Refactoring: rename duplicated Util classes

[jabaws.git] / testsrc / compbio / runner / predictors / JpredTester.java

diff --git a/testsrc/compbio/runner/predictors/JpredTester.java b/testsrc/compbio/runner/predictors/JpredTester.java
index b1b991f..1bf753b 100644 (file)
--- a/testsrc/compbio/runner/predictors/JpredTester.java
+++ b/testsrc/compbio/runner/predictors/JpredTester.java
@@ -47,7 +47,7 @@ import compbio.engine.client.ConfExecutable;
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.RunConfiguration;\r
-import compbio.engine.cluster.drmaa.ClusterUtil;\r
+import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
 import compbio.engine.cluster.drmaa.JobRunner;\r
 import compbio.engine.cluster.drmaa.StatisticManager;\r
 import compbio.engine.local.LocalRunner;\r
@@ -61,7 +61,7 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.RunnerConfig;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
 import compbio.util.FileWatcher;\r
 import compbio.util.SysPrefs;\r
 \r
@@ -85,7 +85,7 @@ public class JpredTester {
        public void RunOnCluster() {\r
                assertFalse(SysPrefs.isWindows, "Cluster execution can only be in unix environment");\r
                try {\r
-                       PresetManager<Jpred> jpredPreset = Util.getPresets(Jpred.class);\r
+                       PresetManager<Jpred> jpredPreset = RunnerUtil.getPresets(Jpred.class);\r
                        assert jpredPreset != null;\r
                        ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Cluster);\r
                        Preset<Jpred> conf = jpredPreset.getPresetByName("cluster configuration");\r
@@ -104,7 +104,7 @@ public class JpredTester {
                                String exits = sm.getExitStatus();\r
                                assertNotNull("Exit status is null", exits);\r
                                // cut 4 trailing zeros from the number\r
-                               int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();\r
+                               int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits).intValue();\r
                                assertEquals(0, exitsInt);\r
                                System.out.println(sm.getAllStats());\r
                        } catch (ParseException e) {\r
@@ -194,7 +194,7 @@ public class JpredTester {
        public void RunLocallyWithPreset() {\r
                try {\r
                        ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);\r
-                       PresetManager<Jpred> preset = Util.getPresets(Jpred.class);\r
+                       PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);\r
                        assert preset != null;\r
                        Preset<Jpred> conf = preset.getPresetByName("laptop configuration");\r
                        confpred.addParameters(conf.getOptions());\r
@@ -227,7 +227,7 @@ public class JpredTester {
                        jpred.setInput(test_input);\r
                        jpred.setOutput(test_output);\r
                        ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(jpred, Executable.ExecProvider.Local);\r
-                       PresetManager<Jpred> preset = Util.getPresets(Jpred.class);\r
+                       PresetManager<Jpred> preset = RunnerUtil.getPresets(Jpred.class);\r
                        assert preset != null;\r
                        Preset<Jpred> conf = preset.getPresetByName("laptop configuration");\r
                        confpred.addParameters(conf.getOptions());\r