321 lines
23 KiB
HTML
321 lines
23 KiB
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<div id="projectname">DNA Calib<span id="projectnumber"> 1.1</span>
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<a href="#func-members">Functions</a> </div>
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<div class="headertitle"><div class="title">remove_joint Namespace Reference</div></div>
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</div><!--header-->
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<div class="contents">
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
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Functions</h2></td></tr>
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<tr class="memitem:ade0f539034a1002bcf88699bc699361e"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#ade0f539034a1002bcf88699bc699361e">loadDNA</a> (path)</td></tr>
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<tr class="separator:ade0f539034a1002bcf88699bc699361e"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a43d4e1b299b48a255cac5bc9e7c0b86f"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#a43d4e1b299b48a255cac5bc9e7c0b86f">saveDNA</a> (reader, path)</td></tr>
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<tr class="separator:a43d4e1b299b48a255cac5bc9e7c0b86f"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ade3a3c766635ef3e837512e08e606923"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">getJoints</a> (dna)</td></tr>
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<tr class="memitem:af612e121a4f9c2b1ae64689cfa583682"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#af612e121a4f9c2b1ae64689cfa583682">printJoints</a> (dna)</td></tr>
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<tr class="separator:af612e121a4f9c2b1ae64689cfa583682"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa3e9973ccb6a0b57fd690202006e9a93"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA</a> (inputPath, outputPath)</td></tr>
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<tr class="separator:aa3e9973ccb6a0b57fd690202006e9a93"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a82e2d3e13e2bac1b012f402ea2f13654"><td class="memItemLeft" align="right" valign="top">def </td><td class="memItemRight" valign="bottom"><a class="el" href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">main</a> ()</td></tr>
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</table>
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<h2 class="groupheader">Function Documentation</h2>
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<a id="aa3e9973ccb6a0b57fd690202006e9a93" name="aa3e9973ccb6a0b57fd690202006e9a93"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#aa3e9973ccb6a0b57fd690202006e9a93">◆ </a></span>calibrateDNA()</h2>
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<td class="memname">def remove_joint.calibrateDNA </td>
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<td>(</td>
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<td class="paramtype"> </td>
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<td class="paramname"><em>inputPath</em>, </td>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype"> </td>
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<td class="paramname"><em>outputPath</em> </td>
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<td></td>
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<td>)</td>
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<div class="fragment"><div class="line"><span class="lineno"> 38</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA</a>(inputPath, outputPath):</div>
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<div class="line"><span class="lineno"> 39</span> dna = <a class="code hl_function" href="namespaceremove__joint.html#ade0f539034a1002bcf88699bc699361e">loadDNA</a>(inputPath)</div>
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<div class="line"><span class="lineno"> 40</span> </div>
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<div class="line"><span class="lineno"> 41</span> <span class="comment"># Copies DNA contents and will serve as input/output parameter to command</span></div>
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<div class="line"><span class="lineno"> 42</span> calibrated = <a class="code hl_class" href="classdnac_1_1DNACalibDNAReader.html">dnac.DNACalibDNAReader</a>(dna)</div>
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<div class="line"><span class="lineno"> 43</span> </div>
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<div class="line"><span class="lineno"> 44</span> original_joints = <a class="code hl_function" href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">getJoints</a>(calibrated)</div>
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<div class="line"><span class="lineno"> 45</span> </div>
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<div class="line"><span class="lineno"> 46</span> <span class="comment"># An example joint to remove</span></div>
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<div class="line"><span class="lineno"> 47</span> joint_index = 314</div>
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<div class="line"><span class="lineno"> 48</span> joint_name = calibrated.getJointName(joint_index)</div>
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<div class="line"><span class="lineno"> 49</span> </div>
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<div class="line"><span class="lineno"> 50</span> <span class="comment"># Removes joint with specified index</span></div>
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<div class="line"><span class="lineno"> 51</span> command = <a class="code hl_class" href="classdnac_1_1RemoveJointCommand.html">dnac.RemoveJointCommand</a>(joint_index)</div>
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<div class="line"><span class="lineno"> 52</span> </div>
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<div class="line"><span class="lineno"> 53</span> <span class="comment"># Modifies calibrated DNA in-place</span></div>
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<div class="line"><span class="lineno"> 54</span> command.run(calibrated)</div>
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<div class="line"><span class="lineno"> 55</span> </div>
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<div class="line"><span class="lineno"> 56</span> modified_joints = <a class="code hl_function" href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">getJoints</a>(calibrated)</div>
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<div class="line"><span class="lineno"> 57</span> </div>
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<div class="line"><span class="lineno"> 58</span> <span class="keywordflow">if</span> ((len(modified_joints) != (len(original_joints) - 1)) <span class="keywordflow">or</span> (joint_name <span class="keywordflow">in</span> modified_joints)):</div>
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<div class="line"><span class="lineno"> 59</span> <span class="keywordflow">raise</span> RuntimeError(<span class="stringliteral">"Joint not removed properly!"</span>)</div>
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<div class="line"><span class="lineno"> 60</span> </div>
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<div class="line"><span class="lineno"> 61</span> print(<span class="stringliteral">"Successfully removed joint `{}`."</span>.format(joint_name))</div>
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<div class="line"><span class="lineno"> 62</span> </div>
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<div class="line"><span class="lineno"> 63</span> print(<span class="stringliteral">"Saving DNA..."</span>)</div>
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<div class="line"><span class="lineno"> 64</span> <a class="code hl_function" href="namespaceremove__joint.html#a43d4e1b299b48a255cac5bc9e7c0b86f">saveDNA</a>(calibrated, outputPath)</div>
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<div class="line"><span class="lineno"> 65</span> </div>
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<div class="line"><span class="lineno"> 66</span> print(<span class="stringliteral">"Done."</span>)</div>
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<div class="line"><span class="lineno"> 67</span> </div>
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<div class="ttc" id="aclassdnac_1_1DNACalibDNAReader_html"><div class="ttname"><a href="classdnac_1_1DNACalibDNAReader.html">dnac::DNACalibDNAReader</a></div><div class="ttdef"><b>Definition:</b> DNACalibDNAReader.h:12</div></div>
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<div class="ttc" id="aclassdnac_1_1RemoveJointCommand_html"><div class="ttname"><a href="classdnac_1_1RemoveJointCommand.html">dnac::RemoveJointCommand</a></div><div class="ttdoc">RemoveJointCommand is used to remove a joint.</div><div class="ttdef"><b>Definition:</b> RemoveJointCommand.h:18</div></div>
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<div class="ttc" id="anamespaceremove__joint_html_a43d4e1b299b48a255cac5bc9e7c0b86f"><div class="ttname"><a href="namespaceremove__joint.html#a43d4e1b299b48a255cac5bc9e7c0b86f">remove_joint.saveDNA</a></div><div class="ttdeci">def saveDNA(reader, path)</div><div class="ttdef"><b>Definition:</b> remove_joint.py:18</div></div>
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<div class="ttc" id="anamespaceremove__joint_html_aa3e9973ccb6a0b57fd690202006e9a93"><div class="ttname"><a href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">remove_joint.calibrateDNA</a></div><div class="ttdeci">def calibrateDNA(inputPath, outputPath)</div><div class="ttdef"><b>Definition:</b> remove_joint.py:38</div></div>
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<div class="ttc" id="anamespaceremove__joint_html_ade0f539034a1002bcf88699bc699361e"><div class="ttname"><a href="namespaceremove__joint.html#ade0f539034a1002bcf88699bc699361e">remove_joint.loadDNA</a></div><div class="ttdeci">def loadDNA(path)</div><div class="ttdef"><b>Definition:</b> remove_joint.py:8</div></div>
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<div class="ttc" id="anamespaceremove__joint_html_ade3a3c766635ef3e837512e08e606923"><div class="ttname"><a href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">remove_joint.getJoints</a></div><div class="ttdeci">def getJoints(dna)</div><div class="ttdef"><b>Definition:</b> remove_joint.py:28</div></div>
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</div><!-- fragment -->
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<p class="reference">References <a class="el" href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">getJoints()</a>, <a class="el" href="namespaceremove__joint.html#ade0f539034a1002bcf88699bc699361e">loadDNA()</a>, and <a class="el" href="namespaceremove__joint.html#a43d4e1b299b48a255cac5bc9e7c0b86f">saveDNA()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">main()</a>.</p>
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<a id="ade3a3c766635ef3e837512e08e606923" name="ade3a3c766635ef3e837512e08e606923"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ade3a3c766635ef3e837512e08e606923">◆ </a></span>getJoints()</h2>
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<td class="memname">def remove_joint.getJoints </td>
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<td>(</td>
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<td class="paramtype"> </td>
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<td class="paramname"><em>dna</em></td><td>)</td>
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<div class="fragment"><div class="line"><span class="lineno"> 28</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#ade3a3c766635ef3e837512e08e606923">getJoints</a>(dna):</div>
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<div class="line"><span class="lineno"> 29</span> joints = []</div>
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<div class="line"><span class="lineno"> 30</span> <span class="keywordflow">for</span> jointIndex <span class="keywordflow">in</span> range(dna.getJointCount()):</div>
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<div class="line"><span class="lineno"> 31</span> joints.append(dna.getJointName(jointIndex))</div>
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<div class="line"><span class="lineno"> 32</span> <span class="keywordflow">return</span> joints</div>
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<div class="line"><span class="lineno"> 33</span> </div>
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</div><!-- fragment -->
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<p class="reference">Referenced by <a class="el" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA()</a>.</p>
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<a id="ade0f539034a1002bcf88699bc699361e" name="ade0f539034a1002bcf88699bc699361e"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ade0f539034a1002bcf88699bc699361e">◆ </a></span>loadDNA()</h2>
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<td class="memname">def remove_joint.loadDNA </td>
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<td>(</td>
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<td class="paramtype"> </td>
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<td class="paramname"><em>path</em></td><td>)</td>
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<div class="fragment"><div class="line"><span class="lineno"> 8</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#ade0f539034a1002bcf88699bc699361e">loadDNA</a>(path):</div>
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<div class="line"><span class="lineno"> 9</span> stream = <a class="code hl_class" href="classtrio_1_1FileStream.html">dna.FileStream</a>(path, dna.FileStream.AccessMode_Read, dna.FileStream.OpenMode_Binary)</div>
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<div class="line"><span class="lineno"> 10</span> reader = <a class="code hl_class" href="classdna_1_1BinaryStreamReader.html">dna.BinaryStreamReader</a>(stream, dna.DataLayer_All)</div>
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<div class="line"><span class="lineno"> 11</span> reader.read()</div>
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<div class="line"><span class="lineno"> 12</span> <span class="keywordflow">if</span> <span class="keywordflow">not</span> dna.Status.isOk():</div>
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<div class="line"><span class="lineno"> 13</span> status = dna.Status.get()</div>
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<div class="line"><span class="lineno"> 14</span> <span class="keywordflow">raise</span> RuntimeError(<span class="stringliteral">"Error loading DNA: {}"</span>.format(status.message))</div>
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<div class="line"><span class="lineno"> 15</span> <span class="keywordflow">return</span> reader</div>
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<div class="line"><span class="lineno"> 16</span> </div>
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<div class="line"><span class="lineno"> 17</span> </div>
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<div class="ttc" id="aclassdna_1_1BinaryStreamReader_html"><div class="ttname"><a href="classdna_1_1BinaryStreamReader.html">dna::BinaryStreamReader</a></div><div class="ttdef"><b>Definition:</b> BinaryStreamReader.h:12</div></div>
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<div class="ttc" id="aclasstrio_1_1FileStream_html"><div class="ttname"><a href="classtrio_1_1FileStream.html">trio::FileStream</a></div><div class="ttdoc">Standard file stream.</div><div class="ttdef"><b>Definition:</b> FileStream.h:13</div></div>
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<p class="reference">Referenced by <a class="el" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA()</a>.</p>
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<a id="a82e2d3e13e2bac1b012f402ea2f13654" name="a82e2d3e13e2bac1b012f402ea2f13654"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a82e2d3e13e2bac1b012f402ea2f13654">◆ </a></span>main()</h2>
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<td class="memname">def remove_joint.main </td>
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<td>(</td>
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<div class="fragment"><div class="line"><span class="lineno"> 68</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">main</a>():</div>
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<div class="line"><span class="lineno"> 69</span> parser = argparse.ArgumentParser(description=<span class="stringliteral">"DNACalib remove joint example"</span>)</div>
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<div class="line"><span class="lineno"> 70</span> parser.add_argument(<span class="stringliteral">'input_dna'</span>,</div>
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<div class="line"><span class="lineno"> 71</span> metavar=<span class="stringliteral">'input-dna'</span>,</div>
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<div class="line"><span class="lineno"> 72</span> help=<span class="stringliteral">'Path to DNA file to load'</span>)</div>
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<div class="line"><span class="lineno"> 73</span> parser.add_argument(<span class="stringliteral">'output_dna'</span>,</div>
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<div class="line"><span class="lineno"> 74</span> metavar=<span class="stringliteral">'output-dna'</span>,</div>
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<div class="line"><span class="lineno"> 75</span> help=<span class="stringliteral">'Path where to save modified DNA file'</span>)</div>
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<div class="line"><span class="lineno"> 76</span> </div>
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<div class="line"><span class="lineno"> 77</span> args = parser.parse_args()</div>
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<div class="line"><span class="lineno"> 78</span> </div>
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<div class="line"><span class="lineno"> 79</span> <a class="code hl_function" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA</a>(args.input_dna, args.output_dna)</div>
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<div class="line"><span class="lineno"> 80</span> </div>
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<div class="line"><span class="lineno"> 81</span> </div>
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<div class="ttc" id="anamespaceremove__joint_html_a82e2d3e13e2bac1b012f402ea2f13654"><div class="ttname"><a href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">remove_joint.main</a></div><div class="ttdeci">def main()</div><div class="ttdef"><b>Definition:</b> remove_joint.py:68</div></div>
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<p class="reference">References <a class="el" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA()</a>, and <a class="el" href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">main()</a>.</p>
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<p class="reference">Referenced by <a class="el" href="namespaceremove__joint.html#a82e2d3e13e2bac1b012f402ea2f13654">main()</a>.</p>
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<a id="af612e121a4f9c2b1ae64689cfa583682" name="af612e121a4f9c2b1ae64689cfa583682"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#af612e121a4f9c2b1ae64689cfa583682">◆ </a></span>printJoints()</h2>
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<td class="memname">def remove_joint.printJoints </td>
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<td>(</td>
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<td class="paramtype"> </td>
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<td class="paramname"><em>dna</em></td><td>)</td>
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<td></td>
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<div class="fragment"><div class="line"><span class="lineno"> 34</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#af612e121a4f9c2b1ae64689cfa583682">printJoints</a>(dna):</div>
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<div class="line"><span class="lineno"> 35</span> <span class="keywordflow">for</span> jointIndex <span class="keywordflow">in</span> range(dna.getJointCount()):</div>
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<div class="line"><span class="lineno"> 36</span> print(dna.getJointName(jointIndex))</div>
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<div class="line"><span class="lineno"> 37</span> </div>
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<div class="ttc" id="anamespaceremove__joint_html_af612e121a4f9c2b1ae64689cfa583682"><div class="ttname"><a href="namespaceremove__joint.html#af612e121a4f9c2b1ae64689cfa583682">remove_joint.printJoints</a></div><div class="ttdeci">def printJoints(dna)</div><div class="ttdef"><b>Definition:</b> remove_joint.py:34</div></div>
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<a id="a43d4e1b299b48a255cac5bc9e7c0b86f" name="a43d4e1b299b48a255cac5bc9e7c0b86f"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#a43d4e1b299b48a255cac5bc9e7c0b86f">◆ </a></span>saveDNA()</h2>
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<td class="memname">def remove_joint.saveDNA </td>
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<td class="paramname"><em>reader</em>, </td>
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<td class="paramname"><em>path</em> </td>
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<div class="fragment"><div class="line"><span class="lineno"> 18</span><span class="keyword">def </span><a class="code hl_function" href="namespaceremove__joint.html#a43d4e1b299b48a255cac5bc9e7c0b86f">saveDNA</a>(reader, path):</div>
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<div class="line"><span class="lineno"> 19</span> stream = <a class="code hl_class" href="classtrio_1_1FileStream.html">dna.FileStream</a>(path, dna.FileStream.AccessMode_Write, dna.FileStream.OpenMode_Binary)</div>
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<div class="line"><span class="lineno"> 20</span> writer = <a class="code hl_class" href="classdna_1_1BinaryStreamWriter.html">dna.BinaryStreamWriter</a>(stream)</div>
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<div class="line"><span class="lineno"> 21</span> writer.setFrom(reader)</div>
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<div class="line"><span class="lineno"> 22</span> writer.write()</div>
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<div class="line"><span class="lineno"> 23</span> </div>
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<div class="line"><span class="lineno"> 24</span> <span class="keywordflow">if</span> <span class="keywordflow">not</span> dna.Status.isOk():</div>
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<div class="line"><span class="lineno"> 25</span> status = dna.Status.get()</div>
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<div class="line"><span class="lineno"> 26</span> <span class="keywordflow">raise</span> RuntimeError(<span class="stringliteral">"Error saving DNA: {}"</span>.format(status.message))</div>
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<div class="line"><span class="lineno"> 27</span> </div>
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<div class="ttc" id="aclassdna_1_1BinaryStreamWriter_html"><div class="ttname"><a href="classdna_1_1BinaryStreamWriter.html">dna::BinaryStreamWriter</a></div><div class="ttdef"><b>Definition:</b> BinaryStreamWriter.h:11</div></div>
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</div><!-- fragment -->
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<p class="reference">Referenced by <a class="el" href="namespaceremove__joint.html#aa3e9973ccb6a0b57fd690202006e9a93">calibrateDNA()</a>.</p>
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