/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.io.AnnotationFile.ViewDef;
+import jalview.structure.StructureSelectionManager;
import java.io.File;
+import java.util.Hashtable;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
- 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"}};
+ 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
+ @Test(groups = { "Functional" })
public void exampleAnnotationFileIO() throws Exception
{
- for (String[] testPair:TestFiles)
+ for (String[] testPair : TestFiles)
{
- testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(testPair[2]));
+ testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
+ testPair[2]));
}
}
- public static AlignmentI readAlignmentFile(File f)
+ AlignmentI readAlignmentFile(File f)
{
System.out.println("Reading file: " + f);
String ff = f.getPath();
{
FormatAdapter rf = new FormatAdapter();
- AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
-
+ 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).setDatasetSequence(al.getSequenceAt(i).createDatasetSequence());
+ al.getSequenceAt(i).createDatasetSequence();
}
assertNotNull("Couldn't read supplied alignment data.", al);
return al;
{
e.printStackTrace();
}
- fail("Couln't read the alignment in file '"+f.toString()+"'");
+ 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
* - label for IO class used to write and read back in the data from
* f
*/
- public static 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);
+ System.out.println("Test: " + testname + "\nReading annotation file '"
+ + annotFile + "' onto : " + f);
String af = annotFile.getPath();
try
{
AlignmentI al = readAlignmentFile(f);
-
- assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
-
- String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
- 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");
-
+ 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, FormatAdapter.PASTE));
-
+ 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);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
return;
} catch (Exception e)
{
e.printStackTrace();
}
- fail("Test "+testname+"\nCouldn't complete Annotation file roundtrip input/output/input test for '"+annotFile+"'.");
+ Assert.fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ + annotFile + "'.");
+ }
+
+
+ @BeforeClass(alwaysRun = true)
+ void testProcessStructModel()
+ {
+ 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);
+ ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ 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);
+ String phyre2ModelDesc = AnnotationFile.generatePhyre2InfoHTMLTable(structModelHeader,
+ structModelData);
+ expectedPDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ 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 = "phyre2InfoHTMLTableDataProvider")
+ void testGeneratePhyre2InfoHTMLTable(String caseDescription,
+ String[] header, String[] data, String expectedHtml)
+ {
+ System.out.println(">>>> Testing Case - " + caseDescription);
+ String actualHtmlGenerated = AnnotationFile
+ .generatePhyre2InfoHTMLTable(header, data);
+ System.out.println("-----> " + actualHtmlGenerated);
+ Assert.assertEquals(actualHtmlGenerated, expectedHtml);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ dataProvider = "StructModelHtmlDataProvider")
+ void testIsGenerateStructInfoHtml(String caseDescription,
+ String[] header, String[] data, boolean expectedOutcome)
+ {
+ System.out.println(">>>> Testing Case - " + caseDescription);
+ boolean actual = AnnotationFile.isGenerateStructInfoHtml(header, data);
+ Assert.assertEquals(actual, expectedOutcome);
+ }
+
+ @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