From c491024e7256817870ff7d53f35ea55db045681d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 27 Mar 2019 17:06:12 +0000
Subject: [PATCH 1/1] JAL-2620 improved error reporting on failure to load
 resource files

---
 src/jalview/analysis/GeneticCodes.java |   28 ++++++++++++++++++++++++++--
 1 file changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/GeneticCodes.java b/src/jalview/analysis/GeneticCodes.java
index d07253e..137b7f8 100644
--- a/src/jalview/analysis/GeneticCodes.java
+++ b/src/jalview/analysis/GeneticCodes.java
@@ -65,7 +65,7 @@ public final class GeneticCodes
       loadAmbiguityCodes(AMBIGUITY_CODES_FILE);
       loadCodes(RESOURCE_FILE);
     }
-  };
+  }
 
   /**
    * Returns the singleton instance of this class
@@ -117,6 +117,11 @@ public final class GeneticCodes
     try
     {
       InputStream is = getClass().getResourceAsStream(fileName);
+      if (is == null)
+      {
+        System.err.println("Resource file not found: " + fileName);
+        return;
+      }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
 
       /*
@@ -136,9 +141,15 @@ public final class GeneticCodes
     } catch (IOException | NullPointerException e)
     {
       Cache.log.error(
-              "Error reading genetic codes data file: "
+              "Error reading genetic codes data file " + fileName + ": "
               + e.getMessage());
     }
+    if (codeTables.isEmpty())
+    {
+      System.err.println(
+              "No genetic code tables loaded, check format of file "
+                      + fileName);
+    }
   }
 
   /**
@@ -157,6 +168,11 @@ public final class GeneticCodes
     try
     {
       InputStream is = getClass().getResourceAsStream(fileName);
+      if (is == null)
+      {
+        System.err.println("Resource file not found: " + fileName);
+        return;
+      }
       BufferedReader dataIn = new BufferedReader(new InputStreamReader(is));
       String line = "";
       while (line != null)
@@ -165,8 +181,16 @@ public final class GeneticCodes
         if (line != null && !"DNA".equals(line.toUpperCase()))
         {
           String[] tokens = line.split("\\t");
+          if (tokens.length == 2)
+          {
           ambiguityCodes.put(tokens[0].toUpperCase(),
                   tokens[1].toUpperCase());
+          }
+          else
+          {
+            System.err.println(
+                    "Unexpected data in " + fileName + ": " + line);
+          }
         }
       }
     } catch (IOException e)
-- 
1.7.10.2