X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FTestAlignSeq.java;h=44bea811761f89441dd095ff44945226bf985eb5;hb=a04a7992b1055fa52f5031ef9d10d2228ee78899;hp=ca4f18dbf83959294cb3b4ab10f6c9f24ba9b687;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index ca4f18d..44bea81 100644
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,23 @@
  */
 package jalview.analysis;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+
+import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import com.google.common.base.Charsets;
 
 /**
  * Test the alignment -> Mapping routines
@@ -37,41 +47,119 @@ import org.junit.Test;
 public class TestAlignSeq
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   SequenceI s1, s2, s3;
 
   /**
    * @throws java.lang.Exception
    */
-  @Before
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
     s1.setStart(3);
+    s1.setEnd(18);
     s2 = new Sequence("Seq2", "ASDFA");
     s2.setStart(5);
-    s3 = new Sequence("Seq1", "SDFAQQQSSS");
+    s2.setEnd(9);
+    s3 = new Sequence("Seq3", "SDFAQQQSSS");
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   /**
    * simple test that mapping from alignment corresponds identical positions.
    */
-  public void TestGetMappingForS1()
+  public void testGetMappingForS1()
   {
-    jalview.analysis.AlignSeq as = jalview.analysis.AlignSeq
-            .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
     System.out.println("s1: " + as.getAStr1());
     System.out.println("s2: " + as.getAStr2());
 
+    // aligned results match
+    assertEquals("ASDFA", as.getAStr1());
+    assertEquals(as.getAStr1(), as.getAStr2());
+
     Mapping s1tos2 = as.getMappingFromS1(false);
+    checkMapping(s1tos2,s1,s2);
+  }
+
+  public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+  {
     System.out.println(s1tos2.getMap().toString());
-    for (int i = s2.getStart(); i < s2.getEnd(); i++)
+    for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
     {
-      System.out.println("Position in s2: " + i
-              + " maps to position in s1: " + s1tos2.getPosition(i));
-      assertTrue("", s2.getCharAt(i) == s1.getCharAt(s1tos2.getPosition(i)));
+      int p=s1tos2.getPosition(i);
+      char s2c=_s2.getCharAt(i-_s2.getStart());
+      char s1c=_s1.getCharAt(p-_s1.getStart());
+      System.out.println("Position in s2: " + i +s2c 
+      + " maps to position in s1: " +p+s1c);
+      assertEquals(s1c,s2c);
     }
   }
+  @Test(groups = { "Functional" })
+  /**
+   * simple test that mapping from alignment corresponds identical positions.
+   */
+  public void testGetMappingForS1_withLowerCase()
+  {
+    // make one of the sequences lower case
+    SequenceI ns2 = new Sequence(s2);
+    ns2.replace('D', 'd');
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
+    System.out.println("s1: " + as.getAStr1());
+    System.out.println("s2: " + as.getAStr2());
+
+    // aligned results match
+    assertEquals("ASDFA", as.getAStr1());
+    assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
+
+    Mapping s1tos2 = as.getMappingFromS1(false);
+    assertEquals("ASdFA",as.getAStr2());
+    // verify mapping is consistent between original all-caps sequences
+    checkMapping(s1tos2,s1,s2);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testExtractGaps()
+  {
+    assertNull(AlignSeq.extractGaps(null, null));
+    assertNull(AlignSeq.extractGaps(". -", null));
+    assertNull(AlignSeq.extractGaps(null, "AB-C"));
 
+    assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPrintAlignment()
+  {
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
+    final StringBuilder baos = new StringBuilder();
+    PrintStream ps = new PrintStream(System.out)
+    {
+      @Override
+      public void print(String x)
+      {
+        baos.append(x);
+      }
+
+      @Override
+      public void println()
+      {
+        baos.append("\n");
+      }
+    };
+
+    as.printAlignment(ps);
+    String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
+            + "Seq1/4-13 SDFAQQQRRR\n" + "          |||||||   \n"
+            + "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
+    assertEquals(expected, baos.toString());
+  }
 }