From 97725e865411eec548a4b400ed9277b591f3fb6e Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 22 Feb 2023 14:23:56 +0000
Subject: [PATCH] JAL-3858 simple test for PAE matrix recovery

---
 test/jalview/project/Jalview2xmlTests.java |   56 ++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index c070edb..84af3e4 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -54,6 +54,8 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.HiddenSequences;
@@ -97,6 +99,7 @@ import jalview.util.MapList;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
@@ -1526,4 +1529,57 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     // af exists still but isn't shown
     assertTrue(af.isClosed());
   }
+
+  @Test(groups = { "Functional" })
+  public void testPAEsaveRestore() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+    AlignmentI al = af.getViewport().getAlignment();
+    SequenceI sq = al.getSequenceAt(0);
+    int i = sq.getLength();
+    float[][] paevals = new float[i][i];
+    for (i = i - 1; i >= 0; i--)
+    {
+      for (int j = 0; j <= i; j++)
+      {
+        paevals[i][j] = ((i - j < 2)
+                || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+        paevals[j][i] = paevals[i][j];
+      }
+    }
+    PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+    AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
+    al.addAnnotation(paeCm);
+    File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
+            ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    AlignmentI newAl = af.getViewport().getAlignment();
+    SequenceI newSeq = newAl.getSequenceAt(0);
+    // check annotation of the expected type exists
+    Assert.assertEquals(newSeq.getAnnotation().length, 1);
+    Assert.assertEquals(newSeq.getAnnotation()[0].graph, paeCm.graph);
+
+    // check a contact matrix was recovered
+    Assert.assertEquals(newSeq.getContactMaps().size(), 1);
+    // and can be found for the annotation
+    ContactMatrixI restoredMat = al
+            .getContactMatrixFor(newSeq.getAnnotation()[0]);
+    Assert.assertNotNull(restoredMat);
+    for (i = sq.getLength() - 1; i >= 0; i--)
+    {
+      ContactListI oldCM = dummyMat.getContactList(i),
+              newCM = restoredMat.getContactList(i);
+      for (int j = oldCM.getContactHeight(); j >= 0; j--)
+      {
+        Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
+      }
+    }
+  }
+
 }
-- 
1.7.10.2