Merge branch 'features/JAL-3858_PAEsInProjects' into develop

[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 269fc31..2bc4869 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -49,6 +49,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.EBIAlfaFold;
@@ -73,12 +74,19 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     // BH 2018 File or String for filename
     super(immediate, inFile, sourceType);
+
   }
 
   public JmolParser(Object inFile, DataSourceType sourceType)
           throws IOException
   {
-    super(inFile, sourceType);
+    this(inFile, sourceType, null);
+  }
+
+  public JmolParser(Object inFile, DataSourceType sourceType,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+    super(inFile, sourceType, tempfacType);
   }
 
   public JmolParser(FileParse fp) throws IOException
@@ -243,7 +251,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         {
           AnnotationRowBuilder builder = null;
           String tempFString = null;
-          if (isAlphafoldModel())
+          if (isAlphafoldModel() || StructureImportSettings.TFType.PLDDT
+                  .equals(getTemperatureFactorType()))
           {
             builder = new AlphaFoldAnnotationRowBuilder();
           }
@@ -312,6 +321,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
+  public void setAlphafoldModel(boolean afm)
+  {
+    alphaFoldModel = afm;
+  }
+
   private boolean isAlphafoldModel()
   {
     return alphaFoldModel;