X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=b58a8a6e71f33077a724262db8b49ead6454bc87;hb=e710810610e029b1519d31c6d8a9de26833f59b9;hp=982be0cdbbd16241a3279ed63848dce1a5120e02;hpb=cce9e4df53a94d9e7f841d25a6063c597f7a2ab9;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 982be0c..b58a8a6 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -20,6 +20,7 @@ */ package jalview.io; +import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import jalview.api.AlignmentViewPanel; @@ -51,8 +52,8 @@ public class Jalview2xmlTests @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" }); } /** @@ -84,7 +85,7 @@ public class Jalview2xmlTests return numdsann; } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testRNAStructureRecovery() throws Exception { String inFile = "examples/RF00031_folded.stk"; @@ -119,7 +120,7 @@ public class Jalview2xmlTests af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTCoffeeScores() throws Exception { String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; @@ -155,7 +156,7 @@ public class Jalview2xmlTests .println("T-Coffee score shading successfully recovered from project."); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testColourByAnnotScores() throws Exception { String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; @@ -241,7 +242,7 @@ public class Jalview2xmlTests .println("Per sequence (Group) colourscheme successfully applied and recovered."); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop @@ -254,7 +255,7 @@ public class Jalview2xmlTests } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void viewRefPdbAnnotation() throws Exception { Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", @@ -276,7 +277,8 @@ public class Jalview2xmlTests 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) { @@ -284,7 +286,7 @@ public class Jalview2xmlTests 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 @@ -298,25 +300,25 @@ public class Jalview2xmlTests 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) { - Assert.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" }) + @Test(groups = { "Functional" }) public void testCopyViewSettings() throws Exception { AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( @@ -350,18 +352,16 @@ public class Jalview2xmlTests } /** - * 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. + * 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( + 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(); @@ -369,12 +369,12 @@ public class Jalview2xmlTests final AlignFrame xaf = af; af = null; new Thread(new Runnable() - { - @Override - public void run() { + @Override + public void run() + { Desktop.instance.explodeViews(xaf); - } + } }).start(); Thread.sleep(1000); } @@ -384,8 +384,7 @@ public class Jalview2xmlTests // Thread.sleep(300); // } int oldviews = Desktop.getAlignFrames().length; - Assert.assertEquals( - Desktop.getAlignFrames().length, + Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels(afid).length); File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); try @@ -406,10 +405,64 @@ public class Jalview2xmlTests af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( tfile.getAbsolutePath(), FormatAdapter.FILE); Assert.assertNotNull(af); - Assert.assertEquals(Desktop.getAlignFrames().length, + Assert.assertEquals( + Desktop.getAlignFrames().length, Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); - Assert.assertEquals(oldviews, + Assert.assertEquals( + oldviews, Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); } + @Test(groups = { "Functional" }) + public void testIsVersionStringLaterThan() + { + /* + * No version / development / test / autobuild is leniently assumed to be + * compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan(null, null)); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null)); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "DEVELOPMENT BUILD")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); + assertTrue(Jalview2XML + .isVersionStringLaterThan(null, "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "AUTOMATED BUILD")); + + /* + * same version returns true i.e. compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1")); + + /* + * later version returns true + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1")); + + /* + * earlier version returns false + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + } }