/**
 * 
 */
package org.vamsas.test.objects;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.vamsas.objects.core.*;
import org.vamsas.objects.utils.*;
import org.vamsas.objects.utils.document.*;
import org.vamsas.test.simpleclient.ArchiveReports;

/**
 * @author jim
 * test XSD-Java binding classes in org.vamsas.objects.core
 */
public class Core {
  static Log log = LogFactory.getLog(Core.class);

  /**
   * 
   * complete any automatically completable entries in the dataset
   * @param ds
   */
  public static String user = "org.vamsas.test.objects.Core";
  
  public static void complete(DataSet ds) {
    Sequence[] q = ds.getSequence();
    for (int i=0,j=q.length; i<j; i++) {
      q[i].setStart(i+1);
      q[i].setEnd(q[i].getSequence().length()+i+1);
    }
  }  

  public static VAMSAS getDemoVamsas() {
     VAMSAS v=new VAMSAS();
     DataSet ds = new DataSet();
     ds.addSequence(Seq.newSequence("Dummy1","ASDFLEQ",SymbolDictionary.STANDARD_AA, 5, 11));
     ds.addSequence(Seq.newSequence("Dummy2","ASFLEQ",SymbolDictionary.STANDARD_AA, 5, 10));
     ds.addSequence(Seq.newSequence("Dummy3","ADFEQ",SymbolDictionary.STANDARD_AA, 3, 7));
     ds.setProvenance(ProvenanceStuff.newProvenance(user, "constructed some dummy sequences"));
     complete(ds);
     v.addDataSet(ds);
     Alignment al = new Alignment();
     al.setProvenance(ProvenanceStuff.newProvenance(user, "Created dummy alignment"));
     //   rely on newAlignmentSequence to set start/end correctly
     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds.getSequence(0), -1, -1)); 
     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds.getSequence(1), -1, -1)); 
     al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds.getSequence(2), -1, -1)); 
     al.setGapChar("-");
     ds.addAlignment(al);
     // TODO: create annotations
     // TODO: create tree
     return v;
   }
  /**
   * @param args
   */
  public static void main(String[] args) {
    
    /**
     * test constants and controlled vocab utils
     */
    System.out.println("VersionEntries.compare(invalid, ALPHA) returned "+VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
    System.out.println("VersionEntries.compare(ALPHA, invalid) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));      
    System.out.println("VersionEntries.compare(BETA, ALPHA) returned "+VersionEntries.compare(VersionEntries.BETA_VERSION,VersionEntries.ALPHA_VERSION));
    System.out.println("VersionEntries.compare(ALPHA, BETA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.BETA_VERSION));
    System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.ALPHA_VERSION));
    System.out.println("VersionEntries.compare(invalid, invalid) returned "+VersionEntries.compare("invalid", "invalid"));
    System.out.println("VersionEntries.latestVersion()="+VersionEntries.latestVersion()+
        ", dict_aa="+SymbolDictionary.STANDARD_AA+", dict_na="+SymbolDictionary.STANDARD_NA);
    /**
     * Test utils and autogenerated Vobject interfaces
     */
    
    VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() }, 
        ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
        VersionEntries.latestVersion());
    ArchiveReports.reportDocument(doc, null, true, System.out);
  }
}