X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=924dd37c2c266d1ed433130f74f88a3ff048b907;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=fec7d755d1ee49399a1231e9d54b9653a6da103a;hpb=862a2b1ffe312f1d58a480c438ac5f8daae74468;p=jalview.git

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index fec7d75..924dd37 100644
--- 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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,20 +20,27 @@
  */
 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;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
 import jalview.schemes.AnnotationColourGradient;
 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
 {
@@ -41,11 +48,11 @@ public class Jalview2xmlTests
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
-    { "-props", "test/jalview/io/testProps.jvprops" });
+    jalview.bin.Jalview.main(new String[] { "-props",
+        "test/jalview/io/testProps.jvprops" });
   }
 
   /**
@@ -77,7 +84,7 @@ public class Jalview2xmlTests
     return numdsann;
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
@@ -112,7 +119,7 @@ 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 +155,7 @@ 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";
@@ -234,16 +241,175 @@ 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() == null ? 0 : 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()));
+
+  }
+
+  /**
+   * test store and recovery of expanded views - currently this is disabled
+   * since the Desktop.explodeViews method doesn't seem to result in the views
+   * being expanded to distinct align frames when executed programmatically.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = false)
+  public void testStoreAndRecoverExpandedviews() 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);
+    String afid = af.getViewport().getSequenceSetId();
+    {
+      final AlignFrame xaf = af;
+      af = null;
+      new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          Desktop.instance.explodeViews(xaf);
+        }
+      }).start();
+      Thread.sleep(1000);
+    }
+    // int times = 0;
+    // while (++times < 5 && Desktop.getAlignFrames().length < )
+    // {
+    // Thread.sleep(300);
+    // }
+    int oldviews = Desktop.getAlignFrames().length;
+    Assert.assertEquals(Desktop.getAlignFrames().length,
+            Desktop.getAlignmentPanels(afid).length);
+    File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
+    try
+    {
+      new Jalview2XML(false).saveState(tfile);
+    } catch (Error e)
+    {
+      Assert.fail("Didn't save the expanded view state", e);
+    } catch (Exception e)
+    {
+      Assert.fail("Didn't save the expanded view state", e);
+    }
+    Desktop.instance.closeAll_actionPerformed(null);
+    if (Desktop.getAlignFrames() != null)
+    {
+      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+    }
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), FormatAdapter.FILE);
+    Assert.assertNotNull(af);
+    Assert.assertEquals(
+            Desktop.getAlignFrames().length,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+    Assert.assertEquals(
+            oldviews,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
   }
+
 }