X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=035f4843d099b6c3c73a5c4f224ddbe386f0cb97;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2537002d02b51a02117231293d7954caf3ad6f97;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 2537002..035f484 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -23,6 +23,7 @@ package jalview.io; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; +import static org.testng.AssertJUnit.fail; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -43,24 +44,24 @@ public class StockholmFileTest static String PfamFile = "examples/PF00111_seed.stk", RfamFile = "examples/RF00031_folded.stk"; - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void pfamFileIO() throws Exception { testFileIOwithFormat(new File(PfamFile), "STH", -1, 0); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void pfamFileDataExtraction() throws Exception { AppletFormatAdapter af = new AppletFormatAdapter(); AlignmentI al = af.readFile(PfamFile, af.FILE, - new IdentifyFile().Identify(PfamFile, af.FILE)); + new IdentifyFile().identify(PfamFile, af.FILE)); int numpdb = 0; for (SequenceI sq : al.getSequences()) { - if (sq.getPDBId() != null) + if (sq.getAllPDBEntries() != null) { - numpdb += sq.getPDBId().size(); + numpdb += sq.getAllPDBEntries().size(); } } assertTrue( @@ -68,7 +69,7 @@ public class StockholmFileTest numpdb > 0); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void rfamFileIO() throws Exception { testFileIOwithFormat(new File(RfamFile), "STH", 2, 1); @@ -95,14 +96,14 @@ public class StockholmFileTest AppletFormatAdapter rf = new AppletFormatAdapter(); AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE, - new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE)); + new IdentifyFile().identify(ff, AppletFormatAdapter.FILE)); assertNotNull("Couldn't read supplied alignment data.", al); // make sure dataset is initialised ? not sure about this for (int i = 0; i < al.getSequencesArray().length; ++i) { - al.getSequenceAt(i).setDatasetSequence(al.getSequenceAt(i)); + al.getSequenceAt(i).createDatasetSequence(); } String outputfile = rf.formatSequences(ioformat, al, true); System.out.println("Output file in '" + ioformat + "':\n" @@ -112,7 +113,7 @@ public class StockholmFileTest AppletFormatAdapter.PASTE, ioformat); assertNotNull("Couldn't parse reimported alignment data.", al_input); - String identifyoutput = new IdentifyFile().Identify(outputfile, + String identifyoutput = new IdentifyFile().identify(outputfile, AppletFormatAdapter.PASTE); assertNotNull("Identify routine failed for outputformat " + ioformat, identifyoutput); @@ -136,7 +137,7 @@ public class StockholmFileTest if (naliannot > -1) { assertEquals("Number of alignment annotations", naliannot, - numaliannot); + numaliannot); } assertTrue( @@ -159,7 +160,7 @@ public class StockholmFileTest * 'secondary' or generated alignment from some datapreserving * transformation * @param ignoreFeatures - * when true, differences in seuqence feature annotation are ignored. + * when true, differences in sequence feature annotation are ignored */ public static void testAlignmentEquivalence(AlignmentI al, AlignmentI al_input, boolean ignoreFeatures) @@ -167,12 +168,9 @@ public class StockholmFileTest assertNotNull("Original alignment was null", al); assertNotNull("Generated alignment was null", al_input); - assertTrue( - "Alignment dimension mismatch: originl contains " - + al.getHeight() + " and generated has " - + al_input.getHeight() + " sequences; original has " - + al.getWidth() + " and generated has " - + al_input.getWidth() + " columns.", + assertTrue("Alignment dimension mismatch: original: " + al.getHeight() + + "x" + al.getWidth() + ", generated: " + al_input.getHeight() + + "x" + al_input.getWidth(), al.getHeight() == al_input.getHeight() && al.getWidth() == al_input.getWidth()); @@ -183,9 +181,10 @@ public class StockholmFileTest // note - at moment we do not distinguish between alignment without any // annotation rows and alignment with no annotation row vector // we might want to revise this in future - int aa_new_size = (aa_new == null ? 0 : aa_new.length), aa_original_size = (aa_original == null ? 0 - : aa_original.length); - Map orig_groups = new HashMap(), new_groups = new HashMap(); + int aa_new_size = (aa_new == null ? 0 : aa_new.length); + int aa_original_size = (aa_original == null ? 0 : aa_original.length); + Map orig_groups = new HashMap(); + Map new_groups = new HashMap(); if (aa_new != null && aa_original != null) { @@ -196,20 +195,17 @@ public class StockholmFileTest assertTrue("Different alignment annotation at position " + i, equalss(aa_original[i], aa_new[i])); // compare graphGroup or graph properties - needed to verify JAL-1299 - assertTrue("Graph type not identical.", - aa_original[i].graph == aa_new[i].graph); - assertTrue("Visibility not identical.", - aa_original[i].visible == aa_new[i].visible); - assertTrue( - "Threshold line not identical.", - aa_original[i].threshold == null ? aa_new[i].threshold == null - : aa_original[i].threshold - .equals(aa_new[i].threshold)); + assertEquals("Graph type not identical.", aa_original[i].graph, + aa_new[i].graph); + assertEquals("Visibility not identical.", aa_original[i].visible, + aa_new[i].visible); + assertEquals("Threshold line not identical.", + aa_original[i].threshold, aa_new[i].threshold); // graphGroup may differ, but pattern should be the same - Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2), n_ggrp = new Integer( - aa_new[i].graphGroup + 2); - BitSet orig_g = orig_groups.get(o_ggrp), new_g = new_groups - .get(n_ggrp); + Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2); + Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2); + BitSet orig_g = orig_groups.get(o_ggrp); + BitSet new_g = new_groups.get(n_ggrp); if (orig_g == null) { orig_groups.put(o_ggrp, orig_g = new BitSet()); @@ -218,8 +214,8 @@ public class StockholmFileTest { new_groups.put(n_ggrp, new_g = new BitSet()); } - assertTrue("Graph Group pattern differs at annotation " + i, - orig_g.equals(new_g)); + assertEquals("Graph Group pattern differs at annotation " + i, + orig_g, new_g); orig_g.set(i); new_g.set(i); } @@ -230,10 +226,9 @@ public class StockholmFileTest } } } - assertTrue( - "Generated and imported alignment have different annotation sets (" - + aa_new_size + " != " + aa_original_size + ")", - aa_new_size == aa_original_size); + assertEquals( + "Generated and imported alignment have different annotation sets", + aa_original_size, aa_new_size); // check sequences, annotation and features SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length]; @@ -260,15 +255,15 @@ public class StockholmFileTest { String ss_original = seq_original[i].getSequenceAsString(); String ss_new = seq_new[in].getSequenceAsString(); - assertTrue("The sequences " + name + "/" + start + "-" + end - + " are not equal", ss_original.equals(ss_new)); + assertEquals("The sequences " + name + "/" + start + "-" + end + + " are not equal", ss_original, ss_new); assertTrue( "Sequence Features were not equivalent" + (ignoreFeatures ? " ignoring." : ""), ignoreFeatures || (seq_original[i].getSequenceFeatures() == null && seq_new[in] - .getSequenceFeatures() == null) + .getSequenceFeatures() == null) || (seq_original[i].getSequenceFeatures() != null && seq_new[in] .getSequenceFeatures() != null)); // compare sequence features @@ -284,15 +279,15 @@ public class StockholmFileTest .getSequenceFeatures().length]; sequenceFeatures_new = seq_new[in].getSequenceFeatures(); - assertTrue("different number of features", seq_original[i] - .getSequenceFeatures().length == seq_new[in] - .getSequenceFeatures().length); + assertEquals("different number of features", + seq_original[i].getSequenceFeatures().length, + seq_new[in].getSequenceFeatures().length); for (int feat = 0; feat < seq_original[i].getSequenceFeatures().length; feat++) { - assertTrue("Different features", - sequenceFeatures_original[feat] - .equals(sequenceFeatures_new[feat])); + assertEquals("Different features", + sequenceFeatures_original[feat], + sequenceFeatures_new[feat]); } } // compare alignment annotation @@ -319,9 +314,9 @@ public class StockholmFileTest else if (al.getSequenceAt(i).getAnnotation() != null && al_input.getSequenceAt(in).getAnnotation() == null) { - assertTrue("Annotations differed between sequences (" + fail("Annotations differed between sequences (" + al.getSequenceAt(i).getName() + ") and (" - + al_input.getSequenceAt(i).getName() + ")", false); + + al_input.getSequenceAt(i).getName() + ")"); } break; }