if (argParser.getBoolean(Arg.QUIT))
{
- Jalview.getInstance().exit(
- "Exiting due to " + Arg.QUIT.argString() + " argument.",
+ Jalview.exit("Exiting due to " + Arg.QUIT.argString() + " argument.",
ExitCode.OK);
return true;
}
Boolean isError = Boolean.valueOf(false);
- // set wrap scope here so it can be applied after structures are opened
+ // set wrap, showSSAnnotations, showAnnotations and hideTFrows scope here so
+ // it can be applied after structures are opened
boolean wrap = false;
+ boolean showSSAnnotations = false;
+ boolean showAnnotations = false;
+ boolean hideTFrows = false;
+ AlignFrame af = null;
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
boolean first = true;
boolean progressBarSet = false;
- AlignFrame af;
// Combine the APPEND and OPEN files into one list, along with whether it
// was APPEND or OPEN
List<ArgValue> openAvList = new ArrayList<>();
}
// Show secondary structure annotations?
- boolean showSSAnnotations = avm.getFromSubValArgOrPref(
+ showSSAnnotations = avm.getFromSubValArgOrPref(
Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
-
// Show sequence annotations?
- boolean showAnnotations = avm.getFromSubValArgOrPref(
- Arg.SHOWANNOTATIONS, av.getSubVals(), null,
- "SHOW_ANNOTATIONS", true);
-
- boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
- final AlignFrame _af = af;
- // many of jalview's format/layout methods are only thread safe on the
- // swingworker thread.
- // all these methods should be on the alignViewController so it can
- // coordinate such details
- try
- {
- SwingUtilities.invokeAndWait(new Runnable()
- {
+ showAnnotations = avm.getFromSubValArgOrPref(Arg.SHOWANNOTATIONS,
+ av.getSubVals(), null, "SHOW_ANNOTATIONS", true);
+ // hide the Temperature Factor row?
+ hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
- @Override
- public void run()
- {
- _af.setAnnotationsVisibility(showSSAnnotations, true,
- false);
-
- _af.setAnnotationsVisibility(showAnnotations, false, true);
-
- // show temperature factor annotations?
- if (hideTFrows)
- {
- // do this better (annotation types?)
- List<String> hideThese = new ArrayList<>();
- hideThese.add("Temperature Factor");
- hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
- AlignmentUtils.showOrHideSequenceAnnotations(
- _af.getCurrentView().getAlignment(), hideThese,
- null, false, false);
- }
- }
- });
- } catch (Exception x)
- {
- Console.warn(
- "Unexpected exception adjusting annotation row visibility.",
- x);
- }
+ // showSSAnnotations, showAnnotations, hideTFrows used after opening
+ // structure
// wrap alignment? do this last for formatting reasons
wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
// open the structure (from same PDB file or given PDBfile)
if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
-
- AlignFrame af = afMap.get(id);
+ if (af == null)
+ {
+ af = afMap.get(id);
+ }
if (avm.containsArg(Arg.STRUCTURE))
{
commandArgsProvided = true;
}
}
- if (wrap)
+ if (af == null)
{
+ af = afMap.get(id);
+ }
+ // many of jalview's format/layout methods are only thread safe on the
+ // swingworker thread.
+ // all these methods should be on the alignViewController so it can
+ // coordinate such details
+ if (headless)
+ {
+ showOrHideAnnotations(af, showSSAnnotations, showAnnotations,
+ hideTFrows);
+ }
+ else
+ {
+ try
+ {
+ AlignFrame _af = af;
+ final boolean _showSSAnnotations = showSSAnnotations;
+ final boolean _showAnnotations = showAnnotations;
+ final boolean _hideTFrows = hideTFrows;
+ SwingUtilities.invokeAndWait(() -> {
+ showOrHideAnnotations(_af, _showSSAnnotations, _showAnnotations,
+ _hideTFrows);
+ }
- AlignFrame af = afMap.get(id);
+ );
+ } catch (Exception x)
+ {
+ Console.warn(
+ "Unexpected exception adjusting annotation row visibility.",
+ x);
+ }
+ }
+
+ if (wrap)
+ {
+ if (af == null)
+ {
+ af = afMap.get(id);
+ }
if (af != null)
{
af.setWrapFormat(wrap, true);
return theseArgsWereParsed && !isError;
}
+ private static void showOrHideAnnotations(AlignFrame af,
+ boolean showSSAnnotations, boolean showAnnotations,
+ boolean hideTFrows)
+ {
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
+
+ // show temperature factor annotations?
+ if (hideTFrows)
+ {
+ // do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+ AlignmentUtils.showOrHideSequenceAnnotations(
+ af.getCurrentView().getAlignment(), hideThese, null, false,
+ false);
+ }
+ }
+
protected void processGroovyScript(String id)
{
ArgValuesMap avm = argParser.getLinkedArgs(id);
*/
package jalview.bin;
+import java.awt.image.BufferedImage;
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.imageio.ImageIO;
import javax.swing.SwingUtilities;
import org.testng.Assert;
public static void callJalviewMain(String[] args)
{
- if (Jalview.getInstance() != null)
+ callJalviewMain(args, false);
+ }
+
+ public static void callJalviewMain(String[] args, boolean newJalview)
+ {
+ if (Jalview.getInstance() != null && !newJalview)
{
Jalview.getInstance().doMain(args);
}
}
*/
- @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines", singleThreaded = true)
+ @Test(
+ groups =
+ { "Functional", "testTask3" },
+ dataProvider = "cmdLines",
+ singleThreaded = true)
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
@Test(
groups =
{ "Functional", "testTask3" },
- dataProvider = "structureImageOutputFiles", singleThreaded = true)
+ dataProvider = "structureImageOutputFiles",
+ singleThreaded = true)
public void structureImageOutputTest(String cmdLine, String[] filenames)
throws IOException
{
cleanupFiles(filenames);
- String[] args = (cmdLine + " --gui").split("\\s+");
+ String[] args = (cmdLine + "").split("\\s+");
try
{
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
- File lastFile = null;
- for (String filename : filenames)
+ 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)
{
- 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)
+ CommandLineOperations.Worker runner = CommandLineOperations
+ .getJalviewDesktopRunner(false, cmdLine, 1000);
+ long timeOut = 10000;
+ while (runner.isAlive() && timeOut > 0)
{
- waitForLastWrite(file,25);
-
- if (Files.size(file.toPath()) > Files
- .size(lastFile.toPath()))
- Assert.assertTrue(Files.size(file.toPath()) > Files
- .size(lastFile.toPath()));
+ Thread.sleep(25);
+ timeOut -= 25;
}
- // remember it for next file
- lastFile = file;
}
+ /*
+ * larger margin between IDs and alignment/annotations when in --gui mode
+ *
+ verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames, false);
+ */
+
+ verifySimilarEnoughImages(cmdLines[0] + " vs " + cmdLines[1],
+ filenames, 0.6f, 0f);
} catch (Exception x)
{
Assert.fail("Unexpected exception during structureImageOutputTest",
}
}
+ @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 --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" },
+ 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 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 < w_tolerance_pc,
+ "Height variation (" + (max_h - min_h)
+ + " not within tolerance 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());
+ long lastSize, stableSize = Files.size(file.toPath());
// wait around until we are sure the file has been completely written.
- do {
+ do
+ {
lastSize = stableSize;
- try {
+ try
+ {
Thread.sleep(i);
- } catch (Exception x) {}
- stableSize=Files.size(file.toPath());
- } while (stableSize!=lastSize);
+ } catch (Exception x)
+ {
+ }
+ stableSize = Files.size(file.toPath());
+ } while (stableSize != lastSize);
return stableSize;
}
- @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
+ @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()));
+ System.out.println("this file: " + file + " +"
+ + Files.size(file.toPath()) + " greater than "
+ + Files.size(lastFile.toPath()));
}
// remember it for next file
lastFile = file;
{
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 + "/structureimage1.png "
{ 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"
- }
- }
+ */
+ { "--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" } }
*/
//
};
};
}
+ @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 }, //
+ };
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff