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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 Jws2Client</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.Jws2Client</B>
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100 <DT><PRE>public class <B>Jws2Client</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 JAva Bioinformatics Analysis Web Services
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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/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>
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129 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</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> host,
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130 <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>
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133 Connects to a web service by the host and the service name</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>static void</CODE></FONT></TD>
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138 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.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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141 Starts command line client, if no parameter are supported print help.</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>static boolean</CODE></FONT></TD>
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146 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)">validURL</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> urlstr)</CODE>
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149 Attempt to construct the URL object from the string</TD>
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152 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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155 <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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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <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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170 <B>Method Detail</B></FONT></TH>
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174 <A NAME="validURL(java.lang.String)"><!-- --></A><H3>
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177 public static boolean <B>validURL</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> urlstr)</PRE>
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179 <DD>Attempt to construct the URL object from the string
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182 <DT><B>Parameters:</B><DD><CODE>urlstr</CODE> -
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183 <DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>
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188 <A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>
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191 public static <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A> <B>connect</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> host,
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192 <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)
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193 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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195 <DD>Connects to a web service by the host and the service name
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198 <DT><B>Parameters:</B><DD><CODE>T</CODE> - web service type<DD><CODE>host</CODE> - <DD><CODE>service</CODE> -
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199 <DT><B>Returns:</B><DD>MsaWS<T>
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201 <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></DL>
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206 <A NAME="main(java.lang.String[])"><!-- --></A><H3>
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209 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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211 <DD>Starts command line client, if no parameter are supported print help. Two
212 parameters are required for successfull call the JWS2 host name and a
216 <DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
217 -s=serviceName ACTION [OPTIONS]
219 -h=<host_and_context> - a full URL to the JWS2 web server
220 including context path e.g. http://10.31.1.159:8080/ws
222 -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
223 TcoffeeWS, ProbconsWS] ACTIONS:
225 -i=<inputFile> - full path to fasta formatted sequence file,
226 from which to align sequences
228 -parameters - lists parameters supported by web service
230 -presets - lists presets supported by web service
232 -limits - lists web services limits Please note that if input
233 file is specified other actions are ignored
235 OPTIONS: (only for use with -i action):
237 -r=<presetName> - name of the preset to use
239 -o=<outputFile> - full path to the file where to write an
240 alignment -f=<parameterInputFile> - the name of the file with
241 the list of parameters to use. Please note that -r and -f
242 options cannot be used together. Alignment is done with either
243 preset or a parameters from the file, but not both!</DL>
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