+/*
+ * 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.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.gui.JvOptionPane;
+
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class IdentifyFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" }, dataProvider = "identifyFiles")
- public void Identify(String data, String expectedFileType)
+ public void testIdentify(String data, FileFormatI expectedFileType)
+ throws FileFormatException
{
- String protocol = AppletFormatAdapter.FILE;
+ DataSourceType protocol = DataSourceType.FILE;
IdentifyFile ider = new IdentifyFile();
- String actualFiletype = ider.Identify(data, protocol);
- Assert.assertEquals(actualFiletype, expectedFileType,
+ FileFormatI actualFiletype = ider.identify(data, protocol);
+ Assert.assertSame(actualFiletype, expectedFileType,
"File identification Failed!");
}
+ /**
+ * Additional tests for Jalview features file
+ *
+ * @throws FileFormatException
+ */
+ @Test(groups = "Functional")
+ public void testIdentify_featureFile() throws FileFormatException
+ {
+ IdentifyFile ider = new IdentifyFile();
+
+ /*
+ * Jalview format with features only, no feature colours
+ */
+ String data = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
+
+ /*
+ * Jalview feature colour followed by GFF format feature data
+ */
+ data = "METAL\tcc9900\n" + "GFF\n"
+ + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n";
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
+
+ /*
+ * Feature with '<' in the name (JAL-2098)
+ */
+ data = "kD < 3\tred\n" + "Low kD\tFER_CAPAA\t-1\t39\t39\tkD < 3\n";
+ assertSame(FileFormat.Features,
+ ider.identify(data, DataSourceType.PASTE));
+ }
+
@DataProvider(name = "identifyFiles")
public Object[][] IdentifyFileDP()
{
return new Object[][] {
- { "examples/example.json", "JSON" },
- { "examples/plantfdx.fa", "FASTA" },
- { "examples/dna_interleaved.phy", "PHYLIP" },
- { "examples/2GIS.pdb", "PDB" },
- { "examples/rf00031_folded.stk", "STH" },
- { "examples/testdata/test.rnaml", "RNAML" },
- { "examples/testdata/test.aln", "CLUSTAL" },
- { "examples/testdata/test.pfam", "PFAM" },
- { "examples/testdata/test.msf", "MSF" },
- { "examples/testdata/test.pir", "PIR" },
- { "examples/testdata/test.html", "HTML" },
- { "examples/testdata/test.pileup", "PileUp" },
- { "examples/testdata/test.blc", "BLC" },
- { "examples/testdata/simplegff3.gff", "GFF v2 or v3" },
- { "examples/testdata/test.jvp", "Jalview" },
+ { "examples/example.json", FileFormat.Json },
+ { "examples/plantfdx.fa", FileFormat.Fasta },
+ { "examples/dna_interleaved.phy", FileFormat.Phylip },
+ { "examples/2GIS.pdb", FileFormat.PDB },
+ { "examples/RF00031_folded.stk", FileFormat.Stockholm },
+ { "examples/testdata/test.rnaml", FileFormat.Rnaml },
+ { "examples/testdata/test.aln", FileFormat.Clustal },
+ { "examples/testdata/test.pfam", FileFormat.Pfam },
+ { "examples/testdata/test.msf", FileFormat.MSF },
+ { "examples/testdata/test.pir", FileFormat.PIR },
+ { "examples/testdata/test.html", FileFormat.Html },
+ { "examples/testdata/test.pileup", FileFormat.Pileup },
+ { "examples/testdata/test.blc", FileFormat.BLC },
+ { "examples/exampleFeatures.txt", FileFormat.Features },
+ { "examples/testdata/simpleGff3.gff", FileFormat.Features },
+ { "examples/testdata/test.jvp", FileFormat.Jalview },
+ { "examples/testdata/test.cif", FileFormat.MMCif },
{
"examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316",
- "FASTA" },
-
+ FileFormat.Fasta },
+ { "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix },
+ { "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix }
// { "examples/testdata/test.amsa", "AMSA" },
// { "examples/test.jnet", "JnetFile" },
};
}
+ @Test(groups = "Functional")
+ public void testLooksLikeFeatureData()
+ {
+ IdentifyFile id = new IdentifyFile();
+ assertFalse(id.looksLikeFeatureData(null));
+ assertFalse(id.looksLikeFeatureData(""));
+ // too few columns:
+ assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5"));
+ // GFF format:
+ assertTrue(id
+ .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss"));
+ // Jalview format:
+ assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss"));
+ // non-numeric start column:
+ assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t.\t2462\tss"));
+ // non-numeric start column:
+ assertFalse(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t.\tss"));
+ }
}
git://source.jalview.org / jalview.git / blobdiff