src/uk/ac/vamsas/test/objects/Core.java

   1 /**
   2  *
   3  */
   4 package uk.ac.vamsas.test.objects;
   5
   6 import org.apache.commons.logging.Log;
   7 import org.apache.commons.logging.LogFactory;
   8
   9 import uk.ac.vamsas.objects.core.*;
  10 import uk.ac.vamsas.objects.utils.*;
  11 import uk.ac.vamsas.objects.utils.document.*;
  12 import uk.ac.vamsas.test.simpleclient.ArchiveReports;
  13
  14 /**
  15  * @author jim
  16  * test XSD-Java binding classes in uk.ac.vamsas.objects.core
  17  */
  18 public class Core {
  19   static Log log = LogFactory.getLog(Core.class);
  20
  21   /**
  22    *
  23    * complete any automatically completable entries in the dataset
  24    * @param ds
  25    */
  26   public static String user = "uk.ac.vamsas.test.objects.Core";
  27
  28   public static void complete(DataSet ds) {
  29     Sequence[] q = ds.getSequence();
  30     for (int i=0,j=q.length; i<j; i++) {
  31       q[i].setStart(i+1);
  32       q[i].setEnd(q[i].getSequence().length()+i+1);
  33     }
  34   }
  35
  36   public static VAMSAS getDemoVamsas() {
  37      VAMSAS v=new VAMSAS();
  38      DataSet ds = new DataSet();
  39      ds.addSequence(Seq.newSequence("Dummy1","ASDFLEQ",SymbolDictionary.STANDARD_AA, 5, 11));
  40      ds.addSequence(Seq.newSequence("Dummy2","ASFLEQ",SymbolDictionary.STANDARD_AA, 5, 10));
  41      ds.addSequence(Seq.newSequence("Dummy3","ADFEQ",SymbolDictionary.STANDARD_AA, 3, 7));
  42      ds.setProvenance(ProvenanceStuff.newProvenance(user, "constructed some dummy sequences"));
  43      complete(ds);
  44      v.addDataSet(ds);
  45      Alignment al = new Alignment();
  46      al.setProvenance(ProvenanceStuff.newProvenance(user, "Created dummy alignment"));
  47      //   rely on newAlignmentSequence to set start/end correctly
  48      al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds.getSequence(0), -1, -1));
  49      al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds.getSequence(1), -1, -1));
  50      al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds.getSequence(2), -1, -1));
  51      al.setGapChar("-");
  52      ds.addAlignment(al);
  53      // TODO: create annotations
  54      // TODO: create tree
  55      return v;
  56    }
  57   /**
  58    * @param args
  59    */
  60   public static void main(String[] args) {
  61
  62     /**
  63      * test constants and controlled vocab utils
  64      */
  65     System.out.println("VersionEntries.compare(invalid, ALPHA) returned "+VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
  66     System.out.println("VersionEntries.compare(ALPHA, invalid) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));
  67     System.out.println("VersionEntries.compare(BETA, ALPHA) returned "+VersionEntries.compare(VersionEntries.BETA_VERSION,VersionEntries.ALPHA_VERSION));
  68     System.out.println("VersionEntries.compare(ALPHA, BETA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.BETA_VERSION));
  69     System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.ALPHA_VERSION));
  70     System.out.println("VersionEntries.compare(invalid, invalid) returned "+VersionEntries.compare("invalid", "invalid"));
  71     System.out.println("VersionEntries.latestVersion()="+VersionEntries.latestVersion()+
  72         ", dict_aa="+SymbolDictionary.STANDARD_AA+", dict_na="+SymbolDictionary.STANDARD_NA);
  73     /**
  74      * Test utils and autogenerated Vobject interfaces
  75      */
  76
  77     VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() },
  78         ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
  79         VersionEntries.latestVersion());
  80     ArchiveReports.reportDocument(doc, null, true, System.out);
  81   }
  82 }