X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=5ab4297c8111a92bed413c9a1d72261390a69a86;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=2537002d02b51a02117231293d7954caf3ad6f97;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 2537002..5ab4297 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -43,13 +43,13 @@ 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(); @@ -58,9 +58,9 @@ public class StockholmFileTest 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 +68,7 @@ public class StockholmFileTest numpdb > 0); } - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void rfamFileIO() throws Exception { testFileIOwithFormat(new File(RfamFile), "STH", 2, 1); @@ -136,7 +136,7 @@ public class StockholmFileTest if (naliannot > -1) { assertEquals("Number of alignment annotations", naliannot, - numaliannot); + numaliannot); } assertTrue( @@ -268,7 +268,7 @@ public class StockholmFileTest + (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