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5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->
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10 <META NAME="date" CONTENT="2011-08-12">
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40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>
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82 <A NAME="_T_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa"><B>Tcoffee</B></A> - Class in <A HREF="../compbio/runner/msa/package-summary.html">compbio.runner.msa</A><DD> <DT><A HREF="../compbio/runner/msa/Tcoffee.html#Tcoffee()"><B>Tcoffee()</B></A> -
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86 Constructor for class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>
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88 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server"><B>TcoffeeWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD> <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#TcoffeeWS()"><B>TcoffeeWS()</B></A> -
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89 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>
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91 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#termSignal()"><B>termSignal()</B></A> -
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92 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>
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94 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws"><B>TestAllServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/TestAllServices.html#TestAllServices()"><B>TestAllServices()</B></A> -
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95 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServices.html" title="class in compbio.data.msa.jaxws">TestAllServices</A>
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97 <DT><A HREF="../compbio/data/msa/RegistryWS.html#testAllServices()"><B>testAllServices()</B></A> -
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98 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>
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99 <DD>Test all JABAWS services on the server
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100 <DT><A HREF="../compbio/ws/server/RegistryWS.html#testAllServices()"><B>testAllServices()</B></A> -
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101 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>
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102 <DD>TODO improve reporting.
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103 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>TestAllServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#TestAllServicesResponse()"><B>TestAllServicesResponse()</B></A> -
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104 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>
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106 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws"><B>TestService</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#TestService()"><B>TestService()</B></A> -
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107 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>
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109 <DT><A HREF="../compbio/data/msa/RegistryWS.html#testService(compbio.ws.client.Services)"><B>testService(Services)</B></A> -
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110 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>
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111 <DD>Test a particular service
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112 <DT><A HREF="../compbio/ws/client/Jws2Client.html#testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)"><B>testService(String, Services, PrintWriter)</B></A> -
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113 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>
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114 <DD>Asks registry to test the service on the host hostname
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115 <DT><A HREF="../compbio/ws/server/RegistryWS.html#testService(compbio.ws.client.Services)"><B>testService(Services)</B></A> -
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116 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>
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118 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws"><B>TestServiceResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD> <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#TestServiceResponse()"><B>TestServiceResponse()</B></A> -
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119 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>
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121 <DT><A HREF="../compbio/data/sequence/Range.html#to"><B>to</B></A> -
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122 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>
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124 <DT><A HREF="../compbio/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> -
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125 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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126 <DD>Convert the option to the command string.
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127 <DT><A HREF="../compbio/metadata/Parameter.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> -
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128 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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130 <DT><A HREF="../compbio/data/sequence/Alignment.html#toString()"><B>toString()</B></A> -
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131 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>
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133 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</B></A> -
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134 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>
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135 <DD>Same as oneLineFasta
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136 <DT><A HREF="../compbio/data/sequence/Range.html#toString()"><B>toString()</B></A> -
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137 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>
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139 <DT><A HREF="../compbio/data/sequence/Score.html#toString()"><B>toString()</B></A> -
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140 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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142 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#toString()"><B>toString()</B></A> -
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143 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>
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145 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#toString()"><B>toString()</B></A> -
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146 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>
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148 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#toString()"><B>toString()</B></A> -
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149 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>
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151 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#toString()"><B>toString()</B></A> -
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152 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>
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154 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#toString()"><B>toString()</B></A> -
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155 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>
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157 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#toString()"><B>toString()</B></A> -
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158 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>
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159 <DD><B>Deprecated.</B>
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160 <DT><A HREF="../compbio/engine/conf/_Key.html#toString()"><B>toString()</B></A> -
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161 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/_Key.html" title="class in compbio.engine.conf">_Key</A>
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162 <DD><B>Deprecated.</B>
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163 <DT><A HREF="../compbio/engine/FilePuller.html#toString()"><B>toString()</B></A> -
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164 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>
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166 <DT><A HREF="../compbio/engine/Job.html#toString()"><B>toString()</B></A> -
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167 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>
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169 <DT><A HREF="../compbio/metadata/ChunkHolder.html#toString()"><B>toString()</B></A> -
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170 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
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172 <DT><A HREF="../compbio/metadata/Limit.html#toString()"><B>toString()</B></A> -
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173 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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175 <DT><A HREF="../compbio/metadata/LimitsManager.html#toString()"><B>toString()</B></A> -
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176 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>
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178 <DT><A HREF="../compbio/metadata/Option.html#toString()"><B>toString()</B></A> -
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179 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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181 <DT><A HREF="../compbio/metadata/Parameter.html#toString()"><B>toString()</B></A> -
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182 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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184 <DT><A HREF="../compbio/metadata/Preset.html#toString()"><B>toString()</B></A> -
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185 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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187 <DT><A HREF="../compbio/metadata/PresetManager.html#toString()"><B>toString()</B></A> -
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188 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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190 <DT><A HREF="../compbio/metadata/RunnerConfig.html#toString()"><B>toString()</B></A> -
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191 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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193 <DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</B></A> -
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194 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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196 <DT><A HREF="../compbio/pipeline/_jpred/Hit.html#toString()"><B>toString()</B></A> -
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197 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A>
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199 <DT><A HREF="../compbio/pipeline/_jpred/PScore.html#toString()"><B>toString()</B></A> -
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200 Method in class compbio.pipeline._jpred.<A HREF="../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A>
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202 <DT><A HREF="../compbio/stat/collector/JobStat.html#toString()"><B>toString()</B></A> -
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203 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>
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205 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#toString()"><B>toString()</B></A> -
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206 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>
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208 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#toString()"><B>toString()</B></A> -
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209 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>
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211 <DT><A HREF="../compbio/ws/client/Services.html#toString(java.util.Set)"><B>toString(Set<Services>)</B></A> -
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212 Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>
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214 <DT><A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util"><B>Totals</B></A> - Class in <A HREF="../compbio/stat/servlet/util/package-summary.html">compbio.stat.servlet.util</A><DD> <DT><A HREF="../compbio/stat/servlet/util/Totals.html#Totals()"><B>Totals()</B></A> -
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215 Constructor for class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>
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221 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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222 <A NAME="navbar_bottom"><!-- --></A>
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223 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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227 <A NAME="navbar_bottom_firstrow"><!-- --></A>
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230 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
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231 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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232 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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233 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>
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237 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
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241 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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248 <A HREF="index-18.html"><B>PREV LETTER</B></A>
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253 <SCRIPT type="text/javascript">
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256 document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');
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