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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>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </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 and utility methods
103 that work on the objects of this model. </TD>
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105 <TR BGCOLOR="white" CLASS="TableRowColor">
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106 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
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107 <TD>A meta-data model for multiple sequence alignment web services
108 Classes in this package have no dependencies to other sources in the project. </TD>
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113 <A NAME="compbio.data.msa"><!-- --></A>
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114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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117 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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123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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124 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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125 <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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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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129 <CODE> java.lang.String</CODE></FONT></TD>
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130 <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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133 Align a list of sequences with default settings.</TD>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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137 <CODE> java.lang.String</CODE></FONT></TD>
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138 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</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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141 Analyse the sequences.</TD>
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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#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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147 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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150 Align a list of sequences with options.</TD>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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154 <CODE> java.lang.String</CODE></FONT></TD>
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155 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</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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156 java.util.List<<A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>>> options)</CODE>
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159 Analyse the sequences according to custom settings defined in options
162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <CODE> java.lang.String</CODE></FONT></TD>
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165 <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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166 <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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169 Align a list of sequences with preset.</TD>
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171 <TR BGCOLOR="white" CLASS="TableRowColor">
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172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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173 <CODE> java.lang.String</CODE></FONT></TD>
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174 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../../compbio/data/msa/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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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175 <A HREF="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> preset)</CODE>
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178 Analyse the sequences according to the preset settings.</TD>
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183 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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184 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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185 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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186 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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187 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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193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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194 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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195 <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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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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199 <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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200 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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203 </TD>
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205 <TR BGCOLOR="white" CLASS="TableRowColor">
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206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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207 <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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208 <TD><CODE><B>PresetAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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211 </TD>
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213 <TR BGCOLOR="white" CLASS="TableRowColor">
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214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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215 <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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216 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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219 </TD>
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221 <TR BGCOLOR="white" CLASS="TableRowColor">
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222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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223 <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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224 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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227 </TD>
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229 <TR BGCOLOR="white" CLASS="TableRowColor">
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230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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231 <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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232 <TD><CODE><B>Analize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Analize.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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235 </TD>
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237 <TR BGCOLOR="white" CLASS="TableRowColor">
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238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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239 <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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240 <TD><CODE><B>Align.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Align.html#getFastaSequences()">getFastaSequences</A></B>()</CODE>
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243 </TD>
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249 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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250 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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251 <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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253 <TR BGCOLOR="white" CLASS="TableRowColor">
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254 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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255 <CODE> void</CODE></FONT></TD>
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256 <TD><CODE><B>PresetAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/PresetAnalize.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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259 </TD>
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261 <TR BGCOLOR="white" CLASS="TableRowColor">
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262 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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263 <CODE> void</CODE></FONT></TD>
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264 <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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267 </TD>
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269 <TR BGCOLOR="white" CLASS="TableRowColor">
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270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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271 <CODE> void</CODE></FONT></TD>
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272 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/CustomAnalize.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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275 </TD>
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277 <TR BGCOLOR="white" CLASS="TableRowColor">
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278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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279 <CODE> void</CODE></FONT></TD>
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280 <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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283 </TD>
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285 <TR BGCOLOR="white" CLASS="TableRowColor">
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286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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287 <CODE> void</CODE></FONT></TD>
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288 <TD><CODE><B>Analize.</B><B><A HREF="../../../../compbio/data/msa/jaxws/Analize.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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291 </TD>
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293 <TR BGCOLOR="white" CLASS="TableRowColor">
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294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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295 <CODE> void</CODE></FONT></TD>
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296 <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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299 </TD>
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304 <A NAME="compbio.data.sequence"><!-- --></A>
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305 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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306 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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307 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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308 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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314 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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315 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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316 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>
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318 <TR BGCOLOR="white" CLASS="TableRowColor">
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319 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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320 <CODE> <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></FONT></TD>
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321 <TD><CODE><B>FastaReader.</B><B><A HREF="../../../../compbio/data/sequence/FastaReader.html#next()">next</A></B>()</CODE>
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324 Reads the next FastaSequence from the input</TD>
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330 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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331 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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332 <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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334 <TR BGCOLOR="white" CLASS="TableRowColor">
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335 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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336 <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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337 <TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>
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340 </TD>
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342 <TR BGCOLOR="white" CLASS="TableRowColor">
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343 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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344 <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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345 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)">openInputStream</A></B>(java.lang.String inFilePath)</CODE>
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348 Reads and parses Fasta or Clustal formatted file into a list of
349 FastaSequence objects</TD>
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351 <TR BGCOLOR="white" CLASS="TableRowColor">
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352 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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353 <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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354 <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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357 Reads fasta sequences from inStream into the list of FastaSequence
364 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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365 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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366 <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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368 <TR BGCOLOR="white" CLASS="TableRowColor">
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369 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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370 <CODE>static boolean</CODE></FONT></TD>
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371 <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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374 </TD>
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380 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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381 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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382 <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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384 <TR BGCOLOR="white" CLASS="TableRowColor">
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385 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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386 <CODE>static void</CODE></FONT></TD>
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387 <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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388 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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391 Writes FastaSequence in the file, each sequence will take one line only</TD>
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393 <TR BGCOLOR="white" CLASS="TableRowColor">
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394 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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395 <CODE>static void</CODE></FONT></TD>
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396 <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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397 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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398 int width)</CODE>
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401 Writes list of FastaSequeces into the outstream formatting the sequence
402 so that it contains width chars on each line</TD>
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404 <TR BGCOLOR="white" CLASS="TableRowColor">
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405 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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406 <CODE>static void</CODE></FONT></TD>
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407 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(java.io.OutputStream outstream,
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408 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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409 int width)</CODE>
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412 </TD>
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418 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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419 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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420 <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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422 <TR BGCOLOR="white" CLASS="TableRowColor">
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423 <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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424 <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>
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427 </TD>
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429 <TR BGCOLOR="white" CLASS="TableRowColor">
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430 <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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431 <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,
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432 char gapchar)</CODE>
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435 </TD>
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440 <A NAME="compbio.metadata"><!-- --></A>
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441 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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442 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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443 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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444 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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450 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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451 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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452 <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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454 <TR BGCOLOR="white" CLASS="TableRowColor">
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455 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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456 <CODE>static int</CODE></FONT></TD>
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457 <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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460 Calculates an average sequence length of the dataset</TD>
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462 <TR BGCOLOR="white" CLASS="TableRowColor">
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463 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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464 <CODE> boolean</CODE></FONT></TD>
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465 <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>
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468 Checks if the number of sequences or their average length in the dataset
469 exceeds this limit.</TD>
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471 <TR BGCOLOR="white" CLASS="TableRowColor">
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472 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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473 <CODE>static <A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>
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474 <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,
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475 java.util.List<<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>
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478 </TD>
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