Quick Start.ipynb

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   "source": [
    "# Quick Start"
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    "This page provides an overview of the functionalities of MassDash and shows a highlights a few convience functions to help you get started with the python interface. The python interface is designed to be run in a jupyter notebook so that plots can be reproducibly generated for a particular peptide of interest."
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    "%load_ext autoreload\n",
    "%autoreload 2"
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    "# Please run this before executing any cell\n",
    "import os\n",
    "os.chdir(\"../../test/test_data/\") #### Insert path to data, this is the path to the tutorial data. "
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   "source": [
    "## Plotting a Chromatogram"
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   "source": [
    "Here, we will demonstrate how to plot a chromatogram of the peptide *NKESPT(UniMod:21)KAIVR(UniMod:267)* with a charge state of *3* from multiple different file inputs. The general process is that first the loader object must be initiated and then we can call the `plotChromatogram()` method to fetch an interactive plot for a specified precursor. "
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   "source": [
    "### SqMass Visualization"
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    "Running [OpenSwath](http://www.openswath.org) with a `out_chrom filename.sqMass` will output the extracted chromatograms alongside the OpenSwath results. Since extraction is already performed this is the quickest way to visualize plots. "
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    "Since the .sqMass file does not contain any metadata, to link chromatograms with their corresponding peptide sequence we must link an ``.osw`` file with the ``.sqMass`` file. In MassDash this is done by initiating a :py:class:`~loaders.SqMassLoader` as shown below.  "
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     "text": [
      "Initializing valid scores for selection\n"
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   "source": [
    "from massdash.loaders import SqMassLoader\n",
    "sqMassLoader = SqMassLoader(rsltsFile='osw/test_data.osw', dataFiles='xics/test_chrom_1.sqMass')"
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    "Now that the :py:class:`~plotting.SqMassLoader` is initiated we can use it to plot a chroamtogram. To plot a chromatogram, we use the :py:func:`~structs.SqMassLoader.plotChromatogram` function."
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     "text": [
      "-------- TransitionGroup --------\n",
      "precursor data: 1\n",
      "transition data: 6\n",
      "data type: Chromatogram\n"
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Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"1004\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\nif (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(\"1004\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
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3\"},\"renderers\":[{\"id\":\"1130\"}]},\"id\":\"1168\",\"type\":\"LegendItem\"},{\"attributes\":{},\"id\":\"1192\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"1186\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"1196\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"1193\",\"type\":\"Selection\"},{\"attributes\":{\"label\":{\"value\":\"Feature 4\"},\"renderers\":[{\"id\":\"1149\"}]},\"id\":\"1169\",\"type\":\"LegendItem\"},{\"attributes\":{},\"id\":\"1177\",\"type\":\"AllLabels\"},{\"attributes\":{\"callback\":null,\"names\":[\"leftWidth_apex_point\"],\"tooltips\":[[\"Intensity\",\"@Intensity\"],[\"Left Width\",\"@leftWidth{0.00}\"],[\"Right Width\",\"@rightWidth{0.00}\"],[\"Peak Group Rank\",\"@peakgroup_rank\"],[\"MS2 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Application\",\"version\":\"2.4.3\"}};\n",
       "  const render_items = [{\"docid\":\"cd7c9d9f-7f71-4d8d-ba42-fd753f04b357\",\"root_ids\":[\"1005\"],\"roots\":{\"1005\":\"ca510ad1-f5d7-415b-94a7-d873b2d12f3c\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    let attempts = 0;\n",
       "    const timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
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      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1005"
      }
     },
     "output_type": "display_data"
    },
    {
     "data": {
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style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">below&nbsp;=&nbsp;[LinearAxis(id='1014', ...)],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">center&nbsp;=&nbsp;[Grid(id='1017', ...), Grid(id='1021', ...)],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">css_classes&nbsp;=&nbsp;[],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">disabled&nbsp;=&nbsp;False,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_scales&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_scales&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_height&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_width&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height&nbsp;=&nbsp;450,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">hidpi&nbsp;=&nbsp;True,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_height&nbsp;=&nbsp;0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_width&nbsp;=&nbsp;0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_event_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_property_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">left&nbsp;=&nbsp;[LinearAxis(id='1018', ...)],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_factor&nbsp;=&nbsp;10,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_interval&nbsp;=&nbsp;300,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_threshold&nbsp;=&nbsp;2000,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_timeout&nbsp;=&nbsp;500,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">margin&nbsp;=&nbsp;(0, 0, 0, 0),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">match_aspect&nbsp;=&nbsp;False,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_height&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_width&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border&nbsp;=&nbsp;5,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_bottom&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_left&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_right&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_top&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_height&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_width&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">name&nbsp;=&nbsp;None,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_height&nbsp;=&nbsp;0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_width&nbsp;=&nbsp;0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_cap&nbsp;=&nbsp;'butt',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_color&nbsp;=&nbsp;'#e5e5e5',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash&nbsp;=&nbsp;[],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash_offset&nbsp;=&nbsp;0,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_join&nbsp;=&nbsp;'bevel',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_width&nbsp;=&nbsp;1,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">output_backend&nbsp;=&nbsp;'canvas',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">renderers&nbsp;=&nbsp;[GlyphRenderer(id='1044', ...), GlyphRenderer(id='1051', ...), GlyphRenderer(id='1058', ...), GlyphRenderer(id='1065', ...), GlyphRenderer(id='1072', ...), GlyphRenderer(id='1079', ...), GlyphRenderer(id='1092', ...), GlyphRenderer(id='1098', ...), GlyphRenderer(id='1104', ...), GlyphRenderer(id='1111', ...), GlyphRenderer(id='1117', ...), GlyphRenderer(id='1123', ...), GlyphRenderer(id='1130', ...), GlyphRenderer(id='1136', ...), GlyphRenderer(id='1142', ...), GlyphRenderer(id='1149', ...), GlyphRenderer(id='1155', ...), GlyphRenderer(id='1161', ...)],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">reset_policy&nbsp;=&nbsp;'standard',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">right&nbsp;=&nbsp;[Legend(id='1038', ...)],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">sizing_mode&nbsp;=&nbsp;'scale_width',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">subscribed_events&nbsp;=&nbsp;[],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">syncable&nbsp;=&nbsp;True,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">tags&nbsp;=&nbsp;[],</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title&nbsp;=&nbsp;Title(id='1170', ...),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title_location&nbsp;=&nbsp;'above',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar&nbsp;=&nbsp;Toolbar(id='1030', ...),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_location&nbsp;=&nbsp;'above',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_sticky&nbsp;=&nbsp;True,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">visible&nbsp;=&nbsp;True,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width&nbsp;=&nbsp;800,</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_range&nbsp;=&nbsp;DataRange1d(id='1006', ...),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_scale&nbsp;=&nbsp;LinearScale(id='1010', ...),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_range&nbsp;=&nbsp;DataRange1d(id='1008', ...),</div></div><div class=\"1344\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_scale&nbsp;=&nbsp;LinearScale(id='1012', ...))</div></div></div>\n",
       "<script>\n",
       "(function() {\n",
       "  let expanded = false;\n",
       "  const ellipsis = document.getElementById(\"1345\");\n",
       "  ellipsis.addEventListener(\"click\", function() {\n",
       "    const rows = document.getElementsByClassName(\"1344\");\n",
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       "    }\n",
       "    ellipsis.innerHTML = expanded ? \"&hellip;)\" : \"&lsaquo;&lsaquo;&lsaquo;\";\n",
       "    expanded = !expanded;\n",
       "  });\n",
       "})();\n",
       "</script>\n"
      ],
      "text/plain": [
       "Figure(id='1005', ...)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sqMassLoader.plotChromatogram(\"NKESPT(UniMod:21)KAIVR(UniMod:267)\", 3)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "327371e4-0381-4344-8576-f9ba6b7fb054",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "By default the plot is smoothed and the boundaries of the features found in the OpenSwath file are plotted. The length of the boundary lines is indicative of the intensity of the feature. These can be turned off as shown below. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "caf0ff7e-8fc6-4771-98f1-11ae6b8ac71f",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "GenericChromatogramLoader.plotChromatogram() got an unexpected keyword argument 'title'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[0;32mIn[8], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msqMassLoader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mplotChromatogram\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mNKESPT(UniMod:21)KAIVR(UniMod:267)\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mincludeBoundaries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msmooth\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtitle\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mHello\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgrid\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
      "\u001b[0;31mTypeError\u001b[0m: GenericChromatogramLoader.plotChromatogram() got an unexpected keyword argument 'title'"
     ]
    }
   ],
   "source": [
    "sqMassLoader.plotChromatogram(\"NKESPT(UniMod:21)KAIVR(UniMod:267)\", 3, includeBoundaries=False, smooth=False, title=\"Hello\", grid=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4051ab11-c400-4824-84a7-82ea74dc93cc",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "Furthermore, the MS1 elution can also be shown."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "d4d6e554-f163-419c-b1bb-7b474c6d7546",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "        .bk-notebook-logo {\n",
       "            display: block;\n",
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       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-notebook-logo\"></a>\n",
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     "metadata": {},
     "output_type": "display_data"
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    {
     "data": {
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       "  function now() {\n",
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       "  const force = true;\n",
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       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
       "    root._bokeh_onload_callbacks = [];\n",
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       "  }\n",
       "\n",
       "const JS_MIME_TYPE = 'application/javascript';\n",
       "  const HTML_MIME_TYPE = 'text/html';\n",
       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    const script = document.createElement(\"script\");\n",
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       "\n",
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       "    function drop(id) {\n",
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       "\n",
       "    // Clean up Bokeh references\n",
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       "\n",
       "    if (server_id !== undefined) {\n",
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       "      cell.notebook.kernel.execute(cmd_clean, {\n",
       "        iopub: {\n",
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       "      // Destroy server and session\n",
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       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
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       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
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       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
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       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "      const bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      const script_attrs = bk_div.children[0].attributes;\n",
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       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
       "      }\n",
       "      // store reference to server id on output_area\n",
       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function register_renderer(events, OutputArea) {\n",
       "\n",
       "    function append_mime(data, metadata, element) {\n",
       "      // create a DOM node to render to\n",
       "      const toinsert = this.create_output_subarea(\n",
       "        metadata,\n",
       "        CLASS_NAME,\n",
       "        EXEC_MIME_TYPE\n",
       "      );\n",
       "      this.keyboard_manager.register_events(toinsert);\n",
       "      // Render to node\n",
       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "      render(props, toinsert[toinsert.length - 1]);\n",
       "      element.append(toinsert);\n",
       "      return toinsert\n",
       "    }\n",
       "\n",
       "    /* Handle when an output is cleared or removed */\n",
       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
       "    events.on('delete.Cell', handleClearOutput);\n",
       "\n",
       "    /* Handle when a new output is added */\n",
       "    events.on('output_added.OutputArea', handleAddOutput);\n",
       "\n",
       "    /**\n",
       "     * Register the mime type and append_mime function with output_area\n",
       "     */\n",
       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "      /* Is output safe? */\n",
       "      safe: true,\n",
       "      /* Index of renderer in `output_area.display_order` */\n",
       "      index: 0\n",
       "    });\n",
       "  }\n",
       "\n",
       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
       "  if (root.Jupyter !== undefined) {\n",
       "    const events = require('base/js/events');\n",
       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  }\n",
       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
       "    root._bokeh_timeout = Date.now() + 5000;\n",
       "    root._bokeh_failed_load = false;\n",
       "  }\n",
       "\n",
       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\n\"+\n",
       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded(error = null) {\n",
       "    const el = document.getElementById(\"eff78e8f-fd60-4c83-81ad-64f161daec36\");\n",
       "    if (el != null) {\n",
       "      const html = (() => {\n",
       "        if (typeof root.Bokeh === \"undefined\") {\n",
       "          if (error == null) {\n",
       "            return \"BokehJS is loading ...\";\n",
       "          } else {\n",
       "            return \"BokehJS failed to load.\";\n",
       "          }\n",
       "        } else {\n",
       "          const prefix = `BokehJS ${root.Bokeh.version}`;\n",
       "          if (error == null) {\n",
       "            return `${prefix} successfully loaded.`;\n",
       "          } else {\n",
       "            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n",
       "          }\n",
       "        }\n",
       "      })();\n",
       "      el.innerHTML = html;\n",
       "\n",
       "      if (error != null) {\n",
       "        const wrapper = document.createElement(\"div\");\n",
       "        wrapper.style.overflow = \"auto\";\n",
       "        wrapper.style.height = \"5em\";\n",
       "        wrapper.style.resize = \"vertical\";\n",
       "        const content = document.createElement(\"div\");\n",
       "        content.style.fontFamily = \"monospace\";\n",
       "        content.style.whiteSpace = \"pre-wrap\";\n",
       "        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n",
       "        content.textContent = error.stack ?? error.toString();\n",
       "        wrapper.append(content);\n",
       "        el.append(wrapper);\n",
       "      }\n",
       "    } else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(() => display_loaded(error), 100);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function run_callbacks() {\n",
       "    try {\n",
       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
       "        if (callback != null)\n",
       "          callback();\n",
       "      });\n",
       "    } finally {\n",
       "      delete root._bokeh_onload_callbacks\n",
       "    }\n",
       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
       "  }\n",
       "\n",
       "  function load_libs(css_urls, js_urls, callback) {\n",
       "    if (css_urls == null) css_urls = [];\n",
       "    if (js_urls == null) js_urls = [];\n",
       "\n",
       "    root._bokeh_onload_callbacks.push(callback);\n",
       "    if (root._bokeh_is_loading > 0) {\n",
       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "      return null;\n",
       "    }\n",
       "    if (js_urls == null || js_urls.length === 0) {\n",
       "      run_callbacks();\n",
       "      return null;\n",
       "    }\n",
       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
       "\n",
       "    function on_load() {\n",
       "      root._bokeh_is_loading--;\n",
       "      if (root._bokeh_is_loading === 0) {\n",
       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
       "        run_callbacks()\n",
       "      }\n",
       "    }\n",
       "\n",
       "    function on_error(url) {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (let i = 0; i < css_urls.length; i++) {\n",
       "      const url = css_urls[i];\n",
       "      const element = document.createElement(\"link\");\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\n",
       "      element.rel = \"stylesheet\";\n",
       "      element.type = \"text/css\";\n",
       "      element.href = url;\n",
       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
       "      document.body.appendChild(element);\n",
       "    }\n",
       "\n",
       "    for (let i = 0; i < js_urls.length; i++) {\n",
       "      const url = js_urls[i];\n",
       "      const element = document.createElement('script');\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\n",
       "      element.async = false;\n",
       "      element.src = url;\n",
       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "      document.head.appendChild(element);\n",
       "    }\n",
       "  };\n",
       "\n",
       "  function inject_raw_css(css) {\n",
       "    const element = document.createElement(\"style\");\n",
       "    element.appendChild(document.createTextNode(css));\n",
       "    document.body.appendChild(element);\n",
       "  }\n",
       "\n",
       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.0.min.js\"];\n",
       "  const css_urls = [];\n",
       "\n",
       "  const inline_js = [    function(Bokeh) {\n",
       "      Bokeh.set_log_level(\"info\");\n",
       "    },\n",
       "function(Bokeh) {\n",
       "    }\n",
       "  ];\n",
       "\n",
       "  function run_inline_js() {\n",
       "    if (root.Bokeh !== undefined || force === true) {\n",
       "      try {\n",
       "            for (let i = 0; i < inline_js.length; i++) {\n",
       "      inline_js[i].call(root, root.Bokeh);\n",
       "    }\n",
       "\n",
       "      } catch (error) {display_loaded(error);throw error;\n",
       "      }if (force === true) {\n",
       "        display_loaded();\n",
       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(run_inline_js, 100);\n",
       "    } else if (!root._bokeh_failed_load) {\n",
       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "      root._bokeh_failed_load = true;\n",
       "    } else if (force !== true) {\n",
       "      const cell = $(document.getElementById(\"eff78e8f-fd60-4c83-81ad-64f161daec36\")).parents('.cell').data().cell;\n",
       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "    }\n",
       "  }\n",
       "\n",
       "  if (root._bokeh_is_loading === 0) {\n",
       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
       "  } else {\n",
       "    load_libs(css_urls, js_urls, function() {\n",
       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "      run_inline_js();\n",
       "    });\n",
       "  }\n",
       "}(window));"
      ],
      "application/vnd.bokehjs_load.v0+json": "'use strict';\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded(error = null) {\n    const el = document.getElementById(\"eff78e8f-fd60-4c83-81ad-64f161daec36\");\n    if (el != null) {\n      const html = (() => {\n        if (typeof root.Bokeh === \"undefined\") {\n          if (error == null) {\n            return \"BokehJS is loading ...\";\n          } else {\n            return \"BokehJS failed to load.\";\n          }\n        } else {\n          const prefix = `BokehJS ${root.Bokeh.version}`;\n          if (error == null) {\n            return `${prefix} successfully loaded.`;\n          } else {\n            return `${prefix} <b>encountered errors</b> while loading and may not function as expected.`;\n          }\n        }\n      })();\n      el.innerHTML = html;\n\n      if (error != null) {\n        const wrapper = document.createElement(\"div\");\n        wrapper.style.overflow = \"auto\";\n        wrapper.style.height = \"5em\";\n        wrapper.style.resize = \"vertical\";\n        const content = document.createElement(\"div\");\n        content.style.fontFamily = \"monospace\";\n        content.style.whiteSpace = \"pre-wrap\";\n        content.style.backgroundColor = \"rgb(255, 221, 221)\";\n        content.textContent = error.stack ?? error.toString();\n        wrapper.append(content);\n        el.append(wrapper);\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(() => display_loaded(error), 100);\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.6.0.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n      try {\n            for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n\n      } catch (error) {display_loaded(error);throw error;\n      }if (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(\"eff78e8f-fd60-4c83-81ad-64f161daec36\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Line width not set, defaulting to 2.5\n"
     ]
    },
    {
     "data": {
      "application/vnd.bokehjs_exec.v0+json": "",
      "text/html": [
       "<script id=\"ca5c5945-e0ea-488c-bc96-39b8cfb63d86\">\n",
       "  (function() {\n",
       "    const xhr = new XMLHttpRequest()\n",
       "    xhr.responseType = 'blob';\n",
       "    xhr.open('GET', \"http://localhost:35917/autoload.js?bokeh-autoload-element=ca5c5945-e0ea-488c-bc96-39b8cfb63d86&bokeh-absolute-url=http://localhost:35917&resources=none\", true);\n",
       "    xhr.withCredentials = false;\n",
       "    xhr.onload = function (event) {\n",
       "      const script = document.createElement('script');\n",
       "      const src = URL.createObjectURL(event.target.response);\n",
       "      script.src = src;\n",
       "      document.body.appendChild(script);\n",
       "    };\n",
       "    xhr.send();\n",
       "  })();\n",
       "</script>"
      ]
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "server_id": "22f560209d184ea7a8913c42fc785192"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "sqMassLoader.plotChromatogram(\"NKESPT(UniMod:21)KAIVR(UniMod:267)\", 3, include_ms1=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8b89c240-7cd8-4305-98e9-f59b5f866ccf",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "<div class=\"alert alert-info\">\n",
    "\n",
    "Note\n",
    "\n",
    "Boundaries shown are directly copied from the the OpenSwath output and are not effected by changing smoothing parameters.\n",
    "\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0856df57-0b9d-4dc4-9f25-c09a945a55f3",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "### MzML Visualization"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "18aa614d-6ec3-4d57-b0c2-70c9d8c6ab67",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "Chromatograms can also be extracted on the fly from .mzML files. This is useful for visualizing how a chromatogram would appear if different extraction parameters were used and if chromatograms were not saved upon data analysis. "
   ]
  },
  {
   "cell_type": "raw",
   "id": "73037ef3-9aaf-47bb-a35d-b3473d595c79",
   "metadata": {
    "editable": true,
    "raw_mimetype": "text/restructuredtext",
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "First we must initiate a :py:class:`~loaders.MzMLDataLoader` which links a `.mzML` file with a results file and a library file. Currently supported results files include `.osw` and a DIA-NN `.tsv` report. We can link multiple result files in a single loader object in order to compare the features across software tools as shown below."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "c1facffe-6e96-4248-bcda-4553bbcded82",
   "metadata": {
    "editable": true,
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Initializing valid scores for selection\n",
      "[2024-10-09 15:39:45,148] MzMLDataAccess - INFO - Opening example_dia/raw/test_raw_1.mzML file...: Elapsed 0.35804009437561035 ms\n",
      "[2024-10-09 15:39:45,149] MzMLDataAccess - INFO - There are 3867 spectra and 1 chromatograms.\n",
      "[2024-10-09 15:39:45,173] MzMLDataAccess - INFO - There are 117 MS1 spectra and 3750 MS2 spectra.\n"
     ]
    }
   ],
   "source": [
    "from massdash.loaders import MzMLDataLoader\n",
    "mzml_loader = MzMLDataLoader(rsltsFile=[\"example_dia/diann/report/test_1_diann_report.tsv\", \"example_dia/openswath/osw/test.osw\"], \n",
    "                            dataFiles=\"example_dia/raw/test_raw_1.mzML\",\n",
    "                            libraryFile=\"example_dia/diann/lib/test_1_lib.tsv\")"
   ]
  },
  {
   "cell_type": "raw",
   "id": "9da9da90-e397-46d6-ac76-fa1219edeb76",
   "metadata": {
    "editable": true,
    "raw_mimetype": "text/restructuredtext",
    "slideshow": {
     "slide_type": ""
    },
    "tags": []
   },
   "source": [
    "Now we can plot each of these using the :py:func:`~structs.MzMLLoader.plotChromatogram` function. Here, we must also specify extraction parameters such as mz_tol (in ppm) and rt_window (in seconds)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "f1028997-16e1-4313-9b77-e1b02c018d59",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div class=\"bk-root\">\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
       "        <span id=\"1348\">Loading BokehJS ...</span>\n",
       "    </div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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     "data": {
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       "(function(root) {\n",
       "  function now() {\n",
       "    return new Date();\n",
       "  }\n",
       "\n",
       "  const force = true;\n",
       "\n",
       "  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n",
       "    root._bokeh_onload_callbacks = [];\n",
       "    root._bokeh_is_loading = undefined;\n",
       "  }\n",
       "\n",
       "const JS_MIME_TYPE = 'application/javascript';\n",
       "  const HTML_MIME_TYPE = 'text/html';\n",
       "  const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  const CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    const script = document.createElement(\"script\");\n",
       "    node.appendChild(script);\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when an output is cleared or removed\n",
       "   */\n",
       "  function handleClearOutput(event, handle) {\n",
       "    const cell = handle.cell;\n",
       "\n",
       "    const id = cell.output_area._bokeh_element_id;\n",
       "    const server_id = cell.output_area._bokeh_server_id;\n",
       "    // Clean up Bokeh references\n",
       "    if (id != null && id in Bokeh.index) {\n",
       "      Bokeh.index[id].model.document.clear();\n",
       "      delete Bokeh.index[id];\n",
       "    }\n",
       "\n",
       "    if (server_id !== undefined) {\n",
       "      // Clean up Bokeh references\n",
       "      const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
       "      cell.notebook.kernel.execute(cmd_clean, {\n",
       "        iopub: {\n",
       "          output: function(msg) {\n",
       "            const id = msg.content.text.trim();\n",
       "            if (id in Bokeh.index) {\n",
       "              Bokeh.index[id].model.document.clear();\n",
       "              delete Bokeh.index[id];\n",
       "            }\n",
       "          }\n",
       "        }\n",
       "      });\n",
       "      // Destroy server and session\n",
       "      const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
       "      cell.notebook.kernel.execute(cmd_destroy);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when a new output is added\n",
       "   */\n",
       "  function handleAddOutput(event, handle) {\n",
       "    const output_area = handle.output_area;\n",
       "    const output = handle.output;\n",
       "\n",
       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
       "    if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n",
       "      return\n",
       "    }\n",
       "\n",
       "    const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
       "\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
       "      // store reference to embed id on output_area\n",
       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
       "    }\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "      const bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      const script_attrs = bk_div.children[0].attributes;\n",
       "      for (let i = 0; i < script_attrs.length; i++) {\n",
       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n",
       "      }\n",
       "      // store reference to server id on output_area\n",
       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function register_renderer(events, OutputArea) {\n",
       "\n",
       "    function append_mime(data, metadata, element) {\n",
       "      // create a DOM node to render to\n",
       "      const toinsert = this.create_output_subarea(\n",
       "        metadata,\n",
       "        CLASS_NAME,\n",
       "        EXEC_MIME_TYPE\n",
       "      );\n",
       "      this.keyboard_manager.register_events(toinsert);\n",
       "      // Render to node\n",
       "      const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "      render(props, toinsert[toinsert.length - 1]);\n",
       "      element.append(toinsert);\n",
       "      return toinsert\n",
       "    }\n",
       "\n",
       "    /* Handle when an output is cleared or removed */\n",
       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
       "    events.on('delete.Cell', handleClearOutput);\n",
       "\n",
       "    /* Handle when a new output is added */\n",
       "    events.on('output_added.OutputArea', handleAddOutput);\n",
       "\n",
       "    /**\n",
       "     * Register the mime type and append_mime function with output_area\n",
       "     */\n",
       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "      /* Is output safe? */\n",
       "      safe: true,\n",
       "      /* Index of renderer in `output_area.display_order` */\n",
       "      index: 0\n",
       "    });\n",
       "  }\n",
       "\n",
       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
       "  if (root.Jupyter !== undefined) {\n",
       "    const events = require('base/js/events');\n",
       "    const OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  }\n",
       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
       "    root._bokeh_timeout = Date.now() + 5000;\n",
       "    root._bokeh_failed_load = false;\n",
       "  }\n",
       "\n",
       "  const NB_LOAD_WARNING = {'data': {'text/html':\n",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\n\"+\n",
       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded() {\n",
       "    const el = document.getElementById(\"1348\");\n",
       "    if (el != null) {\n",
       "      el.textContent = \"BokehJS is loading...\";\n",
       "    }\n",
       "    if (root.Bokeh !== undefined) {\n",
       "      if (el != null) {\n",
       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
       "      }\n",
       "    } else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(display_loaded, 100)\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function run_callbacks() {\n",
       "    try {\n",
       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
       "        if (callback != null)\n",
       "          callback();\n",
       "      });\n",
       "    } finally {\n",
       "      delete root._bokeh_onload_callbacks\n",
       "    }\n",
       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
       "  }\n",
       "\n",
       "  function load_libs(css_urls, js_urls, callback) {\n",
       "    if (css_urls == null) css_urls = [];\n",
       "    if (js_urls == null) js_urls = [];\n",
       "\n",
       "    root._bokeh_onload_callbacks.push(callback);\n",
       "    if (root._bokeh_is_loading > 0) {\n",
       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "      return null;\n",
       "    }\n",
       "    if (js_urls == null || js_urls.length === 0) {\n",
       "      run_callbacks();\n",
       "      return null;\n",
       "    }\n",
       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
       "\n",
       "    function on_load() {\n",
       "      root._bokeh_is_loading--;\n",
       "      if (root._bokeh_is_loading === 0) {\n",
       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
       "        run_callbacks()\n",
       "      }\n",
       "    }\n",
       "\n",
       "    function on_error(url) {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (let i = 0; i < css_urls.length; i++) {\n",
       "      const url = css_urls[i];\n",
       "      const element = document.createElement(\"link\");\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\n",
       "      element.rel = \"stylesheet\";\n",
       "      element.type = \"text/css\";\n",
       "      element.href = url;\n",
       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
       "      document.body.appendChild(element);\n",
       "    }\n",
       "\n",
       "    for (let i = 0; i < js_urls.length; i++) {\n",
       "      const url = js_urls[i];\n",
       "      const element = document.createElement('script');\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error.bind(null, url);\n",
       "      element.async = false;\n",
       "      element.src = url;\n",
       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "      document.head.appendChild(element);\n",
       "    }\n",
       "  };\n",
       "\n",
       "  function inject_raw_css(css) {\n",
       "    const element = document.createElement(\"style\");\n",
       "    element.appendChild(document.createTextNode(css));\n",
       "    document.body.appendChild(element);\n",
       "  }\n",
       "\n",
       "  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\"];\n",
       "  const css_urls = [];\n",
       "\n",
       "  const inline_js = [    function(Bokeh) {\n",
       "      Bokeh.set_log_level(\"info\");\n",
       "    },\n",
       "function(Bokeh) {\n",
       "    }\n",
       "  ];\n",
       "\n",
       "  function run_inline_js() {\n",
       "    if (root.Bokeh !== undefined || force === true) {\n",
       "          for (let i = 0; i < inline_js.length; i++) {\n",
       "      inline_js[i].call(root, root.Bokeh);\n",
       "    }\n",
       "if (force === true) {\n",
       "        display_loaded();\n",
       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(run_inline_js, 100);\n",
       "    } else if (!root._bokeh_failed_load) {\n",
       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "      root._bokeh_failed_load = true;\n",
       "    } else if (force !== true) {\n",
       "      const cell = $(document.getElementById(\"1348\")).parents('.cell').data().cell;\n",
       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "    }\n",
       "  }\n",
       "\n",
       "  if (root._bokeh_is_loading === 0) {\n",
       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
       "  } else {\n",
       "    load_libs(css_urls, js_urls, function() {\n",
       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "      run_inline_js();\n",
       "    });\n",
       "  }\n",
       "}(window));"
      ],
      "application/vnd.bokehjs_load.v0+json": "(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  const force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n\n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  const NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    const el = document.getElementById(\"1348\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error(url) {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (let i = 0; i < css_urls.length; i++) {\n      const url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (let i = 0; i < js_urls.length; i++) {\n      const url = js_urls[i];\n      const element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error.bind(null, url);\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.4.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-2.4.3.min.js\"];\n  const css_urls = [];\n\n  const inline_js = [    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\nfunction(Bokeh) {\n    }\n  ];\n\n  function run_inline_js() {\n    if (root.Bokeh !== undefined || force === true) {\n          for (let i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\nif (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      const cell = $(document.getElementById(\"1348\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "  <div class=\"bk-root\" id=\"dc0fcb40-1810-45f9-b572-3907cc6f205a\" data-root-id=\"1349\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
       "  const docs_json = 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\"attributes\":{\"label\":{\"value\":\"b7^1\"},\"renderers\":[{\"id\":\"1416\"}]},\"id\":\"1485\",\"type\":\"LegendItem\"},{\"attributes\":{\"coordinates\":null,\"data_source\":{\"id\":\"1439\"},\"glyph\":{\"id\":\"1441\"},\"group\":null,\"hover_glyph\":null,\"muted_glyph\":{\"id\":\"1443\"},\"nonselection_glyph\":{\"id\":\"1442\"},\"view\":{\"id\":\"1445\"}},\"id\":\"1444\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"bottom_units\":\"screen\",\"coordinates\":null,\"fill_alpha\":0.5,\"fill_color\":\"lightgrey\",\"group\":null,\"left_units\":\"screen\",\"level\":\"overlay\",\"line_alpha\":1.0,\"line_color\":\"black\",\"line_dash\":[4,4],\"line_width\":2,\"right_units\":\"screen\",\"syncable\":false,\"top_units\":\"screen\"},\"id\":\"1372\",\"type\":\"BoxAnnotation\"},{\"attributes\":{\"label\":{\"value\":\"b8^1\"},\"renderers\":[{\"id\":\"1423\"}]},\"id\":\"1486\",\"type\":\"LegendItem\"},{\"attributes\":{},\"id\":\"1597\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"line_alpha\":0.1,\"line_color\":\"#8c564b\",\"line_width\":2,\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"1456\",\"type\":\"Line\"},{\"attributes\":{},\"id\":\"1574\",\"type\":\"AllLabels\"},{\"attributes\":{\"bottom\":{\"field\":\"bottom_int\"},\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1B9E77\"},\"hatch_alpha\":{\"value\":0.1},\"hatch_color\":{\"value\":\"#1B9E77\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1B9E77\"},\"top\":{\"field\":\"Intensity\"},\"width\":{\"value\":0.3},\"x\":{\"field\":\"rightWidth\"}},\"id\":\"1504\",\"type\":\"VBar\"},{\"attributes\":{\"source\":{\"id\":\"1404\"}},\"id\":\"1410\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"1371\",\"type\":\"HelpTool\"},{\"attributes\":{},\"id\":\"1598\",\"type\":\"Selection\"},{\"attributes\":{\"axis_label\":\"Retention Time\",\"axis_label_text_font_size\":\"11pt\",\"coordinates\":null,\"formatter\":{\"id\":\"1573\"},\"group\":null,\"major_label_policy\":{\"id\":\"1574\"},\"major_label_text_font_size\":\"11pt\",\"ticker\":{\"id\":\"1359\"}},\"id\":\"1358\",\"type\":\"LinearAxis\"},{\"attributes\":{\"line_alpha\":0.2,\"line_color\":\"#98df8a\",\"line_width\":2,\"x\":{\"field\":\"x\"},\"y\":{\"field\":\"y\"}},\"id\":\"1422\",\"type\":\"Line\"},{\"attributes\":{},\"id\":\"1589\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"coordinates\":null,\"data_source\":{\"id\":\"1453\"},\"glyph\":{\"id\":\"1455\"},\"group\":null,\"hover_glyph\":null,\"muted_glyph\":{\"id\":\"1457\"},\"nonselection_glyph\":{\"id\":\"1456\"},\"view\":{\"id\":\"1459\"}},\"id\":\"1458\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"source\":{\"id\":\"1474\"}},\"id\":\"1480\",\"type\":\"CDSView\"}],\"root_ids\":[\"1349\"]},\"title\":\"Bokeh Application\",\"version\":\"2.4.3\"}};\n",
       "  const render_items = [{\"docid\":\"051e568f-09a1-4683-a7d4-fec078dc5c0e\",\"root_ids\":[\"1349\"],\"roots\":{\"1349\":\"dc0fcb40-1810-45f9-b572-3907cc6f205a\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    let attempts = 0;\n",
       "    const timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1349"
      }
     },
     "output_type": "display_data"
    },
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       "<div style=\"display: table;\"><div style=\"display: table-row;\"><div style=\"display: table-cell;\"><b title=\"bokeh.plotting.figure.Figure\">Figure</b>(</div><div style=\"display: table-cell;\">id&nbsp;=&nbsp;'1349', <span id=\"1814\" style=\"cursor: pointer;\">&hellip;)</span></div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">above&nbsp;=&nbsp;[Legend(id='1535', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">align&nbsp;=&nbsp;'start',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">aspect_ratio&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">aspect_scale&nbsp;=&nbsp;1,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">background_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">below&nbsp;=&nbsp;[LinearAxis(id='1358', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">border_fill_color&nbsp;=&nbsp;'#ffffff',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">center&nbsp;=&nbsp;[Grid(id='1361', ...), Grid(id='1365', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">css_classes&nbsp;=&nbsp;[],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">disabled&nbsp;=&nbsp;False,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_x_scales&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_ranges&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">extra_y_scales&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_height&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">frame_width&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height&nbsp;=&nbsp;450,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">height_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">hidpi&nbsp;=&nbsp;True,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_height&nbsp;=&nbsp;0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">inner_width&nbsp;=&nbsp;0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_event_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">js_property_callbacks&nbsp;=&nbsp;{},</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">left&nbsp;=&nbsp;[LinearAxis(id='1362', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_factor&nbsp;=&nbsp;10,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_interval&nbsp;=&nbsp;300,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_threshold&nbsp;=&nbsp;2000,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">lod_timeout&nbsp;=&nbsp;500,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">margin&nbsp;=&nbsp;(0, 0, 0, 0),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">match_aspect&nbsp;=&nbsp;False,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_height&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">max_width&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border&nbsp;=&nbsp;5,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_bottom&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_left&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_right&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_border_top&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_height&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">min_width&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">name&nbsp;=&nbsp;None,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_height&nbsp;=&nbsp;0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outer_width&nbsp;=&nbsp;0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_alpha&nbsp;=&nbsp;1.0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_cap&nbsp;=&nbsp;'butt',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_color&nbsp;=&nbsp;'#e5e5e5',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash&nbsp;=&nbsp;[],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_dash_offset&nbsp;=&nbsp;0,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_join&nbsp;=&nbsp;'bevel',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">outline_line_width&nbsp;=&nbsp;1,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">output_backend&nbsp;=&nbsp;'canvas',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">renderers&nbsp;=&nbsp;[GlyphRenderer(id='1388', ...), GlyphRenderer(id='1395', ...), GlyphRenderer(id='1402', ...), GlyphRenderer(id='1409', ...), GlyphRenderer(id='1416', ...), GlyphRenderer(id='1423', ...), GlyphRenderer(id='1430', ...), GlyphRenderer(id='1437', ...), GlyphRenderer(id='1444', ...), GlyphRenderer(id='1451', ...), GlyphRenderer(id='1458', ...), GlyphRenderer(id='1465', ...), GlyphRenderer(id='1472', ...), GlyphRenderer(id='1479', ...), GlyphRenderer(id='1500', ...), GlyphRenderer(id='1506', ...), GlyphRenderer(id='1512', ...), GlyphRenderer(id='1519', ...), GlyphRenderer(id='1525', ...), GlyphRenderer(id='1531', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">reset_policy&nbsp;=&nbsp;'standard',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">right&nbsp;=&nbsp;[Legend(id='1382', ...)],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">sizing_mode&nbsp;=&nbsp;'scale_width',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">subscribed_events&nbsp;=&nbsp;[],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">syncable&nbsp;=&nbsp;True,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">tags&nbsp;=&nbsp;[],</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title&nbsp;=&nbsp;Title(id='1567', ...),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">title_location&nbsp;=&nbsp;'above',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar&nbsp;=&nbsp;Toolbar(id='1374', ...),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_location&nbsp;=&nbsp;'above',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">toolbar_sticky&nbsp;=&nbsp;True,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">visible&nbsp;=&nbsp;True,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width&nbsp;=&nbsp;800,</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">width_policy&nbsp;=&nbsp;'auto',</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_range&nbsp;=&nbsp;DataRange1d(id='1350', ...),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">x_scale&nbsp;=&nbsp;LinearScale(id='1354', ...),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_range&nbsp;=&nbsp;DataRange1d(id='1352', ...),</div></div><div class=\"1813\" style=\"display: none;\"><div style=\"display: table-cell;\"></div><div style=\"display: table-cell;\">y_scale&nbsp;=&nbsp;LinearScale(id='1356', ...))</div></div></div>\n",
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       "  const ellipsis = document.getElementById(\"1814\");\n",
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      "text/plain": [
       "Figure(id='1349', ...)"
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     "execution_count": 12,
     "metadata": {},
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   ],
   "source": [
    "mzml_loader.plotChromatogram(\"DYASIDAAPEER\", 2, mz_tol=20, rt_window=200, im_window=None, smooth=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "32a1feb3-648e-45a1-9c84-8f97c1d703e5",
   "metadata": {
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    "tags": []
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   "source": [
    "## More Information"
   ]
  },
  {
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   "id": "84302a40-82f1-4344-9a13-29984f5065fc",
   "metadata": {
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    "tags": []
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   "source": [
    "For more details on the implementation please checkout the [Python API](../API.rst)."
   ]
  }
 ],
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