From 08177c20d207f9e34866e220517b168ea517ac5b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 25 Mar 2009 12:01:57 +0000
Subject: [PATCH] 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
---
.../TransferAnnotationToolTest.java | 236 ++++++++++++++++++
1 file changed, 236 insertions(+)
create mode 100644 test/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java
diff --git a/test/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java b/test/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java
new file mode 100644
index 000000000..77bc35d27
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java
@@ -0,0 +1,236 @@
+/* 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;
+ }
+}
+
--
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