+/*
+ * 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;
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Cache.loadProperties("test/jalview/testProps.jvprops");
+ Cache.loadProperties("test/jalview/bin/commandsTest.jvprops");
Date oneHourFromNow = new Date(
System.currentTimeMillis() + 3600 * 1000);
Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- if (Desktop.instance != null)
- Desktop.instance.closeAll_actionPerformed(null);
+ Desktop.closeDesktop();
}
@Test(
groups =
- { "Functional" },
- dataProvider = "structureOpeningArgsParams")
+ { "Functional", "testTask1" },
+ dataProvider = "structureOpeningArgsParams",
+ singleThreaded = true)
public void structureOpeningArgsTest(String cmdLine, int seqNum,
int annNum, int viewerNum)
{
String[] args = cmdLine.split("\\s+");
- Jalview.main(args);
- AlignFrame[] afs = Desktop.getAlignFrames();
+ 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);
AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
int visibleAnn = 0;
+ int dcount = 0;
for (AlignmentAnnotation aa : aas)
{
if (aa.visible)
if (viewerNum > -1)
{
- try
- {
- Thread.sleep(100);
- } catch (InterruptedException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
List<StructureViewerBase> openViewers = Desktop.instance
.getStructureViewers(ap, null);
Assert.assertNotNull(openViewers);
- Assert.assertEquals(openViewers.size(), viewerNum,
+ int count = 0;
+ for (StructureViewerBase svb : openViewers)
+ {
+ if (svb.isVisible())
+ count++;
+ }
+ Assert.assertEquals(count, viewerNum,
"Wrong number of structure viewers opened");
}
}
String cmdLine,
int seqNum,
int annNum,
- int viewerNum,
- String propsFile
+ int structureViewerNum,
*/
- return new Object[][] { { "--nonews --nosplash --debug "
- + "--open=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 " + "--open=examples/uniref50.fa "
- + "--colour=gecos:flower "
+ 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 },
- { "--nonews --nosplash --debug " + "--open=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 " + "--open=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 " + "--open=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 " + "--open=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 },
- { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
- { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
+ { "--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