From 82eb22b5c4cc991fad95822c71ab3ed90da759a6 Mon Sep 17 00:00:00 2001 From: Renia Correya Date: Wed, 15 May 2024 16:56:22 +0100 Subject: [PATCH] JAL-4386 Fixed failed test cases --- test/jalview/bin/CommandsTest2.java | 12 ++--- test/jalview/gui/AnnotationChooserTest.java | 67 +++++++++++++-------------- test/jalview/gui/StructureChooserTest.java | 12 ++--- 3 files changed, 43 insertions(+), 48 deletions(-) diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java index a732254..aa3c834 100644 --- a/test/jalview/bin/CommandsTest2.java +++ b/test/jalview/bin/CommandsTest2.java @@ -167,14 +167,14 @@ public class CommandsTest2 + "--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, 8, 1 }, + 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, 5, 1 }, + 15, 4, 1 }, { "--gui --nonews --nosplash --debug " + "--append=examples/uniref50.fa " + "--colour=gecos-flower " @@ -182,7 +182,7 @@ public class CommandsTest2 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json " + "--noshowssannotations " + "--props=test/jalview/bin/commandsTest2.jvprops1 ", - 15, 5, 1 }, + 15, 4, 1 }, { "--gui --nonews --nosplash --debug " + "--append=examples/uniref50.fa " + "--colour=gecos-flower " @@ -208,7 +208,7 @@ public class CommandsTest2 + "--props=test/jalview/bin/commandsTest2.jvprops1 ", 15, 0, 1 }, { "--gui --nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ", - 16, 20, 3 }, + 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 " @@ -217,14 +217,14 @@ public class CommandsTest2 + "--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, 11, 0 }, + 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, 11, 2 }, + 16, 10, 2 }, /* */ // diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java index c8208ca..f3c0dee 100644 --- a/test/jalview/gui/AnnotationChooserTest.java +++ b/test/jalview/gui/AnnotationChooserTest.java @@ -325,7 +325,7 @@ public class AnnotationChooserTest types = AnnotationChooser.getAnnotationTypes(parentPanel.getAlignment(), false); - assertEquals("Not six annotation types", 8, types.size()); + assertEquals("Not six annotation types", 7, types.size()); assertTrue("IUPRED missing", types.contains("IUPRED")); assertTrue("JMol missing", types.contains("JMol")); assertTrue("Beauty missing", types.contains("Beauty")); @@ -365,13 +365,12 @@ public class AnnotationChooserTest assertTrue(anns[0].visible); // Conservation assertTrue(anns[1].visible); // Quality assertTrue(anns[2].visible); // Consensus - assertTrue(anns[3].visible); // SS Consensus - assertTrue(anns[4].visible); // Occupancy - assertTrue(anns[5].visible); // IUPred for seq0 - assertTrue(anns[6].visible); // Beauty - assertFalse(anns[7].visible); // JMol for seq3 - not selected but hidden - assertTrue(anns[8].visible); // IUPRED for seq2 - assertFalse(anns[9].visible); // JMol for seq1 - selected and hidden + assertTrue(anns[3].visible); // Occupancy + assertTrue(anns[4].visible); // IUPred for seq0 + assertTrue(anns[5].visible); // Beauty + assertFalse(anns[6].visible); // JMol for seq3 - not selected but hidden + assertTrue(anns[7].visible); // IUPRED for seq2 + assertFalse(anns[8].visible); // JMol for seq1 - selected and hidden } /** @@ -405,13 +404,12 @@ public class AnnotationChooserTest assertTrue(anns[0].visible); // Conservation assertTrue(anns[1].visible); // Quality assertTrue(anns[2].visible); // Consensus - assertTrue(anns[3].visible); // SS ßConsensus - assertTrue(anns[4].visible); // Occupancy - assertTrue(anns[5].visible); // IUPred for seq0 - assertTrue(anns[6].visible); // Beauty - assertTrue(anns[7].visible); // JMol for seq3 not in selection group - assertTrue(anns[8].visible); // IUPRED for seq2 - assertFalse(anns[9].visible); // JMol for seq1 in selection group + assertTrue(anns[3].visible); // Occupancy + assertTrue(anns[4].visible); // IUPred for seq0 + assertTrue(anns[5].visible); // Beauty + assertTrue(anns[6].visible); // JMol for seq3 not in selection group + assertTrue(anns[7].visible); // IUPRED for seq2 + assertFalse(anns[8].visible); // JMol for seq1 in selection group } /** @@ -617,13 +615,12 @@ public class AnnotationChooserTest assertTrue(anns[0].visible); // Conservation assertTrue(anns[1].visible); // Quality assertTrue(anns[2].visible); // Consensus - assertTrue(anns[3].visible); // Consensus - assertTrue(anns[4].visible); // Occupancy - assertTrue(anns[5].visible); // IUPred for seq0 - assertTrue(anns[6].visible); // Beauty - assertFalse(anns[7].visible); // JMol for seq3 - assertTrue(anns[8].visible); // IUPRED for seq2 - assertFalse(anns[9].visible); // JMol for seq1 + assertTrue(anns[3].visible); // Occupancy + assertTrue(anns[4].visible); // IUPred for seq0 + assertTrue(anns[5].visible); // Beauty + assertFalse(anns[6].visible); // JMol for seq3 + assertTrue(anns[7].visible); // IUPRED for seq2 + assertFalse(anns[8].visible); // JMol for seq1 } /** @@ -661,13 +658,12 @@ public class AnnotationChooserTest assertTrue(anns[0].visible); // Conservation assertTrue(anns[1].visible); // Quality assertTrue(anns[2].visible); // Consensus - assertTrue(anns[3].visible); // Consensus - assertTrue(anns[4].visible); // Occupancy - assertTrue(anns[5].visible); // IUPred for seq0 - assertTrue(anns[6].visible); // Beauty - assertTrue(anns[7].visible); // JMol for seq3 not in selection group - assertTrue(anns[8].visible); // IUPRED for seq2 - assertFalse(anns[9].visible); // JMol for seq1 in selection group + assertTrue(anns[3].visible); // Occupancy + assertTrue(anns[4].visible); // IUPred for seq0 + assertTrue(anns[5].visible); // Beauty + assertTrue(anns[6].visible); // JMol for seq3 not in selection group + assertTrue(anns[7].visible); // IUPRED for seq2 + assertFalse(anns[8].visible); // JMol for seq1 in selection group } /** @@ -809,13 +805,12 @@ public class AnnotationChooserTest assertTrue(anns[0].visible); // Conservation assertTrue(anns[1].visible); // Quality assertTrue(anns[2].visible); // Consensus - assertTrue(anns[3].visible); // SS Consensus - assertTrue(anns[4].visible); // Occupancy - assertFalse(anns[5].visible); // IUPRED - assertTrue(anns[6].visible); // Beauty (not seq-related) - assertFalse(anns[7].visible); // JMol - assertFalse(anns[8].visible); // IUPRED - assertFalse(anns[9].visible); // JMol + assertTrue(anns[3].visible); // Occupancy + assertFalse(anns[4].visible); // IUPRED + assertTrue(anns[5].visible); // Beauty (not seq-related) + assertFalse(anns[6].visible); // JMol + assertFalse(anns[7].visible); // IUPRED + assertFalse(anns[8].visible); // JMol // reset - should all be visible testee.resetOriginalState(); diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java index 91c8bbc..dd5cd4c 100644 --- a/test/jalview/gui/StructureChooserTest.java +++ b/test/jalview/gui/StructureChooserTest.java @@ -394,27 +394,27 @@ public class StructureChooserTest { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - true, false, null, 15, 8, 0, null }, + true, false, null, 15, 7, 0, null }, { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - true, false, null, 15, 8, 0, null }, + true, false, null, 15, 7, 0, null }, { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - false, false, null, 15, 5, 0, null }, + false, false, null, 15, 4, 0, null }, { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - true, false, ViewerType.JMOL, 15, 8, 1, null }, + true, false, ViewerType.JMOL, 15, 7, 1, null }, { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - true, false, ViewerType.JMOL, 15, 8, 1, null }, + true, false, ViewerType.JMOL, 15, 7, 1, null }, { "examples/uniref50.fa", "FER1_SPIOL", "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT, "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json", - false, false, ViewerType.JMOL, 15, 5, 1, null }, }; + false, false, ViewerType.JMOL, 15, 4, 1, null }, }; } } -- 1.7.10.2