@Test
public void testMultipleRemoval() {
bag.add(test, 5);
Assert.assertTrue(bag.remove(test, 3));
Assert.assertEquals(2, bag.size());
Assert.assertTrue(bag.remove(test));
Assert.assertEquals(1, bag.size());
}
@Test
public void testSizeIncrement() {
bag.add(test, 1);
bag.add(test1, 1);
Assert.assertEquals(2, bag.size());
bag.add(test1, 3);
Assert.assertEquals(5, bag.size());
}
@Test
public void testSingularRemoval() {
bag.add(test, 5);
Assert.assertTrue(bag.remove(test));
Assert.assertEquals(4, bag.size());
}
private void assignStudent(Student s) {
for (int y = 0; y < dorms.size(); y++) {
if (s.hasRoom()) {
break;
}
Dorm d = (Dorm) dorms.get(y);
if (d.isFull()) {
continue;
}
if (d.isFemaleOnly() && s.getGender() == Student.Gender.MALE) {
continue;
}
int i = 0;
while (i < d.getNumRooms()) {
if (s.hasRoom()) {
break;
}
try {
d.getRoomByIndex(i).addResident(s);
} catch (IllegalArgumentException e) {
}
i++;
}
}
}
@Test
public void testAddAll() {
Set<String> expected = new HashSet<>();
addStringsToCollection(expected);
bag.addAll(expected);
Assert.assertEquals(expected.size(), bag.size());
}
@Test
public void testRemoveAllFail() {
addStringsToCollection(bag);
Set<String> remove = new HashSet<>();
remove.add("Not in the list");
Assert.assertFalse(bag.removeAll(remove));
Assert.assertEquals(4, bag.size());
}
@Test
public void testRemoveAllWithCollection() {
addStringsToCollection(bag);
Set<String> remove = new HashSet<>();
addStringsToCollection(remove);
Assert.assertTrue(bag.removeAll(remove));
Assert.assertEquals(0, bag.size());
}
@Test
public void testRetainAll() {
addStringsToCollection(bag);
List<String> retain = new ArrayList<>(2);
retain.add(test);
retain.add(test1);
bag.retainAll(retain);
Assert.assertTrue(bag.containsAll(retain));
Assert.assertEquals(2, bag.size());
}
@Test
public void testClear() {
addStringsToCollection(bag);
bag.clear();
Assert.assertEquals(0, bag.size());
}
// main CELL CA loop************
public boolean iterateCells() {
/*
// modify consumption matrix
for (int i=0;i<size;i++)
for (int j=0;j<size;j++) consumption[i][j] = consumptionBasal[Cells[i][j]];
*/
//
if (cellList == null) cellList = new Bag(size * size);
for (int i = 0; i < size; i++)
for (int j = 0; j < size; j++) {
if (Cells[i][j]
< 4) { // All tumour cell types have Cell > 0, now 0 corresponds to 'healthy cells' that
// consume at basal rate only
int[] p = new int[2];
p[0] = i;
p[1] = j;
cellList.add(p);
if (Cells[i][j] == 1) {
stem_cells_this_TS++;
} else if (Cells[i][j] == 2 || Cells[i][j] == 3) {
non_stem_cells_this_TS++;
}
}
}
while (cellList.size() != 0) {
// Select the next lattice element at random
int randomElemIndex = 0;
if (cellList.size() > 1) randomElemIndex = random.nextInt(cellList.size() - 1);
int[] point = (int[]) cellList.get(randomElemIndex);
int rI = point[0];
int rJ = point[1];
cellList.remove(randomElemIndex); // Remove it from the cell list
int cell = Cells[rI][rJ];
// Cell death
// if ((Oxygen[rI][rJ]<hypoxia)) {
if ((random.nextFloat() < deathprob) && Cells[rI][rJ] > 0) { // x% chances of dying
Age[rI][rJ] = 0;
if (Cells[rI][rJ] == 1) stemDeathCounter[rI][rJ]++;
if (Cells[rI][rJ] < 4) {
// TACDeathCounter[rI][rJ]++;
Cells[rI][rJ] = 4; // was 0, now making necrotic area (truly empty)
deaths++;
stemBirthCounter[rI][rJ] = 0;
carriedmutation[rI][rJ] = 0; // empty space now has no mutations
carriedGenome[rI][rJ] = initGenome; // empty space now has no mutations
}
} else if ((cell == 3)
&& (Age[rI][rJ]
> 100 * maxMatureCellAge)) { // added * to allow for an update each celltimestep/x
// **************************
Age[rI][rJ] = 0;
Cells[rI][rJ] = 4; // was 0, now making necrotic area (truly empty)
// TACDeathCounter[rI][rJ]++;
deaths++;
} else if ((radiotherapy) && (cell == 2) && (random.nextFloat() > Oxygen[rI][rJ])) {
// Radiotherapy
Age[rI][rJ] = 0;
if (Cells[rI][rJ] == 1) stemDeathCounter[rI][rJ]++;
if ((Cells[rI][rJ] == 2) || (Cells[rI][rJ] == 3))
// TACDeathCounter[rI][rJ]++;
Cells[rI][rJ] = 4; // make necrotic
stemBirthCounter[rI][rJ] = 0;
deaths++;
}
// healthy division
else if ((cell == 0) && (vacantSites(rI, rJ) > 0)) {
if (proliferation[cell]
>= random.nextFloat()) { // If tossing the coin we are to proliferate...
// if (Oxygen[rI][rJ]>prolifThreshold) { // AND the oxygen concentration is enough for
// division..
// consumption[rI][rJ]=consumptionDivision[Cells[rI][rJ]];
int[] daughter = findEmptySite(rI, rJ);
births++;
Cells[daughter[0]][daughter[1]] = 0;
carriedmutation[daughter[0]][daughter[1]] = 0;
carriedGenome[daughter[0]][daughter[1]] =
initGenome; // resetting space to healthy cell with no mutations
}
}
// }
// cancer division
else if ((vacantSitesCancer(rI, rJ) > 0) && (cell > 0))
if (proliferation[cell]
>= random.nextFloat()) { // If tossing the coin we are to proliferate...
if ((cell == 1)
|| ((cell == 2)
&& (Age[rI][rJ] < maxProDivisions))) { // AND the cell is stem or TAC ...
// if (Oxygen[rI][rJ]>prolifThreshold) { // AND the oxygen concentration is enough for
// division..
// consumption[rI][rJ]=consumptionDivision[Cells[rI][rJ]];
int[] daughter = findEmptySiteCancer(rI, rJ); // and there is space (for cancer)
// if ((daughter[0]==0) || (daughter[0]==size) ||
// (daughter[1]==0)||(daughter[1]==size)) {simulationFinished=true;} // stop sim if a
// cell hits the edge
births++;
if (cell == 1) { // stem cell
stemBirthsTotal[rI][rJ]++;
stemBirthCounter[rI][rJ]++;
if (asymmetricRatio > random.nextFloat()) {
Cells[daughter[0]][daughter[1]] = 1; // placing the stem daughter
stemBirthCounter[daughter[0]][daughter[1]] =
stemBirthCounter[rI][rJ]; // update stem birth counter
carriedmutation[daughter[0]][daughter[1]] =
carriedmutation[rI][rJ]; // inherit mutational status of parent
carriedGenome[daughter[0]][daughter[1]] =
carriedGenome[rI][rJ]; // inherit mutational status of parent
if (mutfreq > random.nextFloat()) { // small chance of mutation
mutationNum++; // advance mutation number
System.out.println(
+carriedmutation[rI][rJ]
+ ", "
+ mutationNum
+ ", "
+ stem_cells_this_TS
+ ", "
+ non_stem_cells_this_TS
+ ", "
+ timestep); // print (parent,child) pair
// tree.put(carriedmutation[rI][rJ], mutationNum);
// timeTree.put(mutationNum, timestep); // hash table stuff
if (0.5 > random.nextFloat()) {
carriedmutation[daughter[0]][daughter[1]] = mutationNum;
genomeToMod = new StringBuilder(carriedGenome[daughter[0]][daughter[1]]);
genomeToMod.setCharAt(
mutationNum - 1, '1'); // daughter carries new carriedGenome
carriedGenome[daughter[0]][daughter[1]] = genomeToMod;
// System.out.println (carriedGenome[rI][rJ]);
// System.out.println (carriedGenome[daughter[0]][daughter[1]]);
} // 50:50 mutate new position daughter
else {
carriedmutation[rI][rJ] = mutationNum; // else mutate original position daughter
genomeToMod = new StringBuilder(carriedGenome[rI][rJ]);
// genomeToMod = carriedGenome[rI][rJ];
carriedGenome[rI][rJ] = genomeToMod;
genomeToMod.setCharAt(
mutationNum - 1, '1'); // original carries new carriedGenome
// System.out.println (carriedGenome[rI][rJ]);
// System.out.println (carriedGenome[daughter[0]][daughter[1]]);
}
}
} else {
Cells[daughter[0]][daughter[1]] = 2; // asymmetric division, daughter is TAC
stemBirthCounter[daughter[0]][daughter[1]] = 0; // reset stem counter
carriedmutation[daughter[0]][daughter[1]] =
carriedmutation[rI][rJ]; // TAC carries parental mutation flag
carriedGenome[daughter[0]][daughter[1]] = carriedGenome[rI][rJ];
} // TAC carries parental genome
// } // redundant from above
// else { // Only if there's hypoxia induced change of symmetric division ratio
// float newASR=asymmetricRatio+0*(hypoxia-Oxygen[rI][rJ]);
// currently OFF by way of 0 the ^^ multiplier.
// if (newASR>random.nextFloat())
// {Cells[daughter[0]][daughter[1]]=1;stemBirthCounter[daughter[0]][daughter[1]]=stemBirthCounter[rI][rJ];}
// else
// {Cells[daughter[0]][daughter[1]]=2;stemBirthCounter[daughter[0]][daughter[1]]=0;}
// // Otherwise differentiate
// }
} else if (cell == 2) { // non-stem division
// TACBirthCounter[rI][rJ]++;
if (Age[rI][rJ] < maxProDivisions - 1) {
Cells[daughter[0]][daughter[1]] = 2;
Age[rI][rJ]++;
Age[daughter[0]][daughter[1]] = Age[rI][rJ];
carriedmutation[daughter[0]][daughter[1]] =
carriedmutation[rI][rJ]; // TAC carries parental mutation flag
carriedGenome[daughter[0]][daughter[1]] =
carriedGenome[rI][rJ]; // TAC carries parental genome
} else {
Cells[daughter[0]][daughter[1]] = 3;
Cells[rI][rJ] = 3;
Age[rI][rJ] = 0;
Age[daughter[0]][daughter[1]] = Age[rI][rJ];
carriedmutation[daughter[0]][daughter[1]] =
carriedmutation[rI][rJ]; // TAC carries parental mutation flag
carriedGenome[daughter[0]][daughter[1]] =
carriedGenome[rI][rJ]; // TAC carries parental genome
}
}
}
} else if (pMotility > random.nextFloat()) { // Migration = not in use
int[] daughter = findEmptySite(rI, rJ);
Cells[daughter[0]][daughter[1]] = cell;
Cells[rI][rJ] = 0;
Age[daughter[0]][daughter[1]] = Age[rI][rJ];
Age[rI][rJ] = 0;
System.err.println("moving " + rI + ", " + rJ);
}
// Aging for mature cells
if (cell == 3) Age[rI][rJ]++;
}
return true;
}
/**
* Assign the set of students (presumably non-incoming-freshmen, but this is not checked) passed
* to their dorm rooms, in a way that does not take race into account. (compare {@link
* #assignByRace}.) As a precursor (side effect) to this, any students already existing in
* upperclass dorms will be removed.
*/
public void assign(Bag students) {
emptyDorms();
// Purge all freshmen. (We're not assigning those.)
Bag upperclassmen = null;
try {
upperclassmen = (Bag) students.clone();
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
for (int x = upperclassmen.size() - 1; x >= 0; x--) {
Student s = (Student) upperclassmen.get(x);
if (s.getGrade() < 2) {
upperclassmen.remove(s);
}
}
for (int x = 0; x < upperclassmen.size(); x++) {
Student s = (Student) upperclassmen.get(x);
if (s.getGrade() < 2) {
// We're only assigning upperclassmen here.
continue;
}
s.leaveRoom();
for (int y = 0; y < dorms.size(); y++) {
if (s.hasRoom()) {
break;
}
Dorm d = (Dorm) dorms.get(y);
if (d.isFull()) {
continue;
}
if (d.isFemaleOnly() && s.getGender() == Student.Gender.MALE) {
continue;
}
int i = 0;
while (i < d.getNumRooms()) {
if (s.hasRoom()) {
break;
}
try {
d.getRoomByIndex(i).addResident(s);
} catch (IllegalArgumentException e) { // System.out.println(e);
}
i++;
}
}
}
// Error testing to see if there are upperclassmen who don't have a
// room/dorms that aren't full
// int q=0;
for (int x = 0; x < upperclassmen.size(); x++) {
Student s = (Student) upperclassmen.get(x);
if (!s.hasRoom()) {
System.out.println(s + " has no upperclass dorm room!");
}
}
}
private void emptyDorms() {
for (int y = 0; y < dorms.size(); y++) {
Dorm d = (Dorm) dorms.get(y);
d.emptyAllRooms();
}
}
/**
* Assign the set of students (presumably non-incoming-freshmen, but this is not checked) students
* passed to their dorm rooms, in a way that <i>does</i> take race into account. (compare {@link
* #assign}.) Minorities will have a higher probability of rooming with other minorities than they
* would otherwise have had. As a precursor (side effect) to this, any students already existing
* in upperclass dorms will be removed.
*/
public void assignByRace(Bag upperclassmen) {
emptyDorms();
boolean foundRoomie;
for (int x = 0; x < upperclassmen.size(); x++) {
foundRoomie = false;
Student s = (Student) upperclassmen.get(x);
// need to leave current room so that they can get a new room
s.leaveRoom();
if (s.getRace() == Student.Race.MINORITY) {
double rollDice = Sim.instance().random.nextDouble();
if (rollDice < Sim.PROB_DUAL_MINORITY) {
for (int m = 0; m < upperclassmen.size(); m++) {
Student r = (Student) upperclassmen.get(m);
// if the potential roommate is the same gender, is a
// minority, and has no room
if (r.getId() == s.getId()) {
continue;
}
if (r.getRace() == Student.Race.MINORITY
&& r.getGender() == s.getGender()
&& !(r.hasRoom())
&& !(s.hasRoom())) {
// find a room that is completely empty
foundRoomie = true;
for (int y = 0; y < dorms.size(); y++) {
Dorm d = (Dorm) dorms.get(y);
if (d.isFull()) {
continue;
}
if (d.isFemaleOnly() && s.getGender() == Student.Gender.MALE) {
continue;
}
int i = 0;
while (i < d.getNumRooms()) {
if (s.hasRoom() && r.hasRoom()) {
break;
}
try {
if (d.getRoomByIndex(i).isEmpty()) {
try {
d.getRoomByIndex(i).addResidents(s, r);
} catch (IllegalArgumentException e) {
System.out.println(e);
}
}
} catch (IllegalArgumentException e) {
}
i++;
}
}
if (!s.hasRoom()) {
// no empty room has been found to put these
// students in; just assign them normally
assignStudent(s);
}
if (!r.hasRoom()) {
assignStudent(r);
}
}
}
if (foundRoomie == false) {
// no same-minority, same-sex, roomless roommate found
assignStudent(s);
}
} else {
// dice roll not under PROB_DUAL_MINORITY
assignStudent(s);
}
} else {
// not a minority, assign normally
assignStudent(s);
}
}
}