-package compbio.runner.structure;
-
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.List;
-
-
-
-
-
-import org.apache.log4j.Logger;
-
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.RNAStruct;
-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);
-
- // May not be necessary as defult is "<space>" but still dont know
- // How to deal with different key value separators for different params
- public static final String KEY_VALUE_SEPARATOR = " ";
-
- public RNAalifold() {
- super(KEY_VALUE_SEPARATOR);
- }
-
- @Override
- public RNAalifold setOutput(String outFile) {
- super.setOutput(outFile);
- return this;
- }
-
- @Override
- public RNAalifold setInput(String inFile) {
- 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 ScoreManager getResults(String workDirectory)
- throws ResultNotAvailableException {
- try {
- return Util.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);
- }
- }
-
-
- // the new currently used methods for reading are found in
- // - compbio.data.sequence.SequenceUtil and
- // - compbio.runner.Util
-
- // Simple and generic methods for reading a whole file
-// 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
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+\r
+\r
+\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+\r
+import compbio.engine.client.CommandBuilder;\r
+\r
+public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
+ implements PipedExecutable<RNAalifold> {\r
+ \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 Util.readRNAStruct(workDirectory, getOutput());\r
+ \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
git://source.jalview.org / jabaws.git / blobdiff