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41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
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82 <A NAME="_G_"><!-- --></A><H2>
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85 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> -
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86 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
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87 <DD>Dash char to be used as gap char in the alignments
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88 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> -
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89 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>
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91 <DT><A HREF="../compbio/data/msa/Annotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> -
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92 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>
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93 <DD>Return the result of the job.
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94 <DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#getAnnotation()"><B>getAnnotation()</B></A> -
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95 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>
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97 <DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#getAnnotations()"><B>getAnnotations()</B></A> -
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98 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>
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100 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> -
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101 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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102 <DD>Returns the argument by its name if found, NULL otherwise.
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103 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> -
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104 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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105 <DD>Returns the argument by option name, NULL if the argument is not found
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106 <DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig<T>)</B></A> -
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107 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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108 <DD>Converts list of options as String to type Option
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109 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> -
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110 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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111 <DD>Returns list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
113 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> -
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114 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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116 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List<FastaSequence>)</B></A> -
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117 Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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118 <DD>Calculates an average sequence length of the dataset
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119 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> -
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120 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
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122 <DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> -
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123 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>
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125 <DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> -
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126 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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128 <DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> -
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129 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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130 <DD>A default value of the option.
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131 <DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> -
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132 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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134 <DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> -
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135 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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136 <DD>A long description of the Option
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137 <DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> -
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138 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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140 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> -
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141 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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142 <DD>Format sequence per width letter in one string.
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143 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> -
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144 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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146 <DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> -
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147 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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149 <DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> -
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150 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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151 <DD>The URL where further details about the option can be found
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152 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> -
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153 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>
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155 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> -
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156 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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157 <DD>Gets the value of id
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158 <DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> -
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159 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>
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160 <DD>Return the status of the job.
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161 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> -
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162 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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164 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> -
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165 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>
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166 <DD>Get a Limit for a preset.
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167 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> -
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168 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>
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170 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> -
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171 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>
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172 <DD>List Limits supported by a web service.
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173 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> -
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174 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>
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176 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> -
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177 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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179 <DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> -
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180 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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182 <DT><A HREF="../compbio/data/sequence/ConservationMethod.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> -
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183 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>
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185 <DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> -
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186 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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187 <DD>Returns the ConservationMethod
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188 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> -
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189 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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191 <DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> -
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192 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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194 <DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> -
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195 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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196 <DD>Human readable name of the option
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197 <DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> -
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198 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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200 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> -
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201 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>
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203 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> -
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204 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>
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206 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> -
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207 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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209 <DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> -
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210 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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212 <DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> -
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213 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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215 <DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> -
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216 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>
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218 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> -
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219 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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220 <DD>Returns the list of the Options supported by the executable of type T
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221 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> -
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222 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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223 <DD>Returns the list of parameters supported executable of type T.
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224 <DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> -
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225 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>
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227 <DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> -
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228 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
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229 <DD>List of possible optionNames
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230 <DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> -
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231 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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232 <DD>List is more convenient to work with
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233 <DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> -
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234 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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236 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> -
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237 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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239 <DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> -
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240 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>
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241 <DD>Get presets supported by a web service
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242 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> -
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243 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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245 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> -
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246 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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248 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> -
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249 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>
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251 <DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> -
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252 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>
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253 <DD>Return the result of the job.
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254 <DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> -
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255 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>
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257 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> -
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258 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>
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260 <DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> -
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261 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>
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262 <DD>Get options supported by a web service
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263 <DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> -
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264 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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265 <DD>The column scores for the alignment
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266 <DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> -
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267 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
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269 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> -
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270 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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271 <DD>Gets the value of sequence
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272 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> -
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273 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>
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275 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> -
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276 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>
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278 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> -
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279 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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281 <DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> -
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282 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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284 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> -
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285 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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287 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)"><B>getSMERFSColumnScore(String)</B></A> -
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288 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>
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290 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> -
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291 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>
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293 <DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> -
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294 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>
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300 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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