JAL-3438 spotless for 2.11.2.0

[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 2a43244..ab6bbcc 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -117,9 +117,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // }
       // ;
       // instead, we distinguish .cif from non-.cif by filename
-      setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
-              ? PDBEntry.Type.MMCIF.toString()
-              : "PDB");
+      setStructureFileType(
+              getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
+                      ? PDBEntry.Type.MMCIF.toString()
+                      : "PDB");
 
       transformJmolModelToJalview(jmolModel.ms);
     }
@@ -140,7 +141,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
          * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
          * see http://wiki.jmol.org/index.php/Jmol_Application
          */
-        
+
         viewer = JalviewJmolBinding.getJmolData(this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
         viewer.setBooleanProperty("defaultStructureDSSP", true);
@@ -154,28 +155,32 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
     return viewer;
   }
-  
+
   public static Regex getNewAlphafoldValidator()
   {
-    Regex validator =  new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
     validator.setIgnoreCase(true);
     return validator;
   }
 
-  PDBEntry.Type jmolFiletype=null;
+  PDBEntry.Type jmolFiletype = null;
+
   /**
-   * resolve a jmol filetype string and update the jmolFiletype field accordingly
+   * resolve a jmol filetype string and update the jmolFiletype field
+   * accordingly
+   * 
    * @param jmolIdentifiedFileType
    * @return true if filetype was identified as MMCIF, PDB
    */
   public boolean updateFileType(String jmolIdentifiedFileType)
   {
-    if (jmolIdentifiedFileType == null 
+    if (jmolIdentifiedFileType == null
             || jmolIdentifiedFileType.trim().equals(""))
     {
       return false;
     }
-    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType))
+    {
       jmolFiletype = PDBEntry.Type.MMCIF;
       return true;
     }
@@ -183,10 +188,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       jmolFiletype = PDBEntry.Type.PDB;
       return true;
-    } 
+    }
     return false;
   }
-  
+
   public void transformJmolModelToJalview(ModelSet ms) throws IOException
   {
     try
@@ -203,9 +208,9 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setStructureFileType(jmolFiletype.toString());
       }
-      
+
       isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
-      
+
       if (pdbId == null)
       {
         setId(safeName(getDataName()));
@@ -215,7 +220,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;  
+        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
 
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
@@ -230,15 +235,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         if (tmpchain != null)
         {
           tmpchain.atoms.addElement(tmpatom);
-        } else
+        }
+        else
         {
-          String tempFString=null;
+          String tempFString = null;
           if (isAlphafoldModel())
           {
             tempFString = "Alphafold Reliability";
           }
 
-          tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
+          tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }