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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
hmmer
/
HmmerCommand.java
diff --git
a/src/jalview/hmmer/HmmerCommand.java
b/src/jalview/hmmer/HmmerCommand.java
index
e241008
..
9db0ae1
100644
(file)
--- a/
src/jalview/hmmer/HmmerCommand.java
+++ b/
src/jalview/hmmer/HmmerCommand.java
@@
-3,6
+3,7
@@
package jalview.hmmer;
import jalview.analysis.SeqsetUtils;
import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
import jalview.analysis.SeqsetUtils;
import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-196,8
+197,8
@@
public abstract class HmmerCommand implements Runnable
int exitValue = p.exitValue();
if (exitValue != 0)
{
int exitValue = p.exitValue();
if (exitValue != 0)
{
- Cache.log.error("Command failed, return code = " + exitValue);
- Cache.log.error("Command/args were: " + args.toString());
+ Console.error("Command failed, return code = " + exitValue);
+ Console.error("Command/args were: " + args.toString());
}
return exitValue == 0; // 0 is success, by convention
} catch (Exception e)
}
return exitValue == 0; // 0 is success, by convention
} catch (Exception e)
@@
-220,7
+221,7
@@
public abstract class HmmerCommand implements Runnable
Cache.getProperty(Preferences.CYGWIN_PATH));
if (bash == null)
{
Cache.getProperty(Preferences.CYGWIN_PATH));
if (bash == null)
{
- Cache.log.error("Cygwin shell not found");
+ Console.error("Cygwin shell not found");
return commands;
}
return commands;
}