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package pp2.go;
import java.io.BufferedReader;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
/**
* example constructor:
* Relations test = new Relations("./../data/deductiveClosureGO.txt","./../data/goterm.txt",true);
* noCC stands for no Cellular Component (for CAFA, true, since CC is ignored)
* @author Mark Heron
*
*/
public class Relations {
HashMap<String, String[]> ahnen;
HashMap<String, String> type;
boolean noCC;
public Relations(String closure, String terms, boolean noCC) {
BufferedReader input;
this.noCC = noCC;
// create type
type = new HashMap<String, String>();
input = pp2.tools.Tools.openFile(terms);
try {
String line;
while((line = input.readLine()) != null) {
String[] split = line.split("\t");
if(split.length > 4) {
String gokey = split[3];
String typevalue = split[2];
type.put(gokey, typevalue);
}
}
input.close();
} catch (Exception e) {
e.printStackTrace();
}
// create ancestors/parents
ahnen = new HashMap<String, String[]>();
HashMap<String, HashSet<String>> ahnen_tmp = new HashMap<String, HashSet<String>>();
input = pp2.tools.Tools.openFile(closure);
try {
String line;
while((line = input.readLine()) != null) {
if(line.startsWith("GO:")) {
String[] split = line.split("\t");
String key = split[0];
String value = split[2];
if(getType(key).length() > 0 && getType(value).length() > 0 ) {
if(isTypeofInterst(key) && isTypeofInterst(value)) {
if(ahnen_tmp.containsKey(key)) {
ahnen_tmp.get(key).add(value);
} else {
HashSet<String> ll = new HashSet<String>();
ll.add(value);
ahnen_tmp.put(key, ll);
}
}
}
}
}
input.close();
} catch (Exception e) {
e.printStackTrace();
}
for (String key : ahnen_tmp.keySet()) {
String[] values = new String[0];
values = ahnen_tmp.get(key).toArray(values);
ahnen.put(key, values);
}
}
public String[] getAncestors(String goterm) {
if(ahnen.containsKey(goterm)) {
return ahnen.get(goterm);
} else {
return new String[0];
}
}
public String getType(String goterm) {
if (type.containsKey(goterm)) {
return type.get(goterm);
} else {
return "";
}
}
public boolean isTypeofInterst(String goterm) {
if(!type.containsKey(goterm)) { // only happens for GO:0048220
return true; // no idea why it is missing in goterm.txt
}
String tmp = type.get(goterm);
if(tmp.equals("biological_process") || tmp.equals("molecular_function") || tmp.equals("cellular_component")) {
return true;
} else if (!noCC && tmp.equals("cellular_component")){
return true;
} else {
return false;
}
}
public String[][] getExclusivePaths(String[] goterms) {
String[][] results = new String[goterms.length][];
HashSet<String> allreadydone = new HashSet<String>();
for (int i = 0; i < goterms.length; i++) {
String goterm = goterms[i];
String[] anc = getAncestors(goterm);
HashSet<String> exc = new HashSet<String>();
for (String a : anc) {
if( ! allreadydone.contains(a)) {
exc.add(a);
allreadydone.add(a);
}
}
String[] tmp = new String[0];
results[i] = (String[]) exc.toArray(tmp);
}
return results;
}
public static void main(String[] args) {
Relations test = new Relations("C:\\Dokumente und Einstellungen\\murgs\\Eigene Dateien\\Studium\\9. Semester\\PP2\\ProteinPrediction2\\data\\deductiveClosureGO.txt"
,"C:\\Dokumente und Einstellungen\\murgs\\Eigene Dateien\\Studium\\9. Semester\\PP2\\ProteinPrediction2\\data\\goterm.txt",true);
String[] tmp = {"GO:999","GO:0005737","GO:0019134","GO:0000287","GO:0003977","GO:0000902","GO:0007047","GO:0009103","GO:0009252","GO:0008360","GO:0046872","GO:0008152"};
DAG dag = new DAG(test, tmp);
System.out.println(Arrays.toString(dag.getNodes()));
System.out.println(Arrays.toString(dag.getLeaves()));
System.out.println(Arrays.toString(dag.getAncestors("GO:0005737")));
System.out.println(Arrays.deepToString(test.getExclusivePaths(tmp)));
}
}
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