X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=5eeff504e02cfb1f5997eb1c224f7316232b5eda;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=a2c361b99744eecd25e2a015d5f2d7ddedd107c0;hpb=74d80d8a0a48038556001a997da5f2aba29b841b;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index a2c361b..5eeff50 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -1,32 +1,46 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ws.jabaws; -import static org.junit.Assert.*; - -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 static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; 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 java.awt.Component; +import java.util.ArrayList; +import java.util.List; + +import javax.swing.JMenu; +import javax.swing.JMenuItem; + import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; @@ -48,30 +62,32 @@ public class RNAStructExportImport @BeforeClass public static void setUpBeforeClass() throws Exception { - - + jalview.bin.Cache.initLogger(); - disc = JalviewJabawsTestUtils.getJabawsDiscoverer(); - + disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); + for (Jws2Instance svc : disc.getServices()) { - + if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws")) { rnaalifoldws = svc; } } - + System.out.println("State of rnaalifoldws: " + rnaalifoldws); - - if (rnaalifoldws == null) System.exit(0); - + + if (rnaalifoldws == null) + { + System.exit(0); + } + jalview.io.FileLoader fl = new jalview.io.FileLoader(false); - + af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); - + assertNotNull("Couldn't load test data ('" + testseqs + "')", af); - + } @AfterClass @@ -87,13 +103,11 @@ public class RNAStructExportImport @Test public void testRNAStructExport() { - - + alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null); - + af.getViewport().getCalcManager().startWorker(alifoldClient); - - + do { try @@ -104,10 +118,9 @@ public class RNAStructExportImport } ; } while (af.getViewport().getCalcManager().isWorking()); - - + AlignmentI orig_alig = af.getViewport().getAlignment(); - + testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig); } @@ -116,14 +129,12 @@ public class RNAStructExportImport { try { - // what format would be appropriate for RNAalifold annotations? + // what format would be appropriate for RNAalifold annotations? 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 @@ -185,9 +196,9 @@ public class RNAStructExportImport } } alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts); - + af.getViewport().getCalcManager().startWorker(alifoldClient); - + do { try @@ -198,39 +209,58 @@ 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)); } } }