Refactored client class to accomodate new WS interface and reduce the complexity
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / class-use / Alignment.html
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7 Uses of Class compbio.data.sequence.Alignment\r
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84 <B>Uses of Class<br>compbio.data.sequence.Alignment</B></H2>\r
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90 Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
94 <TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
95 </TR>\r
96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
97 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
98 <TD>A data model for multiple sequence alignment web services and utility methods
99  that work on the objects of this model.&nbsp;</TD>\r
100 </TR>\r
101 </TABLE>\r
102 &nbsp;\r
103 <P>\r
104 <A NAME="compbio.data.msa"><!-- --></A>\r
105 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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107 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
108 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
109 </TR>\r
110 </TABLE>\r
111 &nbsp;\r
112 <P>\r
113 \r
114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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116 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
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120 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
121 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
122 \r
123 <BR>\r
124 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</TD>\r
125 </TR>\r
126 </TABLE>\r
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133 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
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141 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
142 </TR>\r
143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
145 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
146 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)</CODE>\r
147 \r
148 <BR>\r
149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
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153 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
154 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;instream)</CODE>\r
155 \r
156 <BR>\r
157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
158 </TR>\r
159 </TABLE>\r
160 &nbsp;\r
161 <P>\r
162 \r
163 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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165 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
166 </TR>\r
167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
169 <CODE>static&nbsp;void</CODE></FONT></TD>\r
170 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outStream,\r
171                       <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
172 \r
173 <BR>\r
174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Write Clustal formatted alignment Limitations: does not record the
175  consensus.</TD>\r
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