/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.io;

import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;

import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DynamicData;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile.ViewDef;
import jalview.structure.StructureSelectionManager;

import java.io.File;
import java.util.Hashtable;
import java.util.List;

import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

public class AnnotationFileIOTest
{

  private StructureSelectionManager ssm = null;

  private AlignmentI al = null;

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  static String TestFiles[][] = {
      { "Test example annotation import/export", "examples/uniref50.fa",
          "examples/testdata/example_annot_file.jva" },
      { "Test multiple combine annotation statements import/export",
          "examples/uniref50.fa",
          "examples/testdata/test_combine_annot.jva" },
      {
          "Test multiple combine annotation statements with sequence_ref import/export",
          "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
      {
          "Test group only annotation file parsing results in parser indicating annotation was parsed",
          "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
      { "Test hiding/showing of insertions on sequence_ref",
          "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };

  @Test(groups = { "Functional" })
  public void exampleAnnotationFileIO() throws Exception
  {
    for (String[] testPair : TestFiles)
    {
      testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
              testPair[2]));
    }
  }

  AlignmentI readAlignmentFile(File f)
  {
    System.out.println("Reading file: " + f);
    String ff = f.getPath();
    try
    {
      FormatAdapter rf = new FormatAdapter();

      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
              new IdentifyFile().identify(ff, DataSourceType.FILE));

      // make sure dataset is initialised ? not sure about this
      for (int i = 0; i < al.getSequencesArray().length; ++i)
      {
        al.getSequenceAt(i).createDatasetSequence();
      }
      assertNotNull("Couldn't read supplied alignment data.", al);
      return al;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
    return null;
  }

  /**
   * test alignment data in given file can be imported, exported and reimported
   * with no dataloss
   * 
   * @param f
   *          - source datafile (IdentifyFile.identify() should work with it)
   * @param ioformat
   *          - label for IO class used to write and read back in the data from
   *          f
   */
  void testAnnotationFileIO(String testname, File f, File annotFile)
  {
    System.out.println("Test: " + testname + "\nReading annotation file '"
            + annotFile + "' onto : " + f);
    String af = annotFile.getPath();
    try
    {
      AlignmentI al = readAlignmentFile(f);
      ColumnSelection cs = new ColumnSelection();
      assertTrue(
              "Test "
                      + testname
                      + "\nAlignment was not annotated - annotation file not imported.",
              new AnnotationFile().readAnnotationFile(al, cs, af,
                      DataSourceType.FILE));

      AnnotationFile aff = new AnnotationFile();
      ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
              new Hashtable());
      String anfileout = new AnnotationFile().printAnnotations(
              al.getAlignmentAnnotation(), al.getGroups(),
              al.getProperties(), null, al, v);
      assertTrue(
              "Test "
                      + testname
                      + "\nAlignment annotation file was not regenerated. Null string",
              anfileout != null);
      assertTrue(
              "Test "
                      + testname
                      + "\nAlignment annotation file was not regenerated. Empty string",
              anfileout.length() > "JALVIEW_ANNOTATION".length());

      System.out.println("Output annotation file:\n" + anfileout
              + "\n<<EOF\n");

      AlignmentI al_new = readAlignmentFile(f);
      assertTrue(
              "Test "
                      + testname
                      + "\nregenerated annotation file did not annotate alignment.",
              new AnnotationFile().readAnnotationFile(al_new, anfileout,
                      DataSourceType.PASTE));

      // test for consistency in io
      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
      return;
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    Assert.fail("Test "
            + testname
            + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
            + annotFile + "'.");
  }


  @BeforeClass(alwaysRun = true)
  void testProcessStructModel()
  {
    try
    {

      ssm = StructureSelectionManager.getStructureSelectionManager();
    } catch (NullPointerException e)
    {
      ssm = new StructureSelectionManager();
    }
    File alignmentFile = new File(
            "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
    String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
    ColumnSelection cs = new ColumnSelection();
    al = readAlignmentFile(alignmentFile);
    boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
            cs, annotationFile, DataSourceType.FILE);
    Assert.assertTrue(annotationRead);
    System.out.println("bla");
  }
  
  @Test(
    groups = { "Functional" },
    dataProvider = "phyre2ModelPDBEntryDataProvider")
  void testSequence_PDBEntryAssociation(String[] structModelHeader, String baseDir,
          String structModelDataStr)
  {
    String structModelData[] = structModelDataStr.split("\t");
    String templateSeq = structModelData[1];
    String pdbId = structModelData[2];

    SequenceI testSeq = al.findName(templateSeq);
    Assert.assertNotNull(testSeq);
    PDBEntry actualPDBEntry = testSeq.getDatasetSequence().getPDBEntry(
            pdbId);
    Assert.assertNotNull(actualPDBEntry);

    PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
            + pdbId);
    List<DynamicData> phyreDD = AnnotationFile
            .generatePhyreDynamicDataList(structModelHeader,
                    structModelData);
    expectedPDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD);

    Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
  }

  @Test(
    groups = { "Functional" },
    dataProvider = "phyre2ModelMappingDataProvider")
  void testPhyre2ModelRegistration(String phyre2ModelFile,
          String expectedPhyre2FastaMappingFile)
  {

    String actualFastaMappingFile = ssm
            .getPhyre2FastaFileFor(phyre2ModelFile);
    Assert.assertNotNull(actualFastaMappingFile);
    Assert.assertEquals(actualFastaMappingFile,
            expectedPhyre2FastaMappingFile);
  }

  @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
  void testResolveAbsolutePath(String caseDescription, String suppliedPath,
          String baseURI, String expectedURI)
  {
    System.out.println(">>>> Testing Case - " + caseDescription);
    String actualURI = AnnotationFile.resolveAbsolutePath(suppliedPath,
            baseURI);
    Assert.assertEquals(actualURI, expectedURI);
  }
  
  @DataProvider(name = "phyre2ModelPDBEntryDataProvider")
  public static Object[][] phyre2ModelPDBEntryDataProvider()
  {
    String[] structModelHeader = new String[] { "QUERY_SEQ",
            "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
            "% I.D", "Aligned Range", "Other Information"};
    String baseDir = "examples/testdata/phyre2results/56da5616b4559c93/";
    
    return new Object[][] {
        {
            structModelHeader,
            baseDir,
            "FER_CAPAN_1-144\tc4n58A_\tc4n58A_.1.pdb\tc4n58A_.1.fasta\t1\t54\t48-143\t<b>PDB Header: </b>Hyrolase<br><b>Chain: "
                    + "</b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms" },
        {
            structModelHeader,
            baseDir,
            "FER_CAPAN_1-144\td1a70a_\td1a70a_.2.pdb\td1a70a_.2.fasta\t1\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "FER_CAPAN_1-144\td1offa_\td1offa_.3.pdb\td1offa_.3.fasta\t1\t73\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
        {
            structModelHeader,
            baseDir,
            "FER_CAPAN_1-144\tc4itkA_\tc4itkA_.15.pdb\tc4itkA_.15.fasta\t0.999\t57\t50-142\t<b>PDB Header: </b>Electron transport<br>"
                    + "<b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2" },
        {
            structModelHeader,
            baseDir,
            "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: "
                    + "</b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate "
                    + "deoxygenate reductase" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
        {
            structModelHeader,
            baseDir,
            "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>"
                    + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
        {
            structModelHeader,
            baseDir,
            "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: "
                    + "</b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the "
                    + "toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant" },
        {
            structModelHeader,
            baseDir,
            "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: "
                    + "</b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a"
                    + " modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]" }
    };
  }

  @DataProvider(name = "phyre2ModelMappingDataProvider")
  public static Object[][] phyre2ModelMappingDataProvider()
  {
    return new Object[][] {

        { "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.fasta" },

        { "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.fasta" },

        { "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.fasta" },
        { "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta" },
        {
            "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb",
            "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta" }

    };
  }

  @DataProvider(name = "phyre2InfoHTMLTableDataProvider")
  public static Object[][] phyre2InfoHTMLTableDataProvider()
  {
    return new Object[][] {
        {
            "STRUCTMODEL Annotation with no headear information provided",
            null,
            new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
                "d1a70a_.2.fasta", }, "" },
        {
            "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
                "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
            new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
                "d1a70a_.2.fasta", },
            "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr></table></html>" },
        {
            "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
                "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
                "% I.D", "Aligned Range", "Other Information", "Coverage" },
            new String[] {
                "FER_CAPAN_1-144",
                "d1a70a_ d1a70a_.2.pdb",
                "d1a70a_.2.fasta",
                "1",
                "71",
                "48-144",
                "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
            "<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>" } };
  }

  @DataProvider(name = "StructModelHtmlDataProvider")
  public static Object[][] IsGenerateStructInfoHtmlDataProvider()
  {
    return new Object[][] {
        { "STRUCTMODEL Annotation with no headear or data provided", null,
            null, false },
        {
            "STRUCTMODEL Annotation with headear information and no data column provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" }, null,
            false },
        {
            "STRUCTMODEL Annotation with no headear information provided",
            null,
            new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
                "d1a70a_.2.fasta", }, false },
        {
            "STRUCTMODEL Annotation with only two headear information and two data column provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" },
            new String[] { "FER_CAPAN_1-144", "d1a70a_" }, false },
        {
            "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
                "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
            new String[] { "FER_CAPAN_1-144", "d1a70a_", "d1a70a_.2.pdb",
                "d1a70a_.2.fasta", }, true },
        {
            "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
            new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
                "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
                "% I.D", "Aligned Range", "Other Information", "Coverage" },
            new String[] {
                "FER_CAPAN_1-144",
                "d1a70a_",
                "d1a70a_.2.pdb",
                "d1a70a_.2.fasta",
                "1",
                "71",
                "48-144",
                "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
            true } };
  }

  @DataProvider(name = "FilePathProvider")
  public static Object[][] filePathProvider()
  {
    return new Object[][] {
        { "relative local file path resolution", "c4n58A_.1.pdb", "",
            "c4n58A_.1.pdb" },
        { "relative local file path resolution", "c4n58A_.1.pdb",
            "/examples/testdata/phyre2results/",
            "/examples/testdata/phyre2results/c4n58A_.1.pdb" },
        {
            "relative URL path resolution",
            "c4n58A_.1.pdb",
            "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
            "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/c4n58A_.1.pdb" },
        {
            "Absolute local file path resolution",
            "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb",
            "/examples/testdata/phyre2results/",
            "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb" },
        {
            "Absolute URL path resolution",
            "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb",
            "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
            "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb" } };
  }
}