JAL-629 Allow attachment of pAE file to a particular sequence

[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 5314207..5575cb8 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -249,10 +249,11 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
             + "");
     UrlDownloadClient.download(paeURL, pae);
-    addAlphaFoldPAE(pdbAlignment, pae);
+    addAlphaFoldPAE(pdbAlignment, pae, 0, null);
   }
 
-  public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae)
+  public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+          int index, String seqId)
   {
     FileInputStream pae_input = null;
     try
@@ -266,7 +267,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     try
     {
-      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input))
+      if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input, index,
+              seqId))
       {
         Console.warn("Could not import contact matrix from '"
                 + pae.getAbsolutePath() + "'");
@@ -299,18 +301,61 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
           AlignmentI pdbAlignment, InputStream pae_input)
           throws IOException, ParseException
   {
+    return importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+  }
+
+  public static boolean importPaeJSONAsContactMatrix(
+          AlignmentI pdbAlignment, InputStream pae_input, int index,
+          String seqId) throws IOException, ParseException
+  {
 
     List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
     if (pae_obj == null)
     {
+      Console.debug("JSON file did not parse properly.");
       return false;
     }
-    ContactMatrixI matrix = new PAEContactMatrix(
-            pdbAlignment.getSequenceAt(0),
+    SequenceI sequence = null;
+    /* debugging */
+    SequenceI[] seqs = pdbAlignment.getSequencesArray();
+    if (seqs == null)
+      Console.debug("******* sequences is null");
+    else
+    {
+      for (int i = 0; i < seqs.length; i++)
+      {
+        SequenceI s = seqs[i];
+        Console.debug("******* sequences[" + i + "]='" + s.getName() + "'");
+      }
+    }
+    /* end debug */
+    if (seqId == null)
+    {
+      int seqToGet = index > 0 ? index : 0;
+      sequence = pdbAlignment.getSequenceAt(seqToGet);
+      Console.debug("***** Got sequence at index " + seqToGet + ": "
+              + (sequence == null ? null : sequence.getName()));
+    }
+    else
+    {
+      Console.debug("***** Looking for sequence with id '" + seqId + "'");
+
+      SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
+      if (sequences == null || sequences.length < 1)
+      {
+        Console.warn("Could not find sequence with id '" + seqId
+                + "' to attach pAE matrix to. Ignoring matrix.");
+        return false;
+      }
+      else
+      {
+        sequence = sequences[0]; // just use the first sequence with this seqId
+      }
+    }
+    ContactMatrixI matrix = new PAEContactMatrix(sequence,
             (Map<String, Object>) pae_obj.get(0));
 
-    AlignmentAnnotation cmannot = pdbAlignment.getSequenceAt(0)
-            .addContactList(matrix);
+    AlignmentAnnotation cmannot = sequence.addContactList(matrix);
     pdbAlignment.addAnnotation(cmannot);
     return true;
   }