test/jalview/io/AnnotationFileIOTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import static org.testng.AssertJUnit.assertNotNull;
  24 import static org.testng.AssertJUnit.assertTrue;
  25
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.DynamicData;
  28 import jalview.datamodel.HiddenColumns;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.PDBEntry.Type;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.gui.JvOptionPane;
  33 import jalview.io.AnnotationFile.ViewDef;
  34 import jalview.structure.StructureSelectionManager;
  35
  36 import java.io.File;
  37 import java.util.Hashtable;
  38 import java.util.List;
  39
  40 import org.testng.Assert;
  41 import org.testng.annotations.BeforeClass;
  42 import org.testng.annotations.DataProvider;
  43 import org.testng.annotations.Test;
  44
  45 public class AnnotationFileIOTest
  46 {
  47
  48   private StructureSelectionManager ssm = null;
  49
  50   private AlignmentI al = null;
  51
  52   @BeforeClass(alwaysRun = true)
  53   public void setUpJvOptionPane()
  54   {
  55     JvOptionPane.setInteractiveMode(false);
  56     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  57   }
  58
  59   static String TestFiles[][] = {
  60       { "Test example annotation import/export", "examples/uniref50.fa",
  61           "examples/testdata/example_annot_file.jva" },
  62       { "Test multiple combine annotation statements import/export",
  63           "examples/uniref50.fa",
  64           "examples/testdata/test_combine_annot.jva" },
  65       {
  66           "Test multiple combine annotation statements with sequence_ref import/export",
  67           "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
  68       {
  69           "Test group only annotation file parsing results in parser indicating annotation was parsed",
  70           "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
  71       { "Test hiding/showing of insertions on sequence_ref",
  72           "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
  73
  74   @Test(groups = { "Functional" })
  75   public void exampleAnnotationFileIO() throws Exception
  76   {
  77     for (String[] testPair : TestFiles)
  78     {
  79       testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
  80               testPair[2]));
  81     }
  82   }
  83
  84   AlignmentI readAlignmentFile(File f)
  85   {
  86     System.out.println("Reading file: " + f);
  87     String ff = f.getPath();
  88     try
  89     {
  90       FormatAdapter rf = new FormatAdapter();
  91
  92       AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
  93               new IdentifyFile().identify(ff, DataSourceType.FILE));
  94
  95       // make sure dataset is initialised ? not sure about this
  96       for (int i = 0; i < al.getSequencesArray().length; ++i)
  97       {
  98         al.getSequenceAt(i).createDatasetSequence();
  99       }
 100       assertNotNull("Couldn't read supplied alignment data.", al);
 101       return al;
 102     } catch (Exception e)
 103     {
 104       e.printStackTrace();
 105     }
 106     Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
 107     return null;
 108   }
 109
 110   /**
 111    * test alignment data in given file can be imported, exported and reimported
 112    * with no dataloss
 113    *
 114    * @param f
 115    *          - source datafile (IdentifyFile.identify() should work with it)
 116    * @param ioformat
 117    *          - label for IO class used to write and read back in the data from
 118    *          f
 119    */
 120   void testAnnotationFileIO(String testname, File f, File annotFile)
 121   {
 122     System.out.println("Test: " + testname + "\nReading annotation file '"
 123             + annotFile + "' onto : " + f);
 124     String af = annotFile.getPath();
 125     try
 126     {
 127       AlignmentI al = readAlignmentFile(f);
 128       HiddenColumns cs = new HiddenColumns();
 129       assertTrue(
 130               "Test "
 131                       + testname
 132                       + "\nAlignment was not annotated - annotation file not imported.",
 133               new AnnotationFile().readAnnotationFile(al, cs, af,
 134                       DataSourceType.FILE));
 135
 136       AnnotationFile aff = new AnnotationFile();
 137       // ViewDef is not used by Jalview
 138       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
 139               new Hashtable());
 140       String anfileout = new AnnotationFile().printAnnotations(
 141               al.getAlignmentAnnotation(), al.getGroups(),
 142               al.getProperties(), null, al, v);
 143       assertTrue(
 144               "Test "
 145                       + testname
 146                       + "\nAlignment annotation file was not regenerated. Null string",
 147               anfileout != null);
 148       assertTrue(
 149               "Test "
 150                       + testname
 151                       + "\nAlignment annotation file was not regenerated. Empty string",
 152               anfileout.length() > "JALVIEW_ANNOTATION".length());
 153
 154       System.out.println("Output annotation file:\n" + anfileout
 155               + "\n<<EOF\n");
 156
 157       AlignmentI al_new = readAlignmentFile(f);
 158       assertTrue(
 159               "Test "
 160                       + testname
 161                       + "\nregenerated annotation file did not annotate alignment.",
 162               new AnnotationFile().readAnnotationFile(al_new, anfileout,
 163                       DataSourceType.PASTE));
 164
 165       // test for consistency in io
 166       StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
 167               false);
 168       return;
 169     } catch (Exception e)
 170     {
 171       e.printStackTrace();
 172     }
 173     Assert.fail("Test "
 174             + testname
 175             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
 176             + annotFile + "'.");
 177   }
 178
 179
 180   @BeforeClass(alwaysRun = true)
 181   void testProcessStructModel()
 182   {
 183     try
 184     {
 185
 186       ssm = StructureSelectionManager.getStructureSelectionManager();
 187     } catch (NullPointerException e)
 188     {
 189       ssm = new StructureSelectionManager();
 190     }
 191     File alignmentFile = new File(
 192             "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
 193     String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
 194     HiddenColumns cs = new HiddenColumns();
 195     al = readAlignmentFile(alignmentFile);
 196     boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
 197             cs, annotationFile, DataSourceType.FILE);
 198     Assert.assertTrue(annotationRead);
 199     System.out.println("bla");
 200   }
 201
 202   @Test(
 203     groups = { "Functional" },
 204     dataProvider = "phyre2ModelPDBEntryDataProvider")
 205   void testSequence_PDBEntryAssociation(String[] structModelHeader, String baseDir,
 206           String structModelDataStr)
 207   {
 208     String structModelData[] = structModelDataStr.split("\t");
 209     String templateSeq = structModelData[1];
 210     String pdbId = structModelData[2];
 211
 212     SequenceI testSeq = al.findName(templateSeq);
 213     Assert.assertNotNull(testSeq);
 214     PDBEntry actualPDBEntry = testSeq.getDatasetSequence().getPDBEntry(
 215             pdbId);
 216     Assert.assertNotNull(actualPDBEntry);
 217
 218     PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
 219             + pdbId);
 220     List<DynamicData> phyreDD = AnnotationFile
 221             .generatePhyreDynamicDataList(structModelHeader,
 222                     structModelData);
 223     expectedPDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD);
 224
 225     Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
 226   }
 227
 228   @Test(
 229     groups = { "Functional" },
 230     dataProvider = "phyre2ModelMappingDataProvider")
 231   void testPhyre2ModelRegistration(String phyre2ModelFile,
 232           String expectedPhyre2FastaMappingFile)
 233   {
 234
 235     String actualFastaMappingFile = ssm
 236             .getPhyre2FastaFileFor(phyre2ModelFile);
 237     Assert.assertNotNull(actualFastaMappingFile);
 238     Assert.assertEquals(actualFastaMappingFile,
 239             expectedPhyre2FastaMappingFile);
 240   }
 241
 242   @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
 243   void testResolveAbsolutePath(String caseDescription, String suppliedPath,
 244           String baseURI, String expectedURI)
 245   {
 246     System.out.println(">>>> Testing Case - " + caseDescription);
 247     String actualURI = AnnotationFile.resolveAbsolutePath(suppliedPath,
 248             baseURI);
 249     Assert.assertEquals(actualURI, expectedURI);
 250   }
 251
 252   @DataProvider(name = "phyre2ModelPDBEntryDataProvider")
 253   public static Object[][] phyre2ModelPDBEntryDataProvider()
 254   {
 255     String[] structModelHeader = new String[] { "QUERY_SEQ",
 256             "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 257             "% I.D", "Aligned Range", "Other Information"};
 258     String baseDir = "examples/testdata/phyre2results/56da5616b4559c93/";
 259
 260     return new Object[][] {
 261         {
 262             structModelHeader,
 263             baseDir,
 264             "FER_CAPAN_1-144\tc4n58A_\tc4n58A_.1.pdb\tc4n58A_.1.fasta\t1\t54\t48-143\t<b>PDB Header: </b>Hyrolase<br><b>Chain: "
 265                     + "</b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms" },
 266         {
 267             structModelHeader,
 268             baseDir,
 269             "FER_CAPAN_1-144\td1a70a_\td1a70a_.2.pdb\td1a70a_.2.fasta\t1\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 270                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 271         {
 272             structModelHeader,
 273             baseDir,
 274             "FER_CAPAN_1-144\td1offa_\td1offa_.3.pdb\td1offa_.3.fasta\t1\t73\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 275                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 276         {
 277             structModelHeader,
 278             baseDir,
 279             "FER_CAPAN_1-144\td1frra_\td1frra_.4.pdb\td1frra_.4.fasta\t0.999\t62\t49-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 280                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 281         {
 282             structModelHeader,
 283             baseDir,
 284             "FER_CAPAN_1-144\td1pfda_\td1pfda_.5.pdb\td1pfda_.5.fasta\t0.999\t70\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 285                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 286         {
 287             structModelHeader,
 288             baseDir,
 289             "FER_CAPAN_1-144\td1frda_\td1frda_.6.pdb\td1frda_.6.fasta\t0.999\t50\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 290                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 291         {
 292             structModelHeader,
 293             baseDir,
 294             "FER_CAPAN_1-144\td1fxia_\td1fxia_.7.pdb\td1fxia_.7.fasta\t0.999\t62\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 295                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 296         {
 297             structModelHeader,
 298             baseDir,
 299             "FER_CAPAN_1-144\td1gaqb_\td1gaqb_.8.pdb\td1gaqb_.8.fasta\t0.999\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 300                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 301         {
 302             structModelHeader,
 303             baseDir,
 304             "FER_CAPAN_1-144\td1iuea_\td1iuea_.9.pdb\td1iuea_.9.fasta\t0.999\t48\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 305                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 306         {
 307             structModelHeader,
 308             baseDir,
 309             "FER_CAPAN_1-144\td1awda_\td1awda_.10.pdb\td1awda_.10.fasta\t0.999\t68\t50-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 310                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 311         {
 312             structModelHeader,
 313             baseDir,
 314             "FER_CAPAN_1-144\td1wria_\td1wria_.11.pdb\td1wria_.11.fasta\t0.999\t59\t49-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 315                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 316         {
 317             structModelHeader,
 318             baseDir,
 319             "FER_CAPAN_1-144\td1czpa_\td1czpa_.12.pdb\td1czpa_.12.fasta\t0.999\t64\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 320                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 321         {
 322             structModelHeader,
 323             baseDir,
 324             "FER_CAPAN_1-144\td2cjoa_\td2cjoa_.13.pdb\td2cjoa_.13.fasta\t0.999\t63\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 325                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 326         {
 327             structModelHeader,
 328             baseDir,
 329             "FER_CAPAN_1-144\td4fxca_\td4fxca_.14.pdb\td4fxca_.14.fasta\t0.999\t64\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 330                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 331         {
 332             structModelHeader,
 333             baseDir,
 334             "FER_CAPAN_1-144\tc4itkA_\tc4itkA_.15.pdb\tc4itkA_.15.fasta\t0.999\t57\t50-142\t<b>PDB Header: </b>Electron transport<br>"
 335                     + "<b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2" },
 336         {
 337             structModelHeader,
 338             baseDir,
 339             "FER_CAPAN_1-144\tc1krhA_\tc1krhA_.16.pdb\tc1krhA_.16.fasta\t0.999\t25\t48-142\t<b>PDB Header: </b>Oxidoreductase<br><b>Chain: "
 340                     + "</b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate "
 341                     + "deoxygenate reductase" },
 342         {
 343             structModelHeader,
 344             baseDir,
 345             "FER_CAPAN_1-144\td1krha3\td1krha3.17.pdb\td1krha3.17.fasta\t0.999\t24\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 346                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 347         {
 348             structModelHeader,
 349             baseDir,
 350             "FER_CAPAN_1-144\td1jq4a_\td1jq4a_.18.pdb\td1jq4a_.18.fasta\t0.999\t29\t47-138\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 351                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 352         {
 353             structModelHeader,
 354             baseDir,
 355             "FER_CAPAN_1-144\tc4wqmA_\tc4wqmA_.19.pdb\tc4wqmA_.19.fasta\t0.999\t28\t49-144\t<b>PDB header: </b>Oxidoreductase<br><b>Chain: "
 356                     + "</b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the "
 357                     + "toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant" },
 358         {
 359             structModelHeader,
 360             baseDir,
 361             "FER_CAPAN_1-144\tc2piaA_\tc2piaA_.20.pdb\tc2piaA_.20.fasta\t0.999\t22\t1-136\t<b>PDB header: </b>Reductase<br><b>Chain: "
 362                     + "</b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a"
 363                     + " modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]" }
 364     };
 365   }
 366
 367   @DataProvider(name = "phyre2ModelMappingDataProvider")
 368   public static Object[][] phyre2ModelMappingDataProvider()
 369   {
 370     return new Object[][] {
 371
 372         { "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb",
 373             "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta" },
 374         { "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb",
 375             "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta" },
 376         { "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.pdb",
 377             "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.fasta" },
 378         { "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.pdb",
 379             "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.fasta" },
 380         { "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.pdb",
 381             "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.fasta" },
 382         { "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.pdb",
 383             "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.fasta" },
 384
 385         { "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.pdb",
 386             "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.fasta" },
 387
 388         { "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.pdb",
 389             "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.fasta" },
 390         { "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.pdb",
 391             "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.fasta" },
 392         {
 393             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb",
 394             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta" },
 395         {
 396             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.pdb",
 397             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.fasta" },
 398         {
 399             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.pdb",
 400             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.fasta" },
 401         {
 402             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.pdb",
 403             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.fasta" },
 404         {
 405             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb",
 406             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.fasta" },
 407         {
 408             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb",
 409             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta" },
 410         {
 411             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.pdb",
 412             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.fasta" },
 413         {
 414             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.pdb",
 415             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.fasta" },
 416         {
 417             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.pdb",
 418             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.fasta" },
 419         {
 420             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb",
 421             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta" },
 422         {
 423             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb",
 424             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta" }
 425
 426     };
 427   }
 428
 429   @DataProvider(name = "phyre2InfoHTMLTableDataProvider")
 430   public static Object[][] phyre2InfoHTMLTableDataProvider()
 431   {
 432     return new Object[][] {
 433         {
 434             "STRUCTMODEL Annotation with no headear information provided",
 435             null,
 436             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 437                 "d1a70a_.2.fasta", }, "" },
 438         {
 439             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 440             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 441                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 442             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 443                 "d1a70a_.2.fasta", },
 444             "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr></table></html>" },
 445         {
 446             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 447             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 448                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 449                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 450             new String[] {
 451                 "FER_CAPAN_1-144",
 452                 "d1a70a_ d1a70a_.2.pdb",
 453                 "d1a70a_.2.fasta",
 454                 "1",
 455                 "71",
 456                 "48-144",
 457                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 458             "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr><tr><td>MAPPING_FILE</td><td>71</td></tr><tr><td>Confidence</td><td>48-144</td></tr><tr><td>% I.D</td><td><b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related</td></tr></table></html>" } };
 459   }
 460
 461   @DataProvider(name = "StructModelHtmlDataProvider")
 462   public static Object[][] IsGenerateStructInfoHtmlDataProvider()
 463   {
 464     return new Object[][] {
 465         { "STRUCTMODEL Annotation with no headear or data provided", null,
 466             null, false },
 467         {
 468             "STRUCTMODEL Annotation with headear information and no data column provided",
 469             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" }, null,
 470             false },
 471         {
 472             "STRUCTMODEL Annotation with no headear information provided",
 473             null,
 474             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 475                 "d1a70a_.2.fasta", }, false },
 476         {
 477             "STRUCTMODEL Annotation with only two headear information and two data column provided",
 478             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" },
 479             new String[] { "FER_CAPAN_1-144", "d1a70a_" }, false },
 480         {
 481             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 482             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 483                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 484             new String[] { "FER_CAPAN_1-144", "d1a70a_", "d1a70a_.2.pdb",
 485                 "d1a70a_.2.fasta", }, true },
 486         {
 487             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 488             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 489                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 490                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 491             new String[] {
 492                 "FER_CAPAN_1-144",
 493                 "d1a70a_",
 494                 "d1a70a_.2.pdb",
 495                 "d1a70a_.2.fasta",
 496                 "1",
 497                 "71",
 498                 "48-144",
 499                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 500             true } };
 501   }
 502
 503   @DataProvider(name = "FilePathProvider")
 504   public static Object[][] filePathProvider()
 505   {
 506     return new Object[][] {
 507         { "relative local file path resolution", "c4n58A_.1.pdb", "",
 508             "c4n58A_.1.pdb" },
 509         { "relative local file path resolution", "c4n58A_.1.pdb",
 510             "/examples/testdata/phyre2results/",
 511             "/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 512         {
 513             "relative URL path resolution",
 514             "c4n58A_.1.pdb",
 515             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 516             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 517         {
 518             "Absolute local file path resolution",
 519             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb",
 520             "/examples/testdata/phyre2results/",
 521             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb" },
 522         {
 523             "Absolute URL path resolution",
 524             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb",
 525             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 526             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb" } };
 527   }
 528 }