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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>Owczarzy11LockedAcid</title>
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<div class="subTitle">melting.patternModels.specificAcids</div>
<h2 title="Class Owczarzy11LockedAcid" class="title">Class Owczarzy11LockedAcid</h2>
</div>
<div class="contentContainer">
<ul class="inheritance">
<li>java.lang.Object</li>
<li>
<ul class="inheritance">
<li><a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">melting.patternModels.PatternComputation</a></li>
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<ul class="inheritance">
<li>melting.patternModels.specificAcids.Owczarzy11LockedAcid</li>
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<dt>All Implemented Interfaces:</dt>
<dd><a href="../../../melting/methodInterfaces/NamedMethod.html" title="interface in melting.methodInterfaces">NamedMethod</a>, <a href="../../../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></dd>
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<pre>public class <span class="strong">Owczarzy11LockedAcid</span>
extends <a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a>
implements <a href="../../../melting/methodInterfaces/NamedMethod.html" title="interface in melting.methodInterfaces">NamedMethod</a></pre>
<div class="block">This class represents the locked nucleic acid (AL, GL, CL or TL) model owc11. It extends PatternComputation.
 
 McTigue et al.(2004). Biochemistry 43 : 5388-5405</div>
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<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Field and Description</th>
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<td class="colFirst"><code>static java.lang.String</code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#defaultFileName">defaultFileName</a></strong></code>
<div class="block">String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid</div>
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<h3>Fields inherited from class&nbsp;melting.patternModels.<a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></h3>
<code><a href="../../../melting/patternModels/PatternComputation.html#collector">collector</a>, <a href="../../../melting/patternModels/PatternComputation.html#fileName">fileName</a></code></li>
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<td class="colOne"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#Owczarzy11LockedAcid()">Owczarzy11LockedAcid</a></strong>()</code>&nbsp;</td>
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<caption><span>Methods</span><span class="tabEnd">&nbsp;</span></caption>
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<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Method and Description</th>
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<td class="colFirst"><code><a href="../../../melting/ThermoResult.html" title="class in melting">ThermoResult</a></code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#computeThermodynamics(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">computeThermodynamics</a></strong>(<a href="../../../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a>&nbsp;sequences,
                     int&nbsp;pos1,
                     int&nbsp;pos2,
                     <a href="../../../melting/ThermoResult.html" title="class in melting">ThermoResult</a>&nbsp;result)</code>&nbsp;</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>java.lang.String</code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#getName()">getName</a></strong>()</code>
<div class="block">Gets the full name of the method.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#initialiseFileName(java.lang.String)">initialiseFileName</a></strong>(java.lang.String&nbsp;methodName)</code>
<div class="block">If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
 otherwise the default file name of the model is used.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>boolean</code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#isApplicable(melting.Environment, int, int)">isApplicable</a></strong>(<a href="../../../melting/Environment.html" title="class in melting">Environment</a>&nbsp;environment,
            int&nbsp;pos1,
            int&nbsp;pos2)</code>&nbsp;</td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>boolean</code></td>
<td class="colLast"><code><strong><a href="../../../melting/patternModels/specificAcids/Owczarzy11LockedAcid.html#isMissingParameters(melting.sequences.NucleotidSequences, int, int)">isMissingParameters</a></strong>(<a href="../../../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a>&nbsp;sequences,
                   int&nbsp;pos1,
                   int&nbsp;pos2)</code>
<div class="block">Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern 
 at the positions pos1 and pos2.</div>
</td>
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<h3>Methods inherited from class&nbsp;melting.patternModels.<a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></h3>
<code><a href="../../../melting/patternModels/PatternComputation.html#getCollector()">getCollector</a>, <a href="../../../melting/patternModels/PatternComputation.html#getData()">getData</a>, <a href="../../../melting/patternModels/PatternComputation.html#getDataFileName(java.lang.String)">getDataFileName</a>, <a href="../../../melting/patternModels/PatternComputation.html#loadData(java.util.HashMap)">loadData</a>, <a href="../../../melting/patternModels/PatternComputation.html#loadFile(java.lang.String, melting.DataCollect)">loadFile</a></code></li>
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<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
<code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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<h4>defaultFileName</h4>
<pre>public static&nbsp;java.lang.String defaultFileName</pre>
<div class="block">String defaultFileName : default name for the xml file containing the thermodynamic parameters for locked nucleic acid</div>
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<h3>Constructor Detail</h3>
<a name="Owczarzy11LockedAcid()">
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<h4>Owczarzy11LockedAcid</h4>
<pre>public&nbsp;Owczarzy11LockedAcid()</pre>
</li>
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<!-- ============ METHOD DETAIL ========== -->
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<h3>Method Detail</h3>
<a name="isApplicable(melting.Environment, int, int)">
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<h4>isApplicable</h4>
<pre>public&nbsp;boolean&nbsp;isApplicable(<a href="../../../melting/Environment.html" title="class in melting">Environment</a>&nbsp;environment,
                   int&nbsp;pos1,
                   int&nbsp;pos2)</pre>
<dl>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#isApplicable(melting.Environment, int, int)">isApplicable</a></code>&nbsp;in interface&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></code></dd>
<dt><strong>Overrides:</strong></dt>
<dd><code><a href="../../../melting/patternModels/PatternComputation.html#isApplicable(melting.Environment, int, int)">isApplicable</a></code>&nbsp;in class&nbsp;<code><a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></code></dd>
<dt><span class="strong">Returns:</span></dt><dd>false if the model used to compute the enthalpy and entropy of the pattern at the positions pos1 and 
 pos2 is not applicable with the environment. If the environment can make the results less reliable, a warning
 message will appear.</dd></dl>
</li>
</ul>
<a name="computeThermodynamics(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">
<!--   -->
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<h4>computeThermodynamics</h4>
<pre>public&nbsp;<a href="../../../melting/ThermoResult.html" title="class in melting">ThermoResult</a>&nbsp;computeThermodynamics(<a href="../../../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a>&nbsp;sequences,
                                 int&nbsp;pos1,
                                 int&nbsp;pos2,
                                 <a href="../../../melting/ThermoResult.html" title="class in melting">ThermoResult</a>&nbsp;result)</pre>
<dl>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#computeThermodynamics(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">computeThermodynamics</a></code>&nbsp;in interface&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></code></dd>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/patternModels/PatternComputation.html#computeThermodynamics(melting.sequences.NucleotidSequences, int, int, melting.ThermoResult)">computeThermodynamics</a></code>&nbsp;in class&nbsp;<code><a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></code></dd>
<dt><span class="strong">Parameters:</span></dt><dd><code>sequences</code> - which contains the sequences entered by the user.</dd><dd><code>result</code> - which contains the computed enthalpy, entropy and melting temperature.</dd>
<dt><span class="strong">Returns:</span></dt><dd>ThermoResult result which contains the incremented enthalpy and entropy values.</dd></dl>
</li>
</ul>
<a name="isMissingParameters(melting.sequences.NucleotidSequences, int, int)">
<!--   -->
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<ul class="blockList">
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<h4>isMissingParameters</h4>
<pre>public&nbsp;boolean&nbsp;isMissingParameters(<a href="../../../melting/sequences/NucleotidSequences.html" title="class in melting.sequences">NucleotidSequences</a>&nbsp;sequences,
                          int&nbsp;pos1,
                          int&nbsp;pos2)</pre>
<div class="block"><strong>Description copied from interface:&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#isMissingParameters(melting.sequences.NucleotidSequences, int, int)">PatternComputationMethod</a></code></strong></div>
<div class="block">Check if one thermodynamic parameter is missing to compute the enthalpy and entropy of the pattern 
 at the positions pos1 and pos2.</div>
<dl>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#isMissingParameters(melting.sequences.NucleotidSequences, int, int)">isMissingParameters</a></code>&nbsp;in interface&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></code></dd>
<dt><strong>Overrides:</strong></dt>
<dd><code><a href="../../../melting/patternModels/PatternComputation.html#isMissingParameters(melting.sequences.NucleotidSequences, int, int)">isMissingParameters</a></code>&nbsp;in class&nbsp;<code><a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></code></dd>
<dt><span class="strong">Parameters:</span></dt><dd><code>sequences</code> - which contains the sequences entered by the user.</dd>
<dt><span class="strong">Returns:</span></dt><dd>false if one necessary thermodynamic parameter is missing.</dd></dl>
</li>
</ul>
<a name="initialiseFileName(java.lang.String)">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>initialiseFileName</h4>
<pre>public&nbsp;void&nbsp;initialiseFileName(java.lang.String&nbsp;methodName)</pre>
<div class="block"><strong>Description copied from interface:&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#initialiseFileName(java.lang.String)">PatternComputationMethod</a></code></strong></div>
<div class="block">If a file name is entered by the user, the file name of the model becomes the file name entered by the user,
 otherwise the default file name of the model is used.</div>
<dl>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html#initialiseFileName(java.lang.String)">initialiseFileName</a></code>&nbsp;in interface&nbsp;<code><a href="../../../melting/methodInterfaces/PatternComputationMethod.html" title="interface in melting.methodInterfaces">PatternComputationMethod</a></code></dd>
<dt><strong>Overrides:</strong></dt>
<dd><code><a href="../../../melting/patternModels/PatternComputation.html#initialiseFileName(java.lang.String)">initialiseFileName</a></code>&nbsp;in class&nbsp;<code><a href="../../../melting/patternModels/PatternComputation.html" title="class in melting.patternModels">PatternComputation</a></code></dd>
<dt><span class="strong">Parameters:</span></dt><dd><code>methodName</code> - : method or model name entered by the user.</dd></dl>
</li>
</ul>
<a name="getName()">
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<h4>getName</h4>
<pre>public&nbsp;java.lang.String&nbsp;getName()</pre>
<div class="block">Gets the full name of the method.</div>
<dl>
<dt><strong>Specified by:</strong></dt>
<dd><code><a href="../../../melting/methodInterfaces/NamedMethod.html#getName()">getName</a></code>&nbsp;in interface&nbsp;<code><a href="../../../melting/methodInterfaces/NamedMethod.html" title="interface in melting.methodInterfaces">NamedMethod</a></code></dd>
<dt><span class="strong">Returns:</span></dt><dd>The full name of the method.</dd></dl>
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