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76 <li>Summary: </li>
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95 <div class="subTitle">compbio.data.sequence</div>
96 <h2 title="Class ClustalAlignmentUtil" class="title">Class ClustalAlignmentUtil</h2>
98 <div class="contentContainer">
99 <ul class="inheritance">
100 <li>java.lang.Object</li>
102 <ul class="inheritance">
103 <li>compbio.data.sequence.ClustalAlignmentUtil</li>
107 <div class="description">
108 <ul class="blockList">
109 <li class="blockList">
112 <pre>public final class <span class="typeNameLabel">ClustalAlignmentUtil</span>
113 extends java.lang.Object</pre>
114 <div class="block">Tools to read and write clustal formated files</div>
116 <dt><span class="simpleTagLabel">Version:</span></dt>
117 <dd>1.0 September 2009</dd>
118 <dt><span class="simpleTagLabel">Author:</span></dt>
119 <dd>Petr Troshin based on jimp class</dd>
124 <div class="summary">
125 <ul class="blockList">
126 <li class="blockList">
127 <!-- =========== FIELD SUMMARY =========== -->
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132 <h3>Field Summary</h3>
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134 <caption><span>Fields</span><span class="tabEnd"> </span></caption>
136 <th class="colFirst" scope="col">Modifier and Type</th>
137 <th class="colLast" scope="col">Field and Description</th>
139 <tr class="altColor">
140 <td class="colFirst"><code>static char</code></td>
141 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</a></span></code>
142 <div class="block">Dash char to be used as gap char in the alignments</div>
145 <tr class="rowColor">
146 <td class="colFirst"><code>private static java.util.logging.Logger</code></td>
147 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#log">log</a></span></code> </td>
149 <tr class="altColor">
150 <td class="colFirst"><code>private static int</code></td>
151 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#maxNameLength">maxNameLength</a></span></code> </td>
153 <tr class="rowColor">
154 <td class="colFirst"><code>private static int</code></td>
155 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#minNameHolderLength">minNameHolderLength</a></span></code> </td>
157 <tr class="altColor">
158 <td class="colFirst"><code>private static int</code></td>
159 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#oneLineAlignmentLength">oneLineAlignmentLength</a></span></code> </td>
161 <tr class="rowColor">
162 <td class="colFirst"><code>private static java.lang.String</code></td>
163 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#spacer">spacer</a></span></code> </td>
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177 <th class="colOne" scope="col">Constructor and Description</th>
179 <tr class="altColor">
180 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil--">ClustalAlignmentUtil</a></span>()</code> </td>
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190 <h3>Method Summary</h3>
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192 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd"> </span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd"> </span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd"> </span></span></caption>
194 <th class="colFirst" scope="col">Modifier and Type</th>
195 <th class="colLast" scope="col">Method and Description</th>
197 <tr id="i0" class="altColor">
198 <td class="colFirst"><code>static boolean</code></td>
199 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile-java.io.InputStream-">isValidClustalFile</a></span>(java.io.InputStream input)</code>
200 <div class="block">Please note this method closes the input stream provided as a parameter</div>
203 <tr id="i1" class="rowColor">
204 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
205 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.File-">readClustalFile</a></span>(java.io.File file)</code> </td>
207 <tr id="i2" class="altColor">
208 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
209 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.InputStream-">readClustalFile</a></span>(java.io.InputStream instream)</code>
210 <div class="block">Read Clustal formatted alignment.</div>
213 <tr id="i3" class="rowColor">
214 <td class="colFirst"><code>static void</code></td>
215 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment-java.io.Writer-compbio.data.sequence.Alignment-">writeClustalAlignment</a></span>(java.io.Writer out,
216 <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> alignment)</code>
217 <div class="block">Write Clustal formatted alignment Limitations: does not record the
222 <ul class="blockList">
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226 <h3>Methods inherited from class java.lang.Object</h3>
227 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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247 <li class="blockList">
249 <pre>private static final java.util.logging.Logger log</pre>
255 <ul class="blockList">
256 <li class="blockList">
258 <pre>public static final char gapchar</pre>
259 <div class="block">Dash char to be used as gap char in the alignments</div>
261 <dt><span class="seeLabel">See Also:</span></dt>
262 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</a></dd>
269 <ul class="blockList">
270 <li class="blockList">
272 <pre>private static final java.lang.String spacer</pre>
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279 <a name="maxNameLength">
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284 <h4>maxNameLength</h4>
285 <pre>private static final int maxNameLength</pre>
287 <dt><span class="seeLabel">See Also:</span></dt>
288 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.maxNameLength">Constant Field Values</a></dd>
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298 <pre>private static final int minNameHolderLength</pre>
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301 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.minNameHolderLength">Constant Field Values</a></dd>
305 <a name="oneLineAlignmentLength">
308 <ul class="blockListLast">
309 <li class="blockList">
310 <h4>oneLineAlignmentLength</h4>
311 <pre>private static final int oneLineAlignmentLength</pre>
313 <dt><span class="seeLabel">See Also:</span></dt>
314 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.oneLineAlignmentLength">Constant Field Values</a></dd>
320 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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325 <h3>Constructor Detail</h3>
326 <a name="ClustalAlignmentUtil--">
329 <ul class="blockListLast">
330 <li class="blockList">
331 <h4>ClustalAlignmentUtil</h4>
332 <pre>public ClustalAlignmentUtil()</pre>
337 <!-- ============ METHOD DETAIL ========== -->
338 <ul class="blockList">
339 <li class="blockList"><a name="method.detail">
342 <h3>Method Detail</h3>
343 <a name="readClustalFile-java.io.InputStream-">
346 <ul class="blockList">
347 <li class="blockList">
348 <h4>readClustalFile</h4>
349 <pre>public static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> readClustalFile(java.io.InputStream instream)
350 throws java.io.IOException,
351 <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
352 <div class="block">Read Clustal formatted alignment. Limitations: Does not read consensus
354 Sequence names as well as the sequences are not guaranteed to be unique!</div>
356 <dt><span class="throwsLabel">Throws:</span></dt>
357 <dd><code>{@link</code> - IOException}</dd>
358 <dd><code>{@link</code> - UnknownFileFormatException}</dd>
359 <dd><code>java.io.IOException</code></dd>
360 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
364 <a name="isValidClustalFile-java.io.InputStream-">
367 <ul class="blockList">
368 <li class="blockList">
369 <h4>isValidClustalFile</h4>
370 <pre>public static boolean isValidClustalFile(java.io.InputStream input)</pre>
371 <div class="block">Please note this method closes the input stream provided as a parameter</div>
373 <dt><span class="paramLabel">Parameters:</span></dt>
374 <dd><code>input</code> - </dd>
375 <dt><span class="returnLabel">Returns:</span></dt>
376 <dd>true if the file is recognised as Clustal formatted alignment,
381 <a name="writeClustalAlignment-java.io.Writer-compbio.data.sequence.Alignment-">
384 <ul class="blockList">
385 <li class="blockList">
386 <h4>writeClustalAlignment</h4>
387 <pre>public static void writeClustalAlignment(java.io.Writer out,
388 <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> alignment)
389 throws java.io.IOException</pre>
390 <div class="block">Write Clustal formatted alignment Limitations: does not record the
391 consensus. Potential bug - records 60 chars length alignment where
392 Clustal would have recorded 50 chars.</div>
394 <dt><span class="paramLabel">Parameters:</span></dt>
395 <dd><code>out</code> - </dd>
396 <dd><code>alignment</code> - </dd>
397 <dt><span class="throwsLabel">Throws:</span></dt>
398 <dd><code>java.io.IOException</code></dd>
402 <a name="readClustalFile-java.io.File-">
405 <ul class="blockListLast">
406 <li class="blockList">
407 <h4>readClustalFile</h4>
408 <pre>public static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> readClustalFile(java.io.File file)
409 throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
410 java.io.IOException</pre>
412 <dt><span class="throwsLabel">Throws:</span></dt>
413 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
414 <dd><code>java.io.IOException</code></dd>
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