/**
* Set <CODE>Vector</CODE> of <CODE>String</CODE>s describing the cursor location from the cursor
* location; this is invoked when the cursor location changes or the cursor display status changes
*/
public void setCursorStringVector() {
synchronized (cursorStringVector) {
cursorStringVector.removeAllElements();
float[][] cursor = new float[3][1];
double[] cur = getCursor();
cursor[0][0] = (float) cur[0];
cursor[1][0] = (float) cur[1];
cursor[2][0] = (float) cur[2];
Enumeration maps = display.getMapVector().elements();
while (maps.hasMoreElements()) {
try {
ScalarMap map = (ScalarMap) maps.nextElement();
DisplayRealType dreal = map.getDisplayScalar();
DisplayTupleType tuple = dreal.getTuple();
int index = dreal.getTupleIndex();
if (tuple != null
&& (tuple.equals(Display.DisplaySpatialCartesianTuple)
|| (tuple.getCoordinateSystem() != null
&& tuple
.getCoordinateSystem()
.getReference()
.equals(Display.DisplaySpatialCartesianTuple)))) {
float[] fval = new float[1];
if (tuple.equals(Display.DisplaySpatialCartesianTuple)) {
fval[0] = cursor[index][0];
} else {
float[][] new_cursor = tuple.getCoordinateSystem().fromReference(cursor);
fval[0] = new_cursor[index][0];
}
float[] dval = map.inverseScaleValues(fval);
RealType real = (RealType) map.getScalar();
// WLH 31 Aug 2000
Real r = new Real(real, dval[0]);
Unit overrideUnit = map.getOverrideUnit();
Unit rtunit = real.getDefaultUnit();
// units not part of Time string
// DRM 2003-08-19: don't check for equality since toString
// may be different
if (overrideUnit != null
&& // !overrideUnit.equals(rtunit) &&
(!Unit.canConvert(rtunit, CommonUnit.secondsSinceTheEpoch)
|| rtunit.getAbsoluteUnit().equals(rtunit))) {
dval[0] = (float) overrideUnit.toThis((double) dval[0], rtunit);
r = new Real(real, dval[0], overrideUnit);
}
String valueString = r.toValueString();
// WLH 27 Oct 2000
String s = map.getScalarName() + " = " + valueString;
// String s = real.getName() + " = " + valueString;
cursorStringVector.addElement(s);
} // end if (tuple != null && ...)
} catch (VisADException e) {
}
} // end while(maps.hasMoreElements())
} // end synchronized (cursorStringVector)
render_trigger();
}
public void convertToBaf(JimpleToBafContext context, List<Unit> out) {
Unit u = Baf.v().newLoadInst(getType(), context.getBafLocalOfJimpleLocal(this));
out.add(u);
Iterator it = context.getCurrentUnit().getTags().iterator();
while (it.hasNext()) {
u.addTag((Tag) it.next());
}
}
public void convertToBaf(JimpleToBafContext context, List out) {
Unit u = Baf.v().newStaticGetInst(fieldRef);
out.add(u);
Iterator it = context.getCurrentUnit().getTags().iterator();
while (it.hasNext()) {
u.addTag((Tag) it.next());
}
}
public final void visitUnit(final Unit unit) {
float z_offset =
getVisuallyCorrectHeight(unit.getPositionX(), unit.getPositionY()) + unit.getOffsetZ();
visitSelectable(
unit_visitor,
unit,
z_offset,
unit.getUnitTemplate().getSelectionRadius(),
unit.getUnitTemplate().getSelectionHeight());
}
public void attack(Unit enemy) {
if (heatCounter >= heat) {
fireX = enemy.getX();
fireY = enemy.getY();
enemy.freeze(level * 2.0);
effects.add(new CircleTowerEffect(fireX, fireY, Global.MAX_SIZE, 100));
}
}
/**
* Produces a string representation of the puzzle, this shall be a 9 columns and 9 rows in size,
* separated by new line characters.
*
* @return A string representation of this puzzle.
*/
public String toString() {
String out = new String();
for (Unit x : rows) {
out += x.toString() + "\n";
}
return out;
}
public String toString() {
Iterator it = unitChain.iterator();
StringBuffer buf = new StringBuffer();
while (it.hasNext()) {
Unit u = (Unit) it.next();
buf.append("// preds: " + getPredsOf(u) + "\n");
buf.append(u.toString() + '\n');
buf.append("// succs " + getSuccsOf(u) + "\n");
}
return buf.toString();
}
@Override
public List<Unit> getPredsOf(Unit unit) {
if (unit.equals(nIf)) {
return Collections.emptyList();
} else if (unit.equals(n1)) {
return Collections.singletonList(nIf);
} else if (unit.equals(n2)) {
return Collections.singletonList(nIf);
} else {
throw new RuntimeException("UNEXPECTED CASE");
}
}
public void convertToBaf(JimpleToBafContext context, List<Unit> out) {
((ConvertToBaf) getOp()).convertToBaf(context, out);
Unit u;
out.add(u = Baf.v().newThrowInst());
Unit currentUnit = this;
Iterator it = currentUnit.getTags().iterator();
while (it.hasNext()) {
u.addTag((Tag) it.next());
}
}
private int addJimpleLnTags(int lnNum, Unit stmt, int endLn) {
if (endLn - lnNum <= 1) {
stmt.addTag(new JimpleLineNumberTag(lnNum));
// G.v().out.println(stmt.getClass().toString());
lnNum++;
return lnNum;
} else {
stmt.addTag(new JimpleLineNumberTag(lnNum, endLn));
// G.v().out.println("multi-line: "+stmt.getClass().toString());
endLn++;
return endLn;
}
}
/**
* Set display Unit to override default Unit of Scalar; MUST be called before any data are
* displayed
*
* @param unit unit that data will be displayed with
* @throws VisADException <CODE>unit</CODE> is not convertable with the default unit or scalar is
* not a RealType.
*/
public void setOverrideUnit(Unit unit) throws VisADException {
if (!(Scalar instanceof RealType)) {
throw new UnitException("Scalar is not RealType");
}
Unit rtunit = ((RealType) Scalar).getDefaultUnit();
if (!Unit.canConvert(unit, rtunit)) {
throw new UnitException("unit not convertable with RealType default");
}
if (unit != null) {
overrideUnit = unit;
override_offset = overrideUnit.toThis(0.0, rtunit);
override_scale = overrideUnit.toThis(1.0, rtunit) - override_offset;
}
}
/**
* Traverse the statements in the given body, looking for aggregation possibilities; that is,
* given a def d and a use u, d has no other uses, u has no other defs, collapse d and u.
*
* <p>option: only-stack-locals; if this is true, only aggregate variables starting with $
*/
protected void internalTransform(Body b, String phaseName, Map<String, String> options) {
StmtBody body = (StmtBody) b;
boolean onlyStackVars = PhaseOptions.getBoolean(options, "only-stack-locals");
int aggregateCount = 1;
if (Options.v().time()) Timers.v().aggregationTimer.start();
boolean changed = false;
Map<ValueBox, Zone> boxToZone =
new HashMap<ValueBox, Zone>(body.getUnits().size() * 2 + 1, 0.7f);
// Determine the zone of every box
{
Zonation zonation = new Zonation(body);
for (Unit u : body.getUnits()) {
Zone zone = zonation.getZoneOf(u);
for (ValueBox box : u.getUseBoxes()) {
boxToZone.put(box, zone);
}
for (ValueBox box : u.getDefBoxes()) {
boxToZone.put(box, zone);
}
}
}
do {
if (Options.v().verbose())
G.v()
.out
.println(
"["
+ body.getMethod().getName()
+ "] Aggregating iteration "
+ aggregateCount
+ "...");
// body.printTo(new java.io.PrintWriter(G.v().out, true));
changed = internalAggregate(body, boxToZone, onlyStackVars);
aggregateCount++;
} while (changed);
if (Options.v().time()) Timers.v().aggregationTimer.end();
}
/**
* Performs the test function.
*
* @param ctx query context
* @return resulting value
* @throws QueryException query exception
*/
private Item test(final QueryContext ctx) throws QueryException {
final Unit unit = new Unit(ctx, info);
if (expr.length == 0) return unit.test(sc);
final ArrayList<StaticFunc> funcs = new ArrayList<>();
final Iter ir = ctx.iter(expr[0]);
for (Item it; (it = ir.next()) != null; ) {
final FItem fi = checkFunc(it, ctx);
if (fi.funcName() != null) {
final StaticFunc sf = ctx.funcs.get(fi.funcName(), fi.arity(), null, true);
if (sf != null) funcs.add(sf);
}
}
return unit.test(sc, funcs);
}
public final void markDetailPolygon(ElementRenderState render_state, int level) {
Unit unit = (Unit) render_state.model;
super.markDetailPolygon(render_state, level);
UnitSupplyContainer supply_container = unit.getSupplyContainer();
if (!render_state.render_state.isPicking()
&& unit.getAbilities().hasAbilities(Abilities.BUILD)
&& supply_container.getSupplyType() != null) {
if (supply_container.getNumSupplies() > 0) {
SpriteRenderer supply_sprite =
render_state.getRenderer(
supply_container.getSupplySpriteRenderer(supply_container.getSupplyType()));
supply_sprite.addToRenderList(level, render_state, false);
}
}
}
public void convertToBaf(JimpleToBafContext context, List out) {
for (int i = 0; i < argBoxes.size(); i++) {
((ConvertToBaf) (getArg(i))).convertToBaf(context, out);
}
Unit u;
out.add(u = Baf.v().newStaticInvokeInst(methodRef));
Unit currentUnit = context.getCurrentUnit();
Iterator it = currentUnit.getTags().iterator();
while (it.hasNext()) {
u.addTag((Tag) it.next());
}
}
/**
* return an array of display (DisplayRealType) values by linear scaling (if applicable) the
* data_values array (RealType values); results are scaled by the given scale factor
*
* @param values to scale as bytes
* @return array of display values
*/
public byte[] scaleValues(byte[] values, int factor) throws VisADException {
if (values == null) return null;
byte[] new_values = null;
if (badRange()) {
new_values = new byte[values.length];
} else {
if (overrideUnit != null && !overrideUnit.equals(((RealType) Scalar).getDefaultUnit())) {
throw new VisADException("scaleValues(byte[]): non-default units not supported");
}
if (isScaled) {
new_values = new byte[values.length];
for (int i = 0; i < values.length; i++) {
float v = (float) values[i];
if (v < 0) v += 256;
v = (float) (factor * (offset + scale * v));
if (v < 0) v = 0;
else if (v > 255) v = 255;
new_values[i] = (byte) v;
}
} else {
new_values = values;
}
}
return new_values;
}
/**
* return an array of data (RealType) values by inverse linear scaling (if applicable) the
* display_values array (DisplayRealType values); this is useful for direct manipulation and
* cursor labels
*
* @param values display values
* @param newArray false to transform in place
* @return data values
*/
public float[] inverseScaleValues(float[] values, boolean newArray) {
if (values == null) return null;
float[] new_values = (newArray) ? new float[values.length] : values;
if (isScaled) {
for (int i = 0; i < values.length; i++) {
if (values[i] == values[i]) {
new_values[i] = (float) ((values[i] - offset) / scale);
} else {
new_values[i] = Float.NaN;
}
}
} else {
if (newArray) {
for (int i = 0; i < values.length; i++) {
new_values[i] = values[i];
}
}
}
// WLH 31 Aug 2000
if (overrideUnit != null) {
// float[] old_values = new_values;
try {
new_values =
overrideUnit.toThat(
new_values, ((RealType) Scalar).getDefaultUnit(), false); // already copied above
} catch (UnitException e) {
}
/*
System.out.println("inverse values = " + values[0] + " " + old_values[0] + " " +
new_values[0]);
*/
}
return new_values;
}
/**
* return an array of display (DisplayRealType) values by linear scaling (if applicable) the
* data_values array (RealType values)
*
* @param values to scale as floats
* @param newArray false to scale in place
* @return array of display values
*/
public float[] scaleValues(float[] values, boolean newArray) {
/* WLH 23 June 99
if (values == null || badRange()) return null;
*/
if (values == null) return null;
float[] new_values = null;
if (badRange()) {
new_values = (newArray) ? new float[values.length] : values;
for (int i = 0; i < values.length; i++) new_values[i] = Float.NaN;
} else {
// float[] old_values = values;
// WLH 31 Aug 2000
// if (overrideUnit != null) {
// DRM 11 Jun 2003
if (overrideUnit != null && !overrideUnit.equals(((RealType) Scalar).getDefaultUnit())) {
try {
values = overrideUnit.toThis(values, ((RealType) Scalar).getDefaultUnit(), newArray);
} catch (UnitException e) {
}
}
if (isScaled) {
new_values = (newArray) ? new float[values.length] : values;
for (int i = 0; i < values.length; i++) {
if (values[i] == values[i]) {
new_values[i] = (float) (offset + scale * values[i]);
} else {
new_values[i] = Float.NaN;
}
}
} else {
new_values = values;
}
/*
if (overrideUnit != null) {
System.out.println("values = " + old_values[0] + " " + values[0] + " " +
new_values[0]);
}
*/
}
/* SRE 27 Oct 99
System.out.println(
"ScalarMap.scaleValues(double[]): values[0] = " + values[0] +
"; new_values[0] = " + new_values[0]);
*/
return new_values;
}
public void finishedSelectingUnits(TilePanel tilePanel, List<Unit> chosenUnits) {
UnitActionDetector unitActionDetector =
new UnitActionDetector(selectedPanel, selectedUnit, tilePanel, chosenUnits);
if (unitActionDetector.isSelectingUnit()) {
selectedPanel = tilePanel;
selectedPanel.addTileStateFromKey(selectedStateKey);
repaintPanels(selectedPanel);
selectedUnit = getUnit(chosenUnits);
selectValidMovements(selectedPanel.getTile(), selectedUnit);
} else if (unitActionDetector.isDeselectingUnit()) {
selectedPanel.removeTileStateFromKey(selectedStateKey);
deselectValidMovements(selectedPanel.getTile(), selectedUnit);
repaintPanels(selectedPanel);
selectedPanel = null;
selectedUnit = null;
} else if (unitActionDetector.isMovingUnit()) {
Position from = selectedPanel.getTile().getPosition();
Position to = tilePanel.getTile().getPosition();
if (movementStrategy.isValidMove(selectedUnit, from, to, unitMap)) {
deselectValidMovements(selectedPanel.getTile(), selectedUnit);
selectedPanel.removeTileStateFromKey(selectedStateKey);
List<Unit> units = unitMap.get(to);
if (units != null && !units.isEmpty()) {
Unit defending = units.get(0);
BattleStrategy strategy =
battleStrategyConfiguration.getBattleStrategy(
selectedUnit, defending, selectedPanel.getTile(), tilePanel.getTile());
Unit winner = strategy.getWinner(selectedUnit, defending);
if (winner.equals(selectedUnit)) {
units.remove(defending);
}
}
board.move(selectedUnit, from, to);
repaintPanels(selectedPanel);
selectedPanel = null;
selectedUnit = null;
}
}
frame.setEnabled(true);
resetPositions();
}
/**
* Utility method for <tt>UnitGraph</tt> constructors. It computes the edges corresponding to
* unexceptional control flow.
*
* @param unitToSuccs A {@link Map} from {@link Unit}s to {@link List}s of {@link Unit}s. This is
* an ``out parameter''; callers must pass an empty {@link Map}.
* <tt>buildUnexceptionalEdges</tt> will add a mapping for every <tt>Unit</tt> in the body to
* a list of its unexceptional successors.
* @param unitToPreds A {@link Map} from {@link Unit}s to {@link List}s of {@link Unit}s. This is
* an ``out parameter''; callers must pass an empty {@link Map}.
* <tt>buildUnexceptionalEdges</tt> will add a mapping for every <tt>Unit</tt> in the body to
* a list of its unexceptional predecessors.
*/
protected void buildUnexceptionalEdges(Map unitToSuccs, Map unitToPreds) {
// Initialize the predecessor sets to empty
for (Iterator unitIt = unitChain.iterator(); unitIt.hasNext(); ) {
unitToPreds.put(unitIt.next(), new ArrayList());
}
Iterator unitIt = unitChain.iterator();
Unit currentUnit, nextUnit;
nextUnit = unitIt.hasNext() ? (Unit) unitIt.next() : null;
while (nextUnit != null) {
currentUnit = nextUnit;
nextUnit = unitIt.hasNext() ? (Unit) unitIt.next() : null;
List successors = new ArrayList();
if (currentUnit.fallsThrough()) {
// Add the next unit as the successor
if (nextUnit != null) {
successors.add(nextUnit);
((List) unitToPreds.get(nextUnit)).add(currentUnit);
}
}
if (currentUnit.branches()) {
for (Iterator targetIt = currentUnit.getUnitBoxes().iterator(); targetIt.hasNext(); ) {
Unit target = ((UnitBox) targetIt.next()).getUnit();
// Arbitrary bytecode can branch to the same
// target it falls through to, so we screen for duplicates:
if (!successors.contains(target)) {
successors.add(target);
((List) unitToPreds.get(target)).add(currentUnit);
}
}
}
// Store away successors
unitToSuccs.put(currentUnit, successors);
}
}
/**
* This method return the the sum of duplicate values in each unit.
*
* <p>Each unit may contain each number 1 to 9 once. The conflict count is incremented by 1 each
* time a number occurs more than once in a unit. So if a unit contains [1,3,4,1,1], its conflict
* count is 2.
*
* @return The the sum of duplicate values in each unit.
*/
public Integer conflictCount() {
if (modified) {
conflicts = 0;
for (Unit x : rows) {
conflicts += x.conflictCount();
}
for (Unit x : cols) {
conflicts += x.conflictCount();
}
for (Unit x : boxes) {
conflicts += x.conflictCount();
}
}
return conflicts;
}
/** @param args the command line arguments */
public static void main(String[] args) {
// TODO code application logic here
Model model;
String insertstmt;
String insertmodel = "",
insertspecies = "",
insertcompartment = "",
insertfunction = "",
insertunitdef = "",
insertunits = "",
insertreaction = "",
insertreactant = "",
insertproduct = "";
String insertmodifier = "",
insertklaw = "",
insertrules = "",
insertconstraint = "",
insertdelay = "",
inserttrigger = "",
insertevent = "",
inserteventassign = "",
insertparameter = "";
String insertstatement = "";
String server, user, password, dbname, filepath;
String Filedata = "";
String cwd = System.getProperty("user.dir");
if (args.length == 0) {
server = "localhost";
user = "******";
password = "******";
dbname = "sbmldb2";
/**
* Path to extract the SBML files from database, where cwd is
* "github\db2sbml\dbtosbml_standalone_Project\dbtosbml" so add a folder in this directory and
* mention folder name instead of extractedbm folder
*/
filepath = cwd + "\\extractedbm\\";
} else {
server = args[0];
user = args[1];
password = args[2];
dbname = args[3];
filepath = args[4];
}
try {
Filedata = readFileAsString(cwd + "\\sbmldbschema.sql");
} catch (Exception e) {
e.printStackTrace();
}
Mysqlconn sql = new Mysqlconn(server, user, password, dbname);
// String modelids.getId() = "MorrisonAllegra" ;
ASTNode math = null;
int level = 0, version = 0;
ArrayList<modellist> modelidlist = sql.getmodels();
insertstatement =
"LOCK TABLES `model` WRITE,`species` WRITE,`compartment` WRITE,`functiondefinition` WRITE,";
insertstatement =
insertstatement
+ "`listofunitdefinitions` WRITE,`listofunits` WRITE,`reaction` WRITE,`simplespeciesreference` WRITE,";
insertstatement =
insertstatement
+ "`modifierspeciesreference` WRITE,`kineticlaw` WRITE,`parameter` WRITE,`sbmlconstraint` WRITE,";
insertstatement =
insertstatement
+ "`event` WRITE,`sbmltrigger` WRITE,`delay` WRITE,`eventassignment` WRITE,`rules` WRITE"
+ ";";
for (modellist modelids : modelidlist) {
ArrayList<modellist> modellevel = sql.getmodeldetails(modelids.getId());
for (modellist modellv : modellevel) {
level = modellv.getlevel();
version = modellv.getversion();
}
SBMLDocument doc = new SBMLDocument(level, version);
ArrayList<modellist> modellists = sql.getmodeldetails(modelids.getId());
if (!modellists.isEmpty())
insertmodel =
insertmodel
+ "\nInsert Into model (id, name,SBML_level,version,notes,annotation) Values";
for (modellist models : modellists) {
insertmodel =
insertmodel
+ "(\'"
+ models.getId()
+ "\',\'"
+ models.getName()
+ "\',"
+ models.getlevel()
+ ","
+ models.getversion()
+ ",\'"
+ models.getnotes()
+ "\',\'"
+ models.getannotation().toString()
+ "\'),";
model = doc.createModel(models.getId());
model.setName(models.getName());
// System.out.println("model : " + models.getId());
// model.setNotes(models.getnotes()); // there is some null exception is command line run
// but run perfectly from netbeans so ommented out
if (!models.getannotation().equals("")) {
Annotation annot = new Annotation(models.getannotation().toString());
model.setAnnotation(annot);
}
doc.setModel(model);
}
if (!modellists.isEmpty()) {
insertmodel = insertmodel.substring(0, insertmodel.length() - 1);
insertmodel = insertmodel + ';';
}
// insertmodel = insertmodel + "\nUNLOCK TABLES;";
// System.out.println(insertmodel);
ArrayList<SpeciesList> specieslist = sql.getspecies(modelids.getId());
if (!specieslist.isEmpty())
insertspecies =
insertspecies
+ "\nInsert Into species (id, name, compartment, initialAmount, initialConcentration,substanceUnits,hasOnlySubstanceUnits,boundaryCondition,constant,conversionFactor,model_id,annotation) Values";
for (SpeciesList species : specieslist) {
insertspecies =
insertspecies
+ "(\'"
+ species.getId()
+ "\',\'"
+ species.getName()
+ "\',\'"
+ species.getcompartment()
+ "\',"
+ species.getia()
+ ","
+ species.getic()
+ ",\'"
+ species.getsu()
+ "\',"
+ species.gethosu()
+ ","
+ species.getbc()
+ ","
+ species.getconstant()
+ ","
+ species.getcf()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ species.getannotation()
+ "\'),";
Species sp = doc.getModel().createSpecies(species.getId());
sp.setName(species.getName());
sp.setCompartment(species.getcompartment());
sp.setConstant(species.getconstant());
sp.setInitialAmount(species.getia());
sp.setInitialConcentration(species.getic());
sp.setHasOnlySubstanceUnits(species.gethosu());
if (doc.getModel().getLevel() == 3) sp.setConversionFactor(species.getcf());
sp.setBoundaryCondition(species.getbc());
sp.setSubstanceUnits(species.getsu());
if (!species.getannotation().equals("")) {
Annotation annot = new Annotation(species.getannotation().toString());
sp.setAnnotation(annot);
}
// doc.getModel().addSpecies(sp) ;
}
if (!specieslist.isEmpty()) {
insertspecies = insertspecies.substring(0, insertspecies.length() - 1);
insertspecies = insertspecies + ';';
}
ArrayList<CompartmentList> complist = sql.getcompartments(modelids.getId());
if (!complist.isEmpty())
insertcompartment =
insertcompartment
+ "\nInsert Into compartment (id, name,constant,model_id,spacialDimensions,size,units) Values";
for (CompartmentList comp : complist) {
insertcompartment =
insertcompartment
+ "(\'"
+ comp.getId()
+ "\',\'"
+ comp.getName()
+ "\',"
+ comp.getconstant()
+ ",\'"
+ modelids.getId()
+ "\',"
+ comp.getspatialdimensions()
+ ","
+ comp.getsize()
+ ","
+ comp.getunits()
+ "\'),";
Compartment c = doc.getModel().createCompartment(comp.getId());
c.setName(comp.getName());
c.setConstant(comp.getconstant());
c.setSize(comp.getsize());
c.setSpatialDimensions(comp.getspatialdimensions());
if (comp.getspatialdimensions() != 0) c.setUnits(comp.getunits());
// doc.getModel().addSpecies(sp) ;
}
if (!complist.isEmpty()) {
insertcompartment = insertcompartment.substring(0, insertcompartment.length() - 1);
insertcompartment = insertcompartment + ';';
}
ArrayList<functionList> funclist = sql.getfunctions(modelids.getId());
if (!funclist.isEmpty())
insertfunction =
insertfunction + "\nInsert Into functiondefinition (id, xmlns,model_id) Values";
for (functionList func : funclist) {
insertfunction =
insertfunction
+ "(\'"
+ func.getId()
+ "\',\'"
+ func.getxmlns()
+ "\',\'"
+ modelids.getId()
+ "\'),";
FunctionDefinition fd = doc.getModel().createFunctionDefinition(func.getId());
try {
math = ASTNode.parseFormula(func.getxmlns());
fd.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!funclist.isEmpty()) {
insertfunction = insertfunction.substring(0, insertfunction.length() - 1);
insertfunction = insertfunction + ';';
}
ArrayList<unitList> unitlist = sql.getunitlist(modelids.getId());
if (!unitlist.isEmpty())
insertunitdef =
insertunitdef + "\nInsert Into listofunitdefinitions (id,name,model_id) Values";
for (unitList units : unitlist) {
insertunitdef =
insertunitdef
+ "(\'"
+ units.getId()
+ "\',\'"
+ units.getName()
+ "\',\'"
+ modelids.getId()
+ "\'),";
UnitDefinition ud = doc.getModel().createUnitDefinition(units.getId());
ud.setName(units.getName());
ArrayList<unitList> unitdeflist = sql.getunitdef(units.getId());
if (!unitdeflist.isEmpty())
insertunits =
insertunits
+ "\nInsert Into listofunits (listofunitdefinitions_id,kind, scale,exponent,multiplier) Values";
for (unitList unitdef : unitdeflist) {
insertunits =
insertunits
+ "(\'"
+ units.getId()
+ "\',\'"
+ unitdef.getkind()
+ "\',"
+ unitdef.getscale()
+ ","
+ unitdef.getexponent()
+ ","
+ unitdef.getmultiplier()
+ "),";
Unit u = ud.createUnit(Unit.Kind.valueOf(unitdef.getkind()));
u.setScale(unitdef.getscale());
u.setExponent(unitdef.getexponent());
u.setMultiplier(unitdef.getmultiplier());
}
// doc.getModel().addSpecies(sp) ;
if (!unitdeflist.isEmpty()) {
insertunits = insertunits.substring(0, insertunits.length() - 1);
insertunits = insertunits + ';';
}
}
if (!unitlist.isEmpty()) {
insertunitdef = insertunitdef.substring(0, insertunitdef.length() - 1);
insertunitdef = insertunitdef + ';';
}
ArrayList<reactionList> reactionlist = sql.getreactons(modelids.getId());
if (!reactionlist.isEmpty())
insertreaction =
insertreaction
+ "\nInsert Into reaction (id,name, reversible,fast,model_id,compartment,annotation) Values";
for (reactionList reaction : reactionlist) {
insertreaction =
insertreaction
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reaction.getName()
+ "\',"
+ reaction.getreversible()
+ ","
+ reaction.getfast()
+ ",\'"
+ modelids.getId()
+ "\',\'"
+ reaction.getcompartment()
+ "\',\'"
+ reaction.getannotation()
+ "\'),";
Reaction rn = doc.getModel().createReaction(reaction.getId());
rn.setName(reaction.getName());
if (doc.getModel().getLevel() == 3) rn.setCompartment(reaction.getcompartment());
rn.setFast(reaction.getfast());
rn.setReversible(reaction.getreversible());
if (!reaction.getannotation().equals("")) {
Annotation annot = new Annotation(reaction.getannotation().toString());
rn.setAnnotation(annot);
}
ArrayList<reactionList> reactantlist = sql.getreactants(reaction.getId());
if (!reactantlist.isEmpty())
insertreactant =
insertreactant
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,speciestype,constant) Values";
for (reactionList reactant : reactantlist) {
insertreactant =
insertreactant
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ reactant.getspecies()
+ "\',\'"
+ reactant.getsboTerm()
+ "\',"
+ reactant.getstoichometry()
+ ","
+ reactant.getconstant()
+ ",\'reactants\'),";
SpeciesReference rt = new SpeciesReference();
rt.setName(reactant.getspecies());
rt.setSpecies(reactant.getspecies());
// rt.setSBOTerm(reactant.getsboTerm());
rt.setStoichiometry(reactant.getstoichometry());
// rt.setConstant(reactant.getconstant());
rn.addReactant(rt);
}
if (!reactantlist.isEmpty()) {
insertreactant = insertreactant.substring(0, insertreactant.length() - 1);
insertreactant = insertreactant + ';';
}
ArrayList<reactionList> productlist = sql.getproducts(reaction.getId());
if (!productlist.isEmpty())
insertproduct =
insertproduct
+ "\nInsert Into simplespeciesreference (reaction_id,species, sboTerm,stoichiometry,constant,speciestype) Values";
for (reactionList product : productlist) {
insertproduct =
insertproduct
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ product.getspecies()
+ "\',\'"
+ product.getsboTerm()
+ "\',"
+ product.getstoichometry()
+ ","
+ product.getconstant()
+ ",\'products\'),";
SpeciesReference pr = new SpeciesReference();
pr.setName(product.getspecies());
pr.setSpecies(product.getspecies());
// pr.setSBOTerm(product.getsboTerm());
pr.setStoichiometry(product.getstoichometry());
// pr.setConstant(product.getconstant());
rn.addProduct(pr);
}
if (!productlist.isEmpty()) {
insertproduct = insertproduct.substring(0, insertproduct.length() - 1);
insertproduct = insertproduct + ';';
}
ArrayList<reactionList> modifierlist = sql.getmodifiers(reaction.getId());
if (!modifierlist.isEmpty())
insertmodifier =
insertmodifier
+ "\nInsert Into modifierspeciesreference (reaction_id,species, sboTerm,speciestype) Values";
for (reactionList modifier : modifierlist) {
insertmodifier =
insertmodifier
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ modifier.getspecies()
+ "\',\'"
+ modifier.getsboTerm()
+ "\',\'modifiers\'),";
ModifierSpeciesReference m = new ModifierSpeciesReference();
m.setName(modifier.getspecies());
m.setSpecies(modifier.getspecies());
// m.setSBOTerm(modifier.getsboTerm());
rn.addModifier(m);
}
if (!modifierlist.isEmpty()) {
insertmodifier = insertmodifier.substring(0, insertmodifier.length() - 1);
insertmodifier = insertmodifier + ';';
}
ArrayList<reactionList> klawlist = sql.getkineticlaws(reaction.getId());
if (!klawlist.isEmpty())
insertklaw =
insertklaw + "\nInsert Into kineticlaw (reaction_id,kid, math,annotation) Values";
for (reactionList klaw : klawlist) {
insertklaw =
insertklaw
+ "(\'"
+ reaction.getId()
+ "\',\'"
+ klaw.getId()
+ "\',\'"
+ klaw.getmath()
+ "\',\'"
+ klaw.getannotation()
+ "\'),";
KineticLaw kl = rn.createKineticLaw();
try {
math = ASTNode.parseFormula(klaw.getmath());
kl.setMath(math);
if (!klaw.getannotation().equals("")) {
Annotation annot = new Annotation(klaw.getannotation().toString());
kl.setAnnotation(annot);
}
} catch (Exception e) {
e.printStackTrace();
}
}
if (!klawlist.isEmpty()) {
insertklaw = insertklaw.substring(0, insertklaw.length() - 1);
insertklaw = insertklaw + ';';
}
}
if (!reactionlist.isEmpty()) {
insertreaction = insertreaction.substring(0, insertreaction.length() - 1);
insertreaction = insertreaction + ';';
}
ArrayList<parameterList> paralist = sql.getparameters(modelids.getId());
if (!paralist.isEmpty())
insertparameter =
insertparameter
+ "\nInsert Into parameter (id,name,value,units,constant,model_id) Values";
for (parameterList para : paralist) {
insertparameter =
insertparameter
+ "(\'"
+ para.getId()
+ "\',\'"
+ para.getName()
+ "\',"
+ para.getvalue()
+ ","
+ para.getunits()
+ ","
+ para.getconstant()
+ ",\'"
+ modelids.getId()
+ "\'),";
Parameter par = doc.getModel().createParameter(para.getId());
par.setName(para.getId());
par.setConstant(para.getconstant());
par.setUnits(para.getunits());
par.setValue(para.getvalue());
}
if (!paralist.isEmpty()) {
insertparameter = insertparameter.substring(0, insertparameter.length() - 1);
insertparameter = insertparameter + ';';
}
ArrayList<constraintList> conslist = sql.getconstraints(modelids.getId());
if (!conslist.isEmpty())
insertconstraint =
insertconstraint + "\nInsert Into sbmlconstraint (math,message,model_id) Values";
for (constraintList constraint : conslist) {
insertconstraint =
insertconstraint
+ "(\'"
+ constraint.getmath()
+ "\',\'"
+ constraint.getmessage()
+ "\',\'"
+ modelids.getId()
+ "\'),";
Constraint cons = doc.getModel().createConstraint();
try {
math = ASTNode.parseFormula(constraint.getmath());
cons.setMath(math);
cons.setMessage(constraint.getmessage());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!conslist.isEmpty()) {
insertconstraint = insertconstraint.substring(0, insertconstraint.length() - 1);
insertconstraint = insertconstraint + ';';
}
ArrayList<eventsList> eventlist = sql.getevents(modelids.getId());
if (!eventlist.isEmpty())
insertevent =
insertevent + "\nInsert Into event (id,name,UseValuesFromTriggerTime,model_id) Values";
for (eventsList events : eventlist) {
insertevent =
insertevent
+ "(\'"
+ events.getId()
+ "\',\'"
+ events.getName()
+ "\',"
+ events.getuservalues()
+ ",\'"
+ modelids.getId()
+ "\'),";
Event ev = doc.getModel().createEvent(events.getId());
ev.setName(events.getName());
// ev.setUseValuesFromTriggerTime(events.getuservalues());
ArrayList<eventsList> triggerlist = sql.gettriggers(events.getId());
if (!triggerlist.isEmpty())
inserttrigger =
inserttrigger
+ "\nInsert Into sbmltrigger (event_id,initialvalue,persisent,math) Values";
for (eventsList triggers : triggerlist) {
Trigger tr = doc.getModel().createTrigger();
try {
math = ASTNode.parseFormula(triggers.getmath());
tr.setMath(math);
tr.setInitialValue(triggers.getinitialval());
tr.setPersistent(triggers.getpersistent());
} catch (Exception e) {
e.printStackTrace();
}
}
if (!triggerlist.isEmpty()) {
inserttrigger = inserttrigger.substring(0, insertmodel.length() - 1);
inserttrigger = inserttrigger + ';';
}
ArrayList<eventsList> delaylist = sql.getdelays(events.getId());
if (!delaylist.isEmpty())
insertdelay = insertdelay + "\nInsert Into delay (event_id,math) Values";
for (eventsList delays : delaylist) {
Delay d = doc.getModel().createDelay();
try {
math = ASTNode.parseFormula(delays.getmath());
d.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!delaylist.isEmpty()) {
insertdelay = insertdelay.substring(0, insertdelay.length() - 1);
insertdelay = insertdelay + ';';
}
ArrayList<eventsList> evasslist = sql.geteventassignments(events.getId());
if (!evasslist.isEmpty())
inserteventassign =
inserteventassign + "\nInsert Into eventassignment (event_id,variable,math) Values";
for (eventsList evassign : evasslist) {
EventAssignment ea = doc.getModel().createEventAssignment();
try {
math = ASTNode.parseFormula(evassign.getmath());
ea.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
if (!evasslist.isEmpty()) {
inserteventassign = inserteventassign.substring(0, inserteventassign.length() - 1);
inserteventassign = inserteventassign + ';';
}
}
if (!eventlist.isEmpty()) {
insertevent = insertevent.substring(0, insertevent.length() - 1);
insertevent = insertevent + ';';
}
ArrayList<ruleslist> rulelist = sql.getrules(modelids.getId());
if (!rulelist.isEmpty())
insertrules = insertrules + "\nInsert Into rules (id,math,ruletype,model_id) Values";
for (ruleslist rules : rulelist) {
insertrules =
insertrules
+ "(\'"
+ rules.getId()
+ "\',\'"
+ rules.getmath()
+ "\',\'"
+ rules.getruletype()
+ "\',\'"
+ modelids.getId()
+ "\'),";
if (rules.getruletype().equals("assignmentrule")) {
Rule r = doc.getModel().createAssignmentRule();
r.setMetaId(rules.getId());
try {
math = ASTNode.parseFormula(rules.getmath());
r.setMath(math);
} catch (Exception e) {
e.printStackTrace();
}
}
}
if (!rulelist.isEmpty()) {
insertrules = insertrules.substring(0, insertrules.length() - 1);
insertrules = insertrules + ';';
}
SBMLWriter writer = new SBMLWriter();
try {
String Path = filepath + modelids.getId() + ".xml";
writer.write(doc, Path);
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(Path);
Element root = document.getDocumentElement();
Element newdataset = document.createElement("dataset");
root.appendChild(newdataset);
ArrayList<dataset> datasetlist = sql.getdataset(modelids.getId());
for (dataset ds : datasetlist) {
// System.out.println(ds.getexpcond());
Element name = document.createElement("experimentalcondition");
name.setAttribute("bioelement", ds.getbioel());
name.setAttribute("name", ds.getName());
name.setAttribute("descr", ds.getdescr());
name.setAttribute("expcond", ds.getexpcond());
name.setAttribute("value", String.valueOf(ds.getvalue()));
name.setAttribute("type", ds.gettype());
name.setAttribute("uri", ds.geturi());
newdataset.appendChild(name);
}
root.appendChild(newdataset);
DOMSource source = new DOMSource(document);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.METHOD, "xml");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "4");
StreamResult result = new StreamResult(filepath + modelids.getId() + "d.xml");
transformer.transform(source, result);
System.out.println(
"Files : "
+ modelids.getId()
+ ".xml and "
+ modelids.getId()
+ "d.xml have been generated successfully !!!");
} catch (Exception e) {
e.printStackTrace();
}
insertstatement =
insertstatement
+ "\n\n"
+ insertmodel
+ "\n"
+ insertspecies
+ "\n"
+ insertcompartment
+ "\n"
+ insertfunction;
insertstatement =
insertstatement
+ "\n"
+ insertparameter
+ "\n"
+ insertreaction
+ "\n"
+ insertreactant
+ "\n"
+ insertproduct;
insertstatement =
insertstatement
+ "\n"
+ insertmodifier
+ "\n"
+ insertklaw
+ "\n"
+ insertunitdef
+ "\n"
+ insertunits;
insertstatement =
insertstatement
+ "\n"
+ insertrules
+ "\n"
+ insertconstraint
+ "\n"
+ insertevent
+ "\n"
+ inserttrigger
+ "\n"
+ insertdelay
+ "\n"
+ inserteventassign;
insertcompartment = "";
insertmodel = "";
insertspecies = "";
// System.out.println("document : " + doc);
}
insertstatement = insertstatement + "\nUNLOCK TABLES;";
Filedata = Filedata + "\n\n\n" + insertstatement;
try {
wrtireStringToFile(Filedata, filepath + "sbmldb.sql");
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(insertstatement);
}
SimpleLiveLocalsAnalysis(UnitGraph g) {
super(g);
if (Options.v().time()) Timers.v().liveSetupTimer.start();
emptySet = new ArraySparseSet();
// Create kill sets.
{
unitToKillSet = new HashMap<Unit, FlowSet>(g.size() * 2 + 1, 0.7f);
Iterator unitIt = g.iterator();
while (unitIt.hasNext()) {
Unit s = (Unit) unitIt.next();
FlowSet killSet = emptySet.clone();
Iterator boxIt = s.getDefBoxes().iterator();
while (boxIt.hasNext()) {
ValueBox box = (ValueBox) boxIt.next();
if (box.getValue() instanceof Local) killSet.add(box.getValue(), killSet);
}
unitToKillSet.put(s, killSet);
}
}
// Create generate sets
{
unitToGenerateSet = new HashMap<Unit, FlowSet>(g.size() * 2 + 1, 0.7f);
Iterator unitIt = g.iterator();
while (unitIt.hasNext()) {
Unit s = (Unit) unitIt.next();
FlowSet genSet = emptySet.clone();
Iterator boxIt = s.getUseBoxes().iterator();
while (boxIt.hasNext()) {
ValueBox box = (ValueBox) boxIt.next();
if (box.getValue() instanceof Local) genSet.add(box.getValue(), genSet);
}
unitToGenerateSet.put(s, genSet);
}
}
if (Options.v().time()) Timers.v().liveSetupTimer.end();
if (Options.v().time()) Timers.v().liveAnalysisTimer.start();
doAnalysis();
if (Options.v().time()) Timers.v().liveAnalysisTimer.end();
}
/**
* By default, this will always attempt to call {@link System#exit(int)} at the end of running
* tests, exiting with 0 if all tests pass, 4 if any units have failed, and 5 if any unit failed
* catastrophically (i.e. the entire case was not completed). This behavior and/or those values
* can be overridden by overriding the {@link #succeeded()}, {@link #failed()}, and {@link
* #aborted()} methods, respectively.
*/
public synchronized void run() {
List<Unit> $units = getUnits(); // list is assumed immutable on pain of death or idiocy
$numUnits = $units.size();
$numUnitsRun = 0;
$numUnitsPassed = 0;
$numUnitsFailed = 0;
for (int $i = 0; $i < $units.size(); $i++) {
Unit $unit = $units.get($i);
if ($unit == null) continue;
try {
resetFailures();
$log.info("TEST UNIT " + $unit.getName() + " STARTING...");
$numUnitsRun++;
$unit.call();
if ($unit.expectExceptionType() != null) {
$numUnitsFailed++;
$log.error("EXPECTED EXCEPTION; TEST CASE ABORTED.");
aborted();
}
if ($unitFailures == 0) {
$numUnitsPassed++;
$log.info("TEST UNIT " + $unit.getName() + " PASSED SUCCESSFULLY!\n");
} else {
$numUnitsFailed++;
$log.info(
"TEST UNIT " + $unit.getName() + " FAILED (WITH " + $unitFailures + " FAILURES)!\n");
}
} catch (AssertionFatal $e) {
$numUnitsFailed++;
$log.error("FATAL EXCEPTION; TEST CASE ABORTED.", $e);
aborted();
break;
} catch (AssertionFailed $e) {
$numUnitsFailed++;
$log.error("TEST UNIT " + $unit.getName() + " ABORTED.", $e);
} catch (Throwable $e) {
if ($unit.expectExceptionType() != null) {
// some kind of exception was expected.
if ($unit.expectExceptionType().isAssignableFrom($e.getClass())) {
// and it was this kind that was expected, so this is good.
$numUnitsPassed++;
$unit.assertInstanceOf(
$unit.expectExceptionType(), $e); // generates a normal confirmation message
$log.info("TEST UNIT " + $unit.getName() + " PASSED SUCCESSFULLY!\n");
} else {
// and it wasn't this kind. this represents fatal failure.
$numUnitsFailed++;
$log.error("FATAL EXCEPTION; TEST CASE ABORTED.", $e);
aborted();
break;
}
} else {
// no exception was expected. any exception represents fatal failure.
$numUnitsFailed++;
$log.error("FATAL EXCEPTION; TEST CASE ABORTED.", $e);
aborted();
break;
}
}
}
if ($numUnitsFailed > 0) failed();
else succeeded();
}
/**
* This method pushes all newExpr down to be the stmt directly before every invoke of the init
* only if they are in the types list
*/
public void internalTransform(Body b, String phaseName, Map options) {
JimpleBody body = (JimpleBody) b;
if (Options.v().verbose())
G.v().out.println("[" + body.getMethod().getName() + "] Folding Jimple constructors...");
Chain units = body.getUnits();
List<Unit> stmtList = new ArrayList<Unit>();
stmtList.addAll(units);
Iterator<Unit> it = stmtList.iterator();
Iterator<Unit> nextStmtIt = stmtList.iterator();
// start ahead one
nextStmtIt.next();
SmartLocalDefs localDefs = SmartLocalDefsPool.v().getSmartLocalDefsFor(body);
UnitGraph graph = localDefs.getGraph();
LocalUses localUses = new SimpleLocalUses(graph, localDefs);
/* fold in NewExpr's with specialinvoke's */
while (it.hasNext()) {
Stmt s = (Stmt) it.next();
if (!(s instanceof AssignStmt)) continue;
/* this should be generalized to ArrayRefs */
// only deal with stmts that are an local = newExpr
Value lhs = ((AssignStmt) s).getLeftOp();
if (!(lhs instanceof Local)) continue;
Value rhs = ((AssignStmt) s).getRightOp();
if (!(rhs instanceof NewExpr)) continue;
// check if very next statement is invoke -->
// this indicates there is no control flow between
// new and invoke and should do nothing
if (nextStmtIt.hasNext()) {
Stmt next = (Stmt) nextStmtIt.next();
if (next instanceof InvokeStmt) {
InvokeStmt invoke = (InvokeStmt) next;
if (invoke.getInvokeExpr() instanceof SpecialInvokeExpr) {
SpecialInvokeExpr invokeExpr = (SpecialInvokeExpr) invoke.getInvokeExpr();
if (invokeExpr.getBase() == lhs) {
break;
}
}
}
}
// check if new is in the types list - only process these
if (!types.contains(((NewExpr) rhs).getType())) continue;
List lu = localUses.getUsesOf(s);
Iterator luIter = lu.iterator();
boolean MadeNewInvokeExpr = false;
while (luIter.hasNext()) {
Unit use = ((UnitValueBoxPair) (luIter.next())).unit;
if (!(use instanceof InvokeStmt)) continue;
InvokeStmt is = (InvokeStmt) use;
if (!(is.getInvokeExpr() instanceof SpecialInvokeExpr)
|| lhs != ((SpecialInvokeExpr) is.getInvokeExpr()).getBase()) continue;
// make a new one here
AssignStmt constructStmt =
Jimple.v()
.newAssignStmt(((DefinitionStmt) s).getLeftOp(), ((DefinitionStmt) s).getRightOp());
constructStmt.setRightOp(Jimple.v().newNewExpr(((NewExpr) rhs).getBaseType()));
MadeNewInvokeExpr = true;
// redirect jumps
use.redirectJumpsToThisTo(constructStmt);
// insert new one here
units.insertBefore(constructStmt, use);
constructStmt.addTag(s.getTag("SourceLnPosTag"));
}
if (MadeNewInvokeExpr) {
units.remove(s);
}
}
}
/** set range used for linear map from Scalar to DisplayScalar values */
private synchronized void setRange(
DataShadow shadow, double low, double hi, boolean unit_flag, int remoteId)
throws VisADException, RemoteException {
int i = ScalarIndex;
if (shadow != null) {
// WLH - 23 Sept 99
if (DisplayScalar.equals(Display.Latitude) || DisplayScalar.equals(Display.Longitude)) {
Unit data_unit = (Scalar instanceof RealType) ? ((RealType) Scalar).getDefaultUnit() : null;
Unit display_unit = DisplayScalar.getDefaultUnit();
if (data_unit != null && display_unit != null && Unit.canConvert(data_unit, display_unit)) {
dataRange[0] = data_unit.toThis(displayRange[0], display_unit);
dataRange[1] = data_unit.toThis(displayRange[1], display_unit);
} else {
if (i < 0 || i >= shadow.ranges[0].length) return;
dataRange[0] = shadow.ranges[0][i];
dataRange[1] = shadow.ranges[1][i];
}
} else {
if (i < 0 || i >= shadow.ranges[0].length) return;
dataRange[0] = shadow.ranges[0][i];
dataRange[1] = shadow.ranges[1][i];
}
} else if (unit_flag) {
Unit data_unit = (Scalar instanceof RealType) ? ((RealType) Scalar).getDefaultUnit() : null;
Unit display_unit = DisplayScalar.getDefaultUnit();
if (data_unit == null || display_unit == null) {
throw new UnitException("ScalarMap.setRangeByUnits: null Unit");
}
dataRange[0] = data_unit.toThis(displayRange[0], display_unit);
dataRange[1] = data_unit.toThis(displayRange[1], display_unit);
/*
System.out.println("data_unit = " + data_unit + " display_unit = " + display_unit);
System.out.println("dataRange = " + dataRange[0] + " " + dataRange[1] +
" displayRange = " + displayRange[0] + " " + displayRange[1]);
*/
} else {
dataRange[0] = low;
dataRange[1] = hi;
// WLH 31 Aug 2000
// manual range is in overrideUnit. so convert to Scalar default Unit
if (overrideUnit != null) {
dataRange[0] = (dataRange[0] - override_offset) / override_scale;
dataRange[1] = (dataRange[1] - override_offset) / override_scale;
}
}
/*
if (shadow != null || remoteId != VisADEvent.LOCAL_SOURCE) {
System.out.println(Scalar + " -> " + DisplayScalar + " range: " + dataRange[0] +
" to " + dataRange[1] + " " + display.getName());
}
*/
// at this point dataRange is range for Scalar default Unit
// even if (overrideUnit != null)
// DRM 17 Feb 2006 - so set the defaultUnitRange to be these values.
defaultUnitRange[0] = dataRange[0];
defaultUnitRange[1] = dataRange[1];
if (defaultUnitRange[0] == defaultUnitRange[1]) {
double half = defaultUnitRange[0] / 2000.0;
if (half < 0.5) half = 0.5;
defaultUnitRange[0] -= half;
defaultUnitRange[1] += half;
}
if (isScaled) {
computeScaleAndOffset();
} else { // if (!isScaled)
if (dataRange[0] == Double.MAX_VALUE || dataRange[1] == -Double.MAX_VALUE) {
dataRange[0] = Double.NaN;
dataRange[1] = Double.NaN;
}
// WLH 31 Aug 2000
if (overrideUnit != null) {
// now convert dataRange to overrideUnit
dataRange[0] = defaultUnitRange[0] * override_scale + override_offset;
dataRange[1] = defaultUnitRange[1] * override_scale + override_offset;
}
}
/*
System.out.println(Scalar + " -> " + DisplayScalar + " range: " + dataRange[0] +
" to " + dataRange[1] + " scale: " + scale + " " + offset);
*/
if (DisplayScalar.equals(Display.Animation) && shadow != null) {
if (control != null && ((AnimationControl) control).getComputeSet()) {
Set set = shadow.animationSampling;
/* DRM: 04 Jan 2003
if (set == null) {
return;
}
*/
((AnimationControl) control).setSet(set, true);
}
} else if (DisplayScalar.equals(Display.IsoContour)) {
if (control != null) {
// WLH 10 July 2002
// don't set if application has called control.setLevels()
float[] lowhibase = new float[3];
boolean[] dashes = new boolean[1];
boolean public_set = ((ContourControl) control).getPublicSet();
if (!public_set) {
boolean[] bvalues = new boolean[2];
float[] values = new float[5];
((ContourControl) control).getMainContours(bvalues, values);
if (shadow == null) {
// don't set surface value for auto-scale
values[0] = (float) dataRange[0]; // surfaceValue
}
// CTR: 29 Jul 1999: interval should never be zero
float f = (float) (dataRange[1] - dataRange[0]) / 10.0f;
if (f != 0.0f) values[1] = f; // contourInterval
values[2] = (float) dataRange[0]; // lowLimit
values[3] = (float) dataRange[1]; // hiLimit
values[4] = (float) dataRange[0]; // base
((ContourControl) control).setMainContours(bvalues, values, true, true);
}
}
} else if (DisplayScalar.equals(Display.XAxis)
|| DisplayScalar.equals(Display.YAxis)
|| DisplayScalar.equals(Display.ZAxis)) {
if (dataRange[0] != Double.MAX_VALUE
&& dataRange[1] != -Double.MAX_VALUE
&& dataRange[0] == dataRange[0]
&& dataRange[1] == dataRange[1]
&& dataRange[0] != dataRange[1]
&& scale == scale
&& offset == offset) {
if (display != null) {
makeScale();
} else {
scale_flag = true;
}
back_scale_flag = true;
}
}
if (dataRange[0] == dataRange[0] && dataRange[1] == dataRange[1] && ListenerVector != null) {
ScalarMapEvent evt;
evt =
new ScalarMapEvent(
this, (shadow == null ? ScalarMapEvent.MANUAL : ScalarMapEvent.AUTO_SCALE), remoteId);
Vector listeners_clone = null;
synchronized (ListenerVector) {
listeners_clone = (Vector) ListenerVector.clone();
}
Enumeration listeners = listeners_clone.elements();
while (listeners.hasMoreElements()) {
ScalarMapListener listener = (ScalarMapListener) listeners.nextElement();
listener.mapChanged(evt);
}
}
}
/** Prints the given <code>JimpleBody</code> to the specified <code>PrintWriter</code>. */
private void printStatementsInBody(
Body body, java.io.PrintWriter out, LabeledUnitPrinter up, UnitGraph unitGraph) {
Chain units = body.getUnits();
Iterator unitIt = units.iterator();
Unit currentStmt = null, previousStmt;
while (unitIt.hasNext()) {
previousStmt = currentStmt;
currentStmt = (Unit) unitIt.next();
// Print appropriate header.
{
// Put an empty line if the previous node was a branch node, the current node is a join node
// or the previous statement does not have body statement as a successor, or if
// body statement has a label on it
if (currentStmt != units.getFirst()) {
if (unitGraph.getSuccsOf(previousStmt).size() != 1
|| unitGraph.getPredsOf(currentStmt).size() != 1
|| up.labels().containsKey(currentStmt)) {
up.newline();
} else {
// Or if the previous node does not have body statement as a successor.
List succs = unitGraph.getSuccsOf(previousStmt);
if (succs.get(0) != currentStmt) {
up.newline();
}
}
}
if (up.labels().containsKey(currentStmt)) {
up.unitRef(currentStmt, true);
up.literal(":");
up.newline();
}
if (up.references().containsKey(currentStmt)) {
up.unitRef(currentStmt, false);
}
}
up.startUnit(currentStmt);
currentStmt.toString(up);
up.endUnit(currentStmt);
up.literal(";");
up.newline();
// only print them if not generating attributes files
// because they mess up line number
// if (!addJimpleLn()) {
if (Options.v().print_tags_in_output()) {
Iterator tagIterator = currentStmt.getTags().iterator();
while (tagIterator.hasNext()) {
Tag t = (Tag) tagIterator.next();
up.noIndent();
up.literal("/*");
up.literal(t.toString());
up.literal("*/");
up.newline();
}
/*Iterator udIt = currentStmt.getUseAndDefBoxes().iterator();
while (udIt.hasNext()) {
ValueBox temp = (ValueBox)udIt.next();
Iterator vbtags = temp.getTags().iterator();
while (vbtags.hasNext()) {
Tag t = (Tag) vbtags.next();
up.noIndent();
up.literal("VB Tag: "+t.toString());
up.newline();
}
}*/
}
}
out.print(up.toString());
if (addJimpleLn()) {
setJimpleLnNum(up.getPositionTagger().getEndLn());
}
// Print out exceptions
{
Iterator trapIt = body.getTraps().iterator();
if (trapIt.hasNext()) {
out.println();
incJimpleLnNum();
}
while (trapIt.hasNext()) {
Trap trap = (Trap) trapIt.next();
out.println(
" catch "
+ Scene.v().quotedNameOf(trap.getException().getName())
+ " from "
+ up.labels().get(trap.getBeginUnit())
+ " to "
+ up.labels().get(trap.getEndUnit())
+ " with "
+ up.labels().get(trap.getHandlerUnit())
+ ";");
incJimpleLnNum();
}
}
}
public synchronized void drag_direct(VisADRay ray, boolean first, int mouseModifiers) {
if (barbValues == null || ref == null || shadow == null) return;
if (first) {
stop = false;
} else {
if (stop) return;
}
// modify direction if mshift != 0
// modify speed if mctrl != 0
// modify speed and direction if neither
int mshift = mouseModifiers & InputEvent.SHIFT_MASK;
int mctrl = mouseModifiers & InputEvent.CTRL_MASK;
float o_x = (float) ray.position[0];
float o_y = (float) ray.position[1];
float o_z = (float) ray.position[2];
float d_x = (float) ray.vector[0];
float d_y = (float) ray.vector[1];
float d_z = (float) ray.vector[2];
if (pickCrawlToCursor) {
if (first) {
offset_count = OFFSET_COUNT_INIT;
} else {
if (offset_count > 0) offset_count--;
}
if (offset_count > 0) {
float mult = ((float) offset_count) / ((float) OFFSET_COUNT_INIT);
o_x += mult * offsetx;
o_y += mult * offsety;
o_z += mult * offsetz;
}
}
if (first || refirst) {
point_x = barbValues[2];
point_y = barbValues[3];
point_z = 0.0f;
line_x = 0.0f;
line_y = 0.0f;
line_z = 1.0f; // lineAxis == 2 in DataRenderer.drag_direct
} // end if (first || refirst)
float[] x = new float[3]; // x marks the spot
// DirectManifoldDimension = 2
// intersect ray with plane
float dot = (point_x - o_x) * line_x + (point_y - o_y) * line_y + (point_z - o_z) * line_z;
float dot2 = d_x * line_x + d_y * line_y + d_z * line_z;
if (dot2 == 0.0) return;
dot = dot / dot2;
// x is intersection
x[0] = o_x + dot * d_x;
x[1] = o_y + dot * d_y;
x[2] = o_z + dot * d_z;
/*
System.out.println("x = " + x[0] + " " + x[1] + " " + x[2]);
*/
try {
Tuple data = (Tuple) link.getData();
int n = ((TupleType) data.getType()).getNumberOfRealComponents();
Real[] reals = new Real[n];
int k = 0;
int m = data.getDimension();
for (int i = 0; i < m; i++) {
Data component = data.getComponent(i);
if (component instanceof Real) {
reals[k++] = (Real) component;
} else if (component instanceof RealTuple) {
for (int j = 0; j < ((RealTuple) component).getDimension(); j++) {
reals[k++] = (Real) ((RealTuple) component).getComponent(j);
}
}
}
if (first || refirst) {
// get first Data flow vector
for (int i = 0; i < 3; i++) {
int j = flowToComponent[i];
data_flow[i] = (j >= 0) ? (float) reals[j].getValue() : 0.0f;
}
if (coord != null) {
float[][] ds = {{data_flow[0]}, {data_flow[1]}, {data_flow[2]}};
ds = coord.toReference(ds);
data_flow[0] = ds[0][0];
data_flow[1] = ds[1][0];
data_flow[2] = ds[2][0];
}
data_speed =
(float)
Math.sqrt(
data_flow[0] * data_flow[0]
+ data_flow[1] * data_flow[1]
+ data_flow[2] * data_flow[2]);
float barb0 = barbValues[2] - barbValues[0];
float barb1 = barbValues[3] - barbValues[1];
/*
System.out.println("data_flow = " + data_flow[0] + " " + data_flow[1] +
" " + data_flow[2]);
System.out.println("barbValues = " + barbValues[0] + " " + barbValues[1] +
" " + barbValues[2] + " " + barbValues[3]);
System.out.println("data_speed = " + data_speed);
*/
} // end if (first || refirst)
// convert x to a flow vector, and from spatial to earth
if (getRealVectorTypes(which_barb) instanceof EarthVectorType) {
// don't worry about vector magnitude -
// data_speed & display_speed take care of that
float eps = 0.0001f; // estimate derivative with a little vector
float[][] spatial_locs = {
{barbValues[0], barbValues[0] + eps * (x[0] - barbValues[0])},
{barbValues[1], barbValues[1] + eps * (x[1] - barbValues[1])},
{0.0f, 0.0f}
};
/*
System.out.println("spatial_locs = " + spatial_locs[0][0] + " " +
spatial_locs[0][1] + " " + spatial_locs[1][0] + " " +
spatial_locs[1][1]);
*/
float[][] earth_locs = spatialToEarth(spatial_locs);
// WLH - 18 Aug 99
if (earth_locs == null) return;
/*
System.out.println("earth_locs = " + earth_locs[0][0] + " " +
earth_locs[0][1] + " " + earth_locs[1][0] + " " +
earth_locs[1][1]);
*/
x[2] = 0.0f;
x[0] =
(earth_locs[1][1] - earth_locs[1][0])
* ((float) Math.cos(Data.DEGREES_TO_RADIANS * earth_locs[0][0]));
x[1] = earth_locs[0][1] - earth_locs[0][0];
/*
System.out.println("x = " + x[0] + " " + x[1] + " " + x[2]);
*/
} else { // if (!(getRealVectorTypes(which_barb) instanceof EarthVectorType))
// convert x to vector
x[0] -= barbValues[0];
x[1] -= barbValues[1];
// adjust for spatial map scalings but don't worry about vector
// magnitude - data_speed & display_speed take care of that
// also, spatial is Cartesian
double[] ranges = getRanges();
for (int i = 0; i < 3; i++) {
x[i] /= ranges[i];
}
/*
System.out.println("ranges = " + ranges[0] + " " + ranges[1] +
" " + ranges[2]);
System.out.println("x = " + x[0] + " " + x[1] + " " + x[2]);
*/
}
// WLH 6 August 99
x[0] = -x[0];
x[1] = -x[1];
x[2] = -x[2];
/* may need to do this for performance
float[] xx = {x[0], x[1], x[2]};
addPoint(xx);
*/
float x_speed = (float) Math.sqrt(x[0] * x[0] + x[1] * x[1] + x[2] * x[2]);
/* WLH 16 April 2002 - from Ken
if (x_speed < 0.000001f) x_speed = 0.000001f;
*/
if (x_speed < 0.01f) x_speed = 0.01f;
if (first || refirst) {
display_speed = x_speed;
}
refirst = false;
if (mshift != 0) {
// only modify data_flow direction
float ratio = data_speed / x_speed;
x[0] *= ratio;
x[1] *= ratio;
x[2] *= ratio;
/*
System.out.println("direction, ratio = " + ratio + " " +
data_speed + " " + x_speed);
System.out.println("x = " + x[0] + " " + x[1] + " " + x[2]);
*/
} else if (mctrl != 0) {
// only modify data_flow speed
float ratio = x_speed / display_speed;
if (data_speed < EPS) {
data_flow[0] = 2.0f * EPS;
refirst = true;
}
x[0] = ratio * data_flow[0];
x[1] = ratio * data_flow[1];
x[2] = ratio * data_flow[2];
/*
System.out.println("speed, ratio = " + ratio + " " +
x_speed + " " + display_speed);
System.out.println("x = " + x[0] + " " + x[1] + " " + x[2]);
*/
} else {
// modify data_flow speed and direction
float ratio = data_speed / display_speed;
/*
System.out.println("data_speed = " + data_speed +
" display_speed = " + display_speed +
" ratio = " + ratio + " EPS = " + EPS);
System.out.println("x = " + x[0] + " " + x[1] +" " + x[2] +
" x_speed = " + x_speed);
data_speed = 21.213203 display_speed = 0.01 ratio = 2121.3203 EPS = 0.2
x = 1.6170928E-4 1.6021729E-4 -0.0 x_speed = 0.01
wind = (0.3430372, 0.33987218) at (-35.0, 5.0)
*/
if (data_speed < EPS) {
data_flow[0] = 2.0f * EPS;
x[0] = data_flow[0];
x[1] = data_flow[1];
x[2] = data_flow[2];
refirst = true;
} else {
x[0] *= ratio;
x[1] *= ratio;
x[2] *= ratio;
}
}
if (coord != null) {
float[][] xs = {{x[0]}, {x[1]}, {x[2]}};
xs = coord.fromReference(xs);
x[0] = xs[0][0];
x[1] = xs[1][0];
x[2] = xs[2][0];
}
// now replace flow values
Vector vect = new Vector();
for (int i = 0; i < 3; i++) {
int j = flowToComponent[i];
if (j >= 0) {
RealType rtype = (RealType) reals[j].getType();
reals[j] = new Real(rtype, (double) x[i], rtype.getDefaultUnit(), null);
// WLH 31 Aug 2000
Real r = reals[j];
Unit overrideUnit = null;
if (directMap[i] != null) {
overrideUnit = directMap[i].getOverrideUnit();
}
Unit rtunit = rtype.getDefaultUnit();
// units not part of Time string
if (overrideUnit != null
&& !overrideUnit.equals(rtunit)
&& !RealType.Time.equals(rtype)) {
double d = (float) overrideUnit.toThis((double) x[0], rtunit);
r = new Real(rtype, d, overrideUnit);
String valueString = r.toValueString();
vect.addElement(rtype.getName() + " = " + valueString);
} else {
// create location string
vect.addElement(rtype.getName() + " = " + x[i]);
}
}
}
getDisplayRenderer().setCursorStringVector(vect);
Data newData = null;
// now build new RealTuple or Flat Tuple
if (data instanceof RealTuple) {
newData =
new RealTuple(
((RealTupleType) data.getType()), reals, ((RealTuple) data).getCoordinateSystem());
} else {
Data[] new_components = new Data[m];
k = 0;
for (int i = 0; i < m; i++) {
Data component = data.getComponent(i);
if (component instanceof Real) {
new_components[i] = reals[k++];
} else if (component instanceof RealTuple) {
Real[] sub_reals = new Real[((RealTuple) component).getDimension()];
for (int j = 0; j < ((RealTuple) component).getDimension(); j++) {
sub_reals[j] = reals[k++];
}
new_components[i] =
new RealTuple(
((RealTupleType) component.getType()),
sub_reals,
((RealTuple) component).getCoordinateSystem());
}
}
newData = new Tuple(new_components, false);
}
ref.setData(newData);
} catch (VisADException e) {
// do nothing
System.out.println("drag_direct " + e);
e.printStackTrace();
} catch (RemoteException e) {
// do nothing
System.out.println("drag_direct " + e);
e.printStackTrace();
}
}