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.PDBEntry;
  29 import jalview.datamodel.PDBEntry.Type;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.gui.Desktop;
  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
  39 import org.testng.Assert;
  40 import org.testng.annotations.BeforeClass;
  41 import org.testng.annotations.DataProvider;
  42 import org.testng.annotations.Test;
  43
  44 public class AnnotationFileIOTest
  45 {
  46
  47   private StructureSelectionManager ssm = null;
  48
  49   private AlignmentI al = null;
  50
  51   @BeforeClass(alwaysRun = true)
  52   public void setUpJvOptionPane()
  53   {
  54     JvOptionPane.setInteractiveMode(false);
  55     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  56   }
  57
  58   static String TestFiles[][] = {
  59       { "Test example annotation import/export", "examples/uniref50.fa",
  60           "examples/testdata/example_annot_file.jva" },
  61       { "Test multiple combine annotation statements import/export",
  62           "examples/uniref50.fa",
  63           "examples/testdata/test_combine_annot.jva" },
  64       {
  65           "Test multiple combine annotation statements with sequence_ref import/export",
  66           "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
  67       {
  68           "Test group only annotation file parsing results in parser indicating annotation was parsed",
  69           "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
  70       { "Test hiding/showing of insertions on sequence_ref",
  71           "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
  72
  73   @Test(groups = { "Functional" })
  74   public void exampleAnnotationFileIO() throws Exception
  75   {
  76     for (String[] testPair : TestFiles)
  77     {
  78       testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
  79               testPair[2]));
  80     }
  81   }
  82
  83   AlignmentI readAlignmentFile(File f)
  84   {
  85     System.out.println("Reading file: " + f);
  86     String ff = f.getPath();
  87     try
  88     {
  89       FormatAdapter rf = new FormatAdapter();
  90
  91       AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
  92               new IdentifyFile().identify(ff, DataSourceType.FILE));
  93
  94       // make sure dataset is initialised ? not sure about this
  95       for (int i = 0; i < al.getSequencesArray().length; ++i)
  96       {
  97         al.getSequenceAt(i).createDatasetSequence();
  98       }
  99       assertNotNull("Couldn't read supplied alignment data.", al);
 100       return al;
 101     } catch (Exception e)
 102     {
 103       e.printStackTrace();
 104     }
 105     Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
 106     return null;
 107   }
 108
 109   /**
 110    * test alignment data in given file can be imported, exported and reimported
 111    * with no dataloss
 112    *
 113    * @param f
 114    *          - source datafile (IdentifyFile.identify() should work with it)
 115    * @param ioformat
 116    *          - label for IO class used to write and read back in the data from
 117    *          f
 118    */
 119   void testAnnotationFileIO(String testname, File f, File annotFile)
 120   {
 121     System.out.println("Test: " + testname + "\nReading annotation file '"
 122             + annotFile + "' onto : " + f);
 123     String af = annotFile.getPath();
 124     try
 125     {
 126       AlignmentI al = readAlignmentFile(f);
 127       ColumnSelection cs = new ColumnSelection();
 128       assertTrue(
 129               "Test "
 130                       + testname
 131                       + "\nAlignment was not annotated - annotation file not imported.",
 132               new AnnotationFile().readAnnotationFile(al, cs, af,
 133                       DataSourceType.FILE));
 134
 135       AnnotationFile aff = new AnnotationFile();
 136       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
 137               new Hashtable());
 138       String anfileout = new AnnotationFile().printAnnotations(
 139               al.getAlignmentAnnotation(), al.getGroups(),
 140               al.getProperties(), null, al, v);
 141       assertTrue(
 142               "Test "
 143                       + testname
 144                       + "\nAlignment annotation file was not regenerated. Null string",
 145               anfileout != null);
 146       assertTrue(
 147               "Test "
 148                       + testname
 149                       + "\nAlignment annotation file was not regenerated. Empty string",
 150               anfileout.length() > "JALVIEW_ANNOTATION".length());
 151
 152       System.out.println("Output annotation file:\n" + anfileout
 153               + "\n<<EOF\n");
 154
 155       AlignmentI al_new = readAlignmentFile(f);
 156       assertTrue(
 157               "Test "
 158                       + testname
 159                       + "\nregenerated annotation file did not annotate alignment.",
 160               new AnnotationFile().readAnnotationFile(al_new, anfileout,
 161                       DataSourceType.PASTE));
 162
 163       // test for consistency in io
 164       StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
 165       return;
 166     } catch (Exception e)
 167     {
 168       e.printStackTrace();
 169     }
 170     Assert.fail("Test "
 171             + testname
 172             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
 173             + annotFile + "'.");
 174   }
 175
 176
 177   @BeforeClass(alwaysRun = true)
 178   void testProcessStructModel()
 179   {
 180     File alignmentFile = new File(
 181             "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
 182     String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
 183     ColumnSelection cs = new ColumnSelection();
 184     al = readAlignmentFile(alignmentFile);
 185     boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
 186             cs, annotationFile, DataSourceType.FILE);
 187     Assert.assertTrue(annotationRead);
 188     ssm = StructureSelectionManager
 189             .getStructureSelectionManager(Desktop.instance);
 190     System.out.println("bla");
 191   }
 192
 193   @Test(
 194     groups = { "Functional" },
 195     dataProvider = "phyre2ModelPDBEntryDataProvider")
 196   void testSequence_PDBEntryAssociation(String[] structModelHeader, String baseDir,
 197           String structModelDataStr)
 198   {
 199     String structModelData[] = structModelDataStr.split("\t");
 200     String templateSeq = structModelData[1];
 201     String pdbId = structModelData[2];
 202
 203     SequenceI testSeq = al.findName(templateSeq);
 204     Assert.assertNotNull(testSeq);
 205     PDBEntry actualPDBEntry = testSeq.getDatasetSequence().getPDBEntry(
 206             pdbId);
 207     Assert.assertNotNull(actualPDBEntry);
 208
 209     PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
 210             + pdbId);
 211     String phyre2ModelDesc = AnnotationFile.generatePhyre2InfoHTMLTable(structModelHeader,
 212             structModelData);
 213     expectedPDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
 214     Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
 215   }
 216
 217   @Test(
 218     groups = { "Functional" },
 219     dataProvider = "phyre2ModelMappingDataProvider")
 220   void testPhyre2ModelRegistration(String phyre2ModelFile,
 221           String expectedPhyre2FastaMappingFile)
 222   {
 223
 224     String actualFastaMappingFile = ssm
 225             .getPhyre2FastaFileFor(phyre2ModelFile);
 226     Assert.assertNotNull(actualFastaMappingFile);
 227     Assert.assertEquals(actualFastaMappingFile,
 228             expectedPhyre2FastaMappingFile);
 229   }
 230
 231   @Test(
 232     groups = { "Functional" },
 233     dataProvider = "phyre2InfoHTMLTableDataProvider")
 234   void testGeneratePhyre2InfoHTMLTable(String caseDescription,
 235           String[] header, String[] data, String expectedHtml)
 236   {
 237     System.out.println(">>>> Testing Case - " + caseDescription);
 238     String actualHtmlGenerated = AnnotationFile
 239             .generatePhyre2InfoHTMLTable(header, data);
 240     System.out.println("-----> " + actualHtmlGenerated);
 241     Assert.assertEquals(actualHtmlGenerated, expectedHtml);
 242   }
 243
 244   @Test(
 245     groups = { "Functional" },
 246     dataProvider = "StructModelHtmlDataProvider")
 247   void testIsGenerateStructInfoHtml(String caseDescription,
 248           String[] header, String[] data, boolean expectedOutcome)
 249   {
 250     System.out.println(">>>> Testing Case - " + caseDescription);
 251     boolean actual = AnnotationFile.isGenerateStructInfoHtml(header, data);
 252     Assert.assertEquals(actual, expectedOutcome);
 253   }
 254
 255   @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
 256   void testResolveAbsolutePath(String caseDescription, String suppliedPath,
 257           String baseURI, String expectedURI)
 258   {
 259     System.out.println(">>>> Testing Case - " + caseDescription);
 260     String actualURI = AnnotationFile.resolveAbsolutePath(suppliedPath,
 261             baseURI);
 262     Assert.assertEquals(actualURI, expectedURI);
 263   }
 264
 265   @DataProvider(name = "phyre2ModelPDBEntryDataProvider")
 266   public static Object[][] phyre2ModelPDBEntryDataProvider()
 267   {
 268     String[] structModelHeader = new String[] { "QUERY_SEQ",
 269             "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 270             "% I.D", "Aligned Range", "Other Information"};
 271     String baseDir = "examples/testdata/phyre2results/56da5616b4559c93/";
 272
 273     return new Object[][] {
 274         {
 275             structModelHeader,
 276             baseDir,
 277             "FER_CAPAN_1-144\tc4n58A_\tc4n58A_.1.pdb\tc4n58A_.1.fasta\t1\t54\t48-143\t<b>PDB Header: </b>Hyrolase<br><b>Chain: "
 278                     + "</b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms" },
 279         {
 280             structModelHeader,
 281             baseDir,
 282             "FER_CAPAN_1-144\td1a70a_\td1a70a_.2.pdb\td1a70a_.2.fasta\t1\t71\t48-144\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\td1offa_\td1offa_.3.pdb\td1offa_.3.fasta\t1\t73\t48-142\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\td1frra_\td1frra_.4.pdb\td1frra_.4.fasta\t0.999\t62\t49-142\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\td1pfda_\td1pfda_.5.pdb\td1pfda_.5.fasta\t0.999\t70\t48-143\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\td1frda_\td1frda_.6.pdb\td1frda_.6.fasta\t0.999\t50\t48-143\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\td1fxia_\td1fxia_.7.pdb\td1fxia_.7.fasta\t0.999\t62\t48-142\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\td1gaqb_\td1gaqb_.8.pdb\td1gaqb_.8.fasta\t0.999\t71\t48-144\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\td1iuea_\td1iuea_.9.pdb\td1iuea_.9.fasta\t0.999\t48\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\td1awda_\td1awda_.10.pdb\td1awda_.10.fasta\t0.999\t68\t50-142\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\td1wria_\td1wria_.11.pdb\td1wria_.11.fasta\t0.999\t59\t49-142\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\td1czpa_\td1czpa_.12.pdb\td1czpa_.12.fasta\t0.999\t64\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
 333                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 334         {
 335             structModelHeader,
 336             baseDir,
 337             "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>"
 338                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 339         {
 340             structModelHeader,
 341             baseDir,
 342             "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>"
 343                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 344         {
 345             structModelHeader,
 346             baseDir,
 347             "FER_CAPAN_1-144\tc4itkA_\tc4itkA_.15.pdb\tc4itkA_.15.fasta\t0.999\t57\t50-142\t<b>PDB Header: </b>Electron transport<br>"
 348                     + "<b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2" },
 349         {
 350             structModelHeader,
 351             baseDir,
 352             "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: "
 353                     + "</b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate "
 354                     + "deoxygenate reductase" },
 355         {
 356             structModelHeader,
 357             baseDir,
 358             "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>"
 359                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 360         {
 361             structModelHeader,
 362             baseDir,
 363             "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>"
 364                     + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
 365         {
 366             structModelHeader,
 367             baseDir,
 368             "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: "
 369                     + "</b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the "
 370                     + "toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant" },
 371         {
 372             structModelHeader,
 373             baseDir,
 374             "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: "
 375                     + "</b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a"
 376                     + " modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]" }
 377     };
 378   }
 379
 380   @DataProvider(name = "phyre2ModelMappingDataProvider")
 381   public static Object[][] phyre2ModelMappingDataProvider()
 382   {
 383     return new Object[][] {
 384
 385         { "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb",
 386             "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta" },
 387         { "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb",
 388             "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta" },
 389         { "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.pdb",
 390             "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.fasta" },
 391         { "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.pdb",
 392             "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.fasta" },
 393         { "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.pdb",
 394             "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.fasta" },
 395         { "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.pdb",
 396             "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.fasta" },
 397
 398         { "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.pdb",
 399             "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.fasta" },
 400
 401         { "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.pdb",
 402             "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.fasta" },
 403         { "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.pdb",
 404             "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.fasta" },
 405         {
 406             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb",
 407             "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta" },
 408         {
 409             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.pdb",
 410             "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.fasta" },
 411         {
 412             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.pdb",
 413             "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.fasta" },
 414         {
 415             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.pdb",
 416             "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.fasta" },
 417         {
 418             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb",
 419             "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.fasta" },
 420         {
 421             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb",
 422             "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta" },
 423         {
 424             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.pdb",
 425             "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.fasta" },
 426         {
 427             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.pdb",
 428             "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.fasta" },
 429         {
 430             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.pdb",
 431             "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.fasta" },
 432         {
 433             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb",
 434             "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta" },
 435         {
 436             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb",
 437             "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta" }
 438
 439     };
 440   }
 441
 442   @DataProvider(name = "phyre2InfoHTMLTableDataProvider")
 443   public static Object[][] phyre2InfoHTMLTableDataProvider()
 444   {
 445     return new Object[][] {
 446         {
 447             "STRUCTMODEL Annotation with no headear information provided",
 448             null,
 449             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 450                 "d1a70a_.2.fasta", }, "" },
 451         {
 452             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 453             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 454                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 455             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 456                 "d1a70a_.2.fasta", },
 457             "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr></table></html>" },
 458         {
 459             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 460             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 461                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 462                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 463             new String[] {
 464                 "FER_CAPAN_1-144",
 465                 "d1a70a_ d1a70a_.2.pdb",
 466                 "d1a70a_.2.fasta",
 467                 "1",
 468                 "71",
 469                 "48-144",
 470                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 471             "<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>" } };
 472   }
 473
 474   @DataProvider(name = "StructModelHtmlDataProvider")
 475   public static Object[][] IsGenerateStructInfoHtmlDataProvider()
 476   {
 477     return new Object[][] {
 478         { "STRUCTMODEL Annotation with no headear or data provided", null,
 479             null, false },
 480         {
 481             "STRUCTMODEL Annotation with headear information and no data column provided",
 482             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" }, null,
 483             false },
 484         {
 485             "STRUCTMODEL Annotation with no headear information provided",
 486             null,
 487             new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
 488                 "d1a70a_.2.fasta", }, false },
 489         {
 490             "STRUCTMODEL Annotation with only two headear information and two data column provided",
 491             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" },
 492             new String[] { "FER_CAPAN_1-144", "d1a70a_" }, false },
 493         {
 494             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 495             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 496                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
 497             new String[] { "FER_CAPAN_1-144", "d1a70a_", "d1a70a_.2.pdb",
 498                 "d1a70a_.2.fasta", }, true },
 499         {
 500             "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
 501             new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
 502                 "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
 503                 "% I.D", "Aligned Range", "Other Information", "Coverage" },
 504             new String[] {
 505                 "FER_CAPAN_1-144",
 506                 "d1a70a_",
 507                 "d1a70a_.2.pdb",
 508                 "d1a70a_.2.fasta",
 509                 "1",
 510                 "71",
 511                 "48-144",
 512                 "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
 513             true } };
 514   }
 515
 516   @DataProvider(name = "FilePathProvider")
 517   public static Object[][] filePathProvider()
 518   {
 519     return new Object[][] {
 520         { "relative local file path resolution", "c4n58A_.1.pdb", "",
 521             "c4n58A_.1.pdb" },
 522         { "relative local file path resolution", "c4n58A_.1.pdb",
 523             "/examples/testdata/phyre2results/",
 524             "/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 525         {
 526             "relative URL path resolution",
 527             "c4n58A_.1.pdb",
 528             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 529             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/c4n58A_.1.pdb" },
 530         {
 531             "Absolute local file path resolution",
 532             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb",
 533             "/examples/testdata/phyre2results/",
 534             "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb" },
 535         {
 536             "Absolute URL path resolution",
 537             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb",
 538             "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
 539             "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb" } };
 540   }
 541 }