JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred...

[jalview.git] / src / jalview / ext / jmol / JmolParser.java

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 05c3f7a..269fc31 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -37,18 +37,21 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.annotations.AnnotationRowBuilder.AlphaFoldAnnotationRowBuilder;
-import jalview.datamodel.annotations.AnnotationRowBuilder.AnnotationRowBuilder;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
+import jalview.datamodel.annotations.AnnotationRowBuilder;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -278,6 +281,28 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           createAnnotation(chainseq, chain, ms.at);
         }
       }
+      if (isAlphafoldModel())
+      {
+        // TODO - work out how to handle different ways that pAE is provided
+        //
+        try
+        {
+          Console.info("retrieving pAE for " + pdbId);
+          Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+          EBIAlfaFold.retrieve_AlphaFold_pAE(pdbId, al, null);
+          if (al.getAlignmentAnnotation() != null)
+          {
+            for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+            {
+              annotations.add(alann);
+            }
+          }
+          ;
+        } catch (Throwable t)
+        {
+          Console.error("Couldn't get the pAE for " + pdbId, t);
+        }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println(
@@ -442,8 +467,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         try
         {
-          asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
-                  secstrcode[p], Float.NaN);
+          asecstr[p] = new Annotation(null, null, secstrcode[p], Float.NaN);
           ssFound = true;
         } catch (Exception e)
         {