diff options
Diffstat (limited to 'docs/coverage/coverage.html')
| -rw-r--r-- | docs/coverage/coverage.html | 338 |
1 files changed, 169 insertions, 169 deletions
diff --git a/docs/coverage/coverage.html b/docs/coverage/coverage.html index 1e9d0ad..5b3b3f1 100644 --- a/docs/coverage/coverage.html +++ b/docs/coverage/coverage.html @@ -3,16 +3,16 @@ <head> <meta charset="utf-8"/> <style>body{background-color:white;}</style> -<link href="lib/htmltools-fill-0.5.8.1/fill.css" rel="stylesheet" /> +<link href="lib/htmltools-fill-0.5.9/fill.css" rel="stylesheet" /> <script src="lib/htmlwidgets-1.6.4/htmlwidgets.js"></script> <link href="lib/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" /> -<script src="lib/datatables-binding-0.33/datatables.js"></script> +<script src="lib/datatables-binding-0.34.0/datatables.js"></script> <script src="lib/jquery-3.6.0/jquery-3.6.0.min.js"></script> <link href="lib/dt-core-1.13.6/css/jquery.dataTables.min.css" rel="stylesheet" /> <link href="lib/dt-core-1.13.6/css/jquery.dataTables.extra.css" rel="stylesheet" /> <script src="lib/dt-core-1.13.6/js/jquery.dataTables.min.js"></script> -<link href="lib/crosstalk-1.2.1/css/crosstalk.min.css" rel="stylesheet" /> -<script src="lib/crosstalk-1.2.1/js/crosstalk.min.js"></script> +<link href="lib/crosstalk-1.2.2/css/crosstalk.min.css" rel="stylesheet" /> +<script src="lib/crosstalk-1.2.2/js/crosstalk.min.js"></script> <link href="lib/highlight.js-6.2/rstudio.css" rel="stylesheet" /> <script src="lib/highlight.js-6.2/highlight.pack.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> @@ -95,7 +95,7 @@ table.table-condensed { font-size: 11px; }</style> <div class="col-md-8 col-md-offset-2"> - <h2>chents coverage - 34.64%</h2> + <h2>chents coverage - 33.77%</h2> <div class="tabbable"> <ul class="nav nav-tabs" data-tabsetid="covr"> <li class="active"> @@ -107,8 +107,8 @@ table.table-condensed { </ul> <div class="tab-content" data-tabsetid="covr"> <div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1"> - <div class="datatables html-widget html-fill-item" id="htmlwidget-702167ad1bbf5cac83c0" style="width:100%;height:500px;"></div> - <script type="application/json" data-for="htmlwidget-702167ad1bbf5cac83c0">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/chent.R<\/a>"],[9,828],[7,299],[0,106],[7,193],["0","1"],["0.00%","35.45%"]],"container":"<table class=\"row-border\">\n <thead>\n <tr>\n <th>File<\/th>\n <th>Lines<\/th>\n <th>Relevant<\/th>\n <th>Covered<\/th>\n <th>Missed<\/th>\n <th>Hits / Line<\/th>\n <th>Coverage<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n var percent = cellData.replace(\"%\", \"\");\n if (percent > 90) {\n var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n } else if (percent > 75) {\n var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n } else {\n var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n }\n $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits / Line","targets":5},{"name":"Coverage","targets":6}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n files = $('div#files div');\n files.not('div.hidden').addClass('hidden');\n id = $(this).text();\n files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}"},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script> + <div class="datatables html-widget html-fill-item" id="htmlwidget-1091363a91657664bb06" style="width:100%;height:500px;"></div> + <script type="application/json" data-for="htmlwidget-1091363a91657664bb06">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/chent.R<\/a>"],[9,828],[7,301],[0,104],[7,197],["0","0"],["0.00%","34.55%"]],"container":"<table class=\"row-border\">\n <thead>\n <tr>\n <th>File<\/th>\n <th>Lines<\/th>\n <th>Relevant<\/th>\n <th>Covered<\/th>\n <th>Missed<\/th>\n <th>Hits / Line<\/th>\n <th>Coverage<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n var percent = cellData.replace(\"%\", \"\");\n if (percent > 90) {\n var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n } else if (percent > 75) {\n var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n } else {\n var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n }\n $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits / Line","targets":5},{"name":"Coverage","targets":6}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n files = $('div#files div');\n files.not('div.hidden').addClass('hidden');\n id = $(this).text();\n files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}"},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script> </div> <div class="tab-pane" title="Source" data-value="Source" id="tab-covr-2"> <div id="files"> @@ -990,16 +990,16 @@ table.table-condensed { <pre class="language-r"> if (rdkit) {</pre> </td> </tr> - <tr class="covered"> + <tr class="missed"> <td class="num">126</td> - <td class="coverage">1<em>x</em></td> + <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> if (rdkit_available) {</pre> </td> </tr> - <tr class="covered"> + <tr class="missed"> <td class="num">127</td> - <td class="coverage">1<em>x</em></td> + <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> self$get_rdkit(template = template)</pre> </td> @@ -1692,28 +1692,28 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">226</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> available_smiles <- names(self$smiles)</pre> </td> </tr> <tr class="covered"> <td class="num">227</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> smiles_preference <- c("user", "PubChem", "PubChem_Connectivity")</pre> </td> </tr> <tr class="covered"> <td class="num">228</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> smiles_preferred_i <- min(match(available_smiles, smiles_preference))</pre> </td> </tr> <tr class="covered"> <td class="num">229</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> smiles_preferred <- smiles_preference[smiles_preferred_i]</pre> </td> @@ -1727,56 +1727,56 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">231</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> message("Get chemical information from RDKit using ",</pre> </td> </tr> <tr class="covered"> <td class="num">232</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> smiles_preferred, " SMILES\n",</pre> </td> </tr> <tr class="covered"> <td class="num">233</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$smiles[smiles_preferred])</pre> </td> </tr> <tr class="covered"> <td class="num">234</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$rdkit <- list()</pre> </td> </tr> <tr class="covered"> <td class="num">235</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$mol <- rdkit_module$Chem$MolFromSmiles(self$smiles[1])</pre> </td> </tr> <tr class="covered"> <td class="num">236</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$rdkit$mw <- rdkit_module$Chem$Descriptors$MolWt(self$mol)</pre> </td> </tr> <tr class="covered"> <td class="num">237</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (!is.null(self$mw) && !is.na(self$mw)) {</pre> </td> </tr> <tr class="covered"> <td class="num">238</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {</pre> </td> @@ -1839,14 +1839,14 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">247</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol)</pre> </td> </tr> <tr class="covered"> <td class="num">248</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (!is.null(template)) {</pre> </td> @@ -1881,56 +1881,56 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">253</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> d2d <- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L)</pre> </td> </tr> <tr class="covered"> <td class="num">254</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> d2d$DrawMolecule(self$mol)</pre> </td> </tr> <tr class="covered"> <td class="num">255</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> d2d$FinishDrawing()</pre> </td> </tr> <tr class="covered"> <td class="num">256</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$svg <- d2d$GetDrawingText()</pre> </td> </tr> <tr class="covered"> <td class="num">257</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> svgfile <- tempfile(fileext = ".svg")</pre> </td> </tr> <tr class="covered"> <td class="num">258</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> psfile <- tempfile(fileext = ".ps")</pre> </td> </tr> <tr class="covered"> <td class="num">259</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> writeLines(self$svg, svgfile)</pre> </td> </tr> <tr class="covered"> <td class="num">260</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> rsvg::rsvg_ps(svgfile, psfile)</pre> </td> @@ -1951,21 +1951,21 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">263</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]</pre> </td> </tr> <tr class="covered"> <td class="num">264</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> ps_font_size <- gsub(" .*$", "", ps_font_line)</pre> </td> </tr> <tr class="covered"> <td class="num">265</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$Pict_font_size = as.numeric(ps_font_size)</pre> </td> @@ -1986,35 +1986,35 @@ table.table-condensed { </tr> <tr class="covered"> <td class="num">268</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> xmlfile <- tempfile(fileext = ".xml")</pre> </td> </tr> <tr class="covered"> <td class="num">269</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> PostScriptTrace(psfile, outfilename = xmlfile)</pre> </td> </tr> <tr class="covered"> <td class="num">270</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> unlink(paste0("capture", basename(psfile)))</pre> </td> </tr> <tr class="covered"> <td class="num">271</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$Picture <- readPicture(xmlfile)</pre> </td> </tr> <tr class="covered"> <td class="num">272</td> - <td class="coverage">2<em>x</em></td> + <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> unlink(c(xmlfile, psfile, svgfile))</pre> </td> @@ -4690,126 +4690,126 @@ table.table-condensed { <td class="num">654</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' # On Travis, we get a certificate validation error,</pre> + <pre class="language-r">#' atr <- pai$new("atrazine")</pre> </td> </tr> <tr class="never"> <td class="num">655</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' # likely because the system (xenial) is so old,</pre> + <pre class="language-r">#' print(atr)</pre> </td> </tr> <tr class="never"> <td class="num">656</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' # therefore don't run this example on Travis</pre> + <pre class="language-r">#' if (!is.null(atr$Picture)) {</pre> </td> </tr> <tr class="never"> <td class="num">657</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' if (Sys.getenv("TRAVIS") == "") {</pre> + <pre class="language-r">#' plot(atr)</pre> </td> </tr> <tr class="never"> <td class="num">658</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#'</pre> + <pre class="language-r">#' }</pre> </td> </tr> <tr class="never"> <td class="num">659</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' atr <- pai$new("atrazine")</pre> + <pre class="language-r">#' # We can also define pais that are not found on the BCPC site</pre> </td> </tr> <tr class="never"> <td class="num">660</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' print(atr)</pre> + <pre class="language-r">#' decanol <- pai$new("1-Decanol")</pre> </td> </tr> <tr class="never"> <td class="num">661</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' if (!is.null(atr$Picture)) {</pre> + <pre class="language-r">#' print(decanol)</pre> </td> </tr> <tr class="never"> <td class="num">662</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' plot(atr)</pre> + <pre class="language-r">pai <- R6Class("pai",</pre> </td> </tr> <tr class="never"> <td class="num">663</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' }</pre> + <pre class="language-r"> inherit = chent,</pre> </td> </tr> <tr class="never"> <td class="num">664</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#'</pre> + <pre class="language-r"> public = list(</pre> </td> </tr> <tr class="never"> <td class="num">665</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">#' }</pre> + <pre class="language-r"></pre> </td> </tr> <tr class="never"> <td class="num">666</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r">pai <- R6Class("pai",</pre> + <pre class="language-r"> #' @field iso ISO common name of the active ingredient according to ISO 1750</pre> </td> </tr> <tr class="never"> <td class="num">667</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"> inherit = chent,</pre> + <pre class="language-r"> iso = NULL,</pre> </td> </tr> <tr class="never"> <td class="num">668</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"> public = list(</pre> + <pre class="language-r"></pre> </td> </tr> <tr class="never"> <td class="num">669</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"></pre> + <pre class="language-r"> #' @field bcpc Information retrieved from the BCPC compendium available online</pre> </td> </tr> <tr class="never"> <td class="num">670</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"> #' @field iso ISO common name of the active ingredient according to ISO 1750</pre> + <pre class="language-r"> #' at <pesticidecompendium.bcpc.org></pre> </td> </tr> <tr class="never"> <td class="num">671</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"> iso = NULL,</pre> + <pre class="language-r"> bcpc = NULL,</pre> </td> </tr> <tr class="never"> @@ -4823,602 +4823,602 @@ table.table-condensed { <td class="num">673</td> <td class="coverage"></td> <td class="col-sm-12"> - <pre class="language-r"> #' @field bcpc Information retrieved from the BCPC compendium available online</pre> - </td> - </tr> - <tr class="never"> - <td class="num">674</td> - <td class="coverage"></td> - <td class="col-sm-12"> - <pre class="language-r"> #' at <pesticidecompendium.bcpc.org></pre> - </td> - </tr> - <tr class="never"> - <td class="num">675</td> - <td class="coverage"></td> - <td class="col-sm-12"> - <pre class="language-r"> bcpc = NULL,</pre> - </td> - </tr> - <tr class="never"> - <td class="num">676</td> - <td class="coverage"></td> - <td class="col-sm-12"> - <pre class="language-r"></pre> - </td> - </tr> - <tr class="never"> - <td class="num">677</td> - <td class="coverage"></td> - <td class="col-sm-12"> <pre class="language-r"> #' @description</pre> </td> </tr> <tr class="never"> - <td class="num">678</td> + <td class="num">674</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' Create a new pai object</pre> </td> </tr> <tr class="never"> - <td class="num">679</td> + <td class="num">675</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param iso The ISO common name to be used in the query of the</pre> </td> </tr> <tr class="never"> - <td class="num">680</td> + <td class="num">676</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' BCPC compendium</pre> </td> </tr> <tr class="never"> - <td class="num">681</td> + <td class="num">677</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param identifier Alternative identifier used for querying pubchem</pre> </td> </tr> <tr class="never"> - <td class="num">682</td> + <td class="num">678</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param smiles Optional user provided SMILES code</pre> </td> </tr> <tr class="never"> - <td class="num">683</td> + <td class="num">679</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param inchikey Optional user provided InChI Key</pre> </td> </tr> <tr class="never"> - <td class="num">684</td> + <td class="num">680</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param bcpc Should the BCPC compendium be queried?</pre> </td> </tr> <tr class="never"> - <td class="num">685</td> + <td class="num">681</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param pubchem Should an attempt be made to retrieve chemical</pre> </td> </tr> <tr class="never"> - <td class="num">686</td> + <td class="num">682</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' information from PubChem via the webchem package?</pre> </td> </tr> <tr class="never"> - <td class="num">687</td> + <td class="num">683</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param pubchem_from Possibility to select the argument</pre> </td> </tr> <tr class="never"> - <td class="num">688</td> + <td class="num">684</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' that is used to query pubchem</pre> </td> </tr> <tr class="never"> - <td class="num">689</td> + <td class="num">685</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param rdkit Should an attempt be made to retrieve chemical</pre> </td> </tr> <tr class="never"> - <td class="num">690</td> + <td class="num">686</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' information from a local rdkit installation via python</pre> </td> </tr> <tr class="never"> - <td class="num">691</td> + <td class="num">687</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' and the reticulate package?</pre> </td> </tr> <tr class="never"> - <td class="num">692</td> + <td class="num">688</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param template An optional SMILES code to be used as template for RDKit</pre> </td> </tr> <tr class="never"> - <td class="num">693</td> + <td class="num">689</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> #' @param chyaml Should we look for a identifier.yaml file in the working</pre> </td> </tr> <tr class="never"> - <td class="num">694</td> + <td class="num">690</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> initialize = function(iso, identifier = iso,</pre> </td> </tr> <tr class="never"> - <td class="num">695</td> + <td class="num">691</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> smiles = NULL, inchikey = NULL, bcpc = TRUE,</pre> </td> </tr> <tr class="never"> - <td class="num">696</td> + <td class="num">692</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> pubchem = TRUE, pubchem_from = 'auto',</pre> </td> </tr> <tr class="never"> - <td class="num">697</td> + <td class="num">693</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> rdkit = TRUE, template = NULL,</pre> </td> </tr> <tr class="never"> - <td class="num">698</td> + <td class="num">694</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> chyaml = FALSE)</pre> </td> </tr> <tr class="never"> - <td class="num">699</td> + <td class="num">695</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> {</pre> </td> </tr> <tr class="never"> - <td class="num">700</td> + <td class="num">696</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="covered"> - <td class="num">701</td> + <td class="num">697</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (!is.null(inchikey)) {</pre> </td> </tr> <tr class="missed"> - <td class="num">702</td> + <td class="num">698</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> self$inchikey = inchikey</pre> </td> </tr> <tr class="missed"> - <td class="num">703</td> + <td class="num">699</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> attr(self$inchikey, "source") <- "user"</pre> </td> </tr> <tr class="never"> - <td class="num">704</td> + <td class="num">700</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">705</td> + <td class="num">701</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="covered"> - <td class="num">706</td> + <td class="num">702</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (!missing(iso) & bcpc) {</pre> </td> </tr> <tr class="covered"> - <td class="num">707</td> + <td class="num">703</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> message("Querying BCPC for ", identifier, " ...")</pre> </td> </tr> <tr class="covered"> - <td class="num">708</td> + <td class="num">704</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> bcpc_result = webchem::bcpc_query(identifier, from = "name")</pre> </td> </tr> <tr class="never"> - <td class="num">709</td> + <td class="num">705</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="never"> - <td class="num">710</td> + <td class="num">706</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> # Use first element of list, as we passed a query of length one</pre> </td> </tr> <tr class="covered"> - <td class="num">711</td> + <td class="num">707</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (is.na(bcpc_result[[1]][1])) {</pre> </td> </tr> <tr class="missed"> - <td class="num">712</td> + <td class="num">708</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem")</pre> </td> </tr> <tr class="never"> - <td class="num">713</td> + <td class="num">709</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> } else {</pre> </td> </tr> <tr class="covered"> - <td class="num">714</td> + <td class="num">710</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$bcpc = bcpc_result[[1]]</pre> </td> </tr> <tr class="covered"> - <td class="num">715</td> + <td class="num">711</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$iso = self$bcpc$cname</pre> </td> </tr> <tr class="covered"> - <td class="num">716</td> + <td class="num">712</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> attr(self$iso, "source") <- "bcpc"</pre> </td> </tr> <tr class="covered"> - <td class="num">717</td> + <td class="num">713</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> attr(self$iso, "status") <- self$bcpc$status</pre> </td> </tr> <tr class="covered"> - <td class="num">718</td> + <td class="num">714</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> bcpc_ik = self$bcpc$inchikey</pre> </td> </tr> <tr class="covered"> - <td class="num">719</td> + <td class="num">715</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (length(bcpc_ik) == 1 && !is.na(bcpc_ik)) {</pre> </td> </tr> <tr class="covered"> - <td class="num">720</td> + <td class="num">716</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (is.null(self$inchikey)) {</pre> </td> </tr> <tr class="covered"> - <td class="num">721</td> + <td class="num">717</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> self$inchikey = substr(self$bcpc$inchikey, 1, 27)</pre> </td> </tr> <tr class="covered"> - <td class="num">722</td> + <td class="num">718</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> attr(self$inchikey, "source") <- "bcpc"</pre> </td> </tr> <tr class="never"> - <td class="num">723</td> + <td class="num">719</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> } else {</pre> </td> </tr> <tr class="missed"> - <td class="num">724</td> + <td class="num">720</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> if (bcpc_ik == self$inchikey) {</pre> </td> </tr> <tr class="missed"> - <td class="num">725</td> + <td class="num">721</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc")</pre> </td> </tr> <tr class="never"> - <td class="num">726</td> + <td class="num">722</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> } else {</pre> </td> </tr> <tr class="missed"> - <td class="num">727</td> + <td class="num">723</td> <td class="coverage">!</td> <td class="col-sm-12"> <pre class="language-r"> warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org")</pre> </td> </tr> <tr class="never"> - <td class="num">728</td> + <td class="num">724</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">729</td> + <td class="num">725</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">730</td> + <td class="num">726</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">731</td> + <td class="num">727</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">732</td> + <td class="num">728</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">733</td> + <td class="num">729</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="never"> - <td class="num">734</td> + <td class="num">730</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> # Set pubchem_from if not specified</pre> </td> </tr> <tr class="covered"> - <td class="num">735</td> + <td class="num">731</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (pubchem_from == 'auto') {</pre> </td> </tr> <tr class="covered"> - <td class="num">736</td> + <td class="num">732</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> pubchem_from = 'name'</pre> </td> </tr> <tr class="covered"> - <td class="num">737</td> + <td class="num">733</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> if (!is.null(self$inchikey)) {</pre> </td> </tr> <tr class="covered"> - <td class="num">738</td> + <td class="num">734</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> pubchem_from = 'inchikey'</pre> </td> </tr> <tr class="never"> - <td class="num">739</td> + <td class="num">735</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">740</td> + <td class="num">736</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">741</td> + <td class="num">737</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="covered"> - <td class="num">742</td> + <td class="num">738</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> super$initialize(identifier = identifier,</pre> </td> </tr> <tr class="covered"> - <td class="num">743</td> + <td class="num">739</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> smiles = smiles, inchikey = self$inchikey,</pre> </td> </tr> <tr class="covered"> - <td class="num">744</td> + <td class="num">740</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> pubchem = pubchem, pubchem_from = pubchem_from,</pre> </td> </tr> <tr class="covered"> - <td class="num">745</td> + <td class="num">741</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> rdkit = rdkit, template = template, chyaml = chyaml)</pre> </td> </tr> <tr class="never"> - <td class="num">746</td> + <td class="num">742</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="covered"> - <td class="num">747</td> + <td class="num">743</td> <td class="coverage">1<em>x</em></td> <td class="col-sm-12"> <pre class="language-r"> invisible(self)</pre> </td> </tr> <tr class="never"> - <td class="num">748</td> + <td class="num">744</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> }</pre> </td> </tr> <tr class="never"> - <td class="num">749</td> + <td class="num">745</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"> )</pre> </td> </tr> <tr class="never"> - <td class="num">750</td> + <td class="num">746</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">)</pre> </td> </tr> <tr class="never"> - <td class="num">751</td> + <td class="num">747</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r"></pre> </td> </tr> <tr class="never"> - <td class="num">752</td> + <td class="num">748</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">#' Printing method for pai objects (pesticidal active ingredients)</pre> </td> </tr> <tr class="never"> - <td class="num">753</td> + <td class="num">749</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">#'</pre> </td> </tr> <tr class="never"> - <td class="num">754</td> + <td class="num">750</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">#' @param x The chent object to be printed</pre> </td> </tr> <tr class="never"> - <td class="num">755</td> + <td class="num">751</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">#' @param ... Further arguments for compatibility with the S3 method</pre> </td> </tr> <tr class="never"> - <td class="num">756</td> + <td class="num">752</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">#' @export</pre> </td> </tr> <tr class="never"> - <td class="num">757</td> + <td class="num">753</td> <td class="coverage"></td> <td class="col-sm-12"> <pre class="language-r">print.pai = function(x, ...) {</pre> </td> </tr> <tr class="missed"> - <td class="num">758</td> + <td class="num">754</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(x$iso)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">755</td> <td class="coverage">!</td> <td class="col-sm-12"> - <pre class="language-r"> cat("<pai> with ISO common name $iso", x$iso, "\n")</pre> + <pre class="language-r"> cat("<pai> without ISO common name\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">756</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">757</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<pai> with ISO common name $iso", x$iso, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">758</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> </td> </tr> <tr class="missed"> |