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+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->\r
+<TITLE>\r
+Jws2Client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
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+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
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+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class Jws2Client</H2>\r
+<PRE>\r
+<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>\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<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>\r
+</PRE>\r
+\r
+<P>\r
+A command line client for JAva Bioinformatics Analysis Web Services\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Version:</B></DT>\r
+ <DD>1.0</DD>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>\r
+<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,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
+\r
+<BR>\r
+ Connects to a web service by the host and the service name web service
+ type</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A></CODE></FONT></TD>\r
+<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>\r
+\r
+<BR>\r
+ Get a connection of JABAWS registry</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
+<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>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<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>\r
+\r
+<BR>\r
+ Starts command line client, if no parameter are supported print help.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<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,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service,\r
+ <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>\r
+\r
+<BR>\r
+ Asks registry to test the service on the host hostname</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static boolean</CODE></FONT></TD>\r
+<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>\r
+\r
+<BR>\r
+ Attempt to construct the URL object from the string</TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<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>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<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>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="validURL(java.lang.String)"><!-- --></A><H3>\r
+validURL</H3>\r
+<PRE>\r
+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>\r
+<DL>\r
+<DD>Attempt to construct the URL object from the string\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>urlstr</CODE> - \r
+<DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)"><!-- --></A><H3>\r
+testService</H3>\r
+<PRE>\r
+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,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service,\r
+ <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)\r
+ 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>,\r
+ <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>\r
+<DL>\r
+<DD>Asks registry to test the service on the host hostname\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>hostname</CODE> - <DD><CODE>service</CODE> - <DD><CODE>writer</CODE> - \r
+<DT><B>Throws:</B>\r
+<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>\r
+<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>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getServices(java.lang.String)"><!-- --></A><H3>\r
+getServices</H3>\r
+<PRE>\r
+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)\r
+ 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>,\r
+ <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>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<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>\r
+<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>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>\r
+connect</H3>\r
+<PRE>\r
+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,\r
+ <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)\r
+ 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>,\r
+ <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>\r
+<DL>\r
+<DD>Connects to a web service by the host and the service name web service
+ type\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
+ context name e.g
+ http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba<DD><CODE>service</CODE> - the name of the JABAWS service to connect to\r
+<DT><B>Returns:</B><DD>JABAService<T>\r
+<DT><B>Throws:</B>\r
+<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>\r
+<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>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="connectToRegistry(java.lang.String)"><!-- --></A><H3>\r
+connectToRegistry</H3>\r
+<PRE>\r
+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)\r
+ 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>,\r
+ <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>\r
+<DL>\r
+<DD>Get a connection of JABAWS registry\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
+ context name e.g
+ http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
+<DT><B>Returns:</B><DD>compbio.data.msa.RegistryWS - instance of a RegistryWS web
+ service\r
+<DT><B>Throws:</B>\r
+<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>\r
+<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>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
+main</H3>\r
+<PRE>\r
+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>\r
+<DL>\r
+<DD>Starts command line client, if no parameter are supported print help. Two
+ parameters are required for successful call the JWS2 host name and a
+ service name.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
+ -s=serviceName ACTION [OPTIONS]
+
+ -h=<host_and_context> - a full URL to the JWS2 web server
+ including context path e.g. http://10.31.1.159:8080/ws
+
+ -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
+ TcoffeeWS, ProbconsWS] ACTIONS:
+
+ -i=<inputFile> - full path to fasta formatted sequence file,
+ from which to align sequences
+
+ -parameters - lists parameters supported by web service
+
+ -presets - lists presets supported by web service
+
+ -limits - lists web services limits Please note that if input
+ file is specified other actions are ignored
+
+ OPTIONS: (only for use with -i action):
+
+ -r=<presetName> - name of the preset to use
+
+ -o=<outputFile> - full path to the file where to write an
+ alignment -f=<parameterInputFile> - the name of the file with
+ the list of parameters to use. Please note that -r and -f
+ options cannot be used together. Alignment is done with either
+ preset or a parameters from the file, but not both!</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
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