JAL-629 Removal of unnecessary methods. Set pLTTD tempfac for EBIAlfafold. Simplify...

[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 969d195..f0e477c 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -230,9 +230,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        Console.debug("##### DATASOURCETYPE=" + getDataSourceType());
-        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF
-                && getDataSourceType() == DataSourceType.URL);
+        setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -303,31 +301,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
       }
       // add a PAEMatrix if set (either by above or otherwise)
-      Console.debug("##### hasPAEMatrix()=" + hasPAEMatrix());
-      Console.debug("##### isAlphafoldModel()=" + isAlphafoldModel());
-      Console.debug("##### getPAEMatrix()=" + getPAEMatrix());
       if (hasPAEMatrix())
       {
         Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
-        if (isAlphafoldModel())
-        {
-          EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
-                  null, false, false);
-        }
-        else
-        {
-          EBIAlfaFold.addPAEToStructure(null, this.getInFile(),
-                  new File(this.getPAEMatrix()));
-        }
+        EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
+                null, false, false);
 
-        Console.debug("##### al.getAlignmentAnnotation()="
-                + al.getAlignmentAnnotation());
         if (al.getAlignmentAnnotation() != null)
         {
           for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
           {
-            Console.debug("##### Adding to alann" + alann.annotationId + "("
-                    + alann.getCalcId() + ")");
             annotations.add(alann);
           }
         }