From 27646d2165ec8ef75444519faf0199f2601a7b2a Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 1 May 2024 15:58:21 +0100
Subject: [PATCH] JAL-4407 failing test checking for secondary structure is
 added when calling the associate pdb file routine

---
 test/jalview/gui/AssociatePDBFileTest.java |  142 ++++++++++++++++++++++++++++
 1 file changed, 142 insertions(+)
 create mode 100644 test/jalview/gui/AssociatePDBFileTest.java

diff --git a/test/jalview/gui/AssociatePDBFileTest.java b/test/jalview/gui/AssociatePDBFileTest.java
new file mode 100644
index 0000000..0e6791b
--- /dev/null
+++ b/test/jalview/gui/AssociatePDBFileTest.java
@@ -0,0 +1,142 @@
+/*
+ * 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.gui;
+
+
+import java.awt.Color;
+import java.io.File;
+import java.util.Iterator;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.project.Jalview2xmlTests;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.util.MessageManager;
+
+public class AssociatePDBFileTest
+{
+  AlignFrame af;
+
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    setUpJvOptionPane();
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Jalview.main(new String[] { "--nonews" });
+  }
+
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  /**
+   * configure (read-only) properties for test to ensure Consensus is computed
+   * for colour Above PID testing
+   */
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded(">1GAQ|A/19-314\n"
+            + "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
+            + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+            + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+            + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
+            + "DQWNVEVY\n"
+            + ">1GAQ|B/1-98\n"
+            + "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
+            + "WVLTCHAYPTSDVVIETHKEEELTGA\n"
+            + ">1GAQ|C/19-314\n"
+            + "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
+            + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+            + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+            + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
+            + "DQWNVEVY\n"
+            ,
+            DataSourceType.PASTE);
+
+    /*
+     * wait for Consensus thread to complete
+     */
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+    } while (af.getViewport().getCalcManager().isWorking());
+  }
+
+  public static void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void testAssociatePDBFile()
+  {
+    String assoc_file="examples/1gaq.txt";
+    for (SequenceI toassoc:af.getViewport().getAlignment().getSequences())
+    {
+      PDBEntry pe = new AssociatePdbFileWithSeq()
+              .associatePdbWithSeq(assoc_file,
+                      DataSourceType.FILE, toassoc, false,
+                      Desktop.instance);
+      Assert.assertNotNull(pe);
+      Assert.assertNotEquals(toassoc.getDatasetSequence().getAnnotation().length,0);
+    }
+  }
+}
-- 
1.7.10.2