Clean up logging system

[jabaws.git] / runner / compbio / runner / Util.java

diff --git a/runner/compbio/runner/Util.java b/runner/compbio/runner/Util.java
index f9106ca..a0123a2 100644 (file)
--- a/runner/compbio/runner/Util.java
+++ b/runner/compbio/runner/Util.java
@@ -20,54 +20,33 @@ package compbio.runner;
 \r
 import java.io.File;\r
 import java.io.FileInputStream;\r
-import java.io.FileReader;\r
-import java.io.BufferedReader;\r
 import java.io.FileNotFoundException;\r
 import java.io.FileOutputStream;\r
 import java.io.IOException;\r
-import java.util.Arrays;\r
 import java.util.List;\r
-import java.util.ArrayList;\r
 import java.util.Map;\r
-import java.util.Set;\r
-import java.util.TreeSet;\r
-import java.util.TreeMap;\r
-import java.util.regex.Pattern;\r
-import java.util.regex.Matcher;\r
-import java.util.Scanner;\r
-\r
-\r
 \r
 import org.apache.log4j.Logger;\r
 \r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.ClustalAlignmentUtil;\r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAStruct;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
 import compbio.data.sequence.Score;\r
-import compbio.data.sequence.ScoreManager;\r
-import compbio.data.sequence.Range;\r
 import compbio.data.sequence.RNAStructReader;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.ConfExecutable;\r
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.Executable;\r
-import compbio.engine.conf.PropertyHelperManager;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.PresetManager;\r
 import compbio.metadata.RunnerConfig;\r
-import compbio.util.PropertyHelper;\r
 \r
 public final class Util {\r
 \r
        public static Logger log = Logger.getLogger(Util.class);\r
 \r
-       private static final PropertyHelper ph = PropertyHelperManager\r
-                       .getPropertyHelper();\r
-\r
-       public static final String SPACE = " ";\r
-\r
        public static synchronized <T> RunnerConfig<T> getSupportedOptions(\r
                        Class<? extends Executable<T>> clazz) {\r
                try {\r
@@ -132,7 +111,6 @@ public final class Util {
 \r
        public static void writeInput(List<FastaSequence> sequences,\r
                        ConfiguredExecutable<?> exec) throws JobSubmissionException {\r
-\r
                try {\r
                        File filein = new File(exec.getInput());\r
                        FileOutputStream fout = new FileOutputStream(filein);\r
@@ -147,7 +125,7 @@ public final class Util {
                                                        + e.getLocalizedMessage(), e);\r
                }\r
        }\r
-       \r
+\r
        public static void writeClustalInput(List<FastaSequence> sequences,\r
                        ConfiguredExecutable<?> exec, char gapChar) throws JobSubmissionException {\r
                \r
@@ -166,8 +144,7 @@ public final class Util {
                }\r
        }\r
 \r
-       \r
-       public static ScoreManager readRNAStruct(String workDirectory,\r
+       public static RNAStructScoreManager readRNAStruct(String workDirectory,\r
                        String structFile) throws IOException, FileNotFoundException {\r
                \r
                assert !compbio.util.Util.isEmpty(workDirectory);\r
@@ -195,28 +172,7 @@ public final class Util {
                                        new FileInputStream(aliFile));\r
                }\r
        }\r
-       \r
 \r
-       \r
-       public static String readFile(File inputFile) throws \r
-                       FileNotFoundException, IOException {\r
-\r
-               BufferedReader input    = new BufferedReader(new FileReader(inputFile));\r
-\r
-               String file = new String();\r
-               String line = new String();\r
-\r
-               while (true) {\r
-                       line = input.readLine();\r
-\r
-                       if (line != null) {\r
-                               file = file + line + "\r\n";\r
-                       } else break;\r
-               }\r
-               // Close file\r
-               input.close();\r
-               return file;\r
-       }\r
 }\r
 \r
 \r