\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
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