Clean up logging system

[jabaws.git] / runner / compbio / runner / disorder / IUPred.java

diff --git a/runner/compbio/runner/disorder/IUPred.java b/runner/compbio/runner/disorder/IUPred.java
index 5d20829..2092ab0 100644 (file)
--- a/runner/compbio/runner/disorder/IUPred.java
+++ b/runner/compbio/runner/disorder/IUPred.java
@@ -15,10 +15,7 @@
 package compbio.runner.disorder;\r
 \r
 import java.io.File;\r
-import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
 import java.util.Map;\r
 import java.util.Set;\r
 import java.util.TreeMap;\r
@@ -32,7 +29,6 @@ import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.Mafft;\r
 \r
 /**\r
  * iupred sequenceFile <short long glob >\r
@@ -48,7 +44,6 @@ public class IUPred extends SkeletalExecutable<IUPred> {
        private static final String SHORT_OUTPUT = "out.short";\r
        private static final String LONG_OUTPUT = "out.long";\r
 \r
-       \r
        @Override\r
        @SuppressWarnings("unchecked")\r
        public ScoreManager getResults(String workDirectory)\r
@@ -109,8 +104,6 @@ public class IUPred extends SkeletalExecutable<IUPred> {
                }\r
        }\r
 \r
-       \r
-       \r
        @Override\r
        public IUPred setInput(String inFile) {\r
                super.setInput(inFile);\r
@@ -118,7 +111,6 @@ public class IUPred extends SkeletalExecutable<IUPred> {
                return this;\r
        } \r
 \r
-               \r
        @Override\r
        public IUPred setOutput(String outFile) {\r
                log.warn("IUpred output is predefined and cannot be set!"); \r
@@ -130,6 +122,7 @@ public class IUPred extends SkeletalExecutable<IUPred> {
                                "are always either of those 3 files (depending on the method called): " + GLOB_OUTPUT + ", " \r
                                + SHORT_OUTPUT + ", "+ LONG_OUTPUT);\r
        }\r
+\r
        @Override\r
        public String getOutput() {\r
                log.warn("IUpred output is predefined and is one of the three files " +\r