X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Ftest%2Fobjects%2FCore.java;h=6dce168cd52f7f428f603907c5724c70243bd8e7;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=58ecceaa7483397228e015518e9dce8277a06f6b;hpb=b9f9ec1358f764fc6c3acb2557703b5804a2084e;p=vamsas.git

diff --git a/src/uk/ac/vamsas/test/objects/Core.java b/src/uk/ac/vamsas/test/objects/Core.java
index 58eccea..6dce168 100644
--- a/src/uk/ac/vamsas/test/objects/Core.java
+++ b/src/uk/ac/vamsas/test/objects/Core.java
@@ -1,82 +1,121 @@
-/**
- * 
- */
-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);
-  }
-}
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
+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);
+  }
+}