@Override
public BuildFromXML build(XMLTag tag) {
baseTag = tag;
String logValue = tag.getAttribute("log");
if (logValue != null) {
this.log = Boolean.valueOf(logValue);
}
String closureValue = tag.getAttribute("closure");
if (closureValue != null) {
this.closure = Boolean.valueOf(closureValue);
}
XMLTag nameTag = tag.getTag("name");
if (nameTag != null) {
this.name = nameTag.getValue();
nameTag.removeFromParent();
}
XMLTag commentTag = tag.getTag("comment");
if (commentTag != null) {
this.comment = commentTag.getValue();
commentTag.removeFromParent();
}
return this;
}
public static void writeAuditVariables(
XMLTag oo, PrintWriter PW, XMLTag fg, ArrayList deathReasons, XMLTag theModel) {
boolean found = false;
XMLTag[] species = theModel.getTag("species").getTags("species");
for (int i = 0; i < species.length; i++) {
if (species[i].getAttribute("fg").equals(fg.getValue("name"))) {
if (oo.getTagWhere("audit", "@species", species[i].getAttribute("name"))
.getAttribute("active")
.equals("true")) {
found = true;
i = species.length;
}
}
}
if (found) {
PW.println(" public void _writeAudits() {");
PW.println(" XMLTag _var;");
for (int i = 0; i < species.length; i++) {
if (species[i].getAttribute("fg").equals(fg.getValue("name"))) {
if (oo.getTagWhere("audit", "@species", species[i].getAttribute("name"))
.getAttribute("active")
.equals("true")) {
PW.println(" if (params._type==" + i + ") {");
handleVariables(LOGGING, oo, PW, i, deathReasons, theModel);
PW.println(" } ");
}
}
}
PW.println(" }");
} else {
PW.println(" public void _writeAudits() {}");
}
PW.println("");
}
public static void writeAuditInit(
XMLTag oo, PrintWriter PW, XMLTag fg, ArrayList deathReasons, XMLTag theModel) {
PW.println(" public static void _initialiseAuditOutput() {");
PW.println(" XMLTag _fg;");
PW.println(" XMLTag o;");
// String speciesName = StringTools.nonSpace(speciesText);
XMLTag[] species = theModel.getTag("species").getTags("species");
boolean found = false;
for (int i = 0; i < species.length; i++) {
XMLTag speciesTag = theModel.getTag("species").getTags("species")[i];
String speciesText = speciesTag.getAttribute("name");
XMLTag theAuditLog = oo.getTagWhere("audit", "@species", speciesText);
XMLTag[] theVars = theAuditLog.getTags("var");
if (theVars.length > 0) {
found = true;
i = species.length;
}
}
if (found) PW.println(" XMLTag _var;");
for (int i = 0; i < species.length; i++) {
XMLTag speciesTag = theModel.getTag("species").getTags("species")[i];
if (speciesTag.getAttribute("fg").equals(fg.getValue("name"))) {
String speciesText = speciesTag.getAttribute("name");
String speciesName = StringTools.nonSpace(speciesText);
PW.println(" _fg = new XMLTag(\"functionalgroup\");");
PW.println(" _fg.addTag(new XMLTag(\"data\",\"fg_" + speciesName + ".bin\"));");
PW.println(
" Logging.setFgFile("
+ String.valueOf(i)
+ ",Launcher.JarPath+File.separator+\"fg_"
+ speciesName
+ ".bin\");");
PW.println(
" Logging.setFgTime("
+ String.valueOf(i)
+ ",Launcher.JarPath+File.separator+\"fg_"
+ speciesName
+ "_time.bin\");");
if ((oo.getTag("lineage").getAttribute("active").equals("true"))) {
PW.println(
" Logging.setLineage("
+ String.valueOf(i)
+ ",\"lineage_"
+ speciesName
+ ".bin\");");
PW.println(
" _fg.addTag(new XMLTag(\"lineage\",\"lineage_" + speciesName + ".bin\"));");
}
if ((oo.getTag("lifespan").getAttribute("active").equals("true"))) {
PW.println(
" Logging.setLifespan("
+ String.valueOf(i)
+ ",\"lifespan_"
+ speciesName
+ ".bin\");");
PW.println(
" _fg.addTag(new XMLTag(\"lifespan\",\"lifespan_" + speciesName + ".bin\"));");
}
PW.println(" _fg.addTag(new XMLTag(\"name\",\"" + speciesText + "\"));");
PW.println(" _fg.addTag(new XMLTag(\"time\",\"fg_" + speciesName + "_time.bin\"));");
PW.println(" _fg.addTag(new XMLTag(\"type\",\"" + String.valueOf(i) + "\"));");
PW.println(" _fg.addTag(new XMLTag(\"zip\",\"true\"));");
PW.println(" o = new XMLTag(\"output\");");
XMLTag ooSpecific = oo.getTagWhere("audit", "@species", speciesText);
PW.println(" o.addTag(new XMLTag(\"after\",String.valueOf(SysVars._firstExecTime)));");
PW.println(
" o.addTag(new XMLTag(\"freq\",\"" + ooSpecific.getAttribute("freq") + "\"));");
PW.println(" o.addTag(new XMLTag(\"to\",\"" + ooSpecific.getAttribute("to") + "\"));");
PW.println(" _fg.addTag(o);");
handleVariables(DEFINITIONS, oo, PW, i, deathReasons, theModel);
PW.println(" Logging.dataFormats.addTag(_fg);");
PW.println(" Logging.dataFormats.write();");
}
}
PW.println(" }");
}
public static void handleVariables(
int mode, XMLTag oo, PrintWriter PW, int speciesNo, ArrayList deathReasons, XMLTag theModel) {
int varID = 4;
XMLTag speciesTag = theModel.getTag("species").getTags("species")[speciesNo];
String speciesText = speciesTag.getAttribute("name");
// String speciesName = StringTools.nonSpace(speciesText);
int auditSpeciesNo = speciesNo;
XMLTag fgTag = theModel.getTagWhere("functionalgroup", "name", speciesTag.getAttribute("fg"));
XMLTag theAuditLog = oo.getTagWhere("audit", "@species", speciesText);
XMLTag[] theVars = theAuditLog.getTags("var");
if (theVars.length > 0) {
if (mode == DEFINITIONS) {
PW.println(" _var = new XMLTag(\"var\");");
PW.println(" _var.addTag(new XMLTag(\"id\",\"1\"));");
PW.println(" _var.addTag(new XMLTag(\"name\",\"TimeStep\"));");
PW.println(" _var.addTag(new XMLTag(\"type\",\"long\"));");
PW.println(" _fg.addTag(_var);");
PW.println(" _var = new XMLTag(\"var\");");
PW.println(" _var.addTag(new XMLTag(\"id\",\"2\"));");
PW.println(" _var.addTag(new XMLTag(\"name\",\"id\"));");
PW.println(" _var.addTag(new XMLTag(\"type\",\"long\"));");
PW.println(" _fg.addTag(_var);");
PW.println(" _var = new XMLTag(\"var\");");
PW.println(" _var.addTag(new XMLTag(\"id\",\"3\"));");
PW.println(" _var.addTag(new XMLTag(\"name\",\"Stage\"));");
PW.println(" _var.addTag(new XMLTag(\"desc\",\"State\"));");
PW.println(" _var.addTag(new XMLTag(\"type\",\"int\"));");
PW.println(" _fg.addTag(_var);");
} else {
long auditFreq = SysVarsCompiler.getFreqTS(theModel, theAuditLog);
PW.println(
" if ((log) && (SysVars._stageLogs[params._type][_CurrentStage]) && (Logging.isTime("
+ auditFreq
+ "L,"
+ theAuditLog.getAttribute("from")
+ "L,"
+ theAuditLog.getAttribute("to")
+ "L))) {");
PW.println(
" Logging.writeFGLong(" + String.valueOf(auditSpeciesNo) + ",Kernel.myTime);");
PW.println(" Logging.writeFGLong(" + String.valueOf(auditSpeciesNo) + ",id);");
PW.println(
" Logging.writeFGInt(" + String.valueOf(auditSpeciesNo) + ",_CurrentStage);");
}
for (int i = 0; i < theVars.length; i++) {
XMLTag var = theVars[i];
String varName = var.getAttribute("name");
String scope = var.getAttribute("scope");
if (scope.equals(OutputDialog2.SCOPE_AT_AGENT)) {
String realVar = varName.substring(0, varName.indexOf("("));
if (mode == LOGGING)
PW.println(" Logging.writeFGReal(" + auditSpeciesNo + "," + realVar + "[1]);");
else varID = writeVarEntry(PW, realVar, "real", varID);
} else if (scope.equals(OutputDialog2.SCOPE_AT_INCHEMICAL)) {
String chemicalName = var.getAttribute("chem");
String poolOrGain = var.getAttribute("chemtype");
if (poolOrGain.equals("pool")) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",_"
+ chemicalName
+ "_Pool_Old);");
else varID = writeVarEntry(PW, varName, "real", varID);
} else if (poolOrGain.equals("gain")) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",_" + chemicalName + "_Ing);");
else varID = writeVarEntry(PW, varName, "real", varID);
}
} else if (scope.equals(OutputDialog2.SCOPE_AT_BIOLOGICAL)) { // Always a concentration
final String species = var.getAttribute("species");
final String stage = var.getAttribute("stage");
final XMLTag[] speciesTags = theModel.getTag("species").getTags("species");
int targetSpeciesNo = 0;
while (!speciesTags[targetSpeciesNo].getAttribute("name").equals(species))
targetSpeciesNo++;
final XMLTag[] stages =
theModel
.getTagWhere(
"functionalgroup", "name", speciesTags[targetSpeciesNo].getAttribute("fg"))
.getTags("stage");
int targetStageNo = 0;
while (!stages[targetStageNo].getValue("name").equals(stage)) targetStageNo++;
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",Utils.getStar(blayer,"
+ targetSpeciesNo
+ ", "
+ targetStageNo
+ "));");
else varID = writeVarEntry(PW, varName, "real", varID);
} else if (scope.equals(OutputDialog2.SCOPE_AT_CHEMICAL)) {
final String chemicalName = var.getAttribute("chem");
final String chemType = var.getAttribute("chemtype");
final XMLTag[] chems = theModel.getTags("chemical");
int targetChem = 0;
while (!chems[targetChem].getValue("name").equals(chemicalName)) targetChem++;
if (chemType.equals(OutputDialog2.DEF_SOLN)) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.solution_chem["
+ targetChem
+ "]);");
else varID = writeVarEntry(PW, varName, "real", varID);
} else if (chemType.equals(OutputDialog2.DEF_BIOCONC)) {
if ((var.getAttribute("species") != null) && (var.getAttribute("stage") != null)) {
if (mode == LOGGING) {
final String chemName = var.getAttribute("chem");
final String species = var.getAttribute("species");
final String stage = var.getAttribute("stage");
final String fg =
theModel
.getTag("species")
.getTagWhere("species", "@name", species)
.getAttribute("fg");
int specNo = 0;
while (!theModel
.getTag("species")
.getTags()[specNo]
.getAttribute("name")
.equals(species)) specNo++;
int stageNo = 0;
while (!theModel
.getTagWhere("functionalgroup", "name", fg)
.getTags("stage")[stageNo]
.getValue("name")
.equals(stage)) stageNo++;
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.sumFGPool_"
+ chemName
+ "("
+ specNo
+ ","
+ stageNo
+ "));");
} else varID = writeVarEntry(PW, varName, "real", varID);
} else {
final String chemName = var.getAttribute("chem");
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.sumFGPool_"
+ chemName
+ "());");
else varID = writeVarEntry(PW, varName, "real", varID);
}
} else if (chemType.equals(OutputDialog2.DEF_ING_BY)) {
if (mode == LOGGING) {
if ((var.getAttribute("stage") == null) && (var.getAttribute("species") == null)) {
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.sumFGIng_"
+ chemicalName
+ "();");
} else {
String byStage = var.getAttribute("stage");
String bySpecies = var.getAttribute("species");
int bySpecNo = 0;
while (!theModel
.getTag("species")
.getTags()[bySpecNo]
.getAttribute("name")
.equals(bySpecies)) bySpecNo++;
String fg =
theModel
.getTag("species")
.getTagWhere("species", "@name", bySpecies)
.getAttribute("fg");
int fromStageNo = 0;
while (!theModel
.getTagWhere("functionalgroup", "name", fg)
.getTags("stage")[fromStageNo]
.getValue("name")
.equals(byStage)) fromStageNo++;
}
} else varID = writeVarEntry(PW, varName, "real", varID);
} else if (chemType.equals(OutputDialog2.DEF_ING_FROM)) {
if (mode == LOGGING) {
final String fromSpecies = StringTools.nonSpace(var.getAttribute("fromspecies"));
final String fromStage = StringTools.nonSpace(var.getAttribute("fromstage"));
if ((var.getAttribute("byall") != null)
&& (var.getAttribute("byall").equals("true"))) {
PW.print(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer._"
+ chemicalName
+ "_from_");
PW.println(fromSpecies + "_" + fromStage + "_by_all);");
} else {
final String bySpecies = StringTools.nonSpace(var.getAttribute("byspecies"));
final String byStage = StringTools.nonSpace(var.getAttribute("bystage"));
PW.print(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer._"
+ chemicalName
+ "_from_");
PW.println(
fromSpecies + "_" + fromStage + "_by_" + bySpecies + "_" + byStage + ");");
}
} else varID = writeVarEntry(PW, varName, "real", varID);
}
} else if (scope.equals(OutputDialog2.SCOPE_AT_DEMOGRAPHIC)) {
String species = var.getAttribute("species");
String stage = var.getAttribute("stage");
XMLTag[] speciesTags = theModel.getTag("species").getTags("species");
int targetSpeciesNo = 0;
while (!speciesTags[targetSpeciesNo].getAttribute("name").equals(species))
targetSpeciesNo++;
XMLTag[] stages =
theModel
.getTagWhere(
"functionalgroup", "name", speciesTags[targetSpeciesNo].getAttribute("fg"))
.getTags("stage");
int targetStageNo = 0;
while (!stages[targetStageNo].getValue("name").equals(stage)) targetStageNo++;
if (varName.startsWith(OutputDialog2.AGENT_NO_AGENTS + " : ")) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.AgentCounts["
+ targetSpeciesNo
+ "]["
+ targetStageNo
+ "]);");
else varID = writeVarEntry(PW, varName, "real", varID);
} else if (varName.startsWith(OutputDialog2.AGENT_BEING_INGESTED_ALL + " : ")) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.SpeciesStateDemography["
+ targetSpeciesNo
+ "]["
+ targetStageNo
+ "][SysVars.ingestionAll["
+ targetSpeciesNo
+ "]]);");
else varID = writeVarEntry(PW, varName, "real", varID);
} else if (varName.startsWith(OutputDialog2.AGENT_BEING_INGESTED_BY)) {
if (mode == LOGGING) {
String fg =
theModel
.getTag("species")
.getTagWhere("species", "@name", species)
.getAttribute("fg");
int specNo = 0;
while (!theModel
.getTag("species")
.getTags()[specNo]
.getAttribute("name")
.equals(species)) specNo++;
int stageNo = 0;
while (!theModel
.getTagWhere("functionalgroup", "name", fg)
.getTags("stage")[stageNo]
.getValue("name")
.equals(stage)) stageNo++;
String predator =
varName.substring(OutputDialog2.AGENT_BEING_INGESTED_BY.length() + 3);
final String predatorSpecies = predator.substring(0, predator.indexOf(":") - 1);
predator = predator.substring(predator.indexOf(":") + 2);
final String predatorStage = predator.substring(0, predator.indexOf(":") - 1);
predator = predator.substring(predator.indexOf(":") + 2);
final String preySpecies = predator.substring(0, predator.indexOf(":") - 1);
PW.print(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.SpeciesStateDemography["
+ specNo
+ "]["
+ stageNo
+ "][");
PW.print("SysVars._DR_" + StringTools.nonSpace(preySpecies) + "_");
PW.print(StringTools.nonSpace(OutputDialog2.AGENT_BEING_INGESTED_BY));
PW.print(StringTools.nonSpace(predatorSpecies) + "_");
PW.print(StringTools.nonSpace(predatorStage) + "]);");
} else varID = writeVarEntry(PW, varName, "real", varID);
} else {
String reason = varName.substring(0, varName.indexOf(":") - 1).trim();
String fgName =
theModel
.getTag("species")
.getTagWhere("species", "@name", var.getAttribute("species"))
.getAttribute("fg");
int reasonNo = getDeathReason(fgName, reason, deathReasons);
if (reasonNo == -1) System.out.println("Error getting death reasons");
else {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",blayer.SpeciesStateDemography["
+ targetSpeciesNo
+ "]["
+ targetStageNo
+ "]["
+ reasonNo
+ "]);");
else varID = writeVarEntry(PW, varName, "real", varID);
}
}
} else if (scope.equals(OutputDialog2.SCOPE_AT_PHYSICAL)) {
if (mode == LOGGING) {
if (varName.equals(OutputDialog2.DENSITY))
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",Utils.getDensity(z[1]));");
else if (varName.equals(OutputDialog2.FULL_IRRADIANCE))
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",Utils.getFullIrrad(z[1]));");
else if (varName.equals(OutputDialog2.SALINITY))
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",Utils.getSalinity(z[1]));");
else if (varName.equals(OutputDialog2.TEMPERATURE))
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",Utils.getPureTemperature(z[1]));");
else if (varName.equals(OutputDialog2.TEMPADJ))
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",Utils.getTemperature(z[1]));");
else if (varName.equals(OutputDialog2.VISIBLE_IRRADIANCE))
PW.println(
" Logging.writeFGReal(" + auditSpeciesNo + ",Utils.getVisIrrad(z[1]));");
} else varID = writeVarEntry(PW, varName, "real", varID);
} else if (scope.equals(OutputDialog2.SCOPE_AT_LOCAL)) {
if (varName.indexOf("(") >= 0)
varName = varName.substring(0, varName.indexOf("(") - 1).trim();
XMLTag findVar = fgTag.getTagWhere("local", "name", varName);
if (findVar != null) {
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ","
+ findVar.getValue("name")
+ ");");
else varID = writeVarEntry(PW, findVar.getValue("name"), "real", varID);
}
} else if (scope.equals(OutputDialog2.SCOPE_AT_VARIETYBASED)) {
if (varName.indexOf("(") >= 0)
varName = varName.substring(0, varName.indexOf("(") - 1).trim();
String species = var.getAttribute("species");
String stage = var.getAttribute("stage");
XMLTag[] speciesTags = theModel.getTag("species").getTags("species");
int targetSpeciesNo = 0;
while (!speciesTags[targetSpeciesNo].getAttribute("name").equals(species))
targetSpeciesNo++;
XMLTag[] stages =
theModel
.getTagWhere(
"functionalgroup", "name", speciesTags[targetSpeciesNo].getAttribute("fg"))
.getTags("stage");
int targetStageNo = 0;
while (!stages[targetStageNo].getValue("name").equals(stage)) targetStageNo++;
String link = "";
boolean variableFlag = false;
String realVar = "";
if (varName.equals("IngestedCells")) {
int ingestionID = 0;
for (int j = 0; j < targetSpeciesNo - 1; j++)
ingestionID += getFGForSpeciesNo(j, theModel).getTags("stage").length;
ingestionID += targetStageNo;
if (mode == LOGGING)
PW.println(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ",IngestedCells["
+ ingestionID
+ "]);");
else varID = writeVarEntry(PW, "Ingested " + stage + " " + species, "real", varID);
} else {
String linkString = StringTools.nonSpace(species + "$" + stage);
if (fgTag.getTagWhere("varietyvariable", "name", varName) != null) {
link = fgTag.getTagWhere("varietyvariable", "name", varName).getAttribute("link");
realVar = fgTag.getTagWhere("varietyvariable", "name", varName).getValue("name");
variableFlag = true;
} else {
XMLTag findVar = fgTag.getTagWhere("varietylocal", "name", varName);
if (findVar != null) {
link = findVar.getAttribute("link");
realVar = findVar.getValue("name");
String foodSetName = speciesText + " : " + link;
XMLTag[] foods =
theModel
.getTag("foodsets")
.getTagWhere("foodset", "@name", foodSetName)
.getTags("food");
int j = 0;
boolean found = false;
while ((j < foods.length) && (!found)) {
String potentialFood =
StringTools.nonSpace(
foods[j].getAttribute("species") + "$" + foods[j].getAttribute("stage"));
if (potentialFood.equals(linkString)) found = true;
else j++;
}
if (mode == LOGGING) {
PW.print(
" Logging.writeFGReal("
+ auditSpeciesNo
+ ","
+ realVar
+ "[params._speciesOfFG]["
+ j
+ "]");
if (variableFlag) PW.println(".get());");
else PW.println(");");
} else
varID =
writeVarEntry(PW, realVar + " for " + stage + " " + species, "real", varID);
}
}
}
}
}
if (mode == LOGGING) PW.println(" }");
}
}
public static XMLTag getSpecies(String species, XMLTag model) {
return model.getTag("species").getTagWhere("species", "@name", species);
}
public static XMLTag getSpeciesNo(int i, XMLTag model) {
return model.getTag("species").getTagWhere("species", "@id", String.valueOf(i));
}