import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.program.das.*;

import java.net.*;
import java.io.*;
import java.util.*;

public class TestDASG {
    public static void main(String[] args) throws Exception {
        if (args.length < 4) {
            throw new Exception("java das.TestDAS <url> <seq> <min> <max> [ann*]");
        }
        String dbURLString = args[0];
        String seqName = args[1];
        int min = Integer.parseInt(args[2]);
        int max = Integer.parseInt(args[3]);
        
        URL dbURL = new URL(dbURLString);
        
        DASSequenceDB dasDB = new DASSequenceDB(dbURL);
        
        DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName);
        for(int i = 4; i < args.length; i++) {
            dasSeq.addAnnotationSource(new URL(args[i]));
        }
        // dasSeq.addAnnotationSource(annoURL);
        // dasSeq.addAnnotationSource(miscURL);
        System.out.println("Length: " + dasSeq.length());
        System.out.println("1st 10 bases: " + dasSeq.subStr(1, 10));
        
        printFeatures(dasSeq, new FeatureFilter.OverlapsLocation(new RangeLocation(min, max)), System.out, "");
        // printFeatures(dasSeq, System.out, "");
    }
    
    public static void printFeatures(FeatureHolder fh, 
                                     FeatureFilter ff,
                                     PrintStream pw,
                                     String prefix)
        throws Exception
    {
        
        for (Iterator i = fh.filter(ff, true).features(); i.hasNext(); ) {
            Feature f = (Feature) i.next();
            pw.print(prefix);
            if (f instanceof ComponentFeature) {
                pw.print(f.getType() + " : " + f.getSource() + ":" + ((ComponentFeature)f).getStrand());
            } else if (f instanceof StrandedFeature) {
                pw.print(f.getType() + " : " + f.getSource() + ":" +  ((StrandedFeature)f).getStrand());
            } else {
                pw.print(f.getType() + " : " + f.getSource());
            }
            
            
            
            pw.print(" at ");
            pw.print(f.getLocation().toString());
            try {
                String id=null;
                if (f instanceof ComponentFeature) {
                    id="components/" + ((ComponentFeature)f).getComponentSequence().getName();
                } else {
                    id = (String) f.getAnnotation().getProperty(DASSequence.PROPERTY_FEATUREID);
                }
                pw.print(" (" + id + ')');
            } catch (NoSuchElementException ex) {
            }
            pw.println();
            printFeatures(f, ff, pw, prefix + "    ");
        }
    }
}