Reverted some changes I made for testing back to their original states.

[jabaws.git] / webservices / compbio / ws / server / WSUtil.java

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 9d81a6a..e80b1e5 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -115,27 +115,27 @@ public final class WSUtil {
        \r
        // Hardcoded gapchar '-' in this method\r
        \r
-       public static <T> String fold(Alignment alignment,\r
-                       ConfiguredExecutable<T> confExec, Logger logger,\r
-                       String callingMethod, Limit<T> limit)\r
-                       throws LimitExceededException, JobSubmissionException {\r
-               \r
-               List<FastaSequence> sequences = alignment.getSequences();\r
-               if (limit != null && limit.isExceeded(sequences)) {\r
-                       throw LimitExceededException.newLimitExceeded(limit, sequences);\r
-               }\r
-               compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
-               System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "\r
-                               + confExec.getInput());\r
-               System.out.println("WSUtil-fold: The executable is configured with parameters: " \r
-                               + confExec.getParameters());\r
-//             System.out.println("WSUTil-fold: Dump the configured executable:\n" \r
-//                             + confExec.toString());\r
-               AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
-               String jobId = engine.submitJob(confExec);\r
-               reportUsage(confExec, logger);\r
-               return jobId;\r
-       }\r
+//     public static <T> String fold(Alignment alignment,\r
+//                     ConfiguredExecutable<T> confExec, Logger logger,\r
+//                     String callingMethod, Limit<T> limit)\r
+//                     throws LimitExceededException, JobSubmissionException {\r
+//             \r
+//             List<FastaSequence> sequences = alignment.getSequences();\r
+//             if (limit != null && limit.isExceeded(sequences)) {\r
+//                     throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+//             }\r
+//             compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
+//             System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "\r
+//                             + confExec.getInput());\r
+//             System.out.println("WSUtil-fold: The executable is configured with parameters: " \r
+//                             + confExec.getParameters());\r
+////           System.out.println("WSUTil-fold: Dump the configured executable:\n" \r
+////                           + confExec.toString());\r
+//             AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+//             String jobId = engine.submitJob(confExec);\r
+//             reportUsage(confExec, logger);\r
+//             return jobId;\r
+//     }\r
 \r
        static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
                if (GAUtils.IS_GA_ENABLED) {\r
@@ -153,13 +153,29 @@ public final class WSUtil {
                        throw LimitExceededException.newLimitExceeded(limit, sequences);\r
                }\r
                log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
-\r
                compbio.runner.Util.writeInput(sequences, confExec);\r
                AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
                String jobId = engine.submitJob(confExec);\r
                reportUsage(confExec, log);\r
                return jobId;\r
        }\r
+       \r
+       // Same as analize but Alifold takes clustal input not fasta\r
+       \r
+       public static <T> String fold(List<FastaSequence> sequences,\r
+                       ConfiguredExecutable<T> confExec, Logger log, String method,\r
+                       Limit<T> limit) throws JobSubmissionException {\r
+               if (limit != null && limit.isExceeded(sequences)) {\r
+                       throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+               }\r
+               log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
+               // This line is different from the above method\r
+               compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
+               AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+               String jobId = engine.submitJob(confExec);\r
+               reportUsage(confExec, log);\r
+               return jobId;\r
+       }\r
 \r
        /*\r
         * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
@@ -198,7 +214,10 @@ public final class WSUtil {
                AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
                ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine\r
                                .getResults(jobId);\r
+               \r
+               \r
                ScoreManager mas = aacon.getResults();\r
+               \r
                log.trace(jobId + " getConservation : " + mas);\r
                return mas;\r
        }\r