From: gmungoc Date: Wed, 27 Mar 2019 17:06:12 +0000 (+0000) Subject: JAL-2620 improved error reporting on failure to load resource files X-Git-Tag: Release_2_11_0~17^2~29 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c491024e7256817870ff7d53f35ea55db045681d;p=jalview.git JAL-2620 improved error reporting on failure to load resource files --- 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)