/*
- * Jalview - A Sequence Alignment Editor and Viewer (2.9.0b1)
- * Copyright (C) 2015 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.
*
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FeaturesFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@Test(groups = { "Functional" })
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
- "examples/exampleFeatures.txt", FormatAdapter.FILE);
+ "examples/exampleFeatures.txt", DataSourceType.FILE);
assertTrue("Test " + "Features file test"
+ "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
+ "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
FeaturesFile featuresFile = new FeaturesFile(gffData,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
String ff = f.getPath();
FormatAdapter rf = new FormatAdapter();
- AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
- new IdentifyFile().identify(ff, FormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
al.setDataset(null); // creates dataset sequences
assertNotNull("Couldn't read supplied alignment data.", al);
+ "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
+ "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
FeaturesFile featuresFile = new FeaturesFile(gffData,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
FeaturesFile featuresFile = new FeaturesFile(featureData,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
assertTrue("Failed to parse features file",
featuresFile.parse(al.getDataset(), colours, true));
public void readGff3File() throws IOException
{
FeaturesFile gffreader = new FeaturesFile(true, simpleGffFile,
- FormatAdapter.FILE);
+ DataSourceType.FILE);
Alignment dataset = new Alignment(gffreader.getSeqsAsArray());
gffreader.addProperties(dataset);
checkDatasetfromSimpleGff3(dataset);
public void simpleGff3FileClass() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[] {});
- FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
-
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile,
+ DataSourceType.FILE);
+
boolean parseResult = ffile.parse(dataset, null, false, false);
assertTrue("return result should be true", parseResult);
checkDatasetfromSimpleGff3(dataset);
public void simpleGff3FileLoader() throws IOException
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- simpleGffFile, FormatAdapter.FILE);
+ simpleGffFile, DataSourceType.FILE);
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
public void simpleGff3RelaxedIdMatching() throws IOException
{
AlignmentI dataset = new Alignment(new SequenceI[] {});
- FeaturesFile ffile = new FeaturesFile(simpleGffFile, FormatAdapter.FILE);
-
+ FeaturesFile ffile = new FeaturesFile(simpleGffFile,
+ DataSourceType.FILE);
+
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
parseResult);
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+ "ENDGROUP\tuniprot\n";
FeaturesFile featuresFile = new FeaturesFile(features,
- FormatAdapter.PASTE);
+ DataSourceType.PASTE);
featuresFile.parse(al.getDataset(), colours, false);
/*