tests for transferring annotation

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10275 ee4ac58c-ac51-4696-9907-e4b3aa274f04

test/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java

+/* TransferAnnotationToolTest.java
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2009  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.components;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.net.URL;
+import java.util.List;
+import java.util.Vector;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import javax.swing.JCheckBox;
+
+import junit.framework.Assert;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureKeyQualifierPredicate;
+import uk.ac.sanger.artemis.FeaturePredicate;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.SimpleEntryGroup;
+
+import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.io.Key;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
+import uk.ac.sanger.artemis.util.InputStreamProgressListener;
+import uk.ac.sanger.artemis.util.StringVector;
+
+public class TransferAnnotationToolTest
+{
+  private QualifierPanel qPanel;
+  private Vector genesToTransferTo = new Vector();
+  private String productStr;
+  private EntryGroup entryGroup;
+  private Feature originatingFeature;
+  
+  /**
+   * Open a flat file and create the components in the TransferAnnotaionTool
+   * used to control the transfer of annotation.
+   */
+  @Before
+  public void setup()
+  {
+    entryGroup = readFile();
+    originatingFeature = getFeature("gene", "O", "CDS", entryGroup);
+
+    qPanel = new QualifierPanel(originatingFeature, 
+        originatingFeature.getKey().getKeyString());
+    Hashtable qualifierHash = (Hashtable) qPanel.getQualifierCheckBoxes();
+
+    Enumeration enumQ = qualifierHash.keys();
+    productStr = null;
+    while (enumQ.hasMoreElements())
+    {
+      JCheckBox cbQualifierName = (JCheckBox) enumQ.nextElement();
+
+      if (cbQualifierName.getText().equals("product"))
+      {
+        cbQualifierName.setSelected(true);
+        Vector cbQualifierValues = (Vector) qualifierHash.get(cbQualifierName);
+        for (int i = 0; i < cbQualifierValues.size(); i++)
+        {
+          JCheckBox cbQualifierValue = (JCheckBox) cbQualifierValues.get(i);
+          cbQualifierValue.setSelected(true);
+          productStr = cbQualifierValue.getText();
+        }
+      }
+      else
+        cbQualifierName.setSelected(false);
+    }
+
+    JCheckBox cbNamesToTransferTo = new JCheckBox("N", true);
+    genesToTransferTo.add(cbNamesToTransferTo);
+  }
+  
+
+  /**
+   * Test for appending qualifiers.
+   */
+  @Test
+  public void testAppend()
+  { 
+    // append product
+    TransferAnnotationTool.transferAnnotation(qPanel.getQualifierCheckBoxes(),
+        genesToTransferTo, originatingFeature, entryGroup, true, false);
+
+    testTransferResult(entryGroup, 2, productStr);
+  }
+  
+  /**
+   * Test for appending qualifiers does not create duplicates when run
+   * again.
+   */
+  @Test
+  public void testAppend2()
+  { 
+    testAppend();
+  }
+   
+  /**
+   * Test for overwriting qualifiers.
+   */
+  @Test
+  public void testOverwrite()
+  { 
+    // check it overwrites product
+    TransferAnnotationTool.transferAnnotation(qPanel.getQualifierCheckBoxes(),
+        genesToTransferTo, originatingFeature, entryGroup, true, true);
+
+    testTransferResult(entryGroup, 1, productStr);
+  }
+  
+  /**
+   * Check the result of the annotation transfer is correct.
+   * @param entryGroup
+   * @param nproducts
+   * @param productStr
+   */
+  private void testTransferResult(final EntryGroup entryGroup,
+                                  final int nproducts,
+                                  final String productStr)
+  {
+    final Feature featureN = getFeature("gene", "N", "CDS", entryGroup);
+    boolean hasTransferred = false;
+    StringVector values = null;
+    try
+    {
+      values = featureN.getQualifierByName("product").getValues();
+      for (int j = 0; j < values.size(); j++)
+      {
+        if (((String) values.get(j)).equals(productStr))
+          hasTransferred = true;
+      }
+    }
+    catch (Exception e)
+    {
+      Assert.fail(e.getMessage());
+    }
+
+    assertEquals("Annotation transfer (product), number of values", values.size(), nproducts);
+    assertTrue("Annotation transfer (product)", hasTransferred);
+  }
+  
+  /**
+   * Return an Artemis EntryGroup by reading in an example file
+   * @return
+   */
+  private EntryGroup readFile()
+  {
+    URL url = TransferAnnotationToolTest.class.getResource("/etc/af063097.embl");
+
+    //assertEquals("Number", 4, 4);
+    final EntryInformation artemisEntryInformation =
+      Options.getArtemisEntryInformation();
+    final Document entryDocument =
+        DocumentFactory.makeDocument(url.getFile());
+
+    final uk.ac.sanger.artemis.io.Entry emblEntry =
+      EntryFileDialog.getEntryFromFile(null, entryDocument,
+          artemisEntryInformation, false);
+    try
+    {
+      final Entry entry = new Entry(emblEntry);
+      final EntryGroup entryGroup = new SimpleEntryGroup(entry.getBases());
+      entryGroup.add(entry);
+      return entryGroup;
+    }
+    catch(uk.ac.sanger.artemis.util.OutOfRangeException oore)
+    {
+      Assert.fail(oore.getMessage());
+    }
+    catch(uk.ac.sanger.artemis.sequence.NoSequenceException nse)
+    {
+      Assert.fail(nse.getMessage());
+    }
+    return null;
+  }
+
+  /**
+   * Return a feature in an entry group by searching for the feature
+   * key and a qualifier with a given value.
+   * @param qualifierName
+   * @param qualifierValue
+   * @param key
+   * @param entryGroup
+   * @return
+   */
+  private Feature getFeature(final String qualifierName,
+                             final String qualifierValue, 
+                             final String key, 
+                             final EntryGroup entryGroup)
+  {
+    FeatureVector features = entryGroup.getAllFeatures();
+    FeaturePredicate newPredicate = new FeatureKeyQualifierPredicate(
+        new Key(key), qualifierName, qualifierValue, false, false);
+
+    for (int i = 0; i < features.size(); i++)
+    {
+      Feature f = features.elementAt(i);
+      if (newPredicate.testPredicate(f))
+        return f;
+    }
+    return null;
+  }
+}
+