From 49ae0c9823bb1c450e03460c5714a7db3cdf440b Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 15 May 2017 16:43:12 +0100 Subject: [PATCH] JAL-2507 - required callers to specify exact ignore flags for StockholmFileTest.testAlignmentEquivalent asserts --- test/jalview/io/AnnotationFileIOTest.java | 3 ++- test/jalview/io/PhylipFileTests.java | 3 ++- test/jalview/io/RNAMLfileTest.java | 2 +- test/jalview/io/StockholmFileTest.java | 12 ++++++++---- test/jalview/ws/jabaws/DisorderAnnotExportImport.java | 3 ++- test/jalview/ws/jabaws/JpredJabaStructExportImport.java | 3 ++- test/jalview/ws/jabaws/RNAStructExportImport.java | 3 ++- 7 files changed, 19 insertions(+), 10 deletions(-) diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index c3aa13e..62bd0b9 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -153,7 +153,8 @@ public class AnnotationFileIOTest DataSourceType.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new, false); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false, + false); return; } catch (Exception e) { diff --git a/test/jalview/io/PhylipFileTests.java b/test/jalview/io/PhylipFileTests.java index f99c67a..d853350 100644 --- a/test/jalview/io/PhylipFileTests.java +++ b/test/jalview/io/PhylipFileTests.java @@ -190,7 +190,8 @@ public class PhylipFileTests DataSourceType.PASTE, FileFormat.Phylip); assertNotNull("Couldn't parse reimported alignment data.", al_input); - StockholmFileTest.testAlignmentEquivalence(al, al_input, false); + StockholmFileTest.testAlignmentEquivalence(al, al_input, false, false, + false); } } diff --git a/test/jalview/io/RNAMLfileTest.java b/test/jalview/io/RNAMLfileTest.java index 1c54980..ae72de4 100644 --- a/test/jalview/io/RNAMLfileTest.java +++ b/test/jalview/io/RNAMLfileTest.java @@ -53,7 +53,7 @@ public class RNAMLfileTest { StockholmFileTest.testFileIOwithFormat(new File( "examples/testdata/rna-alignment.xml"), FileFormat.Stockholm, - -1, -1, true); + -1, -1, true, true, true); } diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 1a18fb9..228c935 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -60,7 +60,7 @@ public class StockholmFileTest public void pfamFileIO() throws Exception { testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0, - false); + false, false, false); } @Test(groups = { "Functional" }) @@ -86,7 +86,7 @@ public class StockholmFileTest public void rfamFileIO() throws Exception { testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1, - false); + false, false, false); } /** @@ -98,11 +98,14 @@ public class StockholmFileTest * @param ioformat * - label for IO class used to write and read back in the data from * f + * @param ignoreFeatures * @param ignoreRowVisibility + * @param allowNullAnnotations */ public static void testFileIOwithFormat(File f, FileFormatI ioformat, - int naliannot, int nminseqann, boolean ignoreRowVisibility) + int naliannot, int nminseqann, boolean ignoreFeatures, + boolean ignoreRowVisibility, boolean allowNullAnnotations) { System.out.println("Reading file: " + f); String ff = f.getPath(); @@ -136,7 +139,8 @@ public class StockholmFileTest "Identify routine could not recognise output generated by '" + ioformat + "' writer", ioformat.equals(identifyoutput)); - testAlignmentEquivalence(al, al_input, false); + testAlignmentEquivalence(al, al_input, ignoreFeatures, + ignoreRowVisibility, allowNullAnnotations); int numaliannot = 0, numsqswithali = 0; for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation()) { diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java index 2714d6c..e8b6c2b 100644 --- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java +++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java @@ -177,7 +177,8 @@ public class DisorderAnnotExportImport DataSourceType.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new, true); + StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false, + false); return; } catch (Exception e) { diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java index d5b6ed1..8326687 100644 --- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java +++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java @@ -218,7 +218,8 @@ public class JpredJabaStructExportImport DataSourceType.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new, false); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false, + false); return; } catch (Exception e) { diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 4e9741e..5ea97ff 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -242,7 +242,8 @@ public class RNAStructExportImport DataSourceType.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new, false); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false, + false); return; } catch (Exception e) { -- 1.7.10.2