X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHmmerCommand.java;fp=src%2Fjalview%2Fhmmer%2FHmmerCommand.java;h=02403525aef6d62ebac586a2414b71a314e6b467;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=b311b760ccbe1be9a84637910cfd2a0200ffb76c;hpb=3609d4b908fa64cab35f2348401baab3347188fc;p=jalview.git

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index b311b76..0240352 100644
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -154,14 +154,14 @@ public abstract class HmmerCommand implements Runnable
   public boolean runCommand(List<String> commands)
           throws IOException
   {
-    List<String> args = Platform.isWindows() ? wrapWithCygwin(commands)
+    List<String> args = Platform.isWindowsAndNotJS() ? wrapWithCygwin(commands)
             : commands;
 
     try
     {
       ProcessBuilder pb = new ProcessBuilder(args);
       pb.redirectErrorStream(true); // merge syserr to sysout
-      if (Platform.isWindows())
+      if (Platform.isWindowsAndNotJS())
       {
         String path = pb.environment().get("Path");
         path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path;
@@ -436,7 +436,7 @@ public abstract class HmmerCommand implements Runnable
   protected String getFilePath(File resultFile, boolean isInCygwin)
   {
     String path = resultFile.getAbsolutePath();
-    if (Platform.isWindows() && isInCygwin)
+    if (Platform.isWindowsAndNotJS() && isInCygwin)
     {
       // the first backslash escapes '\' for the regular expression argument
       path = path.replaceAll("\\" + File.separator, "/");