X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=b57e5d0c2d1b030f5433b9c90c12127309dd42bc;hb=d52084e9014ef22f4449e35307a940d0e6f5766d;hp=519a94601ae33d5dfc0f3db5cbc373d2eafcea62;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 519a946..b57e5d0 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.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. * @@ -20,42 +20,38 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.*; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertTrue; -import java.awt.Component; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Vector; - -import javax.swing.JMenu; -import javax.swing.JMenuItem; - -import jalview.api.AlignCalcManagerI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; import jalview.gui.Jalview2XML; import jalview.io.AnnotationFile; import jalview.io.FormatAdapter; import jalview.io.StockholmFileTest; -import jalview.ws.jws2.AADisorderClient; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.RNAalifoldClient; import jalview.ws.jws2.SequenceAnnotationWSClient; -import jalview.ws.jws2.dm.JabaOption; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.AutoCalcSetting; -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; +import java.awt.Component; +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; + +import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; import compbio.metadata.WrongParameterException; public class RNAStructExportImport { - public static String testseqs = "examples/unfolded_RF00031.aln"; + public static String testseqs = "examples/RF00031_folded.stk"; public static Jws2Discoverer disc; @@ -65,12 +61,12 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { jalview.bin.Cache.initLogger(); - disc = JalviewJabawsTestUtils.getJabawsDiscoverer(); + disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); for (Jws2Instance svc : disc.getServices()) { @@ -84,7 +80,9 @@ public class RNAStructExportImport System.out.println("State of rnaalifoldws: " + rnaalifoldws); if (rnaalifoldws == null) - System.exit(0); + { + Assert.fail("no web service"); + } jalview.io.FileLoader fl = new jalview.io.FileLoader(false); @@ -92,6 +90,22 @@ public class RNAStructExportImport assertNotNull("Couldn't load test data ('" + testseqs + "')", af); + // remove any existing annotation + List aal = new ArrayList(); + for (AlignmentAnnotation rna : af.getViewport().getAlignment() + .getAlignmentAnnotation()) + { + if (rna.isRNA()) + { + aal.add(rna); + } + } + for (AlignmentAnnotation rna : aal) + { + af.getViewport().getAlignment().deleteAnnotation(rna); + } + af.getViewport().alignmentChanged(af.alignPanel); // why is af.alignPanel + // public? } @AfterClass @@ -104,7 +118,41 @@ public class RNAStructExportImport } } - @Test + @Test(groups = { "Functional" }) + public void testRNAAliFoldValidStructure() + { + + alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); + + af.getViewport().getCalcManager().startWorker(alifoldClient); + + do + { + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } + ; + } while (af.getViewport().getCalcManager().isWorking()); + + AlignmentI orig_alig = af.getViewport().getAlignment(); + for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) + { + if (alifoldClient.involves(aa)) + { + if (aa.isRNA()) + { + assertTrue( + "Did not create valid structure from RNAALiFold prediction", + aa.isValidStruc()); + } + } + } + } + + @Test(groups = { "Functional" }) public void testRNAStructExport() { @@ -137,9 +185,8 @@ public class RNAStructExportImport String aligfileout = new FormatAdapter().formatSequences("PFAM", al.getSequencesArray()); - String anfileout = new AnnotationFile().printAnnotations( - al.getAlignmentAnnotation(), al.getGroups(), - al.getProperties()); + String anfileout = new AnnotationFile() + .printAnnotationsForAlignment(al); assertTrue( "Test " + testname @@ -165,18 +212,18 @@ public class RNAStructExportImport FormatAdapter.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false); return; } catch (Exception e) { e.printStackTrace(); } - fail("Test " + Assert.fail("Test " + testname + "\nCouldn't complete Annotation file roundtrip input/output/input test."); } - @Test + @Test(groups = { "Functional" }) public void testRnaalifoldSettingsRecovery() { List opts = new ArrayList(); @@ -190,7 +237,7 @@ public class RNAStructExportImport rg.setValue("292"); } catch (WrongParameterException q) { - fail("Couldn't set the temperature parameter " + Assert.fail("Couldn't set the temperature parameter " + q.getStackTrace()); } opts.add(rg); @@ -201,9 +248,9 @@ public class RNAStructExportImport } } alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts); - + af.getViewport().getCalcManager().startWorker(alifoldClient); - + do { try @@ -214,39 +261,58 @@ public class RNAStructExportImport } ; } while (af.getViewport().getCalcManager().isWorking()); - AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); + AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); String oldsettings = oldacs.getWsParamFile(); // write out parameters - jalview.gui.AlignFrame nalf=null; - assertTrue("Couldn't write out the Jar file",new Jalview2XML(false).SaveAlignment(af, "testRnalifold_param.jar","trial parameter writeout")); - assertTrue("Couldn't read back the Jar file",(nalf = new Jalview2XML(false).LoadJalviewAlign("testRnalifold_param.jar"))!=null); - if (nalf!=null) + jalview.gui.AlignFrame nalf = null; + assertTrue("Couldn't write out the Jar file", + new Jalview2XML(false).saveAlignment(af, + "testRnalifold_param.jar", "trial parameter writeout")); + assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML( + false).loadJalviewAlign("testRnalifold_param.jar")) != null); + if (nalf != null) { - AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); - assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs)); - assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings)); - JMenu nmenu=new JMenu(); - new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af); - assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0); - for (Component itm: nmenu.getMenuComponents()) + AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); + assertTrue("Calc ID settings not recovered from viewport stash", + acs.equals(oldacs)); + assertTrue( + "Serialised Calc ID settings not identical to those recovered from viewport stash", + acs.getWsParamFile().equals(oldsettings)); + JMenu nmenu = new JMenu(); + new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, + rnaalifoldws, af); + assertTrue("Couldn't get menu entry for service", + nmenu.getItemCount() > 0); + for (Component itm : nmenu.getMenuComponents()) { if (itm instanceof JMenuItem) { JMenuItem i = (JMenuItem) itm; - if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle())) - { + if (i.getText().equals( + rnaalifoldws.getAlignAnalysisUI().getAAconToggle())) + { i.doClick(); break; - } + } } } while (af.getViewport().isCalcInProgress()) { - try { Thread.sleep(200); - } catch (Exception x) {}; + try + { + Thread.sleep(200); + } catch (Exception x) + { + } + ; } - AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId()); - assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings)); + AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor( + alifoldClient.getCalcId()); + assertTrue( + "Calc ID settings after recalculation has not been recovered.", + acs2.getWsParamFile().equals(oldsettings)); } } }