Biostar45366.java

    import java.io.*;
    import java.util.*;
    
    class Biostar45366
    	{
    	private BufferedReader in;
    	private String buffer;
    	private Map<String,Term> id2term=new HashMap<String,Term>();
    	private class Term
    		{
    		String id;
    		String name;
    		String def;
    		Set<String> children=new HashSet<String>();
    		Set<String> is_a=new HashSet<String>();
    		
    		int depth()
    			{
    			int min_child=0;
    			for(String p:is_a)
    				{
    				Term parent=id2term.get(p);
    				if(parent==null)
    					{
    					System.err.println("Cannot get "+p);
    					continue;
    					}
    				int n2= parent.depth();
    				if(min_child==0 || n2<min_child) min_child=n2;
    				}
    			return 1+ min_child;
    			}
    
    		public String toString()
    			{
    			return id+"\t"+name+"\t"+is_a;
    			}
    		}
    	
    	private Set<String> getAllDescendantById(String id)
    		{
    		Set<String> set=new HashSet<String>();
    		set.add(id);
    		Term t=id2term.get(id);
    		for(String c:t.children)
    			{
    			set.addAll(getAllDescendantById(c));
    			}
    		return set;
    		}
    
    
    	private Term getTermById(String id,boolean create)
    		{
    		Term t= this.id2term.get(id);
    		if(t==null && create)
    			{
    			t=new Term();
    			t.id=id;
    			t.name=id;
    			t.def=id;
    			this.id2term.put(id,t);
    			}
    		return t;
    		}
    	
    	private static String nocomment(String s)
    		{
    		int excl=s.indexOf('!');
    		if(excl!=-1) s=s.substring(0,excl);
    		return s.trim();
    		}
    
    	private String next() throws IOException
    		{
    		if(buffer!=null)
    			{
    			String s=buffer;
    			buffer=null;
    			return s;
    			}
    		return in.readLine();
    		}
    	
    	private void parseTerm() throws IOException
    		{
    		Term t=null;
    		String line;
    		while((line=next())!=null)
    			{
    			if(line.startsWith("["))
    				{
    				this.buffer=line;
    				break;
    				}
    			int colon=line.indexOf(':');
    			if(colon==-1) continue;
    			if(line.startsWith("id:") && t==null)
    				{
    				t=getTermById(line.substring(colon+1).trim(),true);
    				continue;
    				}
    			if(t==null) continue;
    			if(line.startsWith("name:"))
    				{
    				t.name=nocomment(line.substring(colon+1));
    				continue;
    				}
    			else if(line.startsWith("def:"))
    				{
    				t.def=nocomment(line.substring(colon+1));
    				continue;
    				}
    			else if(line.startsWith("is_a:"))
    				{
    				String rel=nocomment(line.substring(colon+1));
    				t.is_a.add(rel);
    				Term parent=getTermById(rel,true);
    				parent.children.add(t.id);
    				continue;
    				}
    			}
    		}
    	private void parse() throws IOException
    		{
    		in=new BufferedReader(new InputStreamReader(System.in));
    		String line;
    		while((line=next())!=null)
    			{
    			if(line.equals("[Term]")) parseTerm();
    			}
    		in.close();
    		}
    	public static void main(String args[]) throws IOException
    		{
    		Biostar45366 app=new Biostar45366();
    		app.parse();
    		int level=1;
    		boolean found=true;
    		while(found)
    			{
    			found=false;
    			for(Term t: app.id2term.values())
    				{
    				if(t.depth()==level)
    					{
    					System.out.println(""+level+"\t"+t);
    					found=true;
    					}
    				}
    			level++;		
    			}
    		for(String id: app.getAllDescendantById("GO:0001783"))
    			{
    			System.out.println(app.id2term.get(id));
    			}
    		}
    	}

thank you very much for this peace of code :) very helpful! cheers from Portugal