition><source ref=\"id0\"/><target ref=\"id0\"/><label kind=\"guard\" x=\"56\" y=\"-24\">globalTime&gt;=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)
                              + "] &amp;reactant1, int &amp;reactant1_nonofficial, int[0,"
                              + m.getReactant(r.get(REACTANT).as(String.class))
                                  .get(NUMBER_OF_LEVELS)
                                  .as(Integer.class)
                              + "] &amp;reactant2, int &amp;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 &amp;update, chan &amp;inform_reacting, chan &amp;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&lt;=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&amp;&amp; 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&amp;&amp; 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&amp;&amp; c&gt;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 &amp;&amp; timeL[reactant2][reactant1] != INFINITE_TIME)\n|| (timeU[reactant2][reactant1] != INFINITE_TIME &amp;&amp; c&lt;=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&gt;=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)
                              + "] &amp;reactant, int &amp;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 &amp;update, chan &amp;inform_reacting, chan &amp;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&lt;=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&amp;&amp; c&gt;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 &amp;&amp; timeL[reactant] != INFINITE_TIME)\n|| (timeU[reactant] != INFINITE_TIME &amp;&amp; c&lt;=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&gt;=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)
                            + "] &amp;official, int &amp;nonofficial, broadcast chan &amp;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&gt;"
                            + 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&lt;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&gt;=0\n&amp;&amp; nonofficial&lt;="
                            + 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)
                    + "] &amp;official"
                    + (i + 1)
                    + ", int &amp;unofficial"
                    + (i + 1)
                    + ", ");
          }
          templateString.append(
              "broadcast chan &amp;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)
                    + "] &amp;official"
                    + (i + 1)
                    + ", int &amp;unofficial"
                    + (i + 1)
                    + ", ");
          }
          templateString.append(
              "int[0,"
                  + v.lastElement().get(NUMBER_OF_LEVELS).as(Integer.class)
                  + "] &amp;official"
                  + v.size()
                  + ", int &amp;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)
                    + " &lt; 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 &gt; "
                  + 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)
                    + " &gt; 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 &amp;reaction_happening[N_REACTIONS], broadcast chan &amp;update, chan &amp;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();
    }
  }
Beispiel #4
0
  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);
    }
  }