From 001922aefa2bcf95471761473d25f4949635691c Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 18 May 2015 09:51:10 +0100 Subject: [PATCH] JAL-1737 updated JUnit so it creates positional annotations --- .../analysis/AlignmentAnnotationUtilsTest.java | 28 ++++++++++++++++---- test/jalview/gui/PopupMenuTest.java | 25 +++++++++++------ 2 files changed, 40 insertions(+), 13 deletions(-) diff --git a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java index 19a5163..c34bb68 100644 --- a/test/jalview/analysis/AlignmentAnnotationUtilsTest.java +++ b/test/jalview/analysis/AlignmentAnnotationUtilsTest.java @@ -3,10 +3,6 @@ package jalview.analysis; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertTrue; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; import java.io.IOException; import java.util.ArrayList; @@ -19,6 +15,12 @@ import java.util.Map; import org.junit.Before; import org.junit.Test; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; + public class AlignmentAnnotationUtilsTest { // 4 sequences x 13 positions @@ -111,6 +113,11 @@ public class AlignmentAnnotationUtilsTest return result; } + /** + * Load the test alignment and generate annotations on it + * + * @throws IOException + */ @Before public void setUp() throws IOException { @@ -120,7 +127,13 @@ public class AlignmentAnnotationUtilsTest AlignmentAnnotation[] anns = new AlignmentAnnotation[SEQ_ANN_COUNT]; for (int i = 0; i < anns.length; i++) { - anns[i] = new AlignmentAnnotation("Label" + i, null, 0d); + /* + * Use the constructor for a positional annotation (with an Annotation + * array) + */ + anns[i] = new AlignmentAnnotation("Label" + i, "Desc " + i, + new Annotation[] + {}); anns[i].setCalcId("CalcId" + i); anns[i].visible = true; alignment.addAnnotation(anns[i]); @@ -304,6 +317,11 @@ public class AlignmentAnnotationUtilsTest anns[9].graph = AlignmentAnnotation.LINE_GRAPH; anns[9].graphGroup = GROUP_4; + /* + * Generate annotations[] arrays to match aligned columns + */ + // adjustForAlignment(anns); + List selected = selectSequences(0, 3); AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, AlignmentAnnotationUtils.asList(anns), diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index f2248a8..e1f0708 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -19,6 +19,7 @@ import org.junit.Test; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.FormatAdapter; @@ -238,28 +239,32 @@ public class PopupMenuTest // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( - "secondary structure", "", 0); + "secondary structure", "", new Annotation[] + {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // JMOL.secondary structure on Sequence0 - hidden - annotation = new AlignmentAnnotation("secondary structure", "", 0); + annotation = new AlignmentAnnotation("secondary structure", "", new Annotation[] + {}); annotation.setCalcId("JMOL"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // Jpred.SSP on Sequence0 - hidden - annotation = new AlignmentAnnotation("SSP", "", 0); + annotation = new AlignmentAnnotation("SSP", "", new Annotation[] + {}); annotation.setCalcId("JPred"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 - annotation = new AlignmentAnnotation("Temp", "", 0); + annotation = new AlignmentAnnotation("Temp", "", new Annotation[] + {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(1).addAlignmentAnnotation(annotation); @@ -316,14 +321,16 @@ public class PopupMenuTest // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( - "secondary structure", "", 0); + "secondary structure", "", new Annotation[] + {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 - annotation = new AlignmentAnnotation("Temp", "", 0); + annotation = new AlignmentAnnotation("Temp", "", new Annotation[] + {}); annotation.setCalcId("PDB"); annotation.visible = true; seqs.get(1).addAlignmentAnnotation(annotation); @@ -373,14 +380,16 @@ public class PopupMenuTest // PDB.secondary structure on Sequence0 AlignmentAnnotation annotation = new AlignmentAnnotation( - "secondary structure", "", 0); + "secondary structure", "", new Annotation[] + {}); annotation.setCalcId("PDB"); annotation.visible = false; seqs.get(0).addAlignmentAnnotation(annotation); parentPanel.getAlignment().addAnnotation(annotation); // PDB.Temp on Sequence1 - annotation = new AlignmentAnnotation("Temp", "", 0); + annotation = new AlignmentAnnotation("Temp", "", new Annotation[] + {}); annotation.setCalcId("PDB2"); annotation.visible = false; seqs.get(1).addAlignmentAnnotation(annotation); -- 1.7.10.2