/*
* 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.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
import javax.imageio.ImageIO;
import javax.swing.SwingUtilities;
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.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.ArrayUtils;
public class CommandsTest
{
private static final String testfiles = "test/jalview/bin/argparser/testfiles";
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
Date oneHourFromNow = new Date(
System.currentTimeMillis() + 3600 * 1000);
Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
}
@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()
{
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)
{
callJalviewMain(args, false);
}
public static void callJalviewMain(String[] args, boolean newJalview)
{
if (Jalview.getInstance() != null && !newJalview)
{
Jalview.getInstance().doMain(args);
}
else
{
Jalview.main(args);
}
}
/* --setprops is currently disabled so this test won't work
@Test(groups = "Functional")
public void setpropsTest()
{
final String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
String[] args = cmdLine.split("\\s+");
Jalview.main(args);
Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
"Earth");
}
*/
@Test(
groups =
{ "Functional", "testTask3" },
dataProvider = "cmdLines",
singleThreaded = true)
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
try
{
String[] args = (cmdLine + " --gui").split("\\s+");
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
"Commands were not provided in the args");
Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
"Overall command parse and operation is false");
Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
"Wrong number of AlignFrames");
if (sequences != null)
{
Set openedSequenceNames = new HashSet<>();
AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
openedSequenceNames.addAll(
af.getViewport().getAlignment().getSequenceNames());
}
for (String sequence : sequences)
{
Assert.assertTrue(openedSequenceNames.contains(sequence),
"Sequence '" + sequence
+ "' was not found in opened alignment files: "
+ cmdLine + ".\nOpened sequence names are:\n"
+ String.join("\n", openedSequenceNames));
}
}
Assert.assertFalse(
lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
} catch (Exception x)
{
Assert.fail("Unexpected exception during commandsOpenTest", x);
} finally
{
tearDown();
}
}
@Test(
groups =
{ "Functional", "testTask3" },
dataProvider = "structureImageOutputFiles",
singleThreaded = true)
public void structureImageOutputTest(String cmdLine, String[] filenames)
throws IOException
{
cleanupFiles(filenames);
String[] args = (cmdLine).split("\\s+");
try
{
callJalviewMain(args, true);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
verifyIncreasingSize(cmdLine, filenames);
} catch (Exception x)
{
Assert.fail("Unexpected exception during structureImageOutputTest",
x);
} finally
{
cleanupFiles(filenames);
tearDown();
}
}
/**
* given two command lines, compare the output files produced - they should
* exist and be equal in size
*/
@Test(
groups =
{ "Functional", "testTask3" },
dataProvider = "compareHeadlessAndGUIOps",
singleThreaded = true)
public void headlessOrGuiImageOutputTest(String[] cmdLines,
String[] filenames) throws IOException
{
cleanupFiles(filenames);
try
{
for (String cmdLine : cmdLines)
{
CommandLineOperations.Worker runner = CommandLineOperations
.getJalviewDesktopRunner(false, cmdLine, 1000);
long timeOut = 10000;
while (runner.isAlive() && timeOut > 0)
{
Thread.sleep(25);
timeOut -= 25;
}
}
verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
false);
verifySimilarEnoughImages(cmdLines[0] + " vs " + cmdLines[1],
filenames, 0f, 0f);
} catch (Exception x)
{
Assert.fail("Unexpected exception during structureImageOutputTest",
x);
} finally
{
cleanupFiles(filenames);
tearDown();
}
}
@DataProvider(name = "compareHeadlessAndGUIOps")
public Object[][] compareHeadlessAndGUIOps()
{
return new Object[][] {
new Object[]
{ new String[] { "--open examples/uniref50.fa "
+ "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
+ "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
+ testfiles + "/"
+ "test-al-pae-ss-gui.png --overwrite --gui --props test/jalview/bin/commandsTest3.jvprops --quit",
"--open examples/uniref50.fa "
+ "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
+ "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
+ testfiles + "/"
+ "test-al-pae-ss-nogui.png --overwrite --nogui --props test/jalview/bin/commandsTest3.jvprops" },
new String[]
{ testfiles + "/test-al-pae-ss-gui.png",
testfiles + "/test-al-pae-ss-nogui.png", } } };
}
private static void verifyIncreasingSize(String cmdLine,
String[] filenames) throws Exception
{
verifyOrderedFileSet(cmdLine, filenames, true);
}
private static void verifyOrderedFileSet(String cmdLine,
String[] filenames, boolean increasingSize) throws Exception
{
File lastFile = null;
for (String filename : filenames)
{
File file = new File(filename);
Assert.assertTrue(file.exists(), "File '" + filename
+ "' was not created by '" + cmdLine + "'");
Assert.assertTrue(file.isFile(), "File '" + filename
+ "' is not a file from '" + cmdLine + "'");
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)
{
waitForLastWrite(file, 25);
if (increasingSize)
{
Assert.assertTrue(
Files.size(file.toPath()) > Files.size(lastFile.toPath()),
"Expected " + file.toPath() + " to be larger than "
+ lastFile.toPath());
}
else
{
Assert.assertEquals(Files.size(file.toPath()),
Files.size(lastFile.toPath()),
"New file " + file.toPath()
+ " (actual size) not same as last file's size "
+ lastFile.toString());
}
}
// remember it for next file
lastFile = file;
}
}
private static void verifySimilarEnoughImages(String cmdLine,
String[] filenames, float w_tolerance_pc, float h_tolerance_pc)
throws Exception
{
int min_w = -1;
int max_w = -1;
int min_h = -1;
int max_h = -1;
for (String filename : filenames)
{
File file = new File(filename);
Assert.assertTrue(file.exists(), "File '" + filename
+ "' was not created by '" + cmdLine + "'");
Assert.assertTrue(file.isFile(), "File '" + filename
+ "' is not a file from '" + cmdLine + "'");
Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ "' has no content from '" + cmdLine + "'");
BufferedImage img = ImageIO.read(file);
if (img.getWidth() < min_w || min_w == -1)
{
min_w = img.getWidth();
}
if (img.getWidth() > max_w || max_w == -1)
{
max_w = img.getWidth();
}
if (img.getHeight() < min_h || min_h == -1)
{
min_h = img.getHeight();
}
if (img.getHeight() > max_h || max_h == -1)
{
max_h = img.getHeight();
}
}
Assert.assertTrue(min_w > 0,
"Minimum width is not positive (" + min_w + ")");
Assert.assertTrue(max_w > 0,
"Maximum width is not positive (" + max_w + ")");
Assert.assertTrue(min_h > 0,
"Minimum height is not positive (" + min_h + ")");
Assert.assertTrue(max_h > 0,
"Maximum height is not positive (" + max_h + ")");
// tolerance
Assert.assertTrue(100 * (max_w - min_w) / min_w <= w_tolerance_pc,
"Width variation (" + (max_w - min_w)
+ " not within tolerance (" + w_tolerance_pc
+ "%) of minimum width (" + min_w + ")");
if (max_w != min_w)
{
System.out.println("Widths within tolerance (" + w_tolerance_pc
+ "%), min_w=" + min_w + " < max_w=" + max_w);
}
Assert.assertTrue(100 * (max_h - min_h) / min_h <= h_tolerance_pc,
"Height variation (" + (max_h - min_h)
+ " not within tolerance (" + h_tolerance_pc
+ "%) of minimum height (" + min_h + ")");
if (max_h != min_h)
{
System.out.println("Heights within tolerance (" + h_tolerance_pc
+ "%), min_h=" + min_h + " < max_h=" + max_h);
}
}
private static long waitForLastWrite(File file, int i) throws IOException
{
long lastSize, stableSize = Files.size(file.toPath());
// wait around until we are sure the file has been completely written.
do
{
lastSize = stableSize;
try
{
Thread.sleep(i);
} catch (Exception x)
{
}
stableSize = Files.size(file.toPath());
} while (stableSize != lastSize);
return stableSize;
}
@Test(
groups = "Functional",
dataProvider = "argfileOutputFiles",
singleThreaded = true)
public void argFilesGlobAndSubstitutionsTest(String cmdLine,
String[] filenames) throws IOException
{
cleanupFiles(filenames);
String[] args = (cmdLine + " --gui").split("\\s+");
try
{
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
File lastFile = null;
for (String filename : filenames)
{
File file = new File(filename);
Assert.assertTrue(file.exists(), "File '" + filename
+ "' was not created by '" + cmdLine + "'");
Assert.assertTrue(file.isFile(), "File '" + filename
+ "' is not a file from '" + cmdLine + "'");
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()));
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)
{
Assert.fail(
"Unexpected exception during argFilesGlobAndSubstitutions",
x);
} finally
{
cleanupFiles(filenames);
tearDown();
}
}
@DataProvider(name = "structureImageOutputFiles")
public Object[][] structureImageOutputFiles()
{
return new Object[][] {
//
/*
*/
{ "--gui --nonews --nosplash --open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
+ "/structureimage0-1.png "
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
+ "/structureimage0-2.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
+ "/structureimage0-3.png --scale=2.0 ",
new String[]
{ testfiles + "/structureimage0-1.png",
testfiles + "/structureimage0-2.png",
testfiles + "/structureimage0-3.png" } },
{ "--headless --noquit --open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
+ "/structureimage1-1.png "
+ "--open=./examples/test_fab41.result/sample.a2m "
+ "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+ "--structureimage=" + testfiles
+ "/structureimage1-2.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
+ "/structureimage1-3.png --scale=2.0 ",
new String[]
{ testfiles + "/structureimage1-1.png",
testfiles + "/structureimage1-2.png",
testfiles + "/structureimage1-3.png" } },
{ "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "
+ "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
+ "--structureimage " + testfiles
+ "/structureimage2-1gaq.png --structure examples/3W5V.pdb "
+ "--seqid \"3W5V|A\" --structureimage " + testfiles
+ "/structureimage2-3w5v.png --overwrite",
new String[]
{ testfiles + "/structureimage2-3w5v.png",
testfiles + "/structureimage2-1gaq.png", } },
{ "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "
+ "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
+ "--structureimage " + testfiles
+ "/structureimage3-1gaq.png --structure examples/3W5V.pdb "
+ "--seqid \"3W5V|A\" --structureimage " + testfiles
+ "/structureimage3-3w5v.png --overwrite",
new String[]
{ testfiles + "/structureimage3-3w5v.png",
testfiles + "/structureimage3-1gaq.png", } }
/*
*/
//
};
}
@DataProvider(name = "argfileOutputFiles")
public Object[][] argfileOutputFiles()
{
return new Object[][] {
//
{ "--gui --argfile=" + testfiles + "/**/*.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
testfiles + "/dir3/subdir/test0.png" } },
{ "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
{ "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[]
{ testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
{ "--gui --initsubstitutions --append examples/uniref50.fa --image "
+ testfiles + "/{basename}.png",
new String[]
{ testfiles + "/uniref50.png" } },
{ "--gui --append examples/uniref50.fa --nosubstitutions --image "
+ testfiles + "/{basename}.png",
new String[]
{ testfiles + "/{basename}.png" } }
//
};
}
@DataProvider(name = "cmdLines")
public Object[][] cmdLines()
{
String[] someUniref50Seqs = new String[] { "FER_CAPAA", "FER_CAPAN",
"FER1_MAIZE", "FER1_SPIOL", "O80429_MAIZE" };
String[] t1 = new String[] { "TEST1" };
String[] t2 = new String[] { "TEST2" };
String[] t3 = new String[] { "TEST3" };
return new Object[][] {
/*
*/
{ "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
{ "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
{ "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
// NOTE we cannot use shell expansion in tests, so list all files!
{ "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
someUniref50Seqs },
{ "--append=[new]examples/uniref50*.fa", true, 2,
someUniref50Seqs },
{ "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
{ "examples/uniref50.fa", true, 1, someUniref50Seqs },
{ "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
ArrayUtils.concatArrays(someUniref50Seqs, t1) },
{ "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
{ "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1,
ArrayUtils.concatArrays(t1, t3) },
{ "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5,
ArrayUtils.concatArrays(t1, t2, t3) },
{ "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3,
ArrayUtils.concatArrays(t1, t2) } };
}
public static boolean lookForSequenceName(String sequenceName)
{
AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
for (String name : af.getViewport().getAlignment().getSequenceNames())
{
if (sequenceName.equals(name))
{
return true;
}
}
}
return false;
}
public static void cleanupFiles(String[] filenames)
{
for (String filename : filenames)
{
File file = new File(filename);
if (file.exists())
{
file.delete();
}
}
}
private final String deleteDir = "test/deleteAfter";
@Test(
groups = "Functional",
dataProvider = "allLinkedIdsData",
singleThreaded = true)
public void allLinkedIdsTest(String cmdLine, String[] filenames,
String[] nonfilenames)
{
String[] args = (cmdLine + " --gui").split("\\s+");
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
for (String filename : filenames)
{
Assert.assertTrue(new File(filename).exists(),
"File '" + filename + "' was not created");
}
cleanupFiles(filenames);
if (nonfilenames != null)
{
for (String nonfilename : nonfilenames)
{
File nonfile = new File(nonfilename);
Assert.assertFalse(nonfile.exists(),
"File " + nonfilename + " exists when it shouldn't!");
}
}
File deleteDirF = new File(deleteDir);
if (deleteDirF.exists())
{
deleteDirF.delete();
}
}
@DataProvider(name = "allLinkedIdsData")
public Object[][] allLinkedIdsData()
{
return new Object[][] {
//
{ "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/test3.stk", },
null },
{ "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.png",
"test/jalview/bin/argparser/testfiles/test2.png",
"test/jalview/bin/argparser/testfiles/test3.png", },
null },
{ "--gui --open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/test1.stk",
"test/jalview/bin/argparser/testfiles/test2.stk",
"test/jalview/bin/argparser/testfiles/test3.stk", },
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
{ "--gui --open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close",
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/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", },
null },
{ "--gui --open=test/jalview/bin/argparser/**/*.fa --output=*/*.stk --close",
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/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", },
null },
{ "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --all --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", },
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/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", }, },
{ "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*/*.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
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/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", }, },
{ "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
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/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
{ "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.stk --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir2/test1.stk",
"test/jalview/bin/argparser/testfiles/dir2/test2.stk",
"test/jalview/bin/argparser/testfiles/dir2/test3.stk", },
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/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.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", }, },
{ "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output {dirname}/{basename}.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output={dirname}/{basename}.aln --close",
new String[]
{ "test/jalview/bin/argparser/testfiles/dir1/test1.stk",
"test/jalview/bin/argparser/testfiles/dir1/test2.stk",
"test/jalview/bin/argparser/testfiles/dir2/test1.aln",
"test/jalview/bin/argparser/testfiles/dir2/test2.aln",
"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", }, },
// --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", }, },
//
};
}
@Test(
groups =
{ "Functional", "testTask3" },
dataProvider = "structureImageAnnotationsOutputFiles",
singleThreaded = true)
public void structureImageAnnotationsOutputTest(String cmdLine,
String filename, int height) throws IOException
{
cleanupFiles(new String[] { filename });
String[] args = (cmdLine).split("\\s+");
callJalviewMain(args, true); // Create new instance of Jalview each time for
// linkedIds
BufferedImage img = ImageIO.read(new File(filename));
Assert.assertEquals(height, img.getHeight(), "Output image '" + filename
+ "' is not in the expected height range, possibly because of the wrong number of annotations");
cleanupFiles(new String[] { filename });
tearDown();
}
@DataProvider(name = "structureImageAnnotationsOutputFiles")
public Object[][] structureImageAnnotationsOutputFiles()
{
String filename = "test/jalview/bin/argparser/testfiles/test_annotations.png";
return new Object[][] {
// MUST use --noquit with --headless to avoid a System.exit()
{ "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--noshowssannotations " + "--noshowannotations", //
filename, //
252 }, //
{ "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--showssannotations " + "--noshowannotations", //
filename, //
368 }, //
{ "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--noshowssannotations " + "--showannotations", //
filename, //
524 }, //
{ "--noquit --headless --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--showssannotations " + "--showannotations", //
filename, //
660 }, //
{ "--gui --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--noshowssannotations " + "--noshowannotations", //
filename, //
252 }, //
{ "--gui --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--showssannotations " + "--noshowannotations", //
filename, //
368 }, //
{ "--gui --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--noshowssannotations " + "--showannotations", //
filename, //
524 }, //
{ "--gui --nonews --nosplash --open=./examples/uniref50.fa "
+ "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ "--seqid=FER1_SPIOL --structureviewer=jmol "
+ "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ "--image=" + filename + " " + "--tempfac=plddt "
+ "--overwrite " //
+ "--showssannotations " + "--showannotations", //
filename, //
660 }, //
};
}
}