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7 Uses of Class compbio.data.sequence.FastaSequence
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18 parent.document.title="Uses of Class compbio.data.sequence.FastaSequence";
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>
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102 <TD>A data model for multiple sequence alignment web services
103 Classes in this package have no dependencies to other sources in the project. </TD>
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105 <TR BGCOLOR="white" CLASS="TableRowColor">
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106 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>
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107 <TD> </TD>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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111 <TD>A meta-data model for multiple sequence alignment web services
112 Classes in this package have no dependencies to other sources in the project. </TD>
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114 <TR BGCOLOR="white" CLASS="TableRowColor">
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115 <TD><A HREF="#compbio.pipeline._jpred"><B>compbio.pipeline._jpred</B></A></TD>
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116 <TD> </TD>
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118 <TR BGCOLOR="white" CLASS="TableRowColor">
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119 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>
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120 <TD>Utilities commonly used by all runners. </TD>
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122 <TR BGCOLOR="white" CLASS="TableRowColor">
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123 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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124 <TD> </TD>
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129 <A NAME="compbio.data.msa"><!-- --></A>
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130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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131 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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132 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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133 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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139 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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140 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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141 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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145 <CODE> java.lang.String</CODE></FONT></TD>
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146 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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149 Align a list of sequences with default settings.</TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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153 <CODE> java.lang.String</CODE></FONT></TD>
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154 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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155 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>
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158 Align a list of sequences with options.</TD>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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162 <CODE> java.lang.String</CODE></FONT></TD>
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163 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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164 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>
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167 Align a list of sequences with preset.</TD>
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172 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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173 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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174 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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175 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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176 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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182 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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183 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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184 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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186 <TR BGCOLOR="white" CLASS="TableRowColor">
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187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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188 <CODE> java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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189 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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192 </TD>
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194 <TR BGCOLOR="white" CLASS="TableRowColor">
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195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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196 <CODE> java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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197 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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200 </TD>
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202 <TR BGCOLOR="white" CLASS="TableRowColor">
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203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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204 <CODE> java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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205 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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208 </TD>
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214 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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215 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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216 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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218 <TR BGCOLOR="white" CLASS="TableRowColor">
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219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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220 <CODE> void</CODE></FONT></TD>
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221 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> fastaSequences)</CODE>
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224 </TD>
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226 <TR BGCOLOR="white" CLASS="TableRowColor">
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227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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228 <CODE> void</CODE></FONT></TD>
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229 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> fastaSequences)</CODE>
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232 </TD>
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234 <TR BGCOLOR="white" CLASS="TableRowColor">
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235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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236 <CODE> void</CODE></FONT></TD>
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237 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#setFastaSequences(java.util.List)">setFastaSequences</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> fastaSequences)</CODE>
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240 </TD>
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245 <A NAME="compbio.data.sequence"><!-- --></A>
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246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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248 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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249 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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257 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <CODE> java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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262 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>
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265 </TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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269 <CODE>static java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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270 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream inStream)</CODE>
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273 Reads fasta sequences from inStream into the list of FastaSequence
280 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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281 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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282 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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284 <TR BGCOLOR="white" CLASS="TableRowColor">
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285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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286 <CODE>static boolean</CODE></FONT></TD>
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287 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>
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290 </TD>
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296 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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297 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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298 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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300 <TR BGCOLOR="white" CLASS="TableRowColor">
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301 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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302 <CODE>static void</CODE></FONT></TD>
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303 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream os,
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304 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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307 Writes FastaSequence in the file, each sequence will take one line only</TD>
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309 <TR BGCOLOR="white" CLASS="TableRowColor">
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310 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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311 <CODE>static void</CODE></FONT></TD>
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312 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream outstream,
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313 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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314 int width)</CODE>
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317 Writes list of FastaSequeces into the outstream formatting the sequence
318 so that it contains width chars on each line</TD>
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324 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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325 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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326 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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328 <TR BGCOLOR="white" CLASS="TableRowColor">
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329 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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330 <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>
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333 </TD>
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335 <TR BGCOLOR="white" CLASS="TableRowColor">
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336 <TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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337 <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,
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338 char gapchar)</CODE>
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341 </TD>
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346 <A NAME="compbio.engine"><!-- --></A>
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347 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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348 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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349 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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350 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>
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356 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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357 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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358 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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360 <TR BGCOLOR="white" CLASS="TableRowColor">
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361 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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363 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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364 <TR ALIGN="right" VALIGN="">
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365 <TD NOWRAP><FONT SIZE="-1">
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366 <CODE><T> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T></CODE></FONT></TD>
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369 </CODE></FONT></TD>
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370 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T> executable,
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371 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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374 </TD>
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376 <TR BGCOLOR="white" CLASS="TableRowColor">
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377 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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379 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
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380 <TR ALIGN="right" VALIGN="">
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381 <TD NOWRAP><FONT SIZE="-1">
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382 <CODE><T,V> <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>
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385 </CODE></FONT></TD>
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386 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><V> executable,
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387 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> dataSet)</CODE>
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390 </TD>
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395 <A NAME="compbio.metadata"><!-- --></A>
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396 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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397 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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398 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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399 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>
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405 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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406 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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407 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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409 <TR BGCOLOR="white" CLASS="TableRowColor">
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410 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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411 <CODE>static int</CODE></FONT></TD>
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412 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>
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415 Calculates an average sequence length of the dataset</TD>
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417 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
418 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
419 <CODE> boolean</CODE></FONT></TD>
\r
420 <TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> data)</CODE>
\r
423 Checks if the number of sequences or their average length in the dataset
424 exceeds limits the values defined by this Limit</TD>
\r
426 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
427 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
428 <CODE>static <A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>
\r
429 <TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,
\r
430 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>
\r
433 </TD>
\r
438 <A NAME="compbio.pipeline._jpred"><!-- --></A>
\r
439 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
440 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
441 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
442 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A></FONT></TH>
\r
448 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
449 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
450 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/pipeline/_jpred/package-summary.html">compbio.pipeline._jpred</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
\r
452 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
453 <TD><CODE><B><A HREF="../../../../compbio/pipeline/_jpred/Pairwise.html#Pairwise(java.util.List)">Pairwise</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
456 </TD>
\r
461 <A NAME="compbio.runner"><!-- --></A>
\r
462 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
463 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
464 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
465 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
\r
471 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
472 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
473 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
\r
475 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
476 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
477 <CODE>static void</CODE></FONT></TD>
\r
478 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
479 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>
\r
482 </TD>
\r
487 <A NAME="compbio.ws.server"><!-- --></A>
\r
488 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
489 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
490 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
491 Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
\r
497 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
498 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
\r
499 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
\r
501 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
502 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
503 <CODE> java.lang.String</CODE></FONT></TD>
\r
504 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
507 </TD>
\r
509 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
510 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
511 <CODE> java.lang.String</CODE></FONT></TD>
\r
512 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
515 </TD>
\r
517 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
518 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
519 <CODE> java.lang.String</CODE></FONT></TD>
\r
520 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
523 </TD>
\r
525 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
526 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
527 <CODE> java.lang.String</CODE></FONT></TD>
\r
528 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
531 </TD>
\r
533 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
534 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
535 <CODE> java.lang.String</CODE></FONT></TD>
\r
536 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
539 </TD>
\r
541 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
542 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
544 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">
\r
545 <TR ALIGN="right" VALIGN="">
\r
546 <TD NOWRAP><FONT SIZE="-1">
\r
547 <CODE><T> java.lang.String</CODE></FONT></TD>
\r
550 </CODE></FONT></TD>
\r
551 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, javax.xml.ws.WebServiceContext, java.lang.String, compbio.metadata.Limit)">align</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
552 <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><T> confExec,
\r
553 org.apache.log4j.Logger statLog,
\r
554 javax.xml.ws.WebServiceContext wsContext,
\r
555 java.lang.String callingMethod,
\r
556 <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><T> limit)</CODE>
\r
559 </TD>
\r
561 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
562 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
563 <CODE> java.lang.String</CODE></FONT></TD>
\r
564 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
565 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)</CODE>
\r
568 </TD>
\r
570 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
571 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
572 <CODE> java.lang.String</CODE></FONT></TD>
\r
573 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
574 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>>> options)</CODE>
\r
577 </TD>
\r
579 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
580 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
581 <CODE> java.lang.String</CODE></FONT></TD>
\r
582 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
583 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>>> options)</CODE>
\r
586 </TD>
\r
588 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
589 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
590 <CODE> java.lang.String</CODE></FONT></TD>
\r
591 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
592 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>>> options)</CODE>
\r
595 </TD>
\r
597 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
598 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
599 <CODE> java.lang.String</CODE></FONT></TD>
\r
600 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
601 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>>> options)</CODE>
\r
604 </TD>
\r
606 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
607 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
608 <CODE> java.lang.String</CODE></FONT></TD>
\r
609 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
610 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)</CODE>
\r
613 </TD>
\r
615 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
616 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
617 <CODE> java.lang.String</CODE></FONT></TD>
\r
618 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
619 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>> preset)</CODE>
\r
622 </TD>
\r
624 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
625 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
626 <CODE> java.lang.String</CODE></FONT></TD>
\r
627 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
628 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>> preset)</CODE>
\r
631 </TD>
\r
633 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
634 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
635 <CODE> java.lang.String</CODE></FONT></TD>
\r
636 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
637 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>> preset)</CODE>
\r
640 </TD>
\r
642 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
643 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
644 <CODE> java.lang.String</CODE></FONT></TD>
\r
645 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
646 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>> preset)</CODE>
\r
649 </TD>
\r
651 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
652 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
653 <CODE>static void</CODE></FONT></TD>
\r
654 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#validateFastaInput(java.util.List)">validateFastaInput</A></B>(java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
657 </TD>
\r
665 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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666 <A NAME="navbar_bottom"><!-- --></A>
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667 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
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693 NEXT</FONT></TD>
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695 <A HREF="../../../../index.html?compbio/data/sequence/\class-useFastaSequence.html" target="_top"><B>FRAMES</B></A>
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696 <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>
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697 <SCRIPT type="text/javascript">
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