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79 SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
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91 compbio.ws.client</FONT>
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93 Class AAConClient</H2>
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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.AAConClient</B>
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100 <DT><PRE>public class <B>AAConClient</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
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104 A command line client for AACon web service
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109 <DT><B>Version:</B></DT>
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111 <DT><B>Author:</B></DT>
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118 <!-- ========== METHOD SUMMARY =========== -->
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123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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124 <B>Method Summary</B></FONT></TH>
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126 <TR BGCOLOR="white" CLASS="TableRowColor">
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127 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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128 <CODE>static <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A><<A HREF="../../../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>></CODE></FONT></TD>
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129 <TD><CODE><B><A HREF="../../../compbio/ws/client/AAConClient.html#connect()">connect</A></B>()</CODE>
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132 Connects to a AACon web service by the host and the service name</TD>
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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>static void</CODE></FONT></TD>
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137 <TD><CODE><B><A HREF="../../../compbio/ws/client/AAConClient.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)</CODE>
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140 Starts command line client, if no parameters are supplied prints help.</TD>
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146 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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161 <B>Method Detail</B></FONT></TH>
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165 <A NAME="connect()"><!-- --></A><H3>
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168 public static <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A><<A HREF="../../../compbio/ws/server/AAConWS.html" title="class in compbio.ws.server">AAConWS</A>> <B>connect</B>()
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169 throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></PRE>
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171 <DD>Connects to a AACon web service by the host and the service name
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175 <DT><B>Returns:</B><DD><CODE>AlignmentAnnotation</CODE>
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177 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></CODE> - if cannot connect to a web service</DL>
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182 <A NAME="main(java.lang.String[])"><!-- --></A><H3>
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185 public static void <B>main</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>[] args)</PRE>
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187 <DD>Starts command line client, if no parameters are supplied prints help.
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190 <DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> ACTION [OPTIONS]
192 -i=<inputFile> - full path to fasta or Clustal formatted
195 -parameters - lists parameters supported by web service
197 -presets - lists presets supported by web service
199 -limits - lists web services limits. Please note that if input
200 file is specified other actions are ignored
202 OPTIONS: (only for use with -i action):
204 -r=<presetName> - name of the preset to use
206 -o=<outputFile> - full path to the file where to write results
207 -f=<parameterInputFile> - the name of the file with the list
208 of parameters to use. Please note that -r and -f options
209 cannot be used together. Conservation is calculated with
210 either a preset or parameters from the file, but not both!</DL>
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