4 package org.vamsas.test.objects;
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;
15 * test XSD-Java binding classes in org.vamsas.objects.core
18 static Log log = LogFactory.getLog("org.vamsas.test.objects.Core");
22 * complete any automatically completable entries in the dataset
25 public static String user = "org.vamsas.test.objects.Core";
27 public static void complete(DataSet ds) {
28 Sequence[] q = ds.getSequence();
29 for (int i=0,j=q.length; i<j; i++) {
31 q[i].setEnd(q[i].getSequence().length()+i+1);
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"));
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));
52 // TODO: create annotations
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);