JAL-3895 alphafold colours via pluggable annotation row builder. Also ensures min...

[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 ab6bbcc..05c3f7a 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,23 +20,11 @@
  */
 package jalview.ext.jmol;
 
-import java.util.Locale;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-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 java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 
@@ -49,6 +37,18 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+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.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -238,13 +238,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         else
         {
+          AnnotationRowBuilder builder = null;
           String tempFString = null;
           if (isAlphafoldModel())
           {
-            tempFString = "Alphafold Reliability";
+            builder = new AlphaFoldAnnotationRowBuilder();
           }
 
-          tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
+          tmpchain = new PDBChain(getId(), tmpatom.chain, builder);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }