JAL-629 refactoring TFType. Remove i18n identification of 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 5575cb8..859ac05 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -43,11 +43,13 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
@@ -249,11 +251,11 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
             + "");
     UrlDownloadClient.download(paeURL, pae);
-    addAlphaFoldPAE(pdbAlignment, pae, 0, null);
+    addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
   }
 
-  public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
-          int index, String seqId)
+  public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+          File pae, int index, String seqId)
   {
     FileInputStream pae_input = null;
     try
@@ -286,6 +288,21 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
   }
 
+  public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+          File pae, int index, String structId)
+  {
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    if (ssm != null)
+    {
+      /*
+      ssm.setAddTempFacAnnot(showTemperatureFactor);
+      ssm.setProcessSecondaryStructure(showSecondaryStructure);
+      */
+    }
+
+  }
+
   /**
    * parses the given pAE matrix and adds it to sequence 0 in the given
    * alignment
@@ -336,7 +353,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
       Console.debug("***** Got sequence at index " + seqToGet + ": "
               + (sequence == null ? null : sequence.getName()));
     }
-    else
+    if (sequence == null)
     {
       Console.debug("***** Looking for sequence with id '" + seqId + "'");