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.ColumnSelection;
  28 import jalview.datamodel.DynamicData;
  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       ColumnSelection cs = new ColumnSelection();
 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 v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
 138               new Hashtable());
 139       String anfileout = new AnnotationFile().printAnnotations(
 140               al.getAlignmentAnnotation(), al.getGroups(),
 141               al.getProperties(), null, al, v);
 142       assertTrue(
 143               "Test "
 144                       + testname
 145                       + "\nAlignment annotation file was not regenerated. Null string",
 146               anfileout != null);
 147       assertTrue(
 148               "Test "
 149                       + testname
 150                       + "\nAlignment annotation file was not regenerated. Empty string",
 151               anfileout.length() > "JALVIEW_ANNOTATION".length());
 152
 153       System.out.println("Output annotation file:\n" + anfileout
 154               + "\n<<EOF\n");
 155
 156       AlignmentI al_new = readAlignmentFile(f);
 157       assertTrue(
 158               "Test "
 159                       + testname
 160                       + "\nregenerated annotation file did not annotate alignment.",
 161               new AnnotationFile().readAnnotationFile(al_new, anfileout,
 162                       DataSourceType.PASTE));
 163
 164       // test for consistency in io
 165       StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
 166       return;
 167     } catch (Exception e)
 168     {
 169       e.printStackTrace();
 170     }
 171     Assert.fail("Test "
 172             + testname
 173             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
 174             + annotFile + "'.");
 175   }
 176
 177
 178   @BeforeClass(alwaysRun = true)
 179   void testProcessStructModel()
 180   {
 181     try
 182     {
 183
 184       ssm = StructureSelectionManager.getStructureSelectionManager();
 185     } catch (NullPointerException e)
 186     {
 187       ssm = new StructureSelectionManager();
 188     }
 189     File alignmentFile = new File(
 190             "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
 191     String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
 192     ColumnSelection cs = new ColumnSelection();
 193     al = readAlignmentFile(alignmentFile);
 194     boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
 195             cs, annotationFile, DataSourceType.FILE);
 196     Assert.assertTrue(annotationRead);
 197     System.out.println("bla");
 198   }
 199
 200   @Test(
 201     groups = { "Functional" },
 202     dataProvider = "phyre2ModelPDBEntryDataProvider")
 203   void testSequence_PDBEntryAssociation(String[] structModelHeader, String baseDir,
 204           String structModelDataStr)
 205   {
 206     String structModelData[] = structModelDataStr.split("\t");
 207     String templateSeq = structModelData[1];
 208     String pdbId = structModelData[2];
 209
 210     SequenceI testSeq = al.findName(templateSeq);
 211     Assert.assertNotNull(testSeq);
 212     PDBEntry actualPDBEntry = testSeq.getDatasetSequence().getPDBEntry(
 213             pdbId);
 214     Assert.assertNotNull(actualPDBEntry);
 215
 216     PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
 217             + pdbId);
 218     List<DynamicData> phyreDD = AnnotationFile
 219             .generatePhyreDynamicDataList(structModelHeader,
 220                     structModelData);
 221     expectedPDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD);
 222
 223     Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
 224   }
 225
 226   @Test(
 227     groups = { "Functional" },
 228     dataProvider = "phyre2ModelMappingDataProvider")
 229   void testPhyre2ModelRegistration(String phyre2ModelFile,
 230           String expectedPhyre2FastaMappingFile)
 231   {
 232
 233     String actualFastaMappingFile = ssm
 234             .getPhyre2FastaFileFor(phyre2ModelFile);
 235     Assert.assertNotNull(actualFastaMappingFile);
 236     Assert.assertEquals(actualFastaMappingFile,
 237             expectedPhyre2FastaMappingFile);
 238   }
 239
 240   @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
 241   void testResolveAbsolutePath(String caseDescription, String suppliedPath,
 242           String baseURI, String expectedURI)
 243   {
 244     System.out.println(">>>> Testing Case - " + caseDescription);
 245     String actualURI = AnnotationFile.resolveAbsolutePath(suppliedPath,
 246             baseURI);
 247     Assert.assertEquals(actualURI, expectedURI);
 248   }
 249
 250   @DataProvider(name = "phyre2ModelPDBEntryDataProvider")
 251   public static Object[][] phyre2ModelPDBEntryDataProvider()
 252   {
 253     String[] structModelHeader = new String[] { "QUERY_SEQ",
 254             "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 255             "% I.D", "Aligned Range", "Other Information"};
 256     String baseDir = "examples/testdata/phyre2results/56da5616b4559c93/";
 257
 258     return new Object[][] {
 259         {
 260             structModelHeader,
 261             baseDir,
 262             "FER_CAPAN_1-144\tc4n58A_\tc4n58A_.1.pdb\tc4n58A_.1.fasta\t1\t54\t48-143\t<b>PDB Header: </b>Hyrolase<br><b>Chain: "
 263                     + "</b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms" },
 264         {
 265             structModelHeader,
 266             baseDir,
 267             "FER_CAPAN_1-144\td1a70a_\td1a70a_.2.pdb\td1a70a_.2.fasta\t1\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 268                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 269         {
 270             structModelHeader,
 271             baseDir,
 272             "FER_CAPAN_1-144\td1offa_\td1offa_.3.pdb\td1offa_.3.fasta\t1\t73\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 273                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 274         {
 275             structModelHeader,
 276             baseDir,
 277             "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>"
 278                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 279         {
 280             structModelHeader,
 281             baseDir,
 282             "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>"
 283                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 284         {
 285             structModelHeader,
 286             baseDir,
 287             "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>"
 288                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 289         {
 290             structModelHeader,
 291             baseDir,
 292             "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>"
 293                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 294         {
 295             structModelHeader,
 296             baseDir,
 297             "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>"
 298                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 299         {
 300             structModelHeader,
 301             baseDir,
 302             "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>"
 303                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 304         {
 305             structModelHeader,
 306             baseDir,
 307             "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>"
 308                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 309         {
 310             structModelHeader,
 311             baseDir,
 312             "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>"
 313                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 314         {
 315             structModelHeader,
 316             baseDir,
 317             "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>"
 318                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 319         {
 320             structModelHeader,
 321             baseDir,
 322             "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>"
 323                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 324         {
 325             structModelHeader,
 326             baseDir,
 327             "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>"
 328                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 329         {
 330             structModelHeader,
 331             baseDir,
 332             "FER_CAPAN_1-144\tc4itkA_\tc4itkA_.15.pdb\tc4itkA_.15.fasta\t0.999\t57\t50-142\t<b>PDB Header: </b>Electron transport<br>"
 333                     + "<b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2" },
 334         {
 335             structModelHeader,
 336             baseDir,
 337             "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: "
 338                     + "</b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate "
 339                     + "deoxygenate reductase" },
 340         {
 341             structModelHeader,
 342             baseDir,
 343             "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>"
 344                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 345         {
 346             structModelHeader,
 347             baseDir,
 348             "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>"
 349                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 350         {
 351             structModelHeader,
 352             baseDir,
 353             "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: "
 354                     + "</b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the "
 355                     + "toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant" },
 356         {
 357             structModelHeader,
 358             baseDir,
 359             "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: "
 360                     + "</b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a"
 361                     + " modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]" }
 362     };
 363   }
 364
 365   @DataProvider(name = "phyre2ModelMappingDataProvider")
 366   public static Object[][] phyre2ModelMappingDataProvider()
 367   {
 368     return new Object[][] {
 369
 370         { "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb",
 371             "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta" },
 372         { "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb",
 373             "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta" },
 374         { "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.pdb",
 375             "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.fasta" },
 376         { "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.pdb",
 377             "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.fasta" },
 378         { "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.pdb",
 379             "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.fasta" },
 380         { "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.pdb",
 381             "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.fasta" },
 382
 383         { "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.pdb",
 384             "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.fasta" },
 385
 386         { "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.pdb",
 387             "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.fasta" },
 388         { "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.pdb",
 389             "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.fasta" },
 390         {
 391             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb",
 392             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta" },
 393         {
 394             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.pdb",
 395             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.fasta" },
 396         {
 397             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.pdb",
 398             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.fasta" },
 399         {
 400             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.pdb",
 401             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.fasta" },
 402         {
 403             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb",
 404             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.fasta" },
 405         {
 406             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb",
 407             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta" },
 408         {
 409             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.pdb",
 410             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.fasta" },
 411         {
 412             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.pdb",
 413             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.fasta" },
 414         {
 415             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.pdb",
 416             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.fasta" },
 417         {
 418             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb",
 419             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta" },
 420         {
 421             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb",
 422             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta" }
 423
 424     };
 425   }
 426
 427   @DataProvider(name = "phyre2InfoHTMLTableDataProvider")
 428   public static Object[][] phyre2InfoHTMLTableDataProvider()
 429   {
 430     return new Object[][] {
 431         {
 432             "STRUCTMODEL Annotation with no headear information provided",
 433             null,
 434             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 435                 "d1a70a_.2.fasta", }, "" },
 436         {
 437             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 438             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 439                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 440             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 441                 "d1a70a_.2.fasta", },
 442             "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr></table></html>" },
 443         {
 444             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 445             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 446                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 447                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 448             new String[] {
 449                 "FER_CAPAN_1-144",
 450                 "d1a70a_ d1a70a_.2.pdb",
 451                 "d1a70a_.2.fasta",
 452                 "1",
 453                 "71",
 454                 "48-144",
 455                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 456             "<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>" } };
 457   }
 458
 459   @DataProvider(name = "StructModelHtmlDataProvider")
 460   public static Object[][] IsGenerateStructInfoHtmlDataProvider()
 461   {
 462     return new Object[][] {
 463         { "STRUCTMODEL Annotation with no headear or data provided", null,
 464             null, false },
 465         {
 466             "STRUCTMODEL Annotation with headear information and no data column provided",
 467             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" }, null,
 468             false },
 469         {
 470             "STRUCTMODEL Annotation with no headear information provided",
 471             null,
 472             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 473                 "d1a70a_.2.fasta", }, false },
 474         {
 475             "STRUCTMODEL Annotation with only two headear information and two data column provided",
 476             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" },
 477             new String[] { "FER_CAPAN_1-144", "d1a70a_" }, false },
 478         {
 479             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 480             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 481                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 482             new String[] { "FER_CAPAN_1-144", "d1a70a_", "d1a70a_.2.pdb",
 483                 "d1a70a_.2.fasta", }, true },
 484         {
 485             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 486             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 487                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 488                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 489             new String[] {
 490                 "FER_CAPAN_1-144",
 491                 "d1a70a_",
 492                 "d1a70a_.2.pdb",
 493                 "d1a70a_.2.fasta",
 494                 "1",
 495                 "71",
 496                 "48-144",
 497                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 498             true } };
 499   }
 500
 501   @DataProvider(name = "FilePathProvider")
 502   public static Object[][] filePathProvider()
 503   {
 504     return new Object[][] {
 505         { "relative local file path resolution", "c4n58A_.1.pdb", "",
 506             "c4n58A_.1.pdb" },
 507         { "relative local file path resolution", "c4n58A_.1.pdb",
 508             "/examples/testdata/phyre2results/",
 509             "/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 510         {
 511             "relative URL path resolution",
 512             "c4n58A_.1.pdb",
 513             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 514             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 515         {
 516             "Absolute local file path resolution",
 517             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb",
 518             "/examples/testdata/phyre2results/",
 519             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb" },
 520         {
 521             "Absolute URL path resolution",
 522             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb",
 523             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 524             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb" } };
 525   }
 526 }