X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FFeatureSettingsTest.java;h=7cc4cc1884e80230308e104c66aaa3b26d3905ee;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=321adf6d238b26ca13d2f1710a91ce0e8f9a53d1;hpb=92bc328cd9eeb2218721fa6caa20f873d5ac5cf3;p=jalview.git

diff --git a/test/jalview/gui/FeatureSettingsTest.java b/test/jalview/gui/FeatureSettingsTest.java
index 321adf6..7cc4cc1 100644
--- a/test/jalview/gui/FeatureSettingsTest.java
+++ b/test/jalview/gui/FeatureSettingsTest.java
@@ -1,30 +1,75 @@
+/*
+ * 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.gui;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcher;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.FeatureColourTest;
 import jalview.util.matcher.Condition;
-
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-
-import org.testng.annotations.Test;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 public class FeatureSettingsTest
 {
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Jalview.main(new String[] { "--nonews" });
+  }
+
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
+  }
+
   /**
    * Test a roundtrip of save and reload of feature colours and filters as XML
    * 
@@ -50,7 +95,7 @@ public class FeatureSettingsTest
     /*
      * set colour schemes for features
      */
-    FeatureRenderer fr = af.getFeatureRenderer();
+    FeatureRendererModel fr = af.getFeatureRenderer();
 
     // type1: red
     fr.setColour("type1", new FeatureColour(Color.red));
@@ -61,8 +106,8 @@ public class FeatureSettingsTest
     fr.setColour("type2", byLabel);
 
     // type3: by score above threshold
-    FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
-            10);
+    FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byScore.setAboveThreshold(true);
     byScore.setThreshold(2f);
     fr.setColour("type3", byScore);
@@ -74,8 +119,8 @@ public class FeatureSettingsTest
     fr.setColour("type4", byAF);
 
     // type5: by attribute CSQ:PolyPhen below threshold
-    FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
-            1, 10);
+    FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byPolyPhen.setBelowThreshold(true);
     byPolyPhen.setThreshold(3f);
     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
@@ -155,11 +200,12 @@ public class FeatureSettingsTest
     assertTrue(fc.isBelowThreshold());
     assertEquals(fc.getThreshold(), 3f);
 
-    assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
+    assertEquals(fr.getFeatureFilter("type1").toStableString(),
+            "Label Contains x");
     assertEquals(fr.getFeatureFilter("type2").toStableString(),
             "(Score LE 2.4) AND (Score GT 1.1)");
     assertEquals(fr.getFeatureFilter("type3").toStableString(),
-            "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+            "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
   }
 
   /**
@@ -219,7 +265,7 @@ public class FeatureSettingsTest
     /*
      * graduated colour with threshold is html-encoded
      */
-    fc = new FeatureColour(Color.red, Color.blue, 2f, 10f);
+    fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
     fc.setBelowThreshold(true);
     fc.setThreshold(4f);
     assertEquals(FeatureSettings.getColorTooltip(fc, false),
@@ -235,4 +281,13 @@ public class FeatureSettingsTest
             "<html>By Score (&gt; 4.0)<br>" + simpleTooltip
                     + "</br></html>");
   }
+  String fsfile="<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">",fsfile2="<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n<ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">";
+  @Test(groups="Functional")
+  public void testIdentifyFeatureSettingsFile() throws Exception
+  {
+    FileFormatI type = new IdentifyFile().identify(fsfile, DataSourceType.PASTE);
+    assertTrue(FileFormat.FeatureSettings==type,"Feature settings file was identified as "+type);
+    type = new IdentifyFile().identify(fsfile2, DataSourceType.PASTE);
+    assertTrue(FileFormat.FeatureSettings==type,"Feature settings file with newline was identified as "+type);
+  }
 }