AAConWS further work

[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 49c87d4..f43db89 100644 (file)
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -25,6 +25,7 @@ import java.util.List;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.sequence.SMERFSConstraints;\r
 import compbio.data.sequence.Score;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.engine.client.CommandBuilder;\r
@@ -61,6 +62,10 @@ 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
@@ -97,7 +102,7 @@ public class AACon extends SkeletalExecutable<AACon> {
                                                        + "and initialize it with the location of jronn jar file");\r
                }\r
                if (new File(settings).isAbsolute()) {\r
-                       // Jronn jar can be found so no actions necessary\r
+                       // the jar can be found so no actions necessary\r
                        // no further actions is necessary\r
                        return settings;\r
                }\r