Lines Matching refs:this

16     $this->name = 'pdb';
18         @require_once(DOKU_PLUGIN.$this->name.'/classes/cache.php');
20         @require_once(DOKU_PLUGIN.$this->name.'/classes/sciencedb.php');
22     $this->ncbi     = new ncbi();
23     $this->rcsb     = new rcsb();
24     $this->xmlCache = new plugin_cache("ncbi_esummary","structure","xml.gz");
25     $this->imgCache = new plugin_cache("rcsb_image",'',"jpg");
26     $this->searchBox= DOKU_PLUGIN.'pdb/pdb_search_box.htm';
27     $this->imageW['small']  =  80;
28     $this->imageW['medium'] = 250;
29     $this->imageW['large']  = 500;
34 …function connectTo($mode) { $this->Lexer->addSpecialPattern('\{\{pdb>[^}]*\}\}',$mode,'plugin_pdb'…
55       $filename = $this->imgCache->GetMediaPath($pdbid);
56       if ($this->rcsb->DownloadImage($pdbid,$filename)!==false)
57         $renderer->doc.= $this->getImageHtml($pdbid,$cmd).NL;
59         $renderer->doc.= $this->getLang('pdb_no_image').NL;
63       $summaryXML = $this->getSummaryXML($pdbid);
65         $renderer->doc.= $this->getTextHtml($pdbid,$cmd,$summaryXML);
67         $renderer->doc.= $this->getLang('pdb_no_summary').NL;
71       $filename = $this->imgCache->GetMediaPath($pdbid);
72       if ($this->rcsb->DownloadImage($pdbid,$filename)!==false)
73         $imageHtml = $this->getImageHtml($pdbid,"small").NL;
75         $imageHtml = $this->getLang('pdb_no_image').NL;
79       $summaryXML = $this->getSummaryXML($pdbid);
81         $textHtml = $this->getTextHtml($pdbid,"long",$summaryXML);
83         $renderer->doc.= $this->getLang('pdb_no_summary').NL;
92         $renderer->doc .= file_get_contents($this->searchBox);
96         $renderer->doc .= $this->rcsb->ExplorerLink($pdbid);
100         $summaryXML = $this->getSummaryXML($pdbid);
105         $summaryXML = $this->getSummaryXML($pdbid);
106         $sid = $this->ncbi->GetSearchItem("Id",$summaryXML);
116         $this->xmlCache->ClearCache();
121         $this->imgCache->ClearCache();
126         $this->xmlCache->RemoveDir();
127         $this->imgCache->RemoveDir();
132 …$renderer->doc.='<div class="pdb_plugin">'.sprintf($this->getLang('plugin_cmd_not_found'),$cmd).'<…
133 …      $renderer->doc.='<div class="pdb_plugin_text">'.$this->getLang('pdb_available_cmd').'</div>';
142     $pdbid = $this->rcsb->PDBformat($pdbid);
144     $url = $this->imgCache->GetMediaLink($pdbid);
145     $w = $this->imageW[$type];
146     $html = '<a href="'.$this->rcsb->ExplorerURL($pdbid).'"><div class="pdb_image'.$w.'">';
156     $PdbAcc   = $this->ncbi->GetSummaryItem("PdbAcc"  ,$summaryXML);
157     $PdbClass = $this->ncbi->GetSummaryItem("PdbClass",$summaryXML);
158     $PdbDescr = $this->ncbi->GetSummaryItem("PdbDescr",$summaryXML);
159     $LigCode  = $this->ncbi->GetSummaryItem("LigCode" ,$summaryXML);
162     $html ='<div class="pdb_plugin"><a href="'.$this->rcsb->ExplorerURL($pdbid).'">';
170             $this->getLang('pdb_ligand'):$this->getlang('pdb_ligands');
183     $cachedXml = $this->xmlCache->GetMediaText($pdbAcc);
187     $eSearchXml = $this->ncbi->SearchXml('structure',$pdbAcc);
188     $ids = $this->ncbi->GetSearchItems("Id",$eSearchXml);
191         $tmpXml   = $this->ncbi->SummaryXML('structure',$ids[$i]);
192         $tmpPdbId = $this->ncbi->GetSummaryItem("PdbAcc",$tmpXml);
200     $summary = $this->ncbi->SummaryXml('structure',$id);
203       $cachePath = $this->xmlCache->GetMediaPath($pdbAcc);
215       $xml = $this->SearchXml('structure',$pdbAcc);
216       $ids = $this->GetSearchItems("Id",$xml);
218           $tmpXml   = $this->SummaryXML('structure',$ids[$i]);
219           $tmpPdbId = $this->GetSummaryItem("PdbAcc",$tmpXml);