-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
+/*\r
+ * Copyright (c) 2011 Peter Troshin JAva Bioinformatics Analysis Web Services\r
+ * (JABAWS) @version: 2.0 This library is free software; you can redistribute it\r
+ * and/or modify it under the terms of the Apache License version 2 as published\r
+ * by the Apache Software Foundation This library is distributed in the hope\r
+ * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * Apache License for more details. A copy of the license is in\r
+ * apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt Any republication or\r
+ * derived work distributed in source code form must include this copyright and\r
+ * license notice.\r
*/\r
\r
package compbio.runner.disorder;\r
\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
-import java.util.Arrays;\r
+import java.io.InputStream;\r
\r
import org.apache.log4j.Logger;\r
\r
-import com.sun.xml.internal.bind.api.impl.NameConverter.Standard;\r
-import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
-import compbio.engine.client.Executable;\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.runner.Util;\r
\r
/**\r
- * @see Standard DisEMBL DisEMBL.py smooth_frame peak_frame join_frame\r
- * fold_coils fold_hotloops fold_rem465 sequence_file print 'A default run\r
- * would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'\r
+ * DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops\r
+ * fold_rem465 sequence_file print\r
+ * \r
+ * 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'\r
+ * \r
+ * This version of DisEMBL is 1.4 (latest available for download in Feb 2011)\r
+ * capable of outputting raw values\r
+ * \r
+ * The values of the parameters are hard coded in DisEMBL.py script.\r
+ * smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4\r
+ * fold_rem465=1.2\r
+ * \r
+ * Changing these values are not recommended by developers, apart from smoothing\r
+ * window. However, 5 orders of magnitude changes in this parameter does not\r
+ * change the output so allowing this change also seems pointless. Finally, the\r
+ * binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to\r
+ * these values, so changing them can lead to problems.\r
+ * \r
* \r
- * new DisEMBL is at /homes/pvtroshin/soft/DisEMBL-1.4raw This is not a\r
- * standard DisEMBL! The script has been modified! DisEMBL.py smooth_frame\r
- * peak_frame join_frame fold_coils fold_hotloops fold_rem465 [mode] <\r
- * fasta_file > out print 'A default run would be: ./DisEMBL.py 8 8 4 1.2\r
- * 1.4 1.2 < fasta_file' print 'Mode: "default"(nothing) or "scores" which\r
- * will give scores per residue in TAB separated format'\r
+ * This is not a standard DisEMBL! The script has been modified!\r
* \r
*/\r
-public class Disembl extends SkeletalExecutable<Disembl> implements\r
- PipedExecutable<Disembl> {\r
-\r
- private static Logger log = Logger.getLogger(Disembl.class);\r
-\r
- // Cache for Limits information\r
- private static LimitsManager<Disembl> limits;\r
-\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
-\r
- public Disembl() {\r
- // remove default input to prevent it to appear in the parameters list\r
- // that could happen if the parameters are set first\r
- // super.setInput("");\r
- addParameters(Arrays.asList("8", "8", "4", "1.2", "1.4", "1.2",\r
- "scores"));\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- public Alignment getResults(String workDirectory)\r
- throws ResultNotAvailableException {\r
- try {\r
- return Util.readClustalFile(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
- } catch (UnknownFileFormatException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (NullPointerException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
+public class Disembl extends SkeletalExecutable<Disembl>\r
+ implements\r
+ PipedExecutable<Disembl> {\r
+\r
+ private static Logger log = Logger.getLogger(Disembl.class);\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+\r
+ /**\r
+ * For the region to be considered disordered the values must exceed these\r
+ */\r
+ public final double COILS_EXPECTATION_THRESHOLD = 0.43;\r
+ public final double REM_EXPECTATION_THRESHOLD = 0.5;\r
+ public final double LOOPS_EXPECTATION_THRESHOLD = 0.086;\r
+\r
+ /* The parameter list there must not contain same values! */\r
+ public Disembl() {\r
+ // remove default input to prevent it to appear in the parameters list\r
+ // that could happen if the parameters are set first\r
+ // super.setInput("");\r
}\r
- }\r
\r
- @Override\r
- public Disembl setInput(String inFile) {\r
- super.setInput(inFile);\r
- cbuilder.setLast(inFile);\r
- return this;\r
- }\r
-\r
- @Override\r
- public Limit<Disembl> getLimit(String presetName) {\r
- if (limits == null) {\r
- limits = getLimits();\r
- }\r
-\r
- Limit<Disembl> limit = null;\r
- if (limits != null) {\r
- // this returns default limit if preset is undefined!\r
- limit = limits.getLimitByName(presetName);\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public ScoreManager getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+\r
+ InputStream inStream = null;\r
+ ScoreManager results = null;\r
+\r
+ try {\r
+ inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
+ results = ScoreManager.newInstance(SequenceUtil\r
+ .readDisembl(inStream));\r
+ inStream.close();\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
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ log.trace("DRESULTS: " + results);\r
+ return results;\r
}\r
- // If limit is not defined for a particular preset, then return default\r
- // limit\r
- if (limit == null) {\r
- log.debug("Limit for the preset " + presetName\r
- + " is not found. Using default");\r
- limit = limits.getDefaultLimit();\r
+ @Override\r
+ public Disembl setInput(String inFile) {\r
+ super.setInput(inFile);\r
+ cbuilder.setLast(inFile);\r
+ return this;\r
}\r
- return limit;\r
- }\r
\r
- @Override\r
- public LimitsManager<Disembl> getLimits() {\r
- // synchronise on static field\r
- synchronized (log) {\r
- if (limits == null) {\r
- limits = Util.getLimits(this.getClass());\r
- }\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<Disembl> getType() {\r
+ return (Class<Disembl>) this.getClass();\r
}\r
- return limits;\r
- }\r
-\r
- @Override\r
- public Class<? extends Executable<?>> getType() {\r
- return this.getClass();\r
- }\r
\r
}\r
git://source.jalview.org / jabaws.git / blobdiff