refactoring org to uk

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@290 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
deleted file mode 100644 (file)
index fb8c6f9..0000000
--- a/src/org/vamsas/test/objects/Core.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/**
- * 
- */
-package org.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 = "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++) {
-      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);
-  }
-}