Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / test / jalview / io / FormatAdapterTest.java

diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
index 6bf954a..d63fb70 100644 (file)
--- a/test/jalview/io/FormatAdapterTest.java
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.assertEquals;
@@ -6,17 +26,26 @@ import static org.testng.AssertJUnit.fail;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 public class FormatAdapterTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * Test saving and re-reading in a specified format
    * 
@@ -27,8 +56,17 @@ public class FormatAdapterTest
   {
     try
     {
-      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+      AlignmentI al;
+      if (format == FileFormat.HMMER3)
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.hmm",
+                DataSourceType.FILE, FileFormat.HMMER3);
+      }
+      else
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.fa",
               DataSourceType.FILE, FileFormat.Fasta);
+      }
 
       /*
        * 'gap' is the gap character used in the alignment data file here,
@@ -44,8 +82,9 @@ public class FormatAdapterTest
       AlignmentI reloaded = new FormatAdapter().readFile(formatted,
               DataSourceType.PASTE, format);
       List<SequenceI> reread = reloaded.getSequences();
-      assertEquals("Wrong number of reloaded sequences", seqs.length,
-              reread.size());
+        assertEquals("Wrong number of reloaded sequences", seqs.length,
+                reread.size());
+
 
       int i = 0;
       for (SequenceI seq : reread)
@@ -56,16 +95,14 @@ public class FormatAdapterTest
          * special case: MSF always uses '.' as gap character
          */
         sequenceString = adjustForGapTreatment(sequenceString, gap, format);
-        assertEquals(
-                String.format("Sequence %d: %s", i,
-                        seqs[i].getName()), seqs[i].getSequenceAsString(),
-                sequenceString);
+        assertEquals(String.format("Sequence %d: %s", i, seqs[i].getName()),
+                seqs[i].getSequenceAsString(), sequenceString);
         i++;
       }
     } catch (IOException e)
     {
-      fail(String
-              .format("Format %s failed with %s", format, e.getMessage()));
+      fail(String.format("Format %s failed with %s", format,
+              e.getMessage()));
     }
   }
 
@@ -83,7 +120,7 @@ public class FormatAdapterTest
   String adjustForGapTreatment(String sequenceString, char gap,
           FileFormatI format)
   {
-    if (format == FileFormat.MSF)
+    if (FileFormat.MSF.equals(format))
     {
       /*
        * MSF forces gap character to '.', so change it back
@@ -96,17 +133,18 @@ public class FormatAdapterTest
 
   /**
    * Data provider that serves alignment formats that are both readable and
-   * writable
+   * (text) writable
    * 
    * @return
    */
   @DataProvider(name = "formats")
   static Object[][] getFormats()
   {
-    List<FileFormatI> both = new ArrayList<FileFormatI>();
-    for (FileFormat format : FileFormat.values())
+    List<FileFormatI> both = new ArrayList<>();
+    for (FileFormatI format : FileFormats.getInstance().getFormats())
     {
-      if (format.isReadable() && format.isWritable())
+      if (format.isReadable() && format.isWritable()
+              && format.isTextFormat())
       {
         both.add(format);
       }