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+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:24 GMT 2011 -->\r
+<TITLE>\r
+AAConClient\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\r
+\r
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+function windowTitle()\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/AAConClient.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.ws.client</FONT>\r
+<BR>\r
+Class AAConClient</H2>\r
+<PRE>\r
+java.lang.Object\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.AAConClient</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>AAConClient</B><DT>extends java.lang.Object</DL>\r
+</PRE>\r
+\r
+<P>\r
+A command line client for AACon web service\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/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A><compbio.ws.server.AAConWS></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/AAConClient.html#connect()">connect</A></B>()</CODE>\r
+\r
+<BR>\r
+ Connects to a AACon 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 void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/ws/client/AAConClient.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE>\r
+\r
+<BR>\r
+ Starts command line client, if no parameters are supplied prints help.</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="connect()"><!-- --></A><H3>\r
+connect</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A><compbio.ws.server.AAConWS> <B>connect</B>()\r
+ throws javax.xml.ws.WebServiceException</PRE>\r
+<DL>\r
+<DD>Connects to a AACon web service by the host and the service name\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD><CODE>AlignmentAnnotation</CODE>\r
+<DT><B>Throws:</B>\r
+<DD><CODE>javax.xml.ws.WebServiceException</CODE> - if cannot connect to a web service</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 parameters are supplied prints help.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> ACTION [OPTIONS]
+
+ -i=<inputFile> - full path to fasta or Clustal formatted
+ alignment file
+
+ -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 results
+ -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. Conservation is calculated with
+ either a preset or 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
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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/AAConClient.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
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+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
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