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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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82 <A NAME="_S_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>Score</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A value class for AACon annotation results storage.<DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)"><B>Score(Enum<?>, ArrayList<Float>)</B></A> -
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86 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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87 <DD>Instantiate the Score
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88 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><B>Score(Enum<?>, ArrayList<Float>, TreeSet<Range>)</B></A> -
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89 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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91 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)"><B>Score(Enum<?>, TreeSet<Range>)</B></A> -
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92 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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94 <DT><A HREF="../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])"><B>Score(Enum<?>, float[])</B></A> -
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95 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>
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97 <DT><A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>ScoreManager</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#scores"><B>scores</B></A> -
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98 Variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>
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100 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa"><B>SequenceAnnotation</B></A><<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)
102 Single, multiple sequences their groups or alignments can be annotated<DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE"><B>SERVICE_NAMESPACE</B></A> -
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103 Static variable in interface compbio.data.msa.<A HREF="../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>
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105 <DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 2<DT><A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client"><B>ServicesUtil</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD> <DT><A HREF="../compbio/ws/client/ServicesUtil.html#ServicesUtil()"><B>ServicesUtil()</B></A> -
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106 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>
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108 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setActualNumberofSequences(int)"><B>setActualNumberofSequences(int)</B></A> -
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109 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
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111 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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112 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>
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114 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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115 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>
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117 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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118 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescription.html" title="class in compbio.data.msa.jaxws">GetServiceDescription</A>
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120 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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121 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>
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123 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#setArg0(compbio.ws.client.Services)"><B>setArg0(Services)</B></A> -
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124 Method in 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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126 <DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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127 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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128 <DD>Sets one of the values defined in optionList as default.
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129 <DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> -
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130 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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132 <DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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133 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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135 <DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> -
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136 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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138 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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139 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>
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141 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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142 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>
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144 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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145 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>
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147 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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148 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>
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150 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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151 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>
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153 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setFastaSequences(java.util.List)"><B>setFastaSequences(List<FastaSequence>)</B></A> -
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154 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>
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156 <DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> -
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157 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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159 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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160 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>
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162 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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163 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>
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165 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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166 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>
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168 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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169 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>
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171 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setJobId(java.lang.String)"><B>setJobId(String)</B></A> -
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172 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>
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174 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> -
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175 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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177 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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178 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>
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180 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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181 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
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183 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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184 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>
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186 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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187 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>
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189 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#setMessage(java.lang.String)"><B>setMessage(String)</B></A> -
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190 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>
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192 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> -
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193 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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195 <DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> -
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196 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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198 <DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> -
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199 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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201 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setNumberOfSequencesAllowed(int)"><B>setNumberOfSequencesAllowed(int)</B></A> -
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202 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
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204 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> -
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205 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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207 <DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
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208 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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210 <DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> -
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211 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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213 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)"><B>setOptions(List<Option>)</B></A> -
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214 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>
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216 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)"><B>setOptions(List<Option>)</B></A> -
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217 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>
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219 <DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List<String>)</B></A> -
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220 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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222 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List<Option<T>>)</B></A> -
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223 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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224 <DD>Adds the list of options or parameters to the internal list of options
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225 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List<Parameter<T>>)</B></A> -
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226 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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227 <DD>Sets the list of parameters as internal list
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228 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#setPosition(long)"><B>setPosition(long)</B></A> -
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229 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>
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231 <DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set<String>)</B></A> -
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232 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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234 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> -
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235 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>
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237 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#setPreset(compbio.metadata.Preset)"><B>setPreset(Preset)</B></A> -
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238 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>
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240 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#setPresetName(java.lang.String)"><B>setPresetName(String)</B></A> -
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241 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>
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243 <DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List<Preset<T>>)</B></A> -
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244 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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246 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> -
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247 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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248 <DD>Sets name value separator character
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249 <DT><A HREF="../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)"><B>setRanges(TreeSet<Range>)</B></A> -
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250 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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252 <DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> -
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253 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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255 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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256 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>
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258 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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259 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>
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261 <DT><A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> -
\r
262 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJobResponse.html" title="class in compbio.data.msa.jaxws">CancelJobResponse</A>
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264 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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265 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>
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267 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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268 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>
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270 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#setReturn(compbio.data.sequence.ScoreManager)"><B>setReturn(ScoreManager)</B></A> -
\r
271 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>
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273 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#setReturn(compbio.metadata.JobStatus)"><B>setReturn(JobStatus)</B></A> -
\r
274 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>
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276 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#setReturn(java.util.Date)"><B>setReturn(Date)</B></A> -
\r
277 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>
\r
279 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#setReturn(int)"><B>setReturn(int)</B></A> -
\r
280 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>
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282 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#setReturn(compbio.metadata.Limit)"><B>setReturn(Limit)</B></A> -
\r
283 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>
\r
285 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#setReturn(compbio.metadata.LimitsManager)"><B>setReturn(LimitsManager)</B></A> -
\r
286 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>
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288 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#setReturn(compbio.metadata.PresetManager)"><B>setReturn(PresetManager)</B></A> -
\r
289 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>
\r
291 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)"><B>setReturn(Alignment)</B></A> -
\r
292 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>
\r
294 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)"><B>setReturn(RunnerConfig)</B></A> -
\r
295 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>
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297 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set<Category>)</B></A> -
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298 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceCategoriesResponse.html" title="class in compbio.data.msa.jaxws">GetServiceCategoriesResponse</A>
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300 <DT><A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
301 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetServiceDescriptionResponse.html" title="class in compbio.data.msa.jaxws">GetServiceDescriptionResponse</A>
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303 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#setReturn(java.util.Set)"><B>setReturn(Set<Services>)</B></A> -
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304 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>
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306 <DT><A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html#setReturn(boolean)"><B>setReturn(boolean)</B></A> -
\r
307 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperatingResponse.html" title="class in compbio.data.msa.jaxws">IsOperatingResponse</A>
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309 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
\r
310 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>
\r
312 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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313 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>
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315 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#setReturn(compbio.metadata.ChunkHolder)"><B>setReturn(ChunkHolder)</B></A> -
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316 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>
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318 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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319 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>
\r
321 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#setReturn(java.lang.String)"><B>setReturn(String)</B></A> -
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322 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>
\r
324 <DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
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325 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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327 <DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> -
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328 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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329 <DD>Set the name of a runner class
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330 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtActual(int)"><B>setSequenceLenghtActual(int)</B></A> -
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331 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
333 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#setSequenceLenghtAllowed(int)"><B>setSequenceLenghtAllowed(int)</B></A> -
\r
334 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>
\r
336 <DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> -
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337 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
\r
339 <DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> -
\r
340 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
\r
342 <DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
\r
343 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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344 <DD>Set default values for the parameter or an option
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345 <DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> -
\r
346 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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348 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY"><B>SINGLE_ENTRY_KEY</B></A> -
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349 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>
\r
351 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><B>SMERFSConstraints</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration defining two constraints for SMERFS columns score calculation.</DL>
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355 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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356 <A NAME="navbar_bottom"><!-- --></A>
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365 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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366 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
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375 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
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