+/*
+ * 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.io.File;
import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
import java.nio.file.Files;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
+import javax.swing.SwingUtilities;
+
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.AfterMethod;
@AfterMethod(alwaysRun = true)
public void tearDown()
{
- Desktop.closeDesktop();
+ try
+ {
+ // occasionally we are blocked by Jmol redraws
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ Desktop.closeDesktop();
+ }
+ });
+ } catch (Exception foo)
+ {
+ System.err.println("Failed during teardown with exception");
+ foo.printStackTrace();
+ }
+
}
public static void callJalviewMain(String[] args)
}
*/
- @Test(groups = "Functional", dataProvider = "cmdLines")
+ @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines", singleThreaded = true)
+
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
"Overall command parse and operation is false");
- Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
"Wrong number of AlignFrames");
if (sequences != null)
{
Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
+ AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
openedSequenceNames.addAll(
@Test(
groups =
- { "Functional", "testTask1" },
- dataProvider = "structureImageOutputFiles")
+ { "Functional", "testTask3" },
+ dataProvider = "structureImageOutputFiles", singleThreaded = true)
public void structureImageOutputTest(String cmdLine, String[] filenames)
throws IOException
{
Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ "' has no content from '" + cmdLine + "'");
// make sure the successive output files get bigger!
- if (lastFile != null)
- Assert.assertTrue(Files.size(file.toPath()) > Files
- .size(lastFile.toPath()));
+ if (lastFile != null) {
+ Assert.assertTrue(Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+ System.out.println("this file: " + file + " +" + Files.size(file.toPath()) + " greater than "
+ + Files.size(lastFile.toPath()));
+ }
+ // remember it for next file
+ lastFile = file;
}
} catch (Exception x)
{
}
}
- @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+ @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
public void argFilesGlobAndSubstitutionsTest(String cmdLine,
String[] filenames) throws IOException
{
Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ "' has no content from '" + cmdLine + "'");
// make sure the successive output files get bigger!
- if (lastFile != null)
+ if (lastFile != null) {
Assert.assertTrue(Files.size(file.toPath()) > Files
.size(lastFile.toPath()));
+ System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
+ }
+ // remember it for next file
+ lastFile = file;
}
} catch (Exception x)
{
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
- + "/structureimage2.png --structureimagescale=1.5"
+ + "/structureimage2.png --scale=1.5 "
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
- + "/structureimage3.png --structureimagescale=2.0",
+ + "/structureimage3.png --scale=2.0 ",
new String[]
{ testfiles + "/structureimage1.png",
testfiles + "/structureimage2.png",
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
- + "/structureimage2.png --structureimagescale=1.5"
+ + "/structureimage2.png --scale=1.5 "
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
- + "/structureimage3.png --structureimagescale=2.0",
+ + "/structureimage3.png --scale=2.0 ",
new String[]
{ testfiles + "/structureimage1.png",
testfiles + "/structureimage2.png",
testfiles + "/structureimage3.png" } },
+ { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+
+ new String[] {
+ testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+ }
+ },
+ { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+
+ new String[] {
+ testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+ }
+ }
+
/*
*/
//
public static boolean lookForSequenceName(String sequenceName)
{
- AlignFrame[] afs = Desktop.getAlignFrames();
+ AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
for (String name : af.getViewport().getAlignment().getSequenceNames())
}
}
+ private final String deleteDir = "test/deleteAfter";
+
@Test(
groups = "Functional",
dataProvider = "allLinkedIdsData",
"File " + nonfilename + " exists when it shouldn't!");
}
}
+
+ File deleteDirF = new File(deleteDir);
+ if (deleteDirF.exists())
+ {
+ deleteDirF.delete();
+ }
}
@DataProvider(name = "allLinkedIdsData")
"test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
"test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
+ // --mkdirs
+ { "--headless --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output "
+ + deleteDir
+ + "/{dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output="
+ + deleteDir
+ + "/{dirname}/{basename}.aln --close --all --mkdirs",
+ new String[]
+ { deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test1.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir1/test2.stk",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test1.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test2.aln",
+ deleteDir
+ + "/test/jalview/bin/argparser/testfiles/dir2/test3.aln", },
+ new String[]
+ { "test/jalview/bin/argparser/testfiles/test1.stk",
+ "test/jalview/bin/argparser/testfiles/test2.stk",
+ "test/jalview/bin/argparser/testfiles/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ "test/jalview/bin/argparser/testfiles/test1.aln",
+ "test/jalview/bin/argparser/testfiles/test2.aln",
+ "test/jalview/bin/argparser/testfiles/test3.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir2/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/test3.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir1/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test0.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test1.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.aln",
+ deleteDir
+ + "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.aln", }, },
//
};
}
git://source.jalview.org / jalview.git / blobdiff