Refactoring: rename duplicated Util classes

[jabaws.git] / runner / compbio / runner / conservation / AACon.java

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index 0f96077..9ff6549 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -28,12 +28,12 @@ import java.util.List;
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.data.sequence.SMERFSConstraints;\r
 import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
+import compbio.engine.client.EngineUtil;\r
 import compbio.metadata.ResultNotAvailableException;\r
 \r
 /**\r
@@ -59,10 +59,6 @@ public class AACon extends SkeletalExecutable<AACon> {
        public static final String KEY_VALUE_SEPARATOR = "=";\r
        public static final String STAT_FILE = "stat.txt";\r
 \r
-       private final int windowWidth = SMERFSConstraints.DEFAULT_WINDOW_SIZE;\r
-       private final SMERFSConstraints colScoreMethod = SMERFSConstraints.MID_SCORE;\r
-       private final double gapTreshold = SMERFSConstraints.DEFAULT_GAP_THRESHOLD;\r
-\r
        public AACon() {\r
                addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,\r
                                "-f=RESULT_NO_ALIGNMENT"));\r
@@ -104,7 +100,7 @@ public class AACon extends SkeletalExecutable<AACon> {
                        // no further actions is necessary\r
                        return settings;\r
                }\r
-               return compbio.engine.client.Util.convertToAbsolute(settings);\r
+               return EngineUtil.convertToAbsolute(settings);\r
        }\r
 \r
        @Override\r