--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+import java.util.Date;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.StructureViewerBase;
+
+@Test
+public class CommandsTest2
+{
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Cache.loadProperties("test/jalview/bin/commandsTest.jvprops");
+ Date oneHourFromNow = new Date(
+ System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.closeDesktop();
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "structureOpeningArgsParams",
+ singleThreaded = true)
+ public void structureOpeningArgsTest(String cmdLine, int seqNum,
+ int annNum, int viewerNum)
+ {
+ String[] args = cmdLine.split("\\s+");
+
+ CommandsTest.callJalviewMain(args);
+ while (Desktop.instance != null
+ && Desktop.instance.operationsAreInProgress())
+ {
+ try
+ {
+ // sleep for slow build server to open annotations and viewer windows
+ Thread.sleep(viewerNum * 50);
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ ;
+
+ AlignFrame[] afs = Desktop.getDesktopAlignFrames();
+ Assert.assertNotNull(afs);
+ Assert.assertTrue(afs.length > 0);
+
+ AlignFrame af = afs[0];
+ Assert.assertNotNull(af);
+
+ AlignmentPanel ap = af.alignPanel;
+ Assert.assertNotNull(ap);
+
+ AlignmentI al = ap.getAlignment();
+ Assert.assertNotNull(al);
+
+ List<SequenceI> seqs = al.getSequences();
+ Assert.assertNotNull(seqs);
+
+ Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
+
+ AlignViewportI av = ap.getAlignViewport();
+ Assert.assertNotNull(av);
+
+ AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
+ int visibleAnn = 0;
+ int dcount = 0;
+ for (AlignmentAnnotation aa : aas)
+ {
+ if (aa.visible)
+ visibleAnn++;
+ }
+
+ Assert.assertEquals(visibleAnn, annNum,
+ "Wrong number of visible annotations");
+
+ if (viewerNum > -1)
+ {
+ List<StructureViewerBase> openViewers = Desktop.instance
+ .getStructureViewers(ap, null);
+ Assert.assertNotNull(openViewers);
+ int count = 0;
+ for (StructureViewerBase svb : openViewers)
+ {
+ if (svb.isVisible())
+ count++;
+ }
+ Assert.assertEquals(count, viewerNum,
+ "Wrong number of structure viewers opened");
+ }
+ }
+
+ @DataProvider(name = "structureOpeningArgsParams")
+ public Object[][] structureOpeningArgsParams()
+ {
+ /*
+ String cmdLine,
+ int seqNum,
+ int annNum,
+ int structureViewerNum,
+ */
+ return new Object[][] {
+ //
+ /*
+ */
+ { "--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 },
+ { "--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 },
+ { "--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 "
+ + "--noshowssannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 4, 1 },
+ { "--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 "
+ + "--noshowannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 3, 1 },
+ { "--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 "
+ + "--noshowannotations " + "--noshowssannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 0, 1 },
+ { "--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 "
+ + "--noshowannotations " + "--noshowssannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 0, 1 },
+ { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
+ 16, 19, 3 },
+ { "--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 },
+ /*
+ */
+ //
+ };
+ }
+}
git://source.jalview.org / jalview.git / blobdiff