4 package uk.ac.vamsas.test.objects;
6 import org.apache.commons.logging.Log;
7 import org.apache.commons.logging.LogFactory;
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;
16 * test XSD-Java binding classes in uk.ac.vamsas.objects.core
19 static Log log = LogFactory.getLog(Core.class);
23 * complete any automatically completable entries in the dataset
26 public static String user = "uk.ac.vamsas.test.objects.Core";
28 public static void complete(DataSet ds) {
29 Sequence[] q = ds.getSequence();
30 for (int i=0,j=q.length; i<j; i++) {
32 q[i].setEnd(q[i].getSequence().length()+i+1);
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"));
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));
53 // TODO: create annotations
60 public static void main(String[] args) {
63 * test constants and controlled vocab utils
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);
74 * Test utils and autogenerated Vobject interfaces
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);