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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
{
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)
public PDBfile(boolean addAlignmentAnnotations,
boolean predictSecondaryStructure, boolean externalSecStr)
@@
-77,15
+77,15
@@
public class PDBfile extends StructureFile
setId(safeName(getDataName()));
setChains(new Vector<PDBChain>());
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 = "";
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
boolean terFlag = false;
String lastID = "";
- int indexx = 0;
+ // int indexx = 0;
String atomnam = null;
try
{
String atomnam = null;
try
{