-package compbio.runner.structure;
-
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-
-//imports for filereader method
-import java.io.FileReader;
-import java.io.BufferedReader;
-import java.io.File;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.PipedExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
-
-
-import compbio.engine.client.CommandBuilder;
-
-public class RNAalifold extends SkeletalExecutable<RNAalifold>
- implements PipedExecutable<RNAalifold> {
-
-
- private static Logger log = Logger.getLogger(RNAalifold.class);
-
-
- @Override
- public RNAalifold setOutput(String outFile) {
- log.info("Set ouput file: " + outFile.toString());
- super.setOutput(outFile);
- return this;
- }
-
- @Override
- public RNAalifold setInput(String inFile) {
- log.info("Set input file: " + inFile.toString());
- cbuilder.setLast(inFile);
- super.setInput(inFile);
- return this;
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public Class<RNAalifold> getType() {
- return (Class<RNAalifold>) this.getClass();
- }
-
- @SuppressWarnings("unchecked")
- @Override
- // PlaceHolder method
- public String getResults(String workDirectory)
- throws ResultNotAvailableException {
- try {
- // System.out.print(readRNAStruct(workDirectory, getOutput()));
- return readRNAStruct(workDirectory, getOutput());
- } catch (FileNotFoundException e) {
- log.error(e.getMessage(), e.getCause());
- throw new ResultNotAvailableException(e);
- } catch (IOException e) {
- log.error(e.getMessage(), e.getCause());
- throw new ResultNotAvailableException(e);
- }
- }
-
-
- // Simple and generic methods for reading a whole file
- // Should surfice until a more detailed datamodel and parser are developed
- private static String readRNAStruct(String workDirectory,
- String structFile) throws IOException, FileNotFoundException {
- assert !compbio.util.Util.isEmpty(workDirectory);
- assert !compbio.util.Util.isEmpty(structFile);
- File sfile = new File(compbio.engine.client.Util.getFullPath(
- workDirectory, structFile));
- log.trace("RNAALIFOLD OUTPUT FILE PATH: " + sfile.getAbsolutePath());
- if(!(sfile.exists() && sfile.length() > 0)) {
- throw new FileNotFoundException("Result for the jobId "
- + workDirectory + "with file name " + structFile
- + " is not found!");
- }
- return readFile(sfile);
- }
-
- private static BufferedReader input;
- public static String readFile(File inputFile) throws
- FileNotFoundException, IOException {
-
- input = new BufferedReader(new FileReader(inputFile));
-
- String file = new String();
- String line = new String();
-
- while (true) {
- line = input.readLine();
-
- if (line != null) {
- file = file + line + "\r\n";
- } else break;
- }
- // Close file
- input.close();
- return file;
- }
-
-}
+package compbio.runner.structure;\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.RunnerUtil;\r
+\r
+public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
+ implements PipedExecutable<RNAalifold> {\r
+\r
+ private static Logger log = Logger.getLogger(RNAalifold.class);\r
+\r
+ // May not be necessary as defult is "<space>" but still dont know\r
+ // How to deal with different key value separators for different params\r
+ public static final String KEY_VALUE_SEPARATOR = " ";\r
+ \r
+ public RNAalifold() {\r
+ super(KEY_VALUE_SEPARATOR);\r
+ }\r
+ \r
+ @Override\r
+ public RNAalifold setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ return this;\r
+ }\r
+ \r
+ @Override\r
+ public RNAalifold setInput(String inFile) {\r
+ cbuilder.setLast(inFile);\r
+ super.setInput(inFile);\r
+ return this;\r
+ }\r
+ \r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<RNAalifold> getType() {\r
+ return (Class<RNAalifold>) this.getClass();\r
+ }\r
+ \r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public RNAStructScoreManager getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return RunnerUtil.readRNAStruct(workDirectory, getOutput());\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ }\r
+\r
+}\r
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