From 84ff3a3c7824890b0a201e6a4ec8fa1c9b6e9e64 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Sat, 27 May 2023 22:47:45 +0100 Subject: [PATCH] JAL-4121 Added a NPE check caught in tests. Added --gui to relevant tests. --- src/jalview/bin/Jalview.java | 9 ++++--- test/jalview/bin/CommandsTest.java | 44 +++++++++++++++++------------------ test/jalview/bin/CommandsTest2.java | 26 +++++++++++++-------- 3 files changed, 44 insertions(+), 35 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 159cf75..7535f60 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -451,11 +451,14 @@ public class Jalview .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false) || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false); StructureViewerBase.setQuitClose(closeExternal); - for (JInternalFrame frame : Desktop.desktop.getAllFrames()) + if (desktop != null) { - if (frame instanceof StructureViewerBase) + for (JInternalFrame frame : Desktop.desktop.getAllFrames()) { - ((StructureViewerBase) frame).closeViewer(closeExternal); + if (frame instanceof StructureViewerBase) + { + ((StructureViewerBase) frame).closeViewer(closeExternal); + } } } diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java index 7ed1ea3..b4c927b 100644 --- a/test/jalview/bin/CommandsTest.java +++ b/test/jalview/bin/CommandsTest.java @@ -70,7 +70,7 @@ public class CommandsTest public void commandsOpenTest(String cmdLine, boolean cmdArgs, int numFrames, String[] sequences) { - String[] args = cmdLine.split("\\s+"); + String[] args = (cmdLine + " --gui").split("\\s+"); Jalview.main(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); @@ -110,7 +110,7 @@ public class CommandsTest throws IOException { cleanupFiles(filenames); - String[] args = cmdLine.split("\\s+"); + String[] args = (cmdLine + " --gui").split("\\s+"); Jalview.main(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); @@ -138,7 +138,7 @@ public class CommandsTest String[] filenames) throws IOException { cleanupFiles(filenames); - String[] args = cmdLine.split("\\s+"); + String[] args = (cmdLine + " --gui").split("\\s+"); Jalview.main(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); @@ -166,7 +166,7 @@ public class CommandsTest { return new Object[][] { // - { "--nonews --nosplash --open=./examples/test_fab41.result/sample.a2m " + { "--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 " + "--open=./examples/test_fab41.result/sample.a2m " @@ -208,18 +208,18 @@ public class CommandsTest { return new Object[][] { // - { "--argfile=" + testfiles + "/**/*.txt", new String[] + { "--gui --argfile=" + testfiles + "/**/*.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png", testfiles + "/dir3/subdir/test0.png" } }, - { "--argfile=" + testfiles + "/**/argfile.txt", new String[] + { "--gui --argfile=" + testfiles + "/**/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, - { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[] + { "--gui --argfile=" + testfiles + "/dir*/argfile.txt", new String[] { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } }, - { "--initsubstitutions --append examples/uniref50.fa --image " + { "--gui --initsubstitutions --append examples/uniref50.fa --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/uniref50.png" } }, - { "--append examples/uniref50.fa --nosubstitutions --image " + { "--gui --append examples/uniref50.fa --nosubstitutions --image " + testfiles + "/{basename}.png", new String[] { testfiles + "/{basename}.png" } } @@ -252,11 +252,11 @@ public class CommandsTest { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, ArrayUtils.concatArrays(someUniref50Seqs, t1) }, { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 }, - { "--argfile=" + testfiles + "/argfile0.txt", true, 1, + { "--gui --argfile=" + testfiles + "/argfile0.txt", true, 1, ArrayUtils.concatArrays(t1, t3) }, - { "--argfile=" + testfiles + "/argfile*.txt", true, 5, + { "--gui --argfile=" + testfiles + "/argfile*.txt", true, 5, ArrayUtils.concatArrays(t1, t2, t3) }, - { "--argfile=" + testfiles + "/argfile.autocounter", true, 3, + { "--gui --argfile=" + testfiles + "/argfile.autocounter", true, 3, ArrayUtils.concatArrays(t1, t2) } }; } @@ -296,7 +296,7 @@ public class CommandsTest public void allLinkedIdsTest(String cmdLine, String[] filenames, String[] nonfilenames) { - String[] args = cmdLine.split("\\s+"); + String[] args = (cmdLine + " --gui").split("\\s+"); Jalview.main(args); Commands cmds = Jalview.getInstance().getCommands(); Assert.assertNotNull(cmds); @@ -324,19 +324,19 @@ public class CommandsTest // /* */ - { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close", + { "--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 }, - { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close", + { "--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 }, - { "--open=test/jalview/bin/argparser/testfiles/*.fa --all --output={dirname}/{basename}.stk --close", + { "--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", @@ -351,7 +351,7 @@ public class CommandsTest "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", }, }, - { "--open=test/jalview/bin/argparser/**/*.fa --all --output={dirname}/{basename}.stk --close", + { "--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", @@ -366,7 +366,7 @@ public class CommandsTest "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, - { "--open=test/jalview/bin/argparser/**/*.fa --output=*.stk --close", + { "--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", @@ -381,7 +381,7 @@ public class CommandsTest "test/jalview/bin/argparser/testfiles/dir3/subdir/test2.stk", "test/jalview/bin/argparser/testfiles/dir3/subdir/test3.stk", }, null }, - { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=*.stk --close", + { "--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/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", @@ -396,7 +396,7 @@ public class CommandsTest "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", }, }, - { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close", + { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", @@ -411,7 +411,7 @@ public class CommandsTest "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", }, }, - { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close", + { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --opened --output={dirname}/{basename}.stk --close", new String[] { "test/jalview/bin/argparser/testfiles/dir2/test1.stk", "test/jalview/bin/argparser/testfiles/dir2/test2.stk", @@ -426,7 +426,7 @@ public class CommandsTest "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", }, }, - { "--open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close", + { "--gui --open=test/jalview/bin/argparser/testfiles/dir1/*.fa --output open*.stk --open=test/jalview/bin/argparser/testfiles/dir2/*.fa --output=open*.aln --close", new String[] { "test/jalview/bin/argparser/testfiles/dir1/test1.stk", "test/jalview/bin/argparser/testfiles/dir1/test2.stk", diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java index a31b77d..0a47700 100644 --- a/test/jalview/bin/CommandsTest2.java +++ b/test/jalview/bin/CommandsTest2.java @@ -137,58 +137,64 @@ public class CommandsTest2 // /* */ - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " + { "--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 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " + { "--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 " + "--append=examples/uniref50.fa " + { "--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 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " + { "--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 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " + { "--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 }, - { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa " + { "--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 }, - { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ", + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 }, - { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ", + { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 }, - { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m " + { "--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 }, - { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m " + { "--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 " -- 1.7.10.2