Refactoring: rename duplicated Util classes

[jabaws.git] / runner / compbio / runner / RunnerUtil.java

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/RunnerUtil.java
similarity index 90%
rename from runner/compbio/runner/Util.java
rename to runner/compbio/runner/RunnerUtil.java
index f8d7b80..5d02a18 100644 (file)
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/RunnerUtil.java
@@ -39,13 +39,14 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.ConfExecutable;\r
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.Executable;\r
+import compbio.engine.client.EngineUtil;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.PresetManager;\r
 import compbio.metadata.RunnerConfig;\r
 \r
-public final class Util {\r
+public final class RunnerUtil {\r
 \r
-       public static Logger log = Logger.getLogger(Util.class);\r
+       public static Logger log = Logger.getLogger(RunnerUtil.class);\r
 \r
        public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
                        Class<? extends Executable<T>> clazz) {\r
@@ -75,7 +76,7 @@ public final class Util {
                                throws UnknownFileFormatException, IOException, FileNotFoundException, NullPointerException {\r
                assert !compbio.util.Util.isEmpty(workDirectory);\r
                assert !compbio.util.Util.isEmpty(clustFile);\r
-               File cfile = new File(compbio.engine.client.Util.getFullPath(workDirectory, clustFile));\r
+               File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));\r
                log.trace("CLUSTAL OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
                if (!(cfile.exists() && cfile.length() > 0)) {\r
                        throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");\r
@@ -88,8 +89,7 @@ public final class Util {
                        FileNotFoundException, NullPointerException {\r
                assert !compbio.util.Util.isEmpty(workDirectory);\r
                assert !compbio.util.Util.isEmpty(clustFile);\r
-               File cfile = new File(compbio.engine.client.Util.getFullPath(\r
-                               workDirectory, clustFile));\r
+               File cfile = new File(EngineUtil.getFullPath(workDirectory, clustFile));\r
                log.trace("Jronn OUTPUT FILE PATH: " + cfile.getAbsolutePath());\r
                if (!(cfile.exists() && cfile.length() > 0)) {\r
                        throw new FileNotFoundException("Result for the jobId " + workDirectory + " with file name " + clustFile + " is not found!");\r
@@ -131,9 +131,9 @@ public final class Util {
                assert !compbio.util.Util.isEmpty(workDirectory);\r
                assert !compbio.util.Util.isEmpty(structFile);\r
                // The stdout from RNAalifold\r
-               File sFile = new File(compbio.engine.client.Util.getFullPath( workDirectory, structFile));\r
+               File sFile = new File(EngineUtil.getFullPath( workDirectory, structFile));\r
                // Base pair probability matrix (-p option)\r
-               File aliFile = new File(compbio.engine.client.Util.getFullPath( workDirectory, "alifold.out"));\r
+               File aliFile = new File(EngineUtil.getFullPath( workDirectory, "alifold.out"));\r
                // Check that stdout file exists\r
                if(!(sFile.exists() && sFile.length() > 0)) {\r
                        throw new FileNotFoundException("Result for the jobId " + workDirectory + "with file name " + structFile + " is not found!");\r