*/
package org.vamsas.test.objects;
-import org.vamsas.objects.core.Alignment;
-import org.vamsas.objects.core.AlignmentSequence;
-import org.vamsas.objects.core.DataSet;
-import org.vamsas.objects.core.Sequence;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.utils.Seq;
-import org.vamsas.objects.utils.SymbolDictionary;
+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("org.vamsas.test.objects.Core");
+
/**
*
* 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++) {
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.addAlignmentSequence(new AlignmentSequence());
+ 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) {
- // TODO Auto-generated method stub
-
+ VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() },
+ ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
+ VersionEntries.latestVersion());
+ ArchiveReports.reportDocument(doc, null, true);
}
-
}