JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / mc_view / PDBfile.java

diff --git a/src/mc_view/PDBfile.java b/src/mc_view/PDBfile.java
index 04eda42..d3e14c7 100755 (executable)
--- a/src/mc_view/PDBfile.java
+++ b/src/mc_view/PDBfile.java
@@ -36,7 +36,7 @@ import java.util.Vector;
 
 public class PDBfile extends StructureFile
 {
-  private static String CALC_ID_PREFIX = "JalviewPDB";
+  private final static String CALC_ID_PREFIX = "JalviewPDB";
 
   public PDBfile(boolean addAlignmentAnnotations,
           boolean predictSecondaryStructure, boolean externalSecStr)
@@ -77,15 +77,15 @@ public class PDBfile extends StructureFile
     setId(safeName(getDataName()));
 
     setChains(new Vector<PDBChain>());
-    List<SequenceI> rna = new ArrayList<SequenceI>();
-    List<SequenceI> prot = new ArrayList<SequenceI>();
+    List<SequenceI> rna = new ArrayList<>();
+    List<SequenceI> prot = new ArrayList<>();
     PDBChain tmpchain;
     String line = null;
     boolean modelFlag = false;
     boolean terFlag = false;
     String lastID = "";
 
-    int indexx = 0;
+    // int indexx = 0;
     String atomnam = null;
     try
     {