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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<TITLE>\r
+Jws2Client\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-02-17">\r
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+ parent.document.title="Jws2Client";\r
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+ <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
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+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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+<NOSCRIPT>\r
+ <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | 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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+<A NAME="skip-navbar_top"></A>\r
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<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
+java.lang.Object\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 java.lang.Object</DL>\r
+</PRE>\r
+\r
+<P>\r
+A command line client for Jalview Web Services version 2\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+<!-- ======== NESTED CLASS SUMMARY ======== -->\r
+\r
+<A NAME="nested_class_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>Nested Class 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 class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A></B></CODE>\r
+\r
+<BR>\r
+ List of web services currently supported by JWS2</TD>\r
+</TR>\r
+</TABLE>\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\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
+<TR ALIGN="right" VALIGN="">\r
+<TD NOWRAP><FONT SIZE="-1">\r
+<CODE><T> <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></CODE></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Jws2Client.Services)">connect</A></B>(java.lang.String host,\r
+ <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> service)</CODE>\r
+\r
+<BR>\r
+ Connects to a web service by the host and the service name</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static java.lang.String</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])">getHost</A></B>(java.lang.String[] cmd)</CODE>\r
+\r
+<BR>\r
+ Extracts host name from the command line</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static java.lang.String</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])">getServiceName</A></B>(java.lang.String[] cmd)</CODE>\r
+\r
+<BR>\r
+ Extracts service name from the command line</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>(java.lang.String[] 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 boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)">validURL</A></B>(java.lang.String 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.Object</B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</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>(java.lang.String 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="getServiceName(java.lang.String[])"><!-- --></A><H3>\r
+getServiceName</H3>\r
+<PRE>\r
+public static java.lang.String <B>getServiceName</B>(java.lang.String[] cmd)</PRE>\r
+<DL>\r
+<DD>Extracts service name from the command line\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
+<DT><B>Returns:</B><DD>service name or null if it is not defined</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getHost(java.lang.String[])"><!-- --></A><H3>\r
+getHost</H3>\r
+<PRE>\r
+public static java.lang.String <B>getHost</B>(java.lang.String[] cmd)</PRE>\r
+<DL>\r
+<DD>Extracts host name from the command line\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
+<DT><B>Returns:</B><DD>host name or null if it is not defined</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="connect(java.lang.String, compbio.ws.client.Jws2Client.Services)"><!-- --></A><H3>\r
+connect</H3>\r
+<PRE>\r
+public static <T> <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T> <B>connect</B>(java.lang.String host,\r
+ <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client">Jws2Client.Services</A> service)\r
+ throws javax.xml.ws.WebServiceException</PRE>\r
+<DL>\r
+<DD>Connects to a web service by the host and the service name\r
+<P>\r
+<DD><DL>\r
+<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>host</CODE> - <DD><CODE>service</CODE> - \r
+<DT><B>Returns:</B><DD>MsaWS<T>\r
+<DT><B>Throws:</B>\r
+<DD><CODE>javax.xml.ws.WebServiceException</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>(java.lang.String[] args)</PRE>\r
+<DL>\r
+<DD>Starts command line client, if no parameter are supported print help. Two
+ parameters are required for successfull 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
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ PREV CLASS \r
+ <A HREF="../../../compbio/ws/client/Jws2Client.Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
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+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | 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
+</TR>\r
+</TABLE>\r
+<A NAME="skip-navbar_bottom"></A>\r
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r
git://source.jalview.org / jabaws.git / blobdiff