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package jasper;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import shared.Timer;
public class TaxCompare {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
public static void main(String[] args) throws FileNotFoundException, IOException {
//Start a timer immediately upon code entrance.
Timer t=new Timer();
TaxCompare x=new TaxCompare(args);
x.process(t);
//Organism cat = new Organism(9, "snake");
//cat.printOrg();
}
/**
* Constructor. Handle inputs.
* @param args Command line arguments
*/
public TaxCompare(String[] args){
String arg=args[0];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(b!=null && b.equalsIgnoreCase("null")){b=null;}
in = b;
}
/*--------------------------------------------------------------*/
/*---------------- Initialization Helpers ----------------*/
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/*---------------- Outer Methods ----------------*/
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/*---------------- Inner Methods ----------------*/
/*--------------------------------------------------------------*/
/**
* Process input sketch comparison file, pass names of organisms (eventually taxon IDs) to matrix.
*
* @param t
* @throws FileNotFoundException
* @throws IOException
*/
void process(Timer t) throws FileNotFoundException, IOException{
//Set for taxon names.
Set<String> nameSet = new HashSet<String>();
//ArrayList of all names in sketch comparison file, not unique values.
ArrayList<String> names = new ArrayList<String>();
//ArrayList of all lines. need these later to fill in values for the matrix
//This will get ugly with large comparisons.
ArrayList<String> lines = new ArrayList<String>();
//Read in file, add header line and add to header variable
try (BufferedReader br = new BufferedReader(new FileReader(in))) {
String line;
while ((line = br.readLine()) != null) {
//if line is the header line, split and assign to variable.
if(line.startsWith("#")) {header=line.split("\t");
} else {
String[] data = line.split("\t");
//make sure the data in column 1 isnt in the header line
//column 1 should be query names
if(!Arrays.asList(header).contains(data[0])) {nameSet.add(data[0]);}
lines.add(line);
}
}
//create matrix and add values
double[][] matrix = new double[nameSet.size() + 1 ][nameSet.size() + 1];
//loop over lines and fill in matrix
for(int i=0; i<lines.size(); i++) {
fillMatrix(matrix, nameSet, lines.toArray()[i]);
}
System.out.println(nameSet);
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
System.out.print(matrix[i][j] + " ");
}
System.out.println();
}
}
t.stop();
System.out.println(t);
}
/**
* Fill matrix with relationship information of organisms output from sketch comparison.
*
* @param matrix Matrix of comparison percentage values.
* @param setNames Set of names of included organisms.
* @param object Line of sketch comparison output file.
*/
void fillMatrix(double[][] matrix, Set<String> setNames, Object object) {
//System.out.println(object);
//cast line as string
String stringLine = (String) object;
//split line
String[] lineData = stringLine.split("\t");
//place both organism names in variables
//qName is the query, column 1
String qName = lineData[0];
String mName = lineData[1];
double similarity = Double.parseDouble(lineData[2]);
//set positions variables
int qPos = -1;
int mPos = -1;
//convert setNames to array that can be iterated over
String[] nameArray = setNames.toArray(new String[setNames.size()]);
//loop over setNames and get each organisms positions within the matrix
for(int i = 0; i<nameArray.length; i++) {
if(nameArray[i].contentEquals(qName)) {qPos = i;}
else if(nameArray[i].contentEquals(mName)) {mPos = i;}
//after finding both name positions, add similarity value to matrix
if(qPos!=-1 && mPos!=-1) {matrix[qPos][mPos] = similarity;}
}
//displays matrix
/*
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
System.out.print(matrix[i][j] + " ");
}
System.out.println();
}*/
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
private String in=null;
private String out=null;
/*--------------------------------------------------------------*/
private long linesProcessed=0;
private long linesOut=0;
private long bytesProcessed=0;
private long bytesOut=0;
/*--------------------------------------------------------------*/
/*---------------- Final Fields ----------------*/
/*--------------------------------------------------------------*/
private String[] header;
//private final FileFormat ffin;
//private final FileFormat ffout;
/*--------------------------------------------------------------*/
/*---------------- Common Fields ----------------*/
/*--------------------------------------------------------------*/
//private PrintStream outstream=System.err;
public static boolean verbose=false;
public boolean errorState=false;
private boolean overwrite=true;
private boolean append=false;
}
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