Merge branch 'bug/JAL-2541cutWithFeatures' into features/JAL-2446NCList

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index af6592b..9f3e7b8 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -36,6 +36,8 @@ import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
@@ -47,6 +49,11 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class Sequence extends ASequence implements SequenceI
 {
+  private static final Regex limitrx = new Regex(
+          "[/][0-9]{1,}[-][0-9]{1,}$");
+
+  private static final Regex endrx = new Regex("[0-9]{1,}$");
+
   SequenceI datasetSequence;
 
   String name;
@@ -129,11 +136,6 @@ public class Sequence extends ASequence implements SequenceI
     checkValidRange();
   }
 
-  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-          "[/][0-9]{1,}[-][0-9]{1,}$");
-
-  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
-
   void parseId()
   {
     if (name == null)
@@ -235,23 +237,28 @@ public class Sequence extends ASequence implements SequenceI
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
-    {
-      char[] oseq = seq.getSequence();
-      initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(), seq.getEnd());
-    }
+    char[] oseq = seq.getSequence();
+    initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+            seq.getStart(), seq.getEnd());
+
     description = seq.getDescription();
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
     }
-    if (datasetSequence == null && seq.getDBRefs() != null)
+    
+    /*
+     * only copy DBRefs and seqfeatures if we really are a dataset sequence
+     */
+    if (datasetSequence == null)
     {
-      // only copy DBRefs and seqfeatures if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRefs();
-      for (int i = 0; i < dbr.length; i++)
+      if (seq.getDBRefs() != null)
       {
-        addDBRef(new DBRefEntry(dbr[i]));
+        DBRefEntry[] dbr = seq.getDBRefs();
+        for (int i = 0; i < dbr.length; i++)
+        {
+          addDBRef(new DBRefEntry(dbr[i]));
+        }
       }
       if (seq.getSequenceFeatures() != null)
       {
@@ -262,6 +269,7 @@ public class Sequence extends ASequence implements SequenceI
         }
       }
     }
+
     if (seq.getAnnotation() != null)
     {
       AlignmentAnnotation[] sqann = seq.getAnnotation();
@@ -1245,11 +1253,11 @@ public class Sequence extends ASequence implements SequenceI
       return null;
     }
 
-    Vector subset = new Vector();
-    Enumeration e = annotation.elements();
+    Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+    Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
-      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      AlignmentAnnotation ann = e.nextElement();
       if (ann.label != null && ann.label.equals(label))
       {
         subset.addElement(ann);
@@ -1264,7 +1272,7 @@ public class Sequence extends ASequence implements SequenceI
     e = subset.elements();
     while (e.hasMoreElements())
     {
-      anns[i++] = (AlignmentAnnotation) e.nextElement();
+      anns[i++] = e.nextElement();
     }
     subset.removeAllElements();
     return anns;
@@ -1335,10 +1343,10 @@ public class Sequence extends ASequence implements SequenceI
     // transfer PDB entries
     if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getAllPDBEntries().elements();
+      Enumeration<PDBEntry> e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
-        PDBEntry pdb = (PDBEntry) e.nextElement();
+        PDBEntry pdb = e.nextElement();
         addPDBId(pdb);
       }
     }