+/*
+ * 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.gui;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureColourTest;
import jalview.util.matcher.Condition;
-
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-
-import org.testng.annotations.Test;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
public class FeatureSettingsTest
{
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ /*
+ * use read-only test properties file
+ */
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
+ Jalview.main(new String[] { "--nonews" });
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
/**
* Test a roundtrip of save and reload of feature colours and filters as XML
*
/*
* set colour schemes for features
*/
- FeatureRenderer fr = af.getFeatureRenderer();
+ FeatureRendererModel fr = af.getFeatureRenderer();
// type1: red
fr.setColour("type1", new FeatureColour(Color.red));
fr.setColour("type2", byLabel);
// type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
- 10);
+ FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byScore.setAboveThreshold(true);
byScore.setThreshold(2f);
fr.setColour("type3", byScore);
fr.setColour("type4", byAF);
// type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
- 1, 10);
+ FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+ Color.BLUE, null, 1, 10);
byPolyPhen.setBelowThreshold(true);
byPolyPhen.setThreshold(3f);
byPolyPhen.setAttributeName("CSQ", "PolyPhen");
assertTrue(fc.isBelowThreshold());
assertEquals(fc.getThreshold(), 3f);
- assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
+ assertEquals(fr.getFeatureFilter("type1").toStableString(),
+ "Label Contains x");
assertEquals(fr.getFeatureFilter("type2").toStableString(),
"(Score LE 2.4) AND (Score GT 1.1)");
assertEquals(fr.getFeatureFilter("type3").toStableString(),
- "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+ "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
}
/**
@Test(groups = "Functional")
public void testGetColorTooltip() throws IOException
{
- assertNull(FeatureSettings.getColorTooltip(null,false));
+ assertNull(FeatureSettings.getColorTooltip(null, false));
/*
* simple colour
*/
FeatureColourI fc = new FeatureColour(Color.black);
String simpleTooltip = "Click to edit, right-click for menu";
- assertEquals(FeatureSettings.getColorTooltip(fc,false), simpleTooltip);
+ assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
+ assertNull(FeatureSettings.getColorTooltip(fc, false));
/*
* graduated colour tooltip includes description of colour
*/
fc.setColourByLabel(true);
- assertEquals(FeatureSettings.getColorTooltip(fc,false),
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Label</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
"<html>By Label<br>" + simpleTooltip + "</br></html>");
/*
* graduated colour with threshold is html-encoded
*/
- fc = new FeatureColour(Color.red, Color.blue, 2f, 10f);
+ fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
fc.setBelowThreshold(true);
fc.setThreshold(4f);
- assertEquals(FeatureSettings.getColorTooltip(fc,false),
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (< 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
"<html>By Score (< 4.0)<br>" + simpleTooltip
+ "</br></html>");
+
fc.setAboveThreshold(true);
- assertEquals(FeatureSettings.getColorTooltip(fc,false),
+ assertEquals(FeatureSettings.getColorTooltip(fc, false),
+ "<html>By Score (> 4.0)</html>");
+ assertEquals(FeatureSettings.getColorTooltip(fc, true),
"<html>By Score (> 4.0)<br>" + simpleTooltip
+ "</br></html>");
}
+
+ String fsfile = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">",
+ fsfile2 = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n<ns2:JalviewUserColours schemeName=\"Sequence Features\" xmlns:ns2=\"www.jalview.org/colours\">";
+
+ @Test(groups = "Functional")
+ public void testIdentifyFeatureSettingsFile() throws Exception
+ {
+ FileFormatI type = new IdentifyFile().identify(fsfile,
+ DataSourceType.PASTE);
+ assertTrue(FileFormat.FeatureSettings == type,
+ "Feature settings file was identified as " + type);
+ type = new IdentifyFile().identify(fsfile2, DataSourceType.PASTE);
+ assertTrue(FileFormat.FeatureSettings == type,
+ "Feature settings file with newline was identified as " + type);
+ }
}
git://source.jalview.org / jalview.git / blobdiff