From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 28 Oct 2015 14:19:02 +0000 (+0000)
Subject: JAL-1954 test PFAM import results in AlignmentI.hasValidSequences()==true with/out... 
X-Git-Tag: Release_2_10_0~343^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab24e67378e61c3ba70fd3bc557259112a87b3ca;p=jalview.git

JAL-1954 test PFAM import results in AlignmentI.hasValidSequences()==true with/out limits.
---

diff --git a/test/jalview/io/PfamFormatInputTest.java b/test/jalview/io/PfamFormatInputTest.java
new file mode 100644
index 0000000..46e5af7
--- /dev/null
+++ b/test/jalview/io/PfamFormatInputTest.java
@@ -0,0 +1,32 @@
+package jalview.io;
+
+import jalview.datamodel.AlignmentI;
+
+import java.io.IOException;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+public class PfamFormatInputTest
+{
+  @Test
+  public void testPfamFormatNoLimits() throws IOException
+  {
+    AlignmentI al = new jalview.io.AppletFormatAdapter().readFile(
+            "ASEQ\t...--FFAFAFF--", AppletFormatAdapter.PASTE, "PFAM");
+    Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
+    Assert.assertTrue(al.hasValidSequence(),
+            "Didn't extract limits from PFAM ID");
+  }
+
+  @Test
+  public void testPfamFormatValidLimits() throws IOException
+  {
+    AlignmentI al = new jalview.io.AppletFormatAdapter()
+            .readFile("ASEQ/15-25\t...--FFAFAFF--",
+                    AppletFormatAdapter.PASTE, "PFAM");
+    Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
+    Assert.assertTrue(al.hasValidSequence(),
+            "Didn't extract limits from PFAM ID");
+  }
+}