import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DynamicData;
import jalview.datamodel.HiddenColumns;
+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()
{
* - label for IO class used to write and read back in the data from
* f
*/
- void testAnnotationFileIO(String testname, File f,
- File annotFile)
+ void testAnnotationFileIO(String testname, File f, File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
+ annotFile + "' onto : " + f);
+ "\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";
+ HiddenColumns cs = new HiddenColumns();
+ 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" } };
+ }
}
git://source.jalview.org / jalview.git / blobdiff