From: Ben Soares Date: Thu, 1 Jun 2023 16:01:36 +0000 (+0100) Subject: JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructure(). not fixed yet X-Git-Tag: Release_2_11_3_0~14^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bda60947eaabb464920b733509ace12e745f3910;p=jalview.git JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructure(). not fixed yet --- diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 753ded2..30fdc30 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -452,14 +452,6 @@ public class Commands Console.debug("Using structure file " + structureFile.getAbsolutePath()); - // ##### Does this need to happen? Follow - // openStructureFileForSequence() below - /* - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(structureFile.getAbsolutePath(), - DataSourceType.FILE, seq, true, Desktop.instance); - */ - // open structure view AlignmentPanel ap = af.alignPanel; if (headless) @@ -505,15 +497,6 @@ public class Commands Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false, true); TFType tft = notempfac ? null : TFType.DEFAULT; - /* - String tftString = subVals.get("tempfac"); - ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm, - af, structureFilepath); - if (tftString == null && tftAv != null) - { - tftString = tftAv.getSubVals().getContent(); - } - */ if (tftString != null && !notempfac) { // get kind of temperature factor annotation diff --git a/test/jalview/ws/dbsources/EBIAlphaFoldTest.java b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java index b737042..74a149b 100644 --- a/test/jalview/ws/dbsources/EBIAlphaFoldTest.java +++ b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java @@ -12,7 +12,11 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.structure.StructureMapping; @@ -62,8 +66,15 @@ public class EBIAlphaFoldTest FileAssert.assertFile(new File(paeFile), "Test file '" + paeFile + "' doesn't seem to exist"); } + SequenceI seq = new Sequence("Dummy/1-2000", + "ASDASDAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); + AlignmentI al = new Alignment(new SequenceI[] { seq }); + AlignFrame af = new AlignFrame(al, seq.getLength(), 1); StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); + StructureMapping sm = new StructureMapping(seq, pdbFile, null, null, + null, null); + ssm.addStructureMapping(sm); StructureMapping[] smArray = ssm.getMapping(pdbFile); @@ -86,8 +97,8 @@ public class EBIAlphaFoldTest // /* */ - { "examples/test_fab41.result/sample.a2m", - "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" }, + { "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb", + "examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3_scores.json" }, /* { "examples/AlphaFold/AF-A0A1U8FD60-F1-model_v4.pdb", "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },