JAL-629 add AF examples for FER1_SPIOL. Link and display PAE matrix annotation

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index bee1ae9..672f0ac 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -358,6 +358,14 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   public static boolean importPaeJSONAsContactMatrixToSequence(
+          AlignmentI pdbAlignment, File paeFile, int index, String seqId)
+          throws FileNotFoundException, IOException, ParseException
+  {
+    return importPaeJSONAsContactMatrixToSequence(pdbAlignment,
+            new FileInputStream(paeFile), index, seqId);
+  }
+
+  public static boolean importPaeJSONAsContactMatrixToSequence(
           AlignmentI pdbAlignment, InputStream pae_input, int index,
           String seqId) throws IOException, ParseException
   {
@@ -431,10 +439,17 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
   }
 
   public static boolean importPaeJSONAsContactMatrixToStructure(
+          StructureMapping sm, File paeFile)
+          throws FileNotFoundException, IOException, ParseException
+  {
+    return importPaeJSONAsContactMatrixToStructure(sm,
+            new FileInputStream(paeFile));
+  }
+
+  public static boolean importPaeJSONAsContactMatrixToStructure(
           StructureMapping sm, InputStream paeInput)
           throws IOException, ParseException
   {
-
     JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
     if (pae_obj == null)
     {