From fa3e116cc4e6c0603454b10c3ce2425c59293256 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Sep 2015 16:36:09 +0100
Subject: [PATCH] JAL-1853 test demonstrating bug

---
 test/jalview/io/JalviewExportPropertiesTests.java |   84 +++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 test/jalview/io/JalviewExportPropertiesTests.java

diff --git a/test/jalview/io/JalviewExportPropertiesTests.java b/test/jalview/io/JalviewExportPropertiesTests.java
new file mode 100644
index 0000000..faf4ef9
--- /dev/null
+++ b/test/jalview/io/JalviewExportPropertiesTests.java
@@ -0,0 +1,84 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+/**
+ * tests which verify that properties and preferences are correctly interpreted
+ * when exporting/importing data
+ * 
+ * @author jprocter
+ *
+ */
+public class JalviewExportPropertiesTests
+{
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    jalview.bin.Jalview.main(new String[]
+    { "-props", "test/jalview/io/testProps.jvprops" });
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+  }
+  @Test(groups ={ "Functional" })
+  public void testImportExportPeriodGaps() throws Exception
+  {
+    jalview.bin.Cache.setProperty("GAP_SYMBOL", ".");
+    assertTrue("Couldn't set gap character to '.'",
+            ".".equals("" + jalview.bin.Cache.getProperty("GAP_SYMBOL")));
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertTrue("Didn't set the gap character correctly", af.getViewport()
+            .getAlignment().getSequenceAt(0).getCharAt(5) == '.');
+
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(0),false);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1),false);
+    sg.setStartRes(1);
+    sg.setEndRes(7);
+    af.getViewport().setSelectionGroup(sg);
+    String fseqs = new FormatAdapter(af.alignPanel).formatSequences(
+            "FASTA", af.alignPanel, true);
+    assertTrue("Couldn't find '.' in the exported region\n" + fseqs,
+            fseqs.indexOf(".") > -1);
+  }
+}
-- 
1.7.10.2