website/full_javadoc/compbio/ws/client/Jws2Client.html

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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.ws.client</FONT>\r
  92 <BR>\r
  93 Class Jws2Client</H2>\r
  94 <PRE>\r
  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>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 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>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 A command line client for JAva Bioinformatics Analysis Web Services\r
 105 <P>\r
 106 \r
 107 <P>\r
 108 <DL>\r
 109 <DT><B>Version:</B></DT>\r
 110   <DD>1.0</DD>\r
 111 <DT><B>Author:</B></DT>\r
 112   <DD>pvtroshin</DD>\r
 113 </DL>\r
 114 <HR>\r
 115 \r
 116 <P>\r
 117 \r
 118 <!-- ========== METHOD SUMMARY =========== -->\r
 119 \r
 120 <A NAME="method_summary"><!-- --></A>\r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 124 <B>Method Summary</B></FONT></TH>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 128 <CODE>static&nbsp;<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></CODE></FONT></TD>\r
 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>&nbsp;host,\r
 130         <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&nbsp;service)</CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Connects to a web service by the host and the service name web service
 134  type</TD>\r
 135 </TR>\r
 136 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 137 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 138 <CODE>static&nbsp;<A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A></CODE></FONT></TD>\r
 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>&nbsp;host)</CODE>\r
 140 \r
 141 <BR>\r
 142 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get a connection of JABAWS registry</TD>\r
 143 </TR>\r
 144 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 145 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 146 <CODE>static&nbsp;<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>&lt;<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&gt;</CODE></FONT></TD>\r
 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>&nbsp;hostname)</CODE>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 154 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 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>[]&nbsp;args)</CODE>\r
 156 \r
 157 <BR>\r
 158 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Starts command line client, if no parameter are supported print help.</TD>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 162 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 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>&nbsp;hostname,\r
 164             <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&nbsp;service,\r
 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>&nbsp;writer)</CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Asks registry to test the service on the host hostname</TD>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 172 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 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>&nbsp;urlstr)</CODE>\r
 174 \r
 175 <BR>\r
 176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Attempt to construct the URL object from the string</TD>\r
 177 </TR>\r
 178 </TABLE>\r
 179 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 181 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 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>\r
 186 </TR>\r
 187 </TABLE>\r
 188 &nbsp;\r
 189 <P>\r
 190 \r
 191 <!-- ============ METHOD DETAIL ========== -->\r
 192 \r
 193 <A NAME="method_detail"><!-- --></A>\r
 194 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 195 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 196 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 197 <B>Method Detail</B></FONT></TH>\r
 198 </TR>\r
 199 </TABLE>\r
 200 \r
 201 <A NAME="validURL(java.lang.String)"><!-- --></A><H3>\r
 202 validURL</H3>\r
 203 <PRE>\r
 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>&nbsp;urlstr)</PRE>\r
 205 <DL>\r
 206 <DD>Attempt to construct the URL object from the string\r
 207 <P>\r
 208 <DD><DL>\r
 209 <DT><B>Parameters:</B><DD><CODE>urlstr</CODE> - \r
 210 <DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>\r
 211 </DD>\r
 212 </DL>\r
 213 <HR>\r
 214 \r
 215 <A NAME="testService(java.lang.String, compbio.ws.client.Services, java.io.PrintWriter)"><!-- --></A><H3>\r
 216 testService</H3>\r
 217 <PRE>\r
 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>&nbsp;hostname,\r
 219                                <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&nbsp;service,\r
 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>&nbsp;writer)\r
 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>,\r
 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>\r
 223 <DL>\r
 224 <DD>Asks registry to test the service on the host hostname\r
 225 <P>\r
 226 <DD><DL>\r
 227 <DT><B>Parameters:</B><DD><CODE>hostname</CODE> - <DD><CODE>service</CODE> - <DD><CODE>writer</CODE> - \r
 228 <DT><B>Throws:</B>\r
 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>\r
 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>\r
 231 </DD>\r
 232 </DL>\r
 233 <HR>\r
 234 \r
 235 <A NAME="getServices(java.lang.String)"><!-- --></A><H3>\r
 236 getServices</H3>\r
 237 <PRE>\r
 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>&lt;<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&gt; <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>&nbsp;hostname)\r
 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>,\r
 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>\r
 241 <DL>\r
 242 <DD><DL>\r
 243 \r
 244 <DT><B>Throws:</B>\r
 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>\r
 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>\r
 247 </DD>\r
 248 </DL>\r
 249 <HR>\r
 250 \r
 251 <A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>\r
 252 connect</H3>\r
 253 <PRE>\r
 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>&nbsp;host,\r
 255                                   <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&nbsp;service)\r
 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>,\r
 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>\r
 258 <DL>\r
 259 <DD>Connects to a web service by the host and the service name web service
 260  type\r
 261 <P>\r
 262 <DD><DL>\r
 263 <DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
 264             context name e.g
 265             http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba<DD><CODE>service</CODE> - the name of the JABAWS service to connect to\r
 266 <DT><B>Returns:</B><DD>JABAService<T>\r
 267 <DT><B>Throws:</B>\r
 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>\r
 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>\r
 270 </DD>\r
 271 </DL>\r
 272 <HR>\r
 273 \r
 274 <A NAME="connectToRegistry(java.lang.String)"><!-- --></A><H3>\r
 275 connectToRegistry</H3>\r
 276 <PRE>\r
 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>&nbsp;host)\r
 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>,\r
 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>\r
 280 <DL>\r
 281 <DD>Get a connection of JABAWS registry\r
 282 <P>\r
 283 <DD><DL>\r
 284 <DT><B>Parameters:</B><DD><CODE>host</CODE> - the fully qualified name of JABAWS server including JABAWS
 285             context name e.g
 286             http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
 287 <DT><B>Returns:</B><DD>compbio.data.msa.RegistryWS - instance of a RegistryWS web
 288          service\r
 289 <DT><B>Throws:</B>\r
 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>\r
 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>\r
 292 </DD>\r
 293 </DL>\r
 294 <HR>\r
 295 \r
 296 <A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
 297 main</H3>\r
 298 <PRE>\r
 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>[]&nbsp;args)</PRE>\r
 300 <DL>\r
 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
 303  service name.\r
 304 <P>\r
 305 <DD><DL>\r
 306 <DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
 307             -s=serviceName ACTION [OPTIONS]
 308
 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
 311
 312             -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
 313             TcoffeeWS, ProbconsWS] ACTIONS:
 314
 315             -i=<inputFile> - full path to fasta formatted sequence file,
 316             from which to align sequences
 317
 318             -parameters - lists parameters supported by web service
 319
 320             -presets - lists presets supported by web service
 321
 322             -limits - lists web services limits Please note that if input
 323             file is specified other actions are ignored
 324
 325             OPTIONS: (only for use with -i action):
 326
 327             -r=<presetName> - name of the preset to use
 328
 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>\r
 334 </DD>\r
 335 </DL>\r
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