public static int writeVarEntry(PrintWriter PW, String name, String type, int varID) {
PW.println(" _var = new XMLTag(\"var\");");
PW.println(" _var.addTag(new XMLTag(\"id\",\"" + (varID++) + "\"));");
PW.println(" _var.addTag(new XMLTag(\"name\",\"" + StringTools.nonSpace(name) + "\"));");
PW.println(" _var.addTag(new XMLTag(\"desc\",\"" + name + "\"));");
PW.println(" _var.addTag(new XMLTag(\"type\",\"" + type + "\"));");
PW.println(" _fg.addTag(_var);");
return varID;
}
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 void writeLoggingJava(String fileName, XMLTag model) {
try {
PrintWriter PW = StringTools.OpenOutputFile(fileName);
PW.println(" package VEW.Sim;");
PW.println("");
PW.println("import gnu.trove.TLongHashSet;");
PW.println("import VEW.Common.Random.*;");
PW.println("import java.io.*;");
PW.println("import java.util.zip.*;");
PW.println("import VEW.Common.XML.*;");
PW.println("import VEW.Sim.Kernel;");
PW.println("import VEW.Sim.SysVars;");
PW.println("");
PW.println("import java.util.GregorianCalendar;");
PW.println("import java.util.TimeZone;");
PW.println("");
PW.println("public class Logging {");
PW.println("");
PW.println(" public static XMLFile dataFormats;");
PW.println(" private static boolean useFloats = true;");
PW.println(" private static DataOutputStream wcFile;");
PW.println(" private static DataOutputStream phFile;");
PW.println(" private static DataOutputStream biFile;");
PW.println(" private static DataOutputStream chFile;");
PW.println(" private static DataOutputStream deFile;");
PW.println(" private static DataOutputStream[] fgFiles;");
PW.println(" private static DataOutputStream[] fgTimes;");
PW.println(" private static DataOutputStream[] lineages;");
PW.println(" private static DataOutputStream[] lifespans;");
PW.println("");
PW.println(" //private static long parishTime = 0;");
PW.println(" private static TLongHashSet[] auditIDs;");
PW.println(" private static boolean auditEnabled = false;");
PW.println(" private static XMLFile auditXMLFile = null;");
PW.println(" private static long firstSnap = 0;");
PW.println(" private static long snapSpace = 0;");
PW.println(" private static boolean newSeed = false;");
PW.println(" private static boolean useSnapRead = false;");
PW.println(" private static boolean useSnapWrite = false;");
PW.println(" public static String snapFile;");
PW.println(" private static boolean zip = true;");
PW.println(" public static int snapVersion = 740;");
PW.println("");
PW.println(" private static final TimeZone GMTTimeZone = TimeZone.getTimeZone(\"GMT\");");
PW.println(
" private static final GregorianCalendar anyDate = new GregorianCalendar(GMTTimeZone);");
PW.println(
" private static final GregorianCalendar compareDate = new GregorianCalendar(GMTTimeZone);");
PW.println("");
PW.println(" private static long[] fgBytesWritten;");
PW.println("");
PW.println(" /* Constants for which file category to write */");
PW.println("");
PW.println(" public static final byte CREATE = 0;");
PW.println(" public static final byte PCHANGEPARENT = 1;");
PW.println(" public static final byte PCHANGECHILD = 2;");
PW.println(" public static final byte SPLIT = 3;");
PW.println(" public static final byte MERGE = 4;");
PW.println(" public static final byte REMOVAL = 5;");
PW.println(" public static final byte INGEST = 6;");
PW.println(" public static final byte DIVIDE = 7;");
PW.println(" public static final byte CHANGE = 8;");
PW.println("");
PW.println(" /* New variables for representing fg logging types */");
PW.println("");
PW.println(" private static boolean lineage = false;");
PW.println(" private static boolean lifespan = false;");
PW.println(" private static long startLSTime = 0;");
PW.println(" private static long stopLSTime= 0;");
PW.println("");
PW.println("");
PW.println(" public static void setLineage(boolean l, long start, long end) {");
PW.println(" lineage = l;");
PW.println(" startLSTime = start;");
PW.println(" stopLSTime = end;");
PW.println(" }");
PW.println("");
PW.println(" public static void setLifespan(boolean l, long start, long end) {");
PW.println(" lifespan = l;");
PW.println(" startLSTime = start;");
PW.println(" stopLSTime = end;");
PW.println(" }");
PW.println("");
PW.println(" public static boolean getLineage() { return lineage; }");
PW.println(" public static boolean getLifespan() { return lifespan; }");
PW.println(" public static void setZip(boolean b) { zip = b; }");
PW.println("");
PW.println(" public static void setFloat(boolean b) {");
PW.println(" useFloats = b;");
PW.println(
" if (dataFormats.getTag(\"format\")!=null) dataFormats.getTag(\"format\").removeFromParent();");
PW.println(" if (b) dataFormats.addTag(new XMLTag(\"format\",\"float\")); else");
PW.println(" dataFormats.addTag(new XMLTag(\"format\",\"double\"));");
PW.println(" dataFormats.write();");
PW.println(" }");
PW.println("");
PW.println(" /* Complete snapshot of current system state*/");
PW.println("");
PW.println(" public static boolean readingFromSnapshot() { return useSnapRead; }");
PW.println("");
PW.println(" public static void setSnap(long t1, long t2) {");
PW.println(" firstSnap = t1;");
PW.println(" snapSpace = t2;");
PW.println(" if (t2!=0) useSnapWrite = true;");
PW.println(" }");
PW.println("");
PW.println(" public static void setSnap(String s, boolean _newSeed) {");
PW.println(" snapFile = s;");
PW.println(" useSnapRead = true;");
PW.println(" newSeed = _newSeed;");
PW.println(" }");
PW.println("");
PW.println(" public static void writeSnapshot(String f) {");
PW.println(" try {");
PW.println(
" BufferedOutputStream buffered = new BufferedOutputStream(new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(f))));");
PW.println(" DataOutputStream snapshot = new DataOutputStream(buffered);");
PW.println(" final String _snap = new String(\"VEW-CP\");");
PW.println(" for (int i=0; i<6; i++) snapshot.writeChar(_snap.charAt(i));");
PW.println(" snapshot.writeInt(snapVersion);");
PW.println(" snapshot.writeLong(Kernel.myTime);");
PW.println(" ObjectOutputStream snapObj = new ObjectOutputStream(buffered);");
PW.println(" snapObj.writeObject(Utils.rnd);");
PW.println(" snapObj.flush();");
PW.println(" Kernel.W.writePhysicsSnapshot(snapshot);");
PW.println(" Kernel.W.writeBiologicalSnapshot(snapshot);");
PW.println(" snapshot.flush();");
PW.println(" snapObj.close();");
PW.println(" snapshot.close();");
PW.println(" } catch (Exception e) { e.printStackTrace();}");
PW.println(" }");
PW.println("");
PW.println(" public static void readSnapshot() {");
PW.println(" try {");
PW.println(" // Empty system");
PW.println(" Kernel.W.clearSystem();");
PW.println(" BufferedInputStream buffered = null;");
PW.println(" if (new File(snapFile).exists()) {");
PW.println(
" buffered = new BufferedInputStream(new GZIPInputStream(new BufferedInputStream(new FileInputStream(snapFile))));");
PW.println(" } else {");
PW.println(" String justFile = snapFile;");
PW.println(
" while (justFile.indexOf(\"/\")>=0) justFile=justFile.substring(justFile.indexOf(\"/\")+1);");
PW.println(
" while (justFile.indexOf(\"\\\\\")>=0) justFile=justFile.substring(justFile.indexOf(\"\\\\\")+1);");
PW.println(
" java.util.jar.JarFile JF = new java.util.jar.JarFile(Launcher.JarPath+File.separator+\"VEW.jar\");");
PW.println(" java.util.jar.JarEntry JE = JF.getJarEntry(justFile);");
PW.println(
" buffered = new BufferedInputStream(new GZIPInputStream(new BufferedInputStream(JF.getInputStream(JE))));");
PW.println(" }");
PW.println(" DataInputStream snapshot = new DataInputStream(buffered);");
PW.println(" StringBuffer s = new StringBuffer();");
PW.println(" for (int i=0; i<6; i++) s.append(snapshot.readChar());");
PW.println(" RanMT r = null;");
PW.println(" if (!s.toString().equals(\"VEW-CP\")) {");
PW.println(" System.out.println(\"Invalid snapshot\");");
PW.println(" } else {");
PW.println(" snapVersion = snapshot.readInt();");
PW.println(" System.out.println(\"Snapshot version: \"+snapVersion);");
PW.println(" SysVars._firstExecTime = snapshot.readLong();");
PW.println(" ObjectInputStream snapObj = new ObjectInputStream(buffered);");
PW.println(" r = (RanMT)snapObj.readObject();");
PW.println(" Kernel.W.readPhysicsSnapshot(snapshot);");
PW.println(" Kernel.W.readBiologicalSnapshot(snapshot);");
PW.println(" snapObj.close();");
PW.println(" snapshot.close();");
PW.println(" }");
PW.println(" if (!SysVars._seedForced) {");
PW.println(" if ((newSeed) || (r==null)) {");
PW.println(" Utils.rnd = new RanMT();");
PW.println(" Utils.rnd.setSeed(SysVars._seed);");
PW.println(" } else {");
PW.println(" Utils.rnd = r;");
PW.println(" }");
PW.println(" }");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void writeBioReal(double v) { writeReal(biFile,v); }");
PW.println(" public static void writeChemReal(double v) { writeReal(chFile,v); }");
PW.println(" public static void writeDemReal(double v) { writeReal(deFile,v); }");
PW.println(" public static void writePhyReal(double v) { writeReal(phFile,v); }");
PW.println(" public static void writeWCReal(double v) { writeReal(wcFile,v); }");
PW.println("");
PW.println(" public static void writeFGReal(int fg, double d) {");
PW.println(" writeReal(fgFiles[fg],d);");
PW.println(" if (useFloats) fgBytesWritten[fg]+=4;");
PW.println(" else fgBytesWritten[fg]+=8;");
PW.println(" }");
PW.println("");
PW.println(" public static void writeFGLong(int fg, long l) {");
PW.println(" try {");
PW.println(" fgFiles[fg].writeLong(l);");
PW.println(" fgBytesWritten[fg]+=8;");
PW.println(" } catch (Exception e) {e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void writeFGInt(int fg, int i) {");
PW.println(" try {");
PW.println(" fgFiles[fg].writeInt(i);");
PW.println(" fgBytesWritten[fg]+=4;");
PW.println(" } catch (Exception e) {e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void writeReal(DataOutputStream dos, double d) {");
PW.println(" try {");
PW.println(" if (useFloats) dos.writeFloat((float)d);");
PW.println(" else dos.writeDouble(d);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void writeLong(DataOutputStream dos, long l) {");
PW.println(" try {");
PW.println(" dos.writeLong(l);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void setLineage(int fg, String file) {");
PW.println(" if (zip) lineages[fg]=makeZip(file);");
PW.println(" else lineages[fg]=makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setLifespan(int fg, String file) {");
PW.println(" if (zip) lifespans[fg]=makeZip(file);");
PW.println(" else lifespans[fg]=makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setFgTime(int fg, String file) {");
PW.println(" if (zip) fgTimes[fg]= makeZip(file);");
PW.println(" else fgTimes[fg] = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setFgFile(int fg, String file) {");
PW.println(" if (zip) fgFiles[fg] = makeZip(file);");
PW.println(" else fgFiles[fg]= makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setWcFile(String file) {");
PW.println(" if (zip) wcFile = makeZip(file);");
PW.println(" else wcFile = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setBioFile(String file) {");
PW.println(" if (zip) biFile = makeZip(file);");
PW.println(" else biFile = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setChemFile(String file) {");
PW.println(" if (zip) chFile = makeZip(file);");
PW.println(" else chFile = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setDemFile(String file) {");
PW.println(" if (zip) deFile = makeZip(file);");
PW.println(" else deFile = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static void setPhyFile(String file) {");
PW.println(" if (zip) phFile = makeZip(file);");
PW.println(" else phFile = makeNonZip(file);");
PW.println(" }");
PW.println("");
PW.println(" public static DataOutputStream makeZip(String file) {");
PW.println(" try {");
PW.println(
" return new DataOutputStream(new BufferedOutputStream(new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(file)))));");
PW.println(" } catch (Exception e) { e.printStackTrace(); return null; }");
PW.println(" }");
PW.println("");
PW.println(" public static DataOutputStream makeNonZip(String file) {");
PW.println(" try {");
PW.println(
" return new DataOutputStream(new BufferedOutputStream(new FileOutputStream(file)));");
PW.println(" } catch (Exception e) { e.printStackTrace(); return null; }");
PW.println(" }");
PW.println("");
PW.println(" /* Perform logging */");
PW.println("");
PW.println(" public static void setAuditFile(String f) {");
PW.println(" auditEnabled = true;");
PW.println(" auditXMLFile = XMLFile.LoadFile(f);");
PW.println(" }");
PW.println("");
PW.println(" public static boolean isAuditEnabled() {");
PW.println(" return auditEnabled;");
PW.println(" }");
PW.println("");
PW.println(" public static boolean shouldLog(long pid, int fgid) {");
PW.println(" return auditIDs[fgid].contains(pid);");
PW.println(" }");
PW.println("");
PW.println(" /* Lineage format:");
PW.println("");
PW.println(" int Time (measured in Times!)");
PW.println(" byte TYPE (constant for create/pchange/split/merge/removal)");
PW.println(" long ParentID");
PW.println(" long ChildID");
PW.println(" // NEW IN 3.1");
PW.println(" int ParentStage");
PW.println(" int ChildStage");
PW.println("");
PW.println(" -> Merge: new particle assumes ParentID, with new cellcount = C1+C2.");
PW.println(" */");
PW.println("");
PW.println("");
PW.println(
" public static void writeCreateToLineage(int RegisterNo, long Time, long ParentID, long ChildID, int ParentStage, int ChildStage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(CREATE);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(ChildID);");
PW.println(" lineages[RegisterNo].writeInt(ParentStage);");
PW.println(" lineages[RegisterNo].writeInt(ChildStage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writePChangeParentToLineage(int RegisterNo, long Time, long ParentID, int ParentStage, int ChildStage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(PCHANGEPARENT);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(-1);");
PW.println(" lineages[RegisterNo].writeInt(ParentStage);");
PW.println(" lineages[RegisterNo].writeInt(ChildStage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writePChangeChildToLineage(int RegisterNo, long Time, long ParentID, long ChildID, int ParentStage, int ChildStage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(PCHANGECHILD);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(ChildID);");
PW.println(" lineages[RegisterNo].writeInt(ParentStage);");
PW.println(" lineages[RegisterNo].writeInt(ChildStage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeSplitToLineage(int RegisterNo, long Time, long ParentID, long ChildID, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(SPLIT);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(ChildID);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeMergeToLineage(int RegisterNo, long Time, long ParentID, long ChildID, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(MERGE);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(ChildID);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeRemovalToLineage(int RegisterNo, long Time, long ParentID, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lineages[RegisterNo].writeLong(Time);");
PW.println(" lineages[RegisterNo].writeByte(REMOVAL);");
PW.println(" lineages[RegisterNo].writeLong(ParentID);");
PW.println(" lineages[RegisterNo].writeLong(0);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" lineages[RegisterNo].writeInt(stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" /* LifeSpan Register format:");
PW.println("");
PW.println(" int Time");
PW.println(" byte TYPE");
PW.println(" int Reason");
PW.println(" long ID1");
PW.println(" long ID2");
PW.println(" f/d CellCount1");
PW.println(" f/d CellCount2");
PW.println("");
PW.println(" -> for ingest/divide, CellCount1 = initial, CellCount2 = after");
PW.println(" -> for change, CellCount2 = (f/d) stageNumber.");
PW.println(" */");
PW.println("");
PW.println(
" public static void writeCreateToLifespan(int RegisterNo, int Reason, long Time, long ParentID, long ChildID, double childC, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(CREATE);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(ChildID);");
PW.println(" writeReal(lifespans[RegisterNo],childC);");
PW.println(" writeReal(lifespans[RegisterNo],stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writePChangeParentToLifespan(int RegisterNo, int Reason, long Time, long ParentID, double childC, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(PCHANGEPARENT);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(-1);");
PW.println(" writeReal(lifespans[RegisterNo],childC);");
PW.println(" writeReal(lifespans[RegisterNo],stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writePChangeChildToLifespan(int RegisterNo, long Time, long ParentID, long ChildID, double childC, int stage) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(PCHANGECHILD);");
PW.println(
" lifespans[RegisterNo].writeInt(-1); // No reason available - multiple reasons merged.");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(ChildID);");
PW.println(" writeReal(lifespans[RegisterNo],childC); // Total new cell count.");
PW.println(" writeReal(lifespans[RegisterNo],stage);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeSplitToLifespan(int RegisterNo, long Time, long ParentID, long ChildID, double childC) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(SPLIT);");
PW.println(" lifespans[RegisterNo].writeInt(-1);");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(ChildID);");
PW.println(" writeReal(lifespans[RegisterNo],childC);");
PW.println(" writeReal(lifespans[RegisterNo],0.0);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeMergeToLifespan(int RegisterNo, long Time, long ParentID, long ChildID, double childC1, double childC2) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(MERGE);");
PW.println(" lifespans[RegisterNo].writeInt(-1);");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(ChildID);");
PW.println(" writeReal(lifespans[RegisterNo],childC1);");
PW.println(" writeReal(lifespans[RegisterNo],childC2);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeRemovalToLifespan(int RegisterNo, int Reason, long Time, long ParentID, double childC1) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(REMOVAL);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ParentID);");
PW.println(" lifespans[RegisterNo].writeLong(-1);");
PW.println(" writeReal(lifespans[RegisterNo],childC1);");
PW.println(" writeReal(lifespans[RegisterNo],-1);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeIngestToLifespan(int RegisterNo, int Reason, long Time, long ID, double C1, double C2) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(INGEST);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ID);");
PW.println(" lifespans[RegisterNo].writeLong(0);");
PW.println(" writeReal(lifespans[RegisterNo],C1);");
PW.println(" writeReal(lifespans[RegisterNo],C2);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeDivideToLifespan(int RegisterNo, int Reason, long Time, long ID, double C1, double C2) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(DIVIDE);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ID);");
PW.println(" lifespans[RegisterNo].writeLong(0);");
PW.println(" writeReal(lifespans[RegisterNo],C1);");
PW.println(" writeReal(lifespans[RegisterNo],C2);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(
" public static void writeChangeToLifespan(int RegisterNo, int Reason, long Time, long ID, double C1, int S) {");
PW.println(" if ((Time>=startLSTime) && (Time<=stopLSTime)) try {");
PW.println(" lifespans[RegisterNo].writeLong(Time);");
PW.println(" lifespans[RegisterNo].writeByte(CHANGE);");
PW.println(" lifespans[RegisterNo].writeInt(Reason);");
PW.println(" lifespans[RegisterNo].writeLong(ID);");
PW.println(" lifespans[RegisterNo].writeLong(0);");
PW.println(" writeReal(lifespans[RegisterNo],C1);");
PW.println(" writeReal(lifespans[RegisterNo],S);");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static boolean isYearlyTime(long freq, long after, long until) {");
PW.println(" // True if the current time is between after and until, but disregard year.");
PW.println(" anyDate.setTimeInMillis(after);");
PW.println(" anyDate.set(GregorianCalendar.YEAR,1960);");
PW.println(" final long start1960=anyDate.getTimeInMillis();");
PW.println(" anyDate.setTimeInMillis(until);");
PW.println(" anyDate.set(GregorianCalendar.YEAR,1960);");
PW.println(" final long end1960=anyDate.getTimeInMillis();");
PW.println(" anyDate.setTimeInMillis(Kernel.myTime);");
PW.println(" anyDate.set(GregorianCalendar.YEAR,1960);");
PW.println(" final long now1960=anyDate.getTimeInMillis();");
PW.println(" if ((now1960<start1960) || (now1960>end1960)) return false;");
PW.println(
" else return (((Kernel.myTime-SysVars.startTime) % (freq * SysVars.stepInMillis))==0);");
PW.println(" }");
PW.println("");
PW.println(" public static void writeTimes() {");
PW.println(" for (int i=0; i<fgTimes.length; i++)");
PW.println(" if (fgTimes[i]!=null) writeLong(fgTimes[i],fgBytesWritten[i]);");
PW.println(" }");
PW.println("");
PW.println(" public static String unitToTex(String u) {");
PW.println(" String pre = \"\";");
PW.println(" String code = \"\";");
PW.println(" String exp = \"\";");
PW.println(" String theunit = \"\";");
PW.println(" while (u.length()>0) {");
PW.println(" pre = u.substring(0,u.indexOf(\",\"));");
PW.println(" u = u.substring(u.indexOf(\",\")+1);");
PW.println(" code = u.substring(0,u.indexOf(\",\"));");
PW.println(" u = u.substring(u.indexOf(\",\")+1);");
PW.println(" if (u.indexOf(\",\")>=1) {");
PW.println(" exp = u.substring(0,u.indexOf(\",\"));");
PW.println(" u= u.substring(u.indexOf(\",\")+1);");
PW.println(" } else {");
PW.println(" exp = u;");
PW.println(" u = \"\";");
PW.println(" }");
PW.println(" if (pre.equals(\"-12\")) pre = \"p\";");
PW.println(" else if (pre.equals(\"-9\")) pre = \"n\";");
PW.println(" else if (pre.equals(\"-6\")) pre = \"\\\\mu\";");
PW.println(" else if (pre.equals(\"-3\")) pre = \"m\";");
PW.println(" else if (pre.equals(\"12\")) pre = \"A\";");
PW.println(" else if (pre.equals(\"9\")) pre = \"G\";");
PW.println(" else if (pre.equals(\"6\")) pre = \"M\";");
PW.println(" else if (pre.equals(\"3\")) pre = \"K\";");
PW.println(" else pre = \"\";");
PW.println(" if (!exp.equals(\"1\")) exp = \"{\"+exp+\"}\";");
PW.println(" if (exp.equals(\"1\")) exp = \"\";");
PW.println(" if (!exp.equals(\"9\")) theunit +=pre+code+exp;");
PW.println("");
PW.println(" }");
PW.println(" return theunit;");
PW.println(" }");
PW.println("");
PW.println(" public static void checkWriteSnap() {");
PW.println(" if (useSnapWrite) {");
PW.println(
" if ((Kernel.myTime>=firstSnap) && (((Kernel.myTime-firstSnap)%snapSpace)==0)) {");
PW.println(" writeSnapshot(Launcher.JarPath+File.separator+\"snap.\"+Kernel.myTime);");
PW.println(" //System.out.println(\"Snap shot write : myTime = \"+Kernel.myTime);");
PW.println(" //System.out.println(\"FIRST SNAP: \"+firstSnap);");
PW.println(" //System.out.println(\"snapSPACE = \"+snapSpace);");
PW.println(
" //System.out.println(\"Timestep = \"+Kernel.timeSteps+\" just written\");");
PW.println(" }");
PW.println(" }");
PW.println(" }");
PW.println("");
PW.println(" public static boolean isTime(long freq, long after, long until) {");
PW.println(" if ((Kernel.myTime<after) || (Kernel.myTime>until)) return false;");
PW.println(" else return (((Kernel.myTime-SysVars.startTime) % freq)==0);");
PW.println(" }");
PW.println("");
PW.println(" public static boolean isYearlyInterval(int years, long after, long until) {");
PW.println(" if ((Kernel.myTime<after) || (Kernel.myTime>until)) return false;");
PW.println(" else if (Kernel.myTime==after) return true;");
PW.println(" else {");
PW.println(" compareDate.setTimeInMillis(after);");
PW.println(" long compareMillis = Kernel.myTime;");
PW.println(" while (compareMillis<=until) {");
PW.println(" compareDate.add(GregorianCalendar.YEAR,years);");
PW.println(" compareMillis=compareDate.getTimeInMillis();");
PW.println(" if (Kernel.myTime==compareMillis) return true;");
PW.println(" }");
PW.println(" }");
PW.println(" return false;");
PW.println(" }");
PW.println("");
PW.println(" public static void update() {");
PW.println(" writeTimes();");
PW.println(" SysVars.logPhyFieldData();");
PW.println(" SysVars.logBioFieldData();");
PW.println(" SysVars.logChemFieldData();");
PW.println(" SysVars.logDemFieldData();");
PW.println(" SysVars.logColData();");
PW.println(" }");
PW.println("");
PW.println(" public static void init(int speciesCount) {");
PW.println(" fgBytesWritten = new long[speciesCount];");
PW.println(
" dataFormats = new XMLFile(Launcher.JarPath+File.separator+\"DataFormats.xml\",\"dataformat\");");
PW.println(" dataFormats.addTag(new XMLTag(\"version\",\"1.1\"));");
PW.println("");
PW.println(" /* Initialise IDs for audits */");
PW.println("");
PW.println(" if (Logging.isAuditEnabled()) {");
PW.println(" auditIDs = new TLongHashSet[speciesCount];");
PW.println(" for (int i=0; i<speciesCount; i++) {");
PW.println(" String name = Kernel.getSpecies(i).name();");
PW.println(" TLongHashSet ids = new TLongHashSet();");
PW.println(
" XMLTag fgAudit = auditXMLFile.getTagWhere(\"functionalgroup\", \"name\", name);");
PW.println(" if (fgAudit != null) {");
PW.println(" XMLTag[] idList = fgAudit.getTags(\"group/id\");");
PW.println(" if (idList != null) {");
PW.println(" for (int j = 0; j < idList.length; j++) {");
PW.println(" ids.add(Integer.parseInt(idList[j].getValue()));");
PW.println(" }");
PW.println(" }");
PW.println("");
PW.println(" idList = fgAudit.getTags(\"group/descendants/id\");");
PW.println(" if (idList != null) {");
PW.println(" for (int j = 0; j < idList.length; j++) {");
PW.println(" ids.add(Integer.parseInt(idList[j].getValue()));");
PW.println(" }");
PW.println(" }");
PW.println(" }");
PW.println("");
PW.println(" auditIDs[i] = ids;");
PW.println(" }");
PW.println(" }");
PW.println("");
PW.println(" fgFiles = new DataOutputStream[speciesCount];");
PW.println(" fgTimes = new DataOutputStream[speciesCount];");
PW.println(" if (lineage) lineages = new DataOutputStream[speciesCount];");
PW.println(" if (lifespan) lifespans = new DataOutputStream[speciesCount];");
PW.println(" dataFormats.addTag(\"deathreasons\");");
PW.println(" dataFormats.addTag(\"states\");");
PW.println(" SysVars.InitDeathReasons(dataFormats.getTag(\"dataformat/deathreasons\"));");
PW.println(" SysVars.InitStates(dataFormats.getTag(\"dataformat/states\"));");
PW.println(" SysVars.initColData();");
PW.println(" SysVars.initBioFieldData();");
PW.println(" SysVars.initChemFieldData();");
PW.println(" SysVars.initDemFieldData();");
PW.println(" SysVars.initPhyFieldData();");
PW.println(" dataFormats.write();");
PW.println(" }");
PW.println("");
PW.println(" public static void flush() {");
PW.println(" try {");
PW.println(" if (wcFile!=null) wcFile.flush();");
PW.println(" if (phFile!=null) phFile.flush();");
PW.println(" if (biFile!=null) biFile.flush();");
PW.println(" if (deFile!=null) deFile.flush();");
PW.println(" if (chFile!=null) chFile.flush();");
PW.println(" for (int i=0; i<fgFiles.length; i++) {");
PW.println(" if (fgFiles[i]!=null) fgFiles[i].flush();");
PW.println(" if (fgTimes[i]!=null) fgTimes[i].flush();");
PW.println(" }");
PW.println(
" if (lifespan) for (int i=0; i<lifespans.length; i++) lifespans[i].flush();");
PW.println(" if (lineage) for (int i=0; i<lineages.length; i++) lineages[i].flush();");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("");
PW.println(" public static void close() {");
PW.println(" try {");
PW.println(" flush();");
PW.println(" if (wcFile!=null) wcFile.close();");
PW.println(" if (phFile!=null) phFile.close();");
PW.println(" if (biFile!=null) biFile.close();");
PW.println(" if (deFile!=null) deFile.close();");
PW.println(" if (chFile!=null) chFile.close();");
PW.println(" for (int i=0; i<fgFiles.length; i++) {");
PW.println(" if (fgFiles[i]!=null) fgFiles[i].close();");
PW.println(" if (fgTimes[i]!=null) fgTimes[i].close();");
PW.println(" }");
PW.println(
" if (lifespan) for (int i=0; i<lifespans.length; i++) lifespans[i].close();");
PW.println(" if (lineage) for (int i=0; i<lineages.length; i++) lineages[i].close();");
PW.println(" } catch (Exception e) { e.printStackTrace(); }");
PW.println(" }");
PW.println("}");
PW.flush();
PW.close();
} catch (Exception e) {
e.printStackTrace();
}
}
