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18 parent.document.title="Jws2Client";
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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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120 <A NAME="method_summary"><!-- --></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 <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 web service
136 <TR BGCOLOR="white" CLASS="TableRowColor">
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137 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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138 <CODE>static <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A></CODE></FONT></TD>
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139 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connectToRegistry(java.lang.String)">connectToRegistry</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)</CODE>
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142 Get a connection of JABAWS registry</TD>
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144 <TR BGCOLOR="white" CLASS="TableRowColor">
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145 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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146 <CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>></CODE></FONT></TD>
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147 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#getServices(java.lang.String)">getServices</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> hostname)</CODE>
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150 </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>static void</CODE></FONT></TD>
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155 <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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158 Starts command line client, if no parameter are supported print help.</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>static void</CODE></FONT></TD>
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163 <TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)">testService</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> hostname,
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164 <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service,
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165 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/PrintWriter.html?is-external=true" title="class or interface in java.io">PrintWriter</A> writer)</CODE>
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168 Asks registry to test the service on the host hostname</TD>
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170 <TR BGCOLOR="white" CLASS="TableRowColor">
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171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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172 <CODE>static boolean</CODE></FONT></TD>
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173 <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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176 Attempt to construct the URL object from the string</TD>
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179 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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182 <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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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <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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197 <B>Method Detail</B></FONT></TH>
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201 <A NAME="validURL(java.lang.String)"><!-- --></A><H3>
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204 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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206 <DD>Attempt to construct the URL object from the string
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209 <DT><B>Parameters:</B><DD><CODE>urlstr</CODE> -
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210 <DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>
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215 <A NAME="testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)"><!-- --></A><H3>
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218 public static void <B>testService</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> hostname,
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219 <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service,
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220 <A HREF="http://java.sun.com/javase/6/docs/api/java/io/PrintWriter.html?is-external=true" title="class or interface in java.io">PrintWriter</A> writer)
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221 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A>,
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222 <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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224 <DD>Asks registry to test the service on the host hostname
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227 <DT><B>Parameters:</B><DD><CODE>hostname</CODE> - <DD><CODE>service</CODE> - <DD><CODE>writer</CODE> -
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229 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></CODE>
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230 <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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235 <A NAME="getServices(java.lang.String)"><!-- --></A><H3>
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238 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>> <B>getServices</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> hostname)
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239 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>,
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240 <A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></PRE>
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245 <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>
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246 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></CODE></DL>
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251 <A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>
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254 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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255 <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)
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256 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>,
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257 <A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></PRE>
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259 <DD>Connects to a web service by the host and the service name web service
263 <DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
265 http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba<DD><CODE>service</CODE> - the name of the JABAWS service to connect to
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266 <DT><B>Returns:</B><DD>JABAService<T>
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268 <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>
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269 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></CODE> - if fails to connect to the service on the host</DL>
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274 <A NAME="connectToRegistry(java.lang.String)"><!-- --></A><H3>
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275 connectToRegistry</H3>
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277 public static <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A> <B>connectToRegistry</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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278 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>,
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279 <A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></PRE>
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281 <DD>Get a connection of JABAWS registry
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284 <DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
286 http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
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287 <DT><B>Returns:</B><DD>compbio.data.msa.RegistryWS - instance of a RegistryWS web
290 <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>
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291 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/net/ConnectException.html?is-external=true" title="class or interface in java.net">ConnectException</A></CODE></DL>
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296 <A NAME="main(java.lang.String[])"><!-- --></A><H3>
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299 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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301 <DD>Starts command line client, if no parameter are supported print help. Two
302 parameters are required for successful call the JWS2 host name and a
306 <DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
307 -s=serviceName ACTION [OPTIONS]
309 -h=<host_and_context> - a full URL to the JWS2 web server
310 including context path e.g. http://10.31.1.159:8080/ws
312 -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
313 TcoffeeWS, ProbconsWS] ACTIONS:
315 -i=<inputFile> - full path to fasta formatted sequence file,
316 from which to align sequences
318 -parameters - lists parameters supported by web service
320 -presets - lists presets supported by web service
322 -limits - lists web services limits Please note that if input
323 file is specified other actions are ignored
325 OPTIONS: (only for use with -i action):
327 -r=<presetName> - name of the preset to use
329 -o=<outputFile> - full path to the file where to write an
330 alignment -f=<parameterInputFile> - the name of the file with
331 the list of parameters to use. Please note that -r and -f
332 options cannot be used together. Alignment is done with either
333 preset or a parameters from the file, but not both!</DL>
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