public int minkeys() {
// if node is the root, minkey is 1
if (getParent() == null) {
return 1;
} else {
return (int) (Math.ceil(degree / 2.0) - 1);
}
}
public static void main(String[] args) {
double a = -191.635;
double b = 43.74;
int c = 16, d = 45;
System.out.printf("The absolute value " + "of %.3f is %.3f%n", a, abs(a));
System.out.printf("The ceiling of " + "%.2f is %.0f%n", b, Math.ceil(b));
System.out.printf("The floor of " + "%.2f is %.0f%n", b, Math.floor(b));
System.out.printf("The rint of %.2f " + "is %.0f%n", b, Math.rint(b));
System.out.printf("The max of %d and " + "%d is %d%n", c, d, Math.max(c, d));
System.out.printf("The min of of %d " + "and %d is %d%n", c, d, Math.min(c, d));
}
/**
* Makes genotype AB calls. <code>genotypeCalling</code> determines which loci are genotype AB
* (heterozygous) based on A and B allelesl signal of the normal sample.
*
* @param p probe set intensity data
*/
private void genotypeCalling(ProbeSetIntensityData[] p) throws IOException {
int numGenotypingProbeSet = 0;
double meanPmA = 0;
double meanPmB = 0;
for (int i = 0; i < p.length; i++) {
if (p[i].probeSetType == FusionGeneChipProbeSetType.GenotypingProbeSetType) {
meanPmA += (p[i].pmA == 0 ? 0 : log2(p[i].pmA));
meanPmB += (p[i].pmB == 0 ? 0 : log2(p[i].pmB));
numGenotypingProbeSet++;
}
}
meanPmA = meanPmA / numGenotypingProbeSet;
meanPmB = meanPmB / numGenotypingProbeSet;
double k = meanPmB / meanPmA;
class DistanceToLine implements Comparable<DistanceToLine> {
public Double dist;
public int index;
public boolean equals(DistanceToLine d) {
return (dist == d.dist);
}
public int compareTo(DistanceToLine d) {
return dist.compareTo(d.dist);
}
}
DistanceToLine[] s = new DistanceToLine[numGenotypingProbeSet];
int j = 0;
for (int i = 0; i < p.length; i++) {
if (p[i].probeSetType == FusionGeneChipProbeSetType.GenotypingProbeSetType) {
s[j] = new DistanceToLine();
s[j].dist = Math.abs(log2(p[i].pmB) - k * log2(p[i].pmA));
s[j].index = i;
j++;
}
}
Arrays.sort(s);
// Add for testing
// BufferedWriter genotypeCallingFile = null;
// try {
// genotypeCallingFile = new BufferedWriter(new FileWriter("genoTypeCalling_s_dist.csv"),
// 30*1024*1024);
//
// for (int i = 0; i < numGenotypingProbeSet; i ++) {
// String entry = s[i].dist + "," + s[i].index;
// genotypeCallingFile.write(entry.toCharArray());
// genotypeCallingFile.newLine();
// }
//
// } finally {
// if (genotypeCallingFile != null) {
// genotypeCallingFile.close();
// }
// }
////
for (int i = 0; i < Math.ceil(numGenotypingProbeSet * 0.20); i++) {
p[s[i].index].isGenotypeAB = true;
}
// BufferedWriter genotypeCallingFile = null;
// try {
// genotypeCallingFile = new BufferedWriter(new
// FileWriter("genoTypeCallingData.csv"), 30*1024*1024);
// for (int i = 0; i < p.length; i ++) {
// if (p[i].probeSetType == FusionGeneChipProbeSetType.GenotypingProbeSetType) {
// String entry = (p[i].pmA == 0 ? 0:log2(p[i].pmA)) + "," + (p[i].pmB == 0 ?
// 0:log2(p[i].pmB))
// + "," + (p[i].isGenotypeAB? 1:0);
// genotypeCallingFile.write(entry.toCharArray());
// genotypeCallingFile.newLine();
// }
// }
// } finally {
// if (genotypeCallingFile != null) {
// genotypeCallingFile.close();
// }
// }
}
public int getW_mls() {
return (int) (Math.ceil(w * mlsPerMm));
}
public int insertionRedistribute() {
// get val and ptr from newly created node
int val = this.getNext().getKey(1);
Node ptr = this.getNext().getPtr(1);
boolean stop = false;
int p = 1;
while (p <= this.getLast() && !stop) {
stop = this.getKey(p) > this.getNext().getKey(1);
if (!stop) {
p++;
}
}
// create two arrays to store keys and ptrs
int size = this.getLast() + this.getNext().getLast() + 1;
int[] allKeys = new int[size];
Node[] allPtrs = new Node[size];
// store keys and ptrs of current node at position 1 to p-1 into array
allPtrs[0] = this.getPtr(0);
for (int k = 1; k < p; k++) {
allKeys[k] = this.getKey(k);
allPtrs[k] = this.getPtr(k);
}
// store first key and ptr of next node
allKeys[p] = val;
allPtrs[p] = ptr;
// store keys and ptrs of current node at position p to lastindex into array
for (int k = p; k <= this.getLast(); k++) {
allKeys[k + 1] = this.getKey(k);
allPtrs[k + 1] = this.getPtr(k);
}
// decide middle position and new size for current and next node
int middle = (int) Math.ceil((size) / 2.0);
int newSize = middle - 1;
int newSizeNext = size - 1 - middle;
// reset lastindex of current node and store keys and ptrs into current node
this.lastindex = newSize;
this.ptrs[0] = allPtrs[0];
this.ptrs[0].setParent(new Reference(this, 0, false));
for (int k = 1; k <= this.getLast(); k++) {
this.keys[k] = allKeys[k];
this.ptrs[k] = allPtrs[k];
this.ptrs[k].setParent(new Reference(this, k, false));
}
// reset lastindex of next node and store keys and ptrs into next node
this.getNext().lastindex = newSizeNext;
this.getNext().ptrs[0] = allPtrs[middle];
this.getNext().ptrs[0].setParent(new Reference(this.getNext(), 0, false));
for (int k = 1; k <= this.getNext().getLast(); k++) {
this.getNext().keys[k] = allKeys[middle + k];
this.getNext().ptrs[k] = allPtrs[middle + k];
this.getNext().ptrs[k].setParent(new Reference(this.getNext(), k, false));
}
// return value to be updated in the parent
return allKeys[middle];
}
public int deletionRedistribute() {
// decide middle position and new size of current and next node
int size = this.getLast() + this.getNext().getLast() + 2;
int middle = (int) Math.ceil(size / 2.0);
int newSize = middle - 1;
int newSizeNext = size - 1 - middle;
// get special key and val to be inserted into array
int val = this.getNext().getParent().getNode().getKey(this.getNext().getParent().getIndex());
Node ptr = this.getNext().getPtr(0);
// create two arrays to store keys and ptrs
int[] allKeys = new int[size];
Node[] allPtrs = new Node[size];
// store keys and ptrs from current node
allPtrs[0] = this.getPtr(0);
for (int k = 1; k <= this.getLast(); k++) {
allKeys[k] = this.getKey(k);
allPtrs[k] = this.getPtr(k);
}
// insert special key and ptr
allKeys[this.getLast() + 1] = val;
allPtrs[this.getLast() + 1] = ptr;
// store keys and ptrs from next node
for (int k = 1; k <= this.getNext().getLast(); k++) {
allKeys[this.getLast() + 1 + k] = this.getNext().getKey(k);
allPtrs[this.getLast() + 1 + k] = this.getNext().getPtr(k);
}
// update lastindex of current and next node
this.lastindex = newSize;
this.getNext().lastindex = newSizeNext;
// update keys and ptrs in current node
this.ptrs[0] = allPtrs[0];
this.ptrs[0].setParent(new Reference(this, 0, false));
for (int k = 1; k <= this.getLast(); k++) {
this.keys[k] = allKeys[k];
this.ptrs[k] = allPtrs[k];
this.ptrs[k].setParent(new Reference(this, k, false));
}
// update parent
this.getNext().getParent().getNode().keys[this.getNext().getParent().getIndex()] =
allKeys[middle];
// update keys and ptrs in next node
this.getNext().ptrs[0] = allPtrs[middle];
this.getNext().ptrs[0].setParent(new Reference(this.getNext(), 0, false));
for (int k = 1; k <= this.getNext().getLast(); k++) {
this.getNext().keys[k] = allKeys[middle + k];
this.getNext().ptrs[k] = allPtrs[middle + k];
this.getNext().ptrs[k].setParent(new Reference(this.getNext(), k, false));
}
// return value to be updated in the parent
return this.getKey(middle);
}