remove old ebi packages

[vamsas.git] / src / org / vamsas / test / objects / Core.java

diff --git a/src/org/vamsas/test/objects/Core.java b/src/org/vamsas/test/objects/Core.java
index 880c8bd..ffc8a23 100644 (file)
--- a/src/org/vamsas/test/objects/Core.java
+++ b/src/org/vamsas/test/objects/Core.java
@@ -3,22 +3,27 @@
  */
 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.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(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++) {
@@ -26,39 +31,51 @@ public class Core {
       q[i].setEnd(q[i].getSequence().length()+i+1);
     }
   }  
-  public static Sequence Sequence(String Name, String Sequence, String Dictionary, int start, int end) {
-    Sequence seq= new Sequence();
-     seq.setDictionary(Dictionary);
-     seq.setName(Name);
-     seq.setSequence(Sequence);
-     seq.setStart(start);
-     if (start<=end) {
-       if ((end-start)!=Sequence.length())
-         seq.setEnd(start+Sequence.length());
-     } else {
-       // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end on Sequence object
-       if ((start-end)!=Sequence.length())
-         seq.setEnd(end+Sequence.length());
-     }
-     return seq;
-  }
+
   public static VAMSAS getDemoVamsas() {
      VAMSAS v=new VAMSAS();
      DataSet ds = new DataSet();
-     ds.addSequence(Sequence("Dummy1","ASDFLEQ","info:iubmb.org/aminoacids", 5, 11));
+     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
-
+    
+    /**
+     * 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);
   }
-
 }