X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest2.java;h=aa3c834430adddf1fc6182c2190b0c214c7d87d7;hb=82eb22b5c4cc991fad95822c71ab3ed90da759a6;hp=535eb7875453284ce78c8e9d624345fec18f9d8d;hpb=a91459d74964f834f5696c5f6a43b31e6bdbcd02;p=jalview.git diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java index 535eb78..aa3c834 100644 --- a/test/jalview/bin/CommandsTest2.java +++ b/test/jalview/bin/CommandsTest2.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.bin; import java.util.Date; @@ -26,7 +46,7 @@ public class CommandsTest2 @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - Cache.loadProperties("test/jalview/bin/commandsTest2.jvprops"); + Cache.loadProperties("test/jalview/bin/commandsTest.jvprops"); Date oneHourFromNow = new Date( System.currentTimeMillis() + 3600 * 1000); Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); @@ -51,13 +71,12 @@ public class CommandsTest2 @AfterMethod(alwaysRun = true) public void tearDown() { - if (Desktop.instance != null) - Desktop.instance.closeAll_actionPerformed(null); + Desktop.closeDesktop(); } @Test( groups = - { "Functional" }, + { "Functional", "testTask1" }, dataProvider = "structureOpeningArgsParams", singleThreaded = true) public void structureOpeningArgsTest(String cmdLine, int seqNum, @@ -65,17 +84,22 @@ public class CommandsTest2 { String[] args = cmdLine.split("\\s+"); - Jalview.main(args); - try + CommandsTest.callJalviewMain(args); + while (Desktop.instance != null + && Desktop.instance.operationsAreInProgress()) { - // sleep for slow build server to open annotations and viewer windows - Thread.sleep(seqNum * 100 + annNum * 200 + viewerNum * 1500); - } catch (InterruptedException e) - { - e.printStackTrace(); + try + { + // sleep for slow build server to open annotations and viewer windows + Thread.sleep(viewerNum * 50); + } catch (InterruptedException e) + { + e.printStackTrace(); + } } + ; - AlignFrame[] afs = Desktop.getAlignFrames(); + AlignFrame[] afs = Desktop.getDesktopAlignFrames(); Assert.assertNotNull(afs); Assert.assertTrue(afs.length > 0); @@ -101,9 +125,6 @@ public class CommandsTest2 int dcount = 0; for (AlignmentAnnotation aa : aas) { - System.err.println("##### DIAGNOSIS: annotation " + ++dcount - + " is labelled '" + aa.label + "'"); - System.err.println("# " + aa.annotationId + ": " + aa.toString()); if (aa.visible) visibleAnn++; } @@ -134,57 +155,78 @@ public class CommandsTest2 String cmdLine, int seqNum, int annNum, - int viewerNum, - String propsFile + int structureViewerNum, */ return new Object[][] { // /* */ - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 7, 1 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--props=test/jalview/bin/commandsTest2.jvprops2 ", 15, 4, 1 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " - + "--nossannotations " + + "--noshowssannotations " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 4, 1 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " - + "--noannotations " + + "--noshowannotations " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 3, 1 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " - + "--noannotations " + "--nossannotations " + + "--noshowannotations " + "--noshowssannotations " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 0, 1 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " - + "--colour=gecos:flower " + { "--gui --nonews --nosplash --debug " + + "--append=examples/uniref50.fa " + + "--colour=gecos-flower " + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif " + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " - + "--noannotations " + "--nossannotations " + + "--noshowannotations " + "--noshowssannotations " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 0, 1 }, - { "--props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ", + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 }, - { "--props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ", + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 }, + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m " + + "--allstructures " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + + "--structureviewer=none " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb", + 16, 10, 0 }, + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m " + + "--allstructures " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb " + + "--noallstructures " + "--structureviewer=none " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb " + + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb", + 16, 10, 2 }, + /* + */ // }; }