package com.ppfold.algo.extradata;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.util.Iterator;
import java.util.List;
import java.util.regex.Pattern;
import com.ppfold.algo.MatrixTools;
public class BinaryStringDataDiffBp implements ExtraData {
private int type = 0;
private int[] data; //contains the actual measurement numbers (data)
//Probabilities must always be given as P(data|unpaired) or P(data|paired).
private float[] dataProbGivenInnerPair; //P(data|model), unpaired case
private float[] dataProbGivenOuterPair;
private float[] dataProbGivenUnpaired; //P(data|model), paired case
public int getType(){
return type;
}
public boolean isEmpty(int i)
{
return data[i]==-999;
}
public float getProbabilityGivenOuterPaired(int position1, int position2) {
return getProbabilityGivenOuterPair(position1)*getProbabilityGivenOuterPair(position2);
}
public float getProbabilityGivenInnerPaired(int position1, int position2) {
return getProbabilityGivenInnerPair(position1)*getProbabilityGivenInnerPair(position2);
}
public float getProbabilityGivenInnerPair(int position) {
return dataProbGivenInnerPair[position];
}
public float getProbabilityGivenOuterPair(int position) {
return dataProbGivenOuterPair[position];
}
public float getProbabilityGivenUnpaired(int position) {
return dataProbGivenUnpaired[position];
}
public void importData(String filename, int sequencelength) throws Exception{
//read the data
BufferedInputStream stream = null;
try {
stream = new BufferedInputStream(new FileInputStream(filename));
} catch (FileNotFoundException e) {
System.err.println("Binary string input file " + filename + " could not be read!");
throw new Exception(e);
}
readData_toStream(stream, sequencelength);
}
public void readData_toStream(BufferedInputStream stream, int sequencelength) throws Exception{
//the CLC import plugin uses the following line:
//public ClcObject[] doImport(BufferedInputStream stream, String name, Activity activity) throws IOException, ParseException, PersistenceException {
//the same stream will be passed here to ease the import process later.
//create the data containers
this.data = new int[sequencelength];
this.dataProbGivenInnerPair = new float[sequencelength];
this.dataProbGivenOuterPair = new float[sequencelength];
this.dataProbGivenUnpaired = new float[sequencelength];
if(stream!=null){
String line = "";
try{
int l = stream.available();
byte[] bytes = new byte[l];
stream.read(bytes);
stream.close();
String data_string = new String(bytes);
String[] lines = data_string.split("\n");
int data_size = lines.length;
int [] readdata_index = new int[data_size];
int [] readdata_data = new int[data_size];
// Create a pattern to match different kinds of separators
Pattern p = Pattern.compile("[,\\s]+");
//DO NOT ignore first line...
for(int i = 0; i<lines.length; i++){
line = lines[i];
String splitline[] = p.split(line.trim());
if(splitline.length == 2){
readdata_index[i] = Integer.valueOf(splitline[0])-1; //SHAPE data files are numbered from 1; Java numbers from 0
readdata_data[i] = Integer.valueOf(splitline[1]);
}
}
//initialize all data values to -999
for(int i = 0; i<this.data.length; i++){
data[i] = -999;
}
//set the appropriate data values to the read ones
for(int i = 0; i<data_size; i++){
//
data[readdata_index[i]] = readdata_data[i];
}
//calculate probabilities
calcProbabilities();
}
catch(Exception e){
System.err.println("An exception occured while attempting to read or interpret the binary string (diffbp) sequence data. ");
throw new Exception(e);
}
}
else{
System.err.println("Input stream was null, binary string (diffbp) sequence data could not be loaded.");
}
}
private void calcProbabilities(){
int n = data.length;
for(int i = 0; i<n; i++){
//For each data point, calculate the probability of data given paired/unpaired.
//If no data, set both to 1 (so other info fills them in)
if(data[i] == -999){
//ignore
dataProbGivenInnerPair[i] = 1;
dataProbGivenOuterPair[i] = 1;
dataProbGivenUnpaired[i] = 1;
//System.out.println("INDETERMINED DATA AT POS " + i);
continue;
}
dataProbGivenInnerPair[i] = data[i]==2?1:Float.MIN_VALUE;
dataProbGivenOuterPair[i] = data[i]==1?1:Float.MIN_VALUE;
dataProbGivenUnpaired[i] = data[i]==0?1:Float.MIN_VALUE;
}
}
public void transformToAlignment(String gappedseq) {
int n = gappedseq.length();
int[] data_a = new int[n];
float[] dataProbGivenInnerPair_a = new float[n];
float[] dataProbGivenOuterPair_a = new float[n];
float[] dataProbGivenUnpaired_a = new float[n];
int cnt = 0; //counts sequence positions
for(int i = 0; i<n; i++){
//step alignment positions
if(MatrixTools.isGap(gappedseq.charAt(i))){
//if there's a gap, set probabilities to 1
data_a[i] = -999; //no data for that column
dataProbGivenInnerPair_a[i] = 1;
dataProbGivenOuterPair_a[i] = 1;
dataProbGivenUnpaired_a[i] = 1;
}
else{
data_a[i] = data[cnt];
dataProbGivenInnerPair_a[i] = dataProbGivenInnerPair[cnt];
dataProbGivenOuterPair_a[i] = dataProbGivenOuterPair[cnt];
dataProbGivenUnpaired_a[i] = dataProbGivenUnpaired[cnt];
cnt++;
}
//Prevent division by zero by setting 0's to a very small finite number instead
if(dataProbGivenInnerPair_a[i]==0 && dataProbGivenOuterPair_a[i]==0 && dataProbGivenUnpaired_a[i]==0){
dataProbGivenInnerPair_a[i]=Float.MIN_VALUE;
dataProbGivenOuterPair_a[i] =Float.MIN_VALUE;
dataProbGivenUnpaired_a[i]=Float.MIN_VALUE;
}
//
// System.out.println("i=" + i + ", data = " + data_a[i] + ": inner pairing="+dataProbGivenInnerPair_a[i] + ", " +
// ": outer pairing="+dataProbGivenOuterPair_a[i] + ", " +
// "unpaired="+dataProbGivenUnpaired_a[i]);
// System.out.println(i + " " + data_a[i] + " "+ dataProbGivenInnerPair_a[i] + " " +
// " "+dataProbGivenOuterPair_a[i] + " " +
// " "+dataProbGivenUnpaired_a[i]);
}
this.data = data_a;
this.dataProbGivenInnerPair = dataProbGivenInnerPair_a;
this.dataProbGivenOuterPair = dataProbGivenOuterPair_a;
this.dataProbGivenUnpaired = dataProbGivenUnpaired_a;
}
public void removeColumns(List<Integer> leftoutcolumns){
Iterator<Integer> iter = leftoutcolumns.iterator();
int leaveout = 0;
int from = 0;
int cnt = 0; //counts position in new thing
int[] data_a = new int[this.data.length - leftoutcolumns.size()];
float[] dataProbGivenInnerPair_a = new float[this.data.length - leftoutcolumns.size()];
float[] dataProbGivenOuterPair_a = new float[this.data.length - leftoutcolumns.size()];
float[] dataProbGivenUnpaired_a = new float[this.data.length - leftoutcolumns.size()];
while(iter.hasNext()){
leaveout = iter.next();
for(int i = from; i<leaveout; i++){
data_a[cnt] = this.data[i];
dataProbGivenInnerPair_a[cnt] = dataProbGivenInnerPair[i];
dataProbGivenOuterPair_a[cnt] = dataProbGivenOuterPair[i];
dataProbGivenUnpaired_a[cnt] = dataProbGivenUnpaired[i];
cnt++;
}
from = leaveout+1;
}
//do the last part part
for(int i = from; i<data.length; i++){
data_a[cnt] = this.data[i];
dataProbGivenInnerPair_a[cnt] = dataProbGivenInnerPair[i];
dataProbGivenOuterPair_a[cnt] = dataProbGivenOuterPair[i];
dataProbGivenUnpaired_a[cnt] = dataProbGivenUnpaired[i];
cnt++;
}
this.data = data_a;
this.dataProbGivenInnerPair = dataProbGivenInnerPair_a;
this.dataProbGivenOuterPair = dataProbGivenOuterPair_a;
this.dataProbGivenUnpaired = dataProbGivenUnpaired_a;
//System.out.println("Size of new auxdata data: " + data.length);
}
}