From 57d5410a932ce5caba3b913c2a27e1a24e012220 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 30 Nov 2023 15:39:14 +0000
Subject: [PATCH] JAL-4342 test and patch checking annotation csv export
 contains the annotations on the alignment or a specific
 exported annotation

---
 src/jalview/gui/AnnotationExporter.java     |   18 +++++--
 test/jalview/io/AnnotationExporterTest.java |   77 +++++++++++++++++++++++++++
 2 files changed, 91 insertions(+), 4 deletions(-)
 create mode 100644 test/jalview/io/AnnotationExporterTest.java

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 894db79..a23496d 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -163,6 +163,14 @@ public class AnnotationExporter extends JPanel
     frame.setTitle(MessageManager.getString("label.export_annotations"));
   }
 
+  public void setExportAsCSV()
+  {
+    if (CSVFormat != null)
+    {
+      CSVFormat.setSelected(true);
+    }
+  }
+
   private void toFile_actionPerformed()
   {
     // TODO: JAL-3048 JalviewFileChooser - Save option
@@ -202,7 +210,7 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getText()
+  public String getText()
   {
     return exportFeatures ? getFeaturesText() : getAnnotationsText();
   }
@@ -213,12 +221,14 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getAnnotationsText()
+  public String getAnnotationsText()
   {
     String text;
     if (CSVFormat.isSelected())
     {
-      text = new AnnotationFile().printCSVAnnotations(annotations);
+      text = new AnnotationFile().printCSVAnnotations(
+              wholeView ? ap.av.getAlignment().getAlignmentAnnotation()
+                      : annotations);
     }
     else
     {
@@ -241,7 +251,7 @@ public class AnnotationExporter extends JPanel
    * 
    * @return
    */
-  private String getFeaturesText()
+  public String getFeaturesText()
   {
     String text;
     SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
diff --git a/test/jalview/io/AnnotationExporterTest.java b/test/jalview/io/AnnotationExporterTest.java
new file mode 100644
index 0000000..6a627d8
--- /dev/null
+++ b/test/jalview/io/AnnotationExporterTest.java
@@ -0,0 +1,77 @@
+/*
+ * 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.io;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertNotNull;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.gui.AlignFrame;
+import jalview.gui.AnnotationExporter;
+import jalview.gui.JvOptionPane;
+
+public class AnnotationExporterTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void testAnnotationExportAsCSV()
+  {
+    /*
+     * JAL-4342 test that export all alignment annotation as CSV or as an annotations file DOES NOT produce empty text box/file
+     */
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">Seq1\nQRSIL\n>Seq2\nFTHND\n>Seq3\nRPVSL\n",
+            DataSourceType.PASTE);
+    AlignmentAnnotation[] annots = af.alignPanel.getAlignment()
+            .getAlignmentAnnotation();
+
+    assertTrue(annots.length > 1);
+    // set up exporter
+    AnnotationExporter ae = new AnnotationExporter(af.alignPanel);
+    ae.exportAnnotations();
+    ae.setExportAsCSV();
+
+    String exported;
+    exported = ae.getAnnotationsText();
+    assertNotNull(exported);
+    assertTrue(exported.contains(annots[0].label));
+    assertTrue(exported.contains(annots[1].label));
+
+    // just one annotation row
+    ae.exportAnnotation(annots[1]);
+    exported = ae.getAnnotationsText();
+    assertNotNull(exported);
+    assertFalse(exported.contains(annots[0].label));
+    assertTrue(exported.contains(annots[1].label));
+
+  }
+}
-- 
1.7.10.2