updated javadoc
[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_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
6 <TITLE>\r
7 All Classes\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2011-08-12">\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/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
25 <BR>\r
26 <A HREF="compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</A>\r
27 <BR>\r
28 <A HREF="compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>\r
29 <BR>\r
30 <A HREF="compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
31 <BR>\r
32 <A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
33 <BR>\r
34 <A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
35 <BR>\r
36 <A HREF="compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
37 <BR>\r
38 <A HREF="compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
39 <BR>\r
40 <A HREF="compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
41 <BR>\r
42 <A HREF="compbio/stat/servlet/AnnualStat.html" title="class in compbio.stat.servlet">AnnualStat</A>\r
43 <BR>\r
44 <A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata"><I>Argument</I></A>\r
45 <BR>\r
46 <A HREF="compbio/engine/AsyncExecutor.html" title="interface in compbio.engine"><I>AsyncExecutor</I></A>\r
47 <BR>\r
48 <A HREF="compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
49 <BR>\r
50 <A HREF="compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
51 <BR>\r
52 <A HREF="compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
53 <BR>\r
54 <A HREF="compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A>\r
55 <BR>\r
56 <A HREF="compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A>\r
57 <BR>\r
58 <A HREF="compbio/runner/_impl/BlastParameters.html" title="class in compbio.runner._impl">BlastParameters</A>\r
59 <BR>\r
60 <A HREF="compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A>\r
61 <BR>\r
62 <A HREF="compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
63 <BR>\r
64 <A HREF="compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>\r
65 <BR>\r
66 <A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
67 <BR>\r
68 <A HREF="compbio/engine/Cleaner.html" title="class in compbio.engine">Cleaner</A>\r
69 <BR>\r
70 <A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
71 <BR>\r
72 <A HREF="compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
73 <BR>\r
74 <A HREF="compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
75 <BR>\r
76 <A HREF="compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
77 <BR>\r
78 <A HREF="compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
79 <BR>\r
80 <A HREF="compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
81 <BR>\r
82 <A HREF="compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
83 <BR>\r
84 <A HREF="compbio/engine/cluster/drmaa/ClusterUtil.html" title="class in compbio.engine.cluster.drmaa">ClusterUtil</A>\r
85 <BR>\r
86 <A HREF="compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
87 <BR>\r
88 <A HREF="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
89 <BR>\r
90 <A HREF="compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
91 <BR>\r
92 <A HREF="compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><I>ConfiguredExecutable</I></A>\r
93 <BR>\r
94 <A HREF="compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>\r
95 <BR>\r
96 <A HREF="compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
97 <BR>\r
98 <A HREF="compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
99 <BR>\r
100 <A HREF="compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
101 <BR>\r
102 <A HREF="compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
103 <BR>\r
104 <A HREF="compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
105 <BR>\r
106 <A HREF="compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
107 <BR>\r
108 <A HREF="compbio/ws/server/DisemblWS.html" title="class in compbio.ws.server">DisemblWS</A>\r
109 <BR>\r
110 <A HREF="compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</A>\r
111 <BR>\r
112 <A HREF="compbio/stat/servlet/DisplayStat.html" title="class in compbio.stat.servlet">DisplayStat</A>\r
113 <BR>\r
114 <A HREF="compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
115 <BR>\r
116 <A HREF="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
117 <BR>\r
118 <A HREF="compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><I>Executable</I></A>\r
119 <BR>\r
120 <A HREF="compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>\r
121 <BR>\r
122 <A HREF="compbio/engine/local/ExecutableWrapper.html" title="class in compbio.engine.local">ExecutableWrapper</A>\r
123 <BR>\r
124 <A HREF="compbio/stat/collector/ExecutionStatCollector.html" title="class in compbio.stat.collector">ExecutionStatCollector</A>\r
125 <BR>\r
126 <A HREF="compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
127 <BR>\r
128 <A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
129 <BR>\r
130 <A HREF="compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
131 <BR>\r
132 <A HREF="compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
133 <BR>\r
134 <A HREF="compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
135 <BR>\r
136 <A HREF="compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
137 <BR>\r
138 <A HREF="compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
139 <BR>\r
140 <A HREF="compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
141 <BR>\r
142 <A HREF="compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
143 <BR>\r
144 <A HREF="compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
145 <BR>\r
146 <A HREF="compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
147 <BR>\r
148 <A HREF="compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
149 <BR>\r
150 <A HREF="compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
151 <BR>\r
152 <A HREF="compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
153 <BR>\r
154 <A HREF="compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
155 <BR>\r
156 <A HREF="compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
157 <BR>\r
158 <A HREF="compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
159 <BR>\r
160 <A HREF="compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
161 <BR>\r
162 <A HREF="compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
163 <BR>\r
164 <A HREF="compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
165 <BR>\r
166 <A HREF="compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
167 <BR>\r
168 <A HREF="compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
169 <BR>\r
170 <A HREF="compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</A>\r
171 <BR>\r
172 <A HREF="compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
173 <BR>\r
174 <A HREF="compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
175 <BR>\r
176 <A HREF="compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
177 <BR>\r
178 <A HREF="compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A>\r
179 <BR>\r
180 <A HREF="compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A>\r
181 <BR>\r
182 <A HREF="compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A>\r
183 <BR>\r
184 <A HREF="compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
185 <BR>\r
186 <A HREF="compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
187 <BR>\r
188 <A HREF="compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>\r
189 <BR>\r
190 <A HREF="compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
191 <BR>\r
192 <A HREF="compbio/ws/server/IUPredWS.html" title="class in compbio.ws.server">IUPredWS</A>\r
193 <BR>\r
194 <A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa"><I>JABAService</I></A>\r
195 <BR>\r
196 <A HREF="compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A>\r
197 <BR>\r
198 <A HREF="compbio/data/msa/JManagement.html" title="interface in compbio.data.msa"><I>JManagement</I></A>\r
199 <BR>\r
200 <A HREF="compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A>\r
201 <BR>\r
202 <A HREF="compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
203 <BR>\r
204 <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
205 <BR>\r
206 <A HREF="compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</A>\r
207 <BR>\r
208 <A HREF="compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
209 <BR>\r
210 <A HREF="compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
211 <BR>\r
212 <A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
213 <BR>\r
214 <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
215 <BR>\r
216 <A HREF="compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
217 <BR>\r
218 <A HREF="compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A>\r
219 <BR>\r
220 <A HREF="compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A>\r
221 <BR>\r
222 <A HREF="compbio/data/_structure/JpredResult.html" title="class in compbio.data._structure">JpredResult</A>\r
223 <BR>\r
224 <A HREF="compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
225 <BR>\r
226 <A HREF="compbio/ws/server/JronnWS.html" title="class in compbio.ws.server">JronnWS</A>\r
227 <BR>\r
228 <A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
229 <BR>\r
230 <A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
231 <BR>\r
232 <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
233 <BR>\r
234 <A HREF="compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
235 <BR>\r
236 <A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
237 <BR>\r
238 <A HREF="compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
239 <BR>\r
240 <A HREF="compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
241 <BR>\r
242 <A HREF="compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
243 <BR>\r
244 <A HREF="compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
245 <BR>\r
246 <A HREF="compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
247 <BR>\r
248 <A HREF="compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
249 <BR>\r
250 <A HREF="compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
251 <BR>\r
252 <A HREF="compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><I>Metadata</I></A>\r
253 <BR>\r
254 <A HREF="compbio/ws/client/MetadataHelper.html" title="class in compbio.ws.client">MetadataHelper</A>\r
255 <BR>\r
256 <A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><I>MsaWS</I></A>\r
257 <BR>\r
258 <A HREF="compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
259 <BR>\r
260 <A HREF="compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
261 <BR>\r
262 <A HREF="compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
263 <BR>\r
264 <A HREF="compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
265 <BR>\r
266 <A HREF="compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
267 <BR>\r
268 <A HREF="compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
269 <BR>\r
270 <A HREF="compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A>\r
271 <BR>\r
272 <A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
273 <BR>\r
274 <A HREF="compbio/engine/client/PathValidator.html" title="class in compbio.engine.client">PathValidator</A>\r
275 <BR>\r
276 <A HREF="compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><I>PipedExecutable</I></A>\r
277 <BR>\r
278 <A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
279 <BR>\r
280 <A HREF="compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
281 <BR>\r
282 <A HREF="compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
283 <BR>\r
284 <A HREF="compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
285 <BR>\r
286 <A HREF="compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
287 <BR>\r
288 <A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
289 <BR>\r
290 <A HREF="compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
291 <BR>\r
292 <A HREF="compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
293 <BR>\r
294 <A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
295 <BR>\r
296 <A HREF="compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
297 <BR>\r
298 <A HREF="compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
299 <BR>\r
300 <A HREF="compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>\r
301 <BR>\r
302 <A HREF="compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
303 <BR>\r
304 <A HREF="compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
305 <BR>\r
306 <A HREF="compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
307 <BR>\r
308 <A HREF="compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
309 <BR>\r
310 <A HREF="compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
311 <BR>\r
312 <A HREF="compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><I>RegistryWS</I></A>\r
313 <BR>\r
314 <A HREF="compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
315 <BR>\r
316 <A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
317 <BR>\r
318 <A HREF="compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
319 <BR>\r
320 <A HREF="compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
321 <BR>\r
322 <A HREF="compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
323 <BR>\r
324 <A HREF="compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
325 <BR>\r
326 <A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
327 <BR>\r
328 <A HREF="compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
329 <BR>\r
330 <A HREF="compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
331 <BR>\r
332 <A HREF="compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
333 <BR>\r
334 <A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
335 <BR>\r
336 <A HREF="compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
337 <BR>\r
338 <A HREF="compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><I>SequenceAnnotation</I></A>\r
339 <BR>\r
340 <A HREF="compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
341 <BR>\r
342 <A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
343 <BR>\r
344 <A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
345 <BR>\r
346 <A HREF="compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
347 <BR>\r
348 <A HREF="compbio/ws/server/ShutdownEngines.html" title="class in compbio.ws.server">ShutdownEngines</A>\r
349 <BR>\r
350 <A HREF="compbio/ws/server/SimpleWSPublisher.html" title="class in compbio.ws.server">SimpleWSPublisher</A>\r
351 <BR>\r
352 <A HREF="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
353 <BR>\r
354 <A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
355 <BR>\r
356 <A HREF="compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
357 <BR>\r
358 <A HREF="compbio/stat/servlet/util/StatCollection.Stattype.html" title="enum in compbio.stat.servlet.util">StatCollection.Stattype</A>\r
359 <BR>\r
360 <A HREF="compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
361 <BR>\r
362 <A HREF="compbio/stat/servlet/StatisticCollector.html" title="class in compbio.stat.servlet">StatisticCollector</A>\r
363 <BR>\r
364 <A HREF="compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
365 <BR>\r
366 <A HREF="compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
367 <BR>\r
368 <A HREF="compbio/engine/local/StreamGobbler.html" title="class in compbio.engine.local">StreamGobbler</A>\r
369 <BR>\r
370 <A HREF="compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
371 <BR>\r
372 <A HREF="compbio/engine/SyncExecutor.html" title="interface in compbio.engine"><I>SyncExecutor</I></A>\r
373 <BR>\r
374 <A HREF="compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
375 <BR>\r
376 <A HREF="compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
377 <BR>\r
378 <A HREF="compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws">TestAllServices</A>\r
379 <BR>\r
380 <A HREF="compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
381 <BR>\r
382 <A HREF="compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
383 <BR>\r
384 <A HREF="compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
385 <BR>\r
386 <A HREF="compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
387 <BR>\r
388 <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
389 <BR>\r
390 <A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
391 <BR>\r
392 <A HREF="compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
393 <BR>\r
394 <A HREF="compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
395 <BR>\r
396 <A HREF="compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
397 <BR>\r
398 <A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
399 <BR>\r
400 <A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
401 <BR>\r
402 <A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
403 <BR>\r
404 <A HREF="compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
405 <BR>\r
406 <A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
407 <BR>\r
408 <A HREF="compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
409 <BR>\r
410 <A HREF="compbio/runner/_jpred/_Jpred.html" title="class in compbio.runner._jpred">_Jpred</A>\r
411 <BR>\r
412 <A HREF="compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>\r
413 <BR>\r
414 <A HREF="compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
415 <BR>\r
416 <A HREF="compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
417 <BR>\r
418 <A HREF="compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
419 <BR>\r
420 <A HREF="compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
421 <BR>\r
422 <A HREF="compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
423 <BR>\r
424 </FONT></TD>\r
425 </TR>\r
426 </TABLE>\r
427 \r
428 </BODY>\r
429 </HTML>\r