From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 6 Jun 2018 10:07:28 +0000 (+0100)
Subject: JAL-3020 limit cache size; handle applet exception
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e31d010863ff0cb2ad9804cf6a2e3a8d388cb07c;p=jalview.git

JAL-3020 limit cache size; handle applet exception
---

diff --git a/src/jalview/datamodel/features/FeatureAttributes.java b/src/jalview/datamodel/features/FeatureAttributes.java
index 833c704..64a13d7 100644
--- a/src/jalview/datamodel/features/FeatureAttributes.java
+++ b/src/jalview/datamodel/features/FeatureAttributes.java
@@ -34,6 +34,7 @@ public class FeatureAttributes
 
   /*
    * default value if property is not specified
+   * (selected VCF/VEP terms which have 'categorical' value ranges)
    */
   private static final String CACHED_ATTS_DEFAULT = "AS_FilterStatus,clinical_significance,consequence_type,"
           + "CSQ:Consequence,CSQ:CLIN_SIG,CSQ:DOMAIN,CSQ:IMPACT";
@@ -43,6 +44,11 @@ public class FeatureAttributes
    */
   private static final String TERM_DELIMITERS = ",&";
 
+  /*
+   * defensive limit to number of attribute values cached per attribute
+   */
+  private static final int MAX_ATT_VALS = 30;
+
   private static FeatureAttributes instance = new FeatureAttributes();
 
   /*
@@ -225,10 +231,12 @@ public class FeatureAttributes
       {
         terms = new HashSet<>();
       }
+      int count = terms.size();
       StringTokenizer st = new StringTokenizer(value, TERM_DELIMITERS);
-      while (st.hasMoreTokens())
+      while (st.hasMoreTokens() && count < MAX_ATT_VALS)
       {
         terms.add(st.nextToken().trim());
+        count++;
       }
     }
 
@@ -341,7 +349,14 @@ public class FeatureAttributes
    */
   public static List<Pattern> getFieldMatchers(String key, String def)
   {
-    String pref = Cache.getDefault(key, def);
+    String pref = def;
+    try
+    {
+      // temporary for applet: handle class loading errors...
+      pref = Cache.getDefault(key, def);
+    } catch (Throwable t)
+    {
+    }
     List<Pattern> patterns = new ArrayList<>();
     String[] tokens = pref.split(",");
     for (String token : tokens)