import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureColourI;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
-import java.awt.Color;
-import java.util.Arrays;
-import java.util.BitSet;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class AlignViewControllerTest
{
/*
* features start/end are base 1
*/
- seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
- null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
- 10f,
- null));
- seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
- 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 2, 4, 0f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Helix", "desc", 1, 15, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 4, 10, 10f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 11, 15, 10f, null));
// disulfide bond is a 'contact feature' - only select its 'start' and 'end'
- seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
- 8, 12, 0f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null));
/*
* select the first five columns --> Metal in seq1 cols 4-5
/*
* set features visible on a viewport as only visible features are selected
*/
- AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
- seq2, seq3, seq4 }), 100, 100);
+ AlignFrame af = new AlignFrame(
+ new Alignment(new SequenceI[]
+ { seq1, seq2, seq3, seq4 }), 100, 100);
af.getFeatureRenderer().findAllFeatures(true);
AlignViewController avc = new AlignViewController(af, af.getViewport(),
* seq1 feature in columns 4-6 is hidden
* seq2 feature in columns 6-7 is shown
*/
- FeatureColourI fc = new FeatureColour(Color.red, Color.blue, 0f, 10f);
+ FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+ 0f, 10f);
fc.setAboveThreshold(true);
fc.setThreshold(5f);
af.getFeatureRenderer().setColour("Metal", fc);
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ "seq3 aaaaaaaaaaMMMMMaaaaa\n"
- + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+ + "seq4 aaaaaaaaaaaaaaaaaaaa\n",
+ DataSourceType.PASTE);
SearchResultsI sr = new SearchResults();
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
/*
* test Match/Find works first
*/
- FinderI f = new Finder(af.getViewport().getAlignment());
- f.findAll("M+", null, true, false);
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false, false, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
AlignViewControllerI avc = af.avc;
avc.markHighlightedColumns(false, false, false);
- assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
- .getViewport().getColumnSelection().getSelectedRanges()
- .toArray(), new int[][] { { 1, 14 } }));
+ assertTrue("Didn't select highlighted columns",
+ Arrays.deepEquals(af.getViewport().getColumnSelection()
+ .getSelectedRanges().toArray(), new int[][]
+ { { 1, 14 } }));
}
}