JAL-629 implementation of --tempfac options

[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..9306388 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -40,6 +40,7 @@ import com.stevesoft.pat.Regex;
 import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -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,
+          AlignmentAnnotation.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()
+                  || this.getTemperatureFactorType() == AlignmentAnnotation.TFType.PLDDT)
           {
             builder = new AlphaFoldAnnotationRowBuilder();
           }