-/*\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
\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
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
// 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