build client source when build all
[jabaws.git] / website / full_javadoc / allclasses-noframe.html
1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
2 <!--NewPage-->\r
3 <HTML>\r
4 <HEAD>\r
5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->\r
6 <TITLE>\r
7 All Classes\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2010-02-17">\r
11 \r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
13 \r
14 \r
15 </HEAD>\r
16 \r
17 <BODY BGCOLOR="white">\r
18 <FONT size="+1" CLASS="FrameHeadingFont">\r
19 <B>All Classes</B></FONT>\r
20 <BR>\r
21 \r
22 <TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
23 <TR>\r
24 <TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
25 <BR>\r
26 <A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
27 <BR>\r
28 <A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
29 <BR>\r
30 <A HREF="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
31 <BR>\r
32 <A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata"><I>Argument</I></A>\r
33 <BR>\r
34 <A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><I>AsyncExecutor</I></A>\r
35 <BR>\r
36 <A HREF="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
37 <BR>\r
38 <A HREF="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
39 <BR>\r
40 <A HREF="compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
41 <BR>\r
42 <A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl">BlastParameters</A>\r
43 <BR>\r
44 <A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>\r
45 <BR>\r
46 <A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
47 <BR>\r
48 <A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
49 <BR>\r
50 <A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
51 <BR>\r
52 <A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
53 <BR>\r
54 <A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
55 <BR>\r
56 <A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
57 <BR>\r
58 <A HREF="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
59 <BR>\r
60 <A HREF="compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
61 <BR>\r
62 <A HREF="compbio/engine/client/ClusterNativeSpecExecutable.html" title="interface in compbio.engine.client"><I>ClusterNativeSpecExecutable</I></A>\r
63 <BR>\r
64 <A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
65 <BR>\r
66 <A HREF="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
67 <BR>\r
68 <A HREF="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
69 <BR>\r
70 <A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
71 <BR>\r
72 <A HREF="compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
73 <BR>\r
74 <A HREF="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><I>ConfiguredExecutable</I></A>\r
75 <BR>\r
76 <A HREF="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
77 <BR>\r
78 <A HREF="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
79 <BR>\r
80 <A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
81 <BR>\r
82 <A HREF="compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>\r
83 <BR>\r
84 <A HREF="compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
85 <BR>\r
86 <A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
87 <BR>\r
88 <A HREF="compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><I>Executable</I></A>\r
89 <BR>\r
90 <A HREF="compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>\r
91 <BR>\r
92 <A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
93 <BR>\r
94 <A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
95 <BR>\r
96 <A HREF="compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
97 <BR>\r
98 <A HREF="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
99 <BR>\r
100 <A HREF="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
101 <BR>\r
102 <A HREF="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
103 <BR>\r
104 <A HREF="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
105 <BR>\r
106 <A HREF="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
107 <BR>\r
108 <A HREF="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
109 <BR>\r
110 <A HREF="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
111 <BR>\r
112 <A HREF="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
113 <BR>\r
114 <A HREF="compbio/data/msa/jaxws/GetProgress.html" title="class in compbio.data.msa.jaxws">GetProgress</A>\r
115 <BR>\r
116 <A HREF="compbio/data/msa/jaxws/GetProgressResponse.html" title="class in compbio.data.msa.jaxws">GetProgressResponse</A>\r
117 <BR>\r
118 <A HREF="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
119 <BR>\r
120 <A HREF="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
121 <BR>\r
122 <A HREF="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
123 <BR>\r
124 <A HREF="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
125 <BR>\r
126 <A HREF="compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>\r
127 <BR>\r
128 <A HREF="compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
129 <BR>\r
130 <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
131 <BR>\r
132 <A HREF="compbio/data/msa/jaxws/JobExecutionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobExecutionExceptionBean</A>\r
133 <BR>\r
134 <A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
135 <BR>\r
136 <A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
137 <BR>\r
138 <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
139 <BR>\r
140 <A HREF="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
141 <BR>\r
142 <A HREF="compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
143 <BR>\r
144 <A HREF="compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>\r
145 <BR>\r
146 <A HREF="compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure">JpredResult</A>\r
147 <BR>\r
148 <A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
149 <BR>\r
150 <A HREF="compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A>\r
151 <BR>\r
152 <A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
153 <BR>\r
154 <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
155 <BR>\r
156 <A HREF="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
157 <BR>\r
158 <A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
159 <BR>\r
160 <A HREF="compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
161 <BR>\r
162 <A HREF="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
163 <BR>\r
164 <A HREF="compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
165 <BR>\r
166 <A HREF="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
167 <BR>\r
168 <A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
169 <BR>\r
170 <A HREF="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
171 <BR>\r
172 <A HREF="compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
173 <BR>\r
174 <A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><I>MsaWS</I></A>\r
175 <BR>\r
176 <A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
177 <BR>\r
178 <A HREF="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
179 <BR>\r
180 <A HREF="compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
181 <BR>\r
182 <A HREF="compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
183 <BR>\r
184 <A HREF="compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
185 <BR>\r
186 <A HREF="compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
187 <BR>\r
188 <A HREF="compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
189 <BR>\r
190 <A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
191 <BR>\r
192 <A HREF="compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
193 <BR>\r
194 <A HREF="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><I>PipedExecutable</I></A>\r
195 <BR>\r
196 <A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
197 <BR>\r
198 <A HREF="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
199 <BR>\r
200 <A HREF="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
201 <BR>\r
202 <A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
203 <BR>\r
204 <A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
205 <BR>\r
206 <A HREF="compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
207 <BR>\r
208 <A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
209 <BR>\r
210 <A HREF="compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
211 <BR>\r
212 <A HREF="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
213 <BR>\r
214 <A HREF="compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
215 <BR>\r
216 <A HREF="compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
217 <BR>\r
218 <A HREF="compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>\r
219 <BR>\r
220 <A HREF="compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
221 <BR>\r
222 <A HREF="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
223 <BR>\r
224 <A HREF="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
225 <BR>\r
226 <A HREF="compbio/data/msa/jaxws/PullFile.html" title="class in compbio.data.msa.jaxws">PullFile</A>\r
227 <BR>\r
228 <A HREF="compbio/data/msa/jaxws/PullFileResponse.html" title="class in compbio.data.msa.jaxws">PullFileResponse</A>\r
229 <BR>\r
230 <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
231 <BR>\r
232 <A HREF="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
233 <BR>\r
234 <A HREF="compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
235 <BR>\r
236 <A HREF="compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
237 <BR>\r
238 <A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
239 <BR>\r
240 <A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
241 <BR>\r
242 <A HREF="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
243 <BR>\r
244 <A HREF="compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
245 <BR>\r
246 <A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
247 <BR>\r
248 <A HREF="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
249 <BR>\r
250 <A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
251 <BR>\r
252 <A HREF="compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
253 <BR>\r
254 <A HREF="compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>\r
255 <BR>\r
256 <A HREF="compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
257 <BR>\r
258 <A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><I>SyncExecutor</I></A>\r
259 <BR>\r
260 <A HREF="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
261 <BR>\r
262 <A HREF="compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
263 <BR>\r
264 <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
265 <BR>\r
266 <A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
267 <BR>\r
268 <A HREF="compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
269 <BR>\r
270 <A HREF="compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
271 <BR>\r
272 <A HREF="compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
273 <BR>\r
274 <A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
275 <BR>\r
276 <A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
277 <BR>\r
278 <A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
279 <BR>\r
280 <A HREF="compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
281 <BR>\r
282 <A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
283 <BR>\r
284 <A HREF="compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
285 <BR>\r
286 <A HREF="compbio/engine/cluster/drmaa/_DrmaaExample.html" title="class in compbio.engine.cluster.drmaa">_DrmaaExample</A>\r
287 <BR>\r
288 <A HREF="compbio/engine/cluster/drmaa/_JobStatus.html" title="class in compbio.engine.cluster.drmaa">_JobStatus</A>\r
289 <BR>\r
290 <A HREF="compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred">_Jpred</A>\r
291 <BR>\r
292 <A HREF="compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
293 <BR>\r
294 <A HREF="compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
295 <BR>\r
296 <A HREF="compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
297 <BR>\r
298 <A HREF="compbio/engine/cluster/dundee/_QueueConstraints.html" title="class in compbio.engine.cluster.dundee">_QueueConstraints</A>\r
299 <BR>\r
300 <A HREF="compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
301 <BR>\r
302 <A HREF="compbio/engine/local/_TrackingExecutor.html" title="class in compbio.engine.local">_TrackingExecutor</A>\r
303 <BR>\r
304 </FONT></TD>\r
305 </TR>\r
306 </TABLE>\r
307 \r
308 </BODY>\r
309 </HTML>\r