src/org/vamsas/test/objects/Core.java

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