Clean up logging system

[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 366b95f..d34bb09 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -1,15 +1,19 @@
-/*\r
- * Copyright (c) 2009 Peter Troshin JAva Bioinformatics Analysis Web Services\r
- * (JABAWS) @version: 1.0 This library is free software; you can redistribute it\r
- * and/or modify it under the terms of the Apache License version 2 as published\r
- * by the Apache Software Foundation This library is distributed in the hope\r
- * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
- * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * Apache License for more details. A copy of the license is in\r
- * apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
- * derived work distributed in source code form must include this copyright and\r
- * license notice.\r
+/* Copyright (c) 2011 Peter Troshin\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
+ * \r
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ *  Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ *  License for more details.\r
+ * \r
+ *  A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
  */\r
 \r
 package compbio.runner.conservation;\r
@@ -24,7 +28,6 @@ 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
@@ -55,10 +58,6 @@ 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
@@ -124,8 +123,8 @@ public class AACon extends SkeletalExecutable<AACon> {
 \r
        @SuppressWarnings("unchecked")\r
        @Override\r
-       public Class<Executable<AACon>> getType() {\r
-               return (Class<Executable<AACon>>) this.getClass();\r
+       public Class<AACon> getType() {\r
+               return (Class<AACon>) this.getClass();\r
        }\r
 \r
        public static String getStatFile() {\r