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Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112
[jalview.git]
/
src
/
jalview
/
hmmer
/
HmmerCommand.java
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
b311b76
..
0240352
100644
(file)
--- 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
{
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
: 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;
{
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();
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, "/");
{
// the first backslash escapes '\' for the regular expression argument
path = path.replaceAll("\\" + File.separator, "/");