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7 Uses of Class compbio.data.sequence.Alignment
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84 <B>Uses of Class<br>compbio.data.sequence.Alignment</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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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/Alignment.html" title="class in compbio.data.sequence">Alignment</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.runner"><B>compbio.runner</B></A></TD>
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107 <TD>Utilities commonly used by all runners. </TD>
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109 <TR BGCOLOR="white" CLASS="TableRowColor">
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110 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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111 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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113 <TR BGCOLOR="white" CLASS="TableRowColor">
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114 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>
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115 <TD> </TD>
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120 <A NAME="compbio.data.msa"><!-- --></A>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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124 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
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130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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131 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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132 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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136 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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137 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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140 Return the result of the job.</TD>
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145 <A NAME="compbio.data.msa.jaxws"><!-- --></A>
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146 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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147 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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148 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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149 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>
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155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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156 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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157 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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161 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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162 <TD><CODE><B>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()">getReturn</A></B>()</CODE>
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165 </TD>
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171 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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172 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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173 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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175 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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177 <CODE> void</CODE></FONT></TD>
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178 <TD><CODE><B>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)">setReturn</A></B>(<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> _return)</CODE>
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181 </TD>
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186 <A NAME="compbio.data.sequence"><!-- --></A>
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187 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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188 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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189 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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190 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>
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196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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197 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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198 <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/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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203 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(java.io.File file)</CODE>
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206 </TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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211 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(java.io.InputStream instream)</CODE>
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214 Read Clustal formatted alignment.</TD>
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220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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221 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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222 <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/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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226 <CODE>static void</CODE></FONT></TD>
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227 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(java.io.OutputStream outStream,
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228 <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)</CODE>
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231 Write Clustal formatted alignment Limitations: does not record the
237 <A NAME="compbio.runner"><!-- --></A>
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238 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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239 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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240 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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241 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>
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247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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248 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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249 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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251 <TR BGCOLOR="white" CLASS="TableRowColor">
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252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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253 <CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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254 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(java.lang.String workDirectory,
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255 java.lang.String clustFile)</CODE>
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258 </TD>
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263 <A NAME="compbio.runner.msa"><!-- --></A>
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264 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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265 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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266 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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267 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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273 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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274 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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275 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>
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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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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280 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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288 <TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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296 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</CODE>
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299 </TD>
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301 <TR BGCOLOR="white" CLASS="TableRowColor">
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302 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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303 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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304 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</CODE>
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307 </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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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312 <TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String workDirectory)</CODE>
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315 </TD>
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320 <A NAME="compbio.ws.server"><!-- --></A>
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321 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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322 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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323 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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324 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>
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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/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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337 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</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> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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345 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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348 </TD>
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350 <TR BGCOLOR="white" CLASS="TableRowColor">
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351 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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352 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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353 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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356 </TD>
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358 <TR BGCOLOR="white" CLASS="TableRowColor">
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359 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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360 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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361 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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364 </TD>
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366 <TR BGCOLOR="white" CLASS="TableRowColor">
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367 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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368 <CODE> <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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369 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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372 </TD>
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408 NEXT</FONT></TD>
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