X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;fp=src%2Fjalview%2Futil%2FDBRefUtils.java;h=197261ac154716b46c73f097d2aa58b160e51f01;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=fb54bbabaad9e6585e5cee0eb3e20f8a91e8c3a2;hpb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index fb54bba..197261a 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -32,7 +32,6 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 import com.stevesoft.pat.Regex;
 
@@ -96,14 +95,14 @@ public class DBRefUtils
 	}
 
 	// BH TODO (what?)
-	HashSet<String> srcs = new HashSet<String>();
+	HashSet<String> srcs = new HashSet<>();
 	for (String src : sources) 
 	{
 	  srcs.add(src.toUpperCase());
 	}
 
 	int nrefs = dbrefs.size();
-	List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+	List<DBRefEntry> res = new ArrayList<>();
 	for (int ib = 0; ib < nrefs; ib++) 
 	{
 	  DBRefEntry dbr = dbrefs.get(ib);
@@ -217,7 +216,7 @@ public class DBRefUtils
 	 * @return
 	 */
 	public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
-		List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+		List<DBRefEntry> rfs = new ArrayList<>();
 		if (refs == null || accId == null) {
 			return rfs;
 		}
@@ -243,7 +242,7 @@ public class DBRefUtils
 	 * @return
 	 */
 	static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
-		List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+		List<DBRefEntry> rfs = new ArrayList<>();
 		if (refs == null || entry == null) {
 			return rfs;
 		}
@@ -450,6 +449,14 @@ public class DBRefUtils
     return matches;
   }
 
+  private static Regex PARSE_REGEX;
+
+  private static Regex getParseRegex()
+  {
+    return (PARSE_REGEX == null ? PARSE_REGEX = Platform.newRegex(
+            "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)", null)
+            : PARSE_REGEX);
+  }
 	/**
 	 * Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
 	 * database is PDB.
@@ -471,7 +478,7 @@ public class DBRefUtils
 				/*
 				 * Check for PFAM style stockhom PDB accession id citation e.g. "1WRI A; 7-80;"
 				 */
-				Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
+        Regex r = getParseRegex();
 				if (r.search(acn.trim())) {
 					String pdbid = r.stringMatched(1);
 					String chaincode = r.stringMatched(2);
@@ -558,7 +565,7 @@ public class DBRefUtils
 	 * @return
 	 */
 	public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
-		List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+		List<DBRefEntry> matches = new ArrayList<>();
 		if (dbRefs != null && source != null) {
 			for (DBRefEntry dbref : dbRefs) {
 				if (source.equalsIgnoreCase(dbref.getSource())) {
@@ -621,7 +628,9 @@ public class DBRefUtils
 		bsSelect.set(0, dbrefs.size());
 
 		if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
-			return;
+    {
+      return;
+    }
 
 //      selfs.addAll(selfArray);
 //    }
@@ -631,7 +640,9 @@ public class DBRefUtils
 			DBRefEntry p = pr.get(ip);
 			for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) {
 				if (dbrefs.get(i) == p)
-					bsSelect.clear(i);
+        {
+          bsSelect.clear(i);
+        }
 			}
 //      while (selfs.contains(p))
 //      {
@@ -655,7 +666,9 @@ public class DBRefUtils
 				// TODO: promote transcript refs ??
 			}
 			if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
-				return;
+      {
+        return;
+      }
 //      if (candidates != null)
 			{
 				for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))