refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@289 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/test/objects/Core.java b/src/uk/ac/vamsas/test/objects/Core.java
new file mode 100644 (file)
index 0000000..58eccea
--- /dev/null
+++ b/src/uk/ac/vamsas/test/objects/Core.java
@@ -0,0 +1,82 @@
+/**
+ * 
+ */
+package uk.ac.vamsas.test.objects;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.objects.utils.*;
+import uk.ac.vamsas.objects.utils.document.*;
+import uk.ac.vamsas.test.simpleclient.ArchiveReports;
+
+/**
+ * @author jim
+ * test XSD-Java binding classes in uk.ac.vamsas.objects.core
+ */
+public class Core {
+  static Log log = LogFactory.getLog(Core.class);
+
+  /**
+   * 
+   * complete any automatically completable entries in the dataset
+   * @param ds
+   */
+  public static String user = "uk.ac.vamsas.test.objects.Core";
+  
+  public static void complete(DataSet ds) {
+    Sequence[] q = ds.getSequence();
+    for (int i=0,j=q.length; i<j; i++) {
+      q[i].setStart(i+1);
+      q[i].setEnd(q[i].getSequence().length()+i+1);
+    }
+  }  
+
+  public static VAMSAS getDemoVamsas() {
+     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.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) {
+    
+    /**
+     * test constants and controlled vocab utils
+     */
+    System.out.println("VersionEntries.compare(invalid, ALPHA) returned "+VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
+    System.out.println("VersionEntries.compare(ALPHA, invalid) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));      
+    System.out.println("VersionEntries.compare(BETA, ALPHA) returned "+VersionEntries.compare(VersionEntries.BETA_VERSION,VersionEntries.ALPHA_VERSION));
+    System.out.println("VersionEntries.compare(ALPHA, BETA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.BETA_VERSION));
+    System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.ALPHA_VERSION));
+    System.out.println("VersionEntries.compare(invalid, invalid) returned "+VersionEntries.compare("invalid", "invalid"));
+    System.out.println("VersionEntries.latestVersion()="+VersionEntries.latestVersion()+
+        ", dict_aa="+SymbolDictionary.STANDARD_AA+", dict_na="+SymbolDictionary.STANDARD_NA);
+    /**
+     * Test utils and autogenerated Vobject interfaces
+     */
+    
+    VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() }, 
+        ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
+        VersionEntries.latestVersion());
+    ArchiveReports.reportDocument(doc, null, true, System.out);
+  }
+}