Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 602ce9f..d6f1e8b 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -34,17 +34,26 @@ import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
 
   @Test(groups = { "Functional" })
@@ -56,7 +65,7 @@ public class FeaturesFileTest
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
     FeaturesFile featuresFile = new FeaturesFile(
-            "examples/exampleFeatures.txt", FormatAdapter.FILE);
+            "examples/exampleFeatures.txt", DataSourceType.FILE);
     assertTrue("Test " + "Features file test"
             + "\nFailed to parse features file.",
             featuresFile.parse(al.getDataset(), colours, true));
@@ -158,7 +167,7 @@ public class FeaturesFileTest
             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
-            FormatAdapter.PASTE);
+            DataSourceType.PASTE);
     assertTrue("Failed to parse features file",
             featuresFile.parse(al.getDataset(), colours, true));
 
@@ -197,8 +206,8 @@ public class FeaturesFileTest
     String ff = f.getPath();
     FormatAdapter rf = new FormatAdapter();
 
-    AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
-            new IdentifyFile().identify(ff, FormatAdapter.FILE));
+    AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+            new IdentifyFile().identify(ff, DataSourceType.FILE));
 
     al.setDataset(null); // creates dataset sequences
     assertNotNull("Couldn't read supplied alignment data.", al);
@@ -224,7 +233,7 @@ public class FeaturesFileTest
             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
-            FormatAdapter.PASTE);
+            DataSourceType.PASTE);
     assertTrue("Failed to parse features file",
             featuresFile.parse(al.getDataset(), colours, true));
 
@@ -277,7 +286,7 @@ public class FeaturesFileTest
     String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
             + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
     FeaturesFile featuresFile = new FeaturesFile(featureData,
-            FormatAdapter.PASTE);
+            DataSourceType.PASTE);
     assertTrue("Failed to parse features file",
             featuresFile.parse(al.getDataset(), colours, true));
 
@@ -343,7 +352,7 @@ public class FeaturesFileTest
   public void readGff3File() throws IOException
   {
     FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
     gffreader.addProperties(dataset);
     checkDatasetfromSimpleGff3(dataset);
@@ -353,8 +362,9 @@ public class FeaturesFileTest
   public void simpleGff3FileClass() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
-
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
+            DataSourceType.FILE);
+  
     boolean parseResult = ffile.parse(dataset, null, false, false);
     assertTrue("return result should be true", parseResult);
     checkDatasetfromSimpleGff3(dataset);
@@ -364,7 +374,7 @@ public class FeaturesFileTest
   public void simpleGff3FileLoader() throws IOException
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
-            simpleGffFile, FormatAdapter.FILE);
+            simpleGffFile, DataSourceType.FILE);
     assertTrue(
             "Didn't read the alignment into an alignframe from Gff3 File",
             af != null);
@@ -375,8 +385,9 @@ public class FeaturesFileTest
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[] {});
-    FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
-
+    FeaturesFile ffile = new FeaturesFile(simpleGffFile,
+            DataSourceType.FILE);
+  
     boolean parseResult = ffile.parse(dataset, null, false, true);
     assertTrue("return result (relaxedID matching) should be true",
             parseResult);
@@ -400,7 +411,7 @@ public class FeaturesFileTest
             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
             + "ENDGROUP\tuniprot\n";
     FeaturesFile featuresFile = new FeaturesFile(features,
-            FormatAdapter.PASTE);
+            DataSourceType.PASTE);
     featuresFile.parse(al.getDataset(), colours, false);
 
     /*