+++ /dev/null
-/* Copyright (c) 2011 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \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
-package compbio.runner;\r
-\r
-import java.net.UnknownServiceException;\r
-\r
-import compbio.engine.cluster.dundee._Queue;\r
-\r
-@Deprecated\r
-public class _NativeSpecHelper {\r
-\r
- int maxCalculationTime;\r
- int requiredMemory;\r
- String queue;\r
-\r
- public _NativeSpecHelper(int requiredMemory) {\r
- this(requiredMemory, 0);\r
- }\r
-\r
- public _NativeSpecHelper(int requiredMemory, int maxCalculationTime) {\r
- this.requiredMemory = requiredMemory;\r
- this.maxCalculationTime = maxCalculationTime;\r
- }\r
-\r
- public void setRequiredMemory(int memory) {\r
- this.requiredMemory = memory;\r
- }\r
-\r
- int getRequiredMemory() {\r
- return requiredMemory;\r
- }\r
-\r
- public void setQueue(String queue) {\r
- this.queue = queue;\r
- }\r
-\r
- public String getQueue() {\r
- return queue;\r
- }\r
-\r
- // -q 64bit.q -l qname=64bit.q -l h_vmem=8000M -l ram=8000M\r
- public String getNativeSpec() throws UnknownServiceException {\r
- if (queue == null) {\r
- queue = getApproprieteQueue().toString();\r
- } else {\r
- // check whether chosen queue suits for memory and runtime settings\r
- _Queue knownQueue = _Queue.BIGINT.getQueue(queue);\r
- if (knownQueue == null) {\r
- throw new UnknownServiceException("Queue " + queue\r
- + " is not regestered in the system! ");\r
- }\r
- if (this.requiredMemory <= knownQueue.getMemoryLimit()) {\r
- throw new UnknownServiceException("Queue " + queue\r
- + " has a memory limit of "\r
- + knownQueue.getMemoryLimit()\r
- + "M - which is smaller than requested!");\r
- }\r
- if (knownQueue.hasTimeLimit()\r
- && this.maxCalculationTime <= knownQueue.getTimeLimit()) {\r
- throw new UnknownServiceException("Queue " + queue\r
- + " has a time limit of " + knownQueue.getTimeLimit()\r
- + "hours - which is smaller than requested!");\r
- }\r
- }\r
- return "-q " + queue.toString() + "-l qname=" + queue.toString()\r
- + ", h_vmem=" + requiredMemory + "M,ram=" + requiredMemory\r
- + "M";\r
- }\r
-\r
- public _Queue getApproprieteQueue() {\r
- return _Queue.getQueue(requiredMemory, maxCalculationTime);\r
- }\r
-\r
-}\r