From 3380595c6eb44d914e9a25958bc09c4e292e1c32 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 21 Oct 2022 16:21:51 +0100
Subject: [PATCH] JAL-2349 JAL-3855 fix failing tests

---
 src/jalview/gui/AnnotationPanel.java |    5 ++---
 src/mc_view/PDBChain.java            |    2 +-
 test/mc_view/PDBfileTest.java        |   20 ++++++++++----------
 3 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 615fbdd..e12cc3f 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1019,15 +1019,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
   {
     int[] res = new int[2];
+    res[0] = -1;
+    res[1] = 0;
     if (aa == null)
     {
-      res[0] = -1;
-      res[1] = 0;
       return res;
     }
     int row = -1;
     int height = 0, lheight = 0;
-
     for (int i = 0; i < aa.length; i++)
     {
       if (aa[i].visible)
diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 035e608..5413a3c 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -82,7 +82,7 @@ public class PDBChain
   public String pdbid = "";
 
   AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder(
-          "TemperatureFactor");
+          "Temperature Factor");
 
   public PDBChain(String thePdbid, String theId,
           AnnotationRowBuilder template)
diff --git a/test/mc_view/PDBfileTest.java b/test/mc_view/PDBfileTest.java
index b636669..cae183a 100644
--- a/test/mc_view/PDBfileTest.java
+++ b/test/mc_view/PDBfileTest.java
@@ -26,6 +26,13 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -37,13 +44,6 @@ import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureImportSettings;
 
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class PDBfileTest
 {
 
@@ -286,10 +286,10 @@ public class PDBfileTest
     for (int i = 0; i < 20; i++)
     {
       assertNull(anns[0].annotations[i]);
-      assertEquals("E", anns[0].annotations[20].displayCharacter);
+      assertNull(anns[0].annotations[20].displayCharacter);
       assertEquals('E', anns[0].annotations[20].secondaryStructure);
-      assertEquals("E", anns[2].annotations[18].displayCharacter);
-      assertEquals("H", anns[2].annotations[23].displayCharacter);
+      assertEquals('E', anns[2].annotations[18].secondaryStructure);
+      assertEquals('H', anns[2].annotations[23].secondaryStructure);
     }
   }
 
-- 
1.7.10.2