+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.assertNotNull;
import jalview.api.AlignExportSettingI;
seqs[3].addSequenceFeature(seqFeature3);
seqs[4].addSequenceFeature(seqFeature4);
-
for (Sequence seq : seqs)
{
seq.setDatasetSequence(seq);
af.changeColour(jf.getColourScheme());
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
-
formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
af.alignPanel.getAlignment(), false);
}
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void methodSetup()
{
passedCount = 0;
jf = null;
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void roundTripTest()
{
assertNotNull("JSON roundtrip test failed!", testJsonFile);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSeqParsed()
{
assertNotNull("Couldn't read supplied alignment data.", testAlignment);
AssertJUnit.assertEquals("Some Sequences did not pass the test",
TEST_SEQ_HEIGHT, passedCount);
}
-
- @Test(groups ={ "Functional" })
+
+ @Test(groups = { "Functional" })
public void hiddenColsTest()
{
ColumnSelection cs = testJsonFile.getColumnSelection();
"Mismatched hidden columns!");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void hiddenSeqsTest()
{
Assert.assertNotNull(testJsonFile.getHiddenSequences(),
"Hidden sequence Expected but found Null");
- Assert.assertEquals(jf.getHiddenSequences().length, 1,
- "Hidden sequece");
+ Assert.assertEquals(jf.getHiddenSequences().length, 1, "Hidden sequece");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void colorSchemeTest()
{
Assert.assertNotNull(testJsonFile.getColourScheme(),
"Zappo colour scheme expected!");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void isShowSeqFeaturesSet()
{
Assert.assertTrue(testJsonFile.isShowSeqFeatures(),
"Sequence feature isDisplayed setting expected to be true");
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testGrpParsed()
{
Assert.assertNotNull(testAlignment.getGroups());
TEST_GRP_HEIGHT, passedCount);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testAnnotationParsed()
{
Assert.assertNotNull(testAlignment.getAlignmentAnnotation());