JAL-1759 merge from develop

[jalview.git] / test / jalview / io / Jalview2xmlTests.java

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 32aa84a..c03dd71 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,11 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -31,9 +35,11 @@ import jalview.schemes.ColourSchemeI;
 
 import java.io.File;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 public class Jalview2xmlTests
 {
@@ -77,7 +83,7 @@ public class Jalview2xmlTests
     return numdsann;
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
@@ -112,7 +118,7 @@ public class Jalview2xmlTests
             af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTCoffeeScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
@@ -148,7 +154,7 @@ public class Jalview2xmlTests
             .println("T-Coffee score shading successfully recovered from project.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testColourByAnnotScores() throws Exception
   {
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
@@ -234,15 +240,111 @@ public class Jalview2xmlTests
             .println("Per sequence (Group) colourscheme successfully applied and recovered.");
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void gatherViewsHere() throws Exception
   {
-    int origCount = Desktop.getAlignframes().length;
+    int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
+            .getAlignFrames().length;
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
     assertTrue("Didn't read in the example file correctly.", af != null);
     assertTrue("Didn't gather the views in the example file.",
-            Desktop.getAlignframes().length == 1 + origCount);
+            Desktop.getAlignFrames().length == 1 + origCount);
+
+  }
+
+  @Test(groups ={ "Functional" })
+  public void viewRefPdbAnnotation() throws Exception
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    AlignmentViewPanel sps = null;
+    for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+    {
+      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+      {
+        sps = ap;
+        break;
+      }
+    }
+    assertTrue("Couldn't find the structure view", sps != null);
+    SequenceI sq = sps.getAlignment().findName("1A70|");
+    AlignmentAnnotation refan = null;
+    for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
+    {
+      if (ra.graph != 0)
+      {
+        refan = ra;
+        break;
+      }
+    }
+    assertTrue("Annotation secondary structure not found.",refan!=null);
+    assertTrue("Couldn't find 1a70 null chain", sq != null);
+    // compare the manually added temperature factor annotation
+    // to the track automatically transferred from the pdb structure on load
+    for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
+    {
+      AlignmentAnnotation alaa;
+      sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala));
+      alaa.adjustForAlignment();
+      if (ala.graph == refan.graph)
+      {
+        for (int p = 0; p < ala.annotations.length; p++)
+        {
+          sq.findPosition(p);
+          try {
+            assertTrue(
+                    "Mismatch at alignment position " + p,
+                  (alaa.annotations[p] == null && refan.annotations[p] == null)
+                            || alaa.annotations[p].value == refan.annotations[p].value);
+          }
+          catch (NullPointerException q)
+          {
+            Assert.fail("Mismatch of alignment annotations at position " + p
+                    + " Ref seq ann: " + refan.annotations[p]
+                    + " alignment " + alaa.annotations[p]);
+          }
+          }
+      }
+    }
+    
+  }
+
+  @Test(groups ={ "Functional" })
+  public void testCopyViewSettings() throws Exception
+  {
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    AlignmentViewPanel sps = null, groups = null;
+    for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+    {
+      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+      {
+        sps = ap;
+      }
+      if (ap.getViewName().contains("MAFFT"))
+      {
+        groups = ap;
+      }
+    }
+    assertTrue("Couldn't find the structure view", sps != null);
+    assertTrue("Couldn't find the MAFFT view", groups != null);
+
+    ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
+    ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
+    AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
+
+    groups.getAlignViewport().setViewStyle(structureStyle);
+    AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+            .getViewStyle()));
+    Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
+            .getViewStyle()));
 
   }
 }