From a1115830030081f29593da857b28ec46581b6e09 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 21 Jan 2008 16:57:16 +0000 Subject: [PATCH] fix regex for annotation subtype to use non-whitespace presence rather than word boundary tokens --- src/jalview/io/StockholmFile.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index e7b1c6e..bac1916 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -97,7 +97,7 @@ public class StockholmFile extends AlignFile rend = new Regex("\\/\\/"); // Find the end of an alignment p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in // id/from/to - s = new Regex("(\\S+)\\s+(\\w{2})\\s+(.*)"); // Parses annotation subtype + s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence @@ -432,7 +432,8 @@ public class StockholmFile extends AlignFile } else { - throw new IOException("Error parsing " + line); + System.err.println("Warning - couldn't parse sequence annotation row line:\n"+line); + // throw new IOException("Error parsing " + line); } } else -- 1.7.10.2