user plots

test/uk/ac/sanger/artemis/plot/UserPlotTest.java

+/* 
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2013  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.plot;
+
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.plot.LineAttributes;
+import uk.ac.sanger.artemis.plot.UserDataAlgorithm;
+import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.io.Utils;
+
+import uk.ac.sanger.artemis.sequence.Strand;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertEquals;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+
+import junit.framework.Assert;
+import org.junit.Test;
+
+public class UserPlotTest
+{
+  @Test
+  /**
+   * Base position user plot.
+   */
+  public void basePosition()
+  {
+    URL gffURL = UserPlotTest.class.getResource("/data/plot/base_position.plot.gz");
+    EntryGroup entryGrp = Utils.getEntryGroup("/data/MAL1.embl.gz");
+    final Strand fwdStrand = entryGrp.getBases ().getForwardStrand ();
+    final FileDocument doc = new FileDocument (new File(gffURL.getFile()));
+    
+    try
+    {
+      final UserDataAlgorithm alg = new UserDataAlgorithm (fwdStrand, doc, false);
+      float [] values = new float [alg.getValueCount()];
+      int start = 278;
+      alg.getValues(start, start+10, values);
+      assertEquals("Number of plots",values.length,6);
+      assertTrue("Value of plot 1 at base position 278",values[0]==804.99f);
+    }
+    catch(IOException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+  
+  @Test
+  /**
+   * Base position (with labels) user plot.
+   */
+  public void labelBasePosition()
+  {
+    URL gffURL = UserPlotTest.class.getResource("/data/plot/base_position_labels.plot.gz");
+    EntryGroup entryGrp = Utils.getEntryGroup("/data/MAL1.embl.gz");
+    final Strand fwdStrand = entryGrp.getBases ().getForwardStrand ();
+    final FileDocument doc = new FileDocument (new File(gffURL.getFile()));
+    
+    try
+    {
+      final UserDataAlgorithm alg = new UserDataAlgorithm (fwdStrand, doc, false);
+      final LineAttributes lines[] = alg.getLineAttributes();
+      assertEquals("Number of lines",lines.length,6);
+      assertEquals("Number of plots",lines[0].getLabel(),"lab1");
+
+      float [] values = new float [alg.getValueCount()];
+      int start = 278;
+      alg.getValues(start, start+10, values);
+      assertEquals("Number of plots",values.length,6);
+      assertTrue("Value of plot 1 at base position 278",values[0]==804.99f);
+    }
+    catch(IOException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+
+}