From dcb4c919fdf50dd481eb411c11a657611ab4f63b Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 10 Feb 2023 16:03:32 +0000
Subject: [PATCH] JAL-4126 failing test - colour scheme appears to be being
 created and configured, but the renderer is not actually
 using the colour scheme to shade the sequence when the
 project is restored.

---
 test/jalview/project/Jalview2xmlTests.java |   93 ++++++++++++++++++++++++++--
 1 file changed, 89 insertions(+), 4 deletions(-)

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 79d622c..e728ca6 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -50,6 +50,7 @@ import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.HiddenSequences;
@@ -233,8 +234,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     boolean diffseqcols = false, diffgseqcols = false;
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
-    for (int p = 0, pSize = af.getViewport().getAlignment()
-            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
@@ -253,8 +255,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0, pSize = af.getViewport().getAlignment()
-            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
@@ -819,6 +822,88 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * @throws IOException
    */
   @Test(groups = { "Functional" })
+  public void testStoreAndRecoverAnnotationRowElementColours()
+          throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ",
+            DataSourceType.PASTE);
+
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    SequenceI fsq;
+    fsq = al.getSequenceAt(0);
+    Annotation annots[] = new Annotation[fsq.getLength()];
+    AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots",
+            annots);
+    annots[0] = new Annotation(1.0f);
+    annots[1] = new Annotation(2.0f);
+    annots[2] = new Annotation(3.0f);
+    annots[0].colour = Color.RED;
+    annots[1].colour = Color.GREEN;
+    annots[2].colour = Color.BLUE;
+    ala.validateRangeAndDisplay();
+    al.getSequenceAt(0).addAlignmentAnnotation(ala);
+    al.addAnnotation(ala);
+    /*
+     * and colour by annotation
+     */
+    AnnotationColourGradient acg = new AnnotationColourGradient(ala,
+            af.alignPanel.av.getGlobalColourScheme(), 0);
+    acg.setSeqAssociated(true);
+    acg.setPredefinedColours(true);
+    af.changeColour(acg);
+    Color seqcol[] = new Color[3];
+    for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
+      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+    }
+    /*
+     * save project, close windows, reload project, verify
+     */
+    File tfile = File.createTempFile(
+            "testStoreAndRecoverAnnotRowElemColors", ".jvp");
+    tfile.deleteOnExit();
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    Assert.assertNotNull(af, "Failed to reload project");
+    /*
+     * verify alignment annotation has colors
+     */
+    av = af.getViewport();
+    
+    ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
+    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+    acg = (AnnotationColourGradient) loadedCscheme;
+    assertTrue(acg.isSeqAssociated());
+    assertTrue(acg.isPredefinedColours());
+
+    al = av.getAlignment();
+    fsq = al.getSequenceAt(0);
+    ala = fsq.getAnnotation()[0];
+    Assert.assertNotNull(ala, "No annotation row recovered");
+    Assert.assertNotNull(ala.annotations);
+    for (int iStart = al.getSequenceAt(0)
+            .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
+    {
+      Assert.assertTrue(ala.annotations[i].colour!=null);
+      Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
+      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+      Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+
+    }
+    
+  }
+
+  /**
+   * Configure an alignment and a sub-group each with distinct colour schemes,
+   * Conservation and PID thresholds, and confirm these are restored from the
+   * saved project.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
   public void testStoreAndRecoverColourThresholds() throws IOException
   {
     Desktop.instance.closeAll_actionPerformed(null);
-- 
1.7.10.2