From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 24 Feb 2023 16:44:48 +0000 (+0000)
Subject: JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of... 
X-Git-Tag: Release_2_11_3_0~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7f98aeaa190d77fd40dcf80d55faedcace024d6f;p=jalview.git

JAL-629 JAL-4124 JAL-3855 test to check we can import PAE matrices in a variety of formats - and fix up a casting issue (again?)
---

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 0349417..48071bd 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -90,24 +90,24 @@ public class PAEContactMatrix implements ContactMatrixI
   @SuppressWarnings("unchecked")
   private void parse_version_2_pAE(Map<String, Object> pae_obj)
   {
-    elements = new float[length][length];
     // this is never going to be reached by the integer rounding.. or is it ?
     maxscore = ((Double) MapUtils.getFirst(pae_obj,
             "max_predicted_aligned_error", "max_pae")).floatValue();
-    Iterator<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
+    List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
             .getFirst(pae_obj, "predicted_aligned_error", "pae"))
-            .iterator();
+            ;
+    elements = new float[scoreRows.size()][scoreRows.size()];
     int row = 0, col = 0;
-    while (scoreRows.hasNext())
+    for (List<Long> scoreRow:scoreRows)
     {
-      Iterator<Long> scores = scoreRows.next().iterator();
+      Iterator<Long> scores = scoreRow.iterator();
       while (scores.hasNext())
       {
         Object d = scores.next();
         if (d instanceof Double)
           elements[row][col++] = ((Double) d).longValue();
         else
-          elements[row][col++] = (float) d;
+          elements[row][col++] = (float) ((Long)d).longValue();
       }
       row++;
       col = 0;
@@ -131,7 +131,7 @@ public class PAEContactMatrix implements ContactMatrixI
     Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
     Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
             .iterator();
-
+    // assume square matrix
     elements = new float[length][length];
     while (scores.hasNext())
     {
diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index b3bcfd9..72fd8d9 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -402,8 +402,26 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       }
     }
 
+    JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
+    if (paeDict == null)
+    {
+      Console.debug("JSON file did not parse properly.");
+      return false;
+    }
+    ContactMatrixI matrix = new PAEContactMatrix(sequence,
+            (Map<String, Object>) paeDict);
+
+    AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+    pdbAlignment.addAnnotation(cmannot);
+
+    return true;
+  }
+
+  public static JSONObject parseJSONtoPAEContactMatrix(
+          InputStream pae_input) throws IOException,ParseException
+  {
     Object paeJson = Platform.parseJSON(pae_input);
-    JSONObject paeDict = null;
+    JSONObject paeDict=null;
     if (paeJson instanceof JSONObject)
     {
       Console.debug("***** paeJson is a JSONObject");
@@ -416,18 +434,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
         paeDict = (JSONObject) jsonArray.get(0);
     }
 
-    if (paeDict == null)
-    {
-      Console.debug("JSON file did not parse properly.");
-      return false;
-    }
-    ContactMatrixI matrix = new PAEContactMatrix(sequence,
-            (Map<String, Object>) paeDict);
-
-    AlignmentAnnotation cmannot = sequence.addContactList(matrix);
-    pdbAlignment.addAnnotation(cmannot);
-
-    return true;
+    return paeDict;
   }
 
   public static boolean importPaeJSONAsContactMatrixToStructure(
@@ -452,7 +459,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           throws IOException, ParseException
   {
 
-    List<Object> pae_obj = (List<Object>) Platform.parseJSON(paeInput);
+    JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
     if (pae_obj == null)
     {
       Console.debug("JSON file did not parse properly.");
@@ -460,7 +467,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     }
 
     ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
-            (Map<String, Object>) pae_obj.get(0));
+            (Map<String, Object>) pae_obj);
 
     AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
     // sm.getSequence().addAlignmentAnnotation(cmannot);
diff --git a/test/jalview/ws/dbsources/EBIAlphaFoldTest.java b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java
new file mode 100644
index 0000000..20435f4
--- /dev/null
+++ b/test/jalview/ws/dbsources/EBIAlphaFoldTest.java
@@ -0,0 +1,44 @@
+package jalview.ws.dbsources;
+
+import java.io.FileInputStream;
+
+import org.junit.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.Sequence;
+import jalview.gui.JvOptionPane;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
+public class EBIAlphaFoldTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @DataProvider(name = "getExamplePAEfiles")
+  public Object[][] getExamplePAEfiles()
+  {
+    return new String[][] { {
+        "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json" },
+        { "examples/AlphaFold/AF-A0A1U8FD60-F1-predicted_aligned_error_v4.json" },
+        { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4.json" },
+        { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4_2023.json" } ,
+        { "examples/AlphaFold/AF-Q5VSL9-F1-predicted_aligned_error_v4B.json" } };
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "getExamplePAEfiles")
+  public void checkPAEimport(String paeFile) throws Exception
+  {
+    PAEContactMatrix cm = new PAEContactMatrix(
+            new Sequence("Dummy/1-2000", "ASDASDA"),
+            EBIAlfaFold.parseJSONtoPAEContactMatrix(
+                    new FileInputStream(paeFile)));
+    Assert.assertNotEquals("No data from " + paeFile, cm.getMax(), 0);
+  }
+}