X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=utils%2FHelpLinksChecker.java;h=dee5322a21eae3827ea448d34d11304615784da6;hb=fc77dfd068b74f1ba81927c098b97667eb01e255;hp=1279b314403927dd2511864ea19afb90091800d4;hpb=1eda02547f8519e1dff46dac06734cba6c77b97f;p=jalview.git

diff --git a/utils/HelpLinksChecker.java b/utils/HelpLinksChecker.java
index 1279b31..dee5322 100644
--- a/utils/HelpLinksChecker.java
+++ b/utils/HelpLinksChecker.java
@@ -282,9 +282,10 @@ public class HelpLinksChecker implements BufferedLineReader.LineCleaner
         else
         {
           internalHrefCount++;
+          String relFile = System.getProperty("os.name").indexOf("Win") > -1 ? href.replace("/", File.separator) : href;
           File hrefFile = href.equals("") ? htmlFile : new File(htmlFolder,
                   href);
-          if (hrefFile != htmlFile && !fileExists(hrefFile, href))
+          if (hrefFile != htmlFile && !fileExists(hrefFile, relFile))
           {
             badLink = true;
             invalidInternalHrefCount++;