/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
*
*/
package jalview.io;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+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
{
/**
* @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" });
}
/**
return numdsann;
}
- @Test
+ @Test(groups = { "Functional" })
public void testRNAStructureRecovery() throws Exception
{
String inFile = "examples/RF00031_folded.stk";
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";
.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";
.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
+ @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);
assertTrue("Couldn't find the structure view", sps != null);
SequenceI sq = sps.getAlignment().findName("1A70|");
AlignmentAnnotation refan = null;
- for (AlignmentAnnotation ra:sps.getAlignment().getAlignmentAnnotation())
+ for (AlignmentAnnotation ra : sps.getAlignment()
+ .getAlignmentAnnotation())
{
if (ra.graph != 0)
{
break;
}
}
- assertTrue("Annotation secondary structure not found.",refan!=null);
+ 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 (int p = 0; p < ala.annotations.length; p++)
{
sq.findPosition(p);
- try {
+ try
+ {
assertTrue(
"Mismatch at alignment position " + p,
- (alaa.annotations[p] == null && refan.annotations[p] == null)
+ (alaa.annotations[p] == null && refan.annotations[p] == null)
|| alaa.annotations[p].value == refan.annotations[p].value);
- }
- catch (NullPointerException q)
+ } catch (NullPointerException q)
{
- fail("Mismatch of alignment annotations at position " + p
- + " Ref seq ann: " + refan.annotations[p]
+ 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);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff