examples/applets.html

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  27
  28 <p align="left">
  29 <h2>JalviewLite Button Examples</h2>
  30 Try out JalviewLite by pressing one of the buttons below.<br/>
  31  For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletDeployment')"><strong>applet deployment,</strong></a> <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters,</strong></a> and other documentation in the links to the left.</p>
  32 <p>&nbsp;</p><div align="center">
  33   <p align="center">
  34     <h2>Ferredoxins, chloroplast precursor related UniRef50
  35       cluster</h2>
  36     <br /> (15 sequences x 150 residues)
  37   </p>
  38   <table width="90%">
  39     <tr>
  40       <td width="10%" valign="center">
  41       <applet
  42         code="jalview.bin.JalviewLite" width="140" height="35"
  43         archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
  44         <param name="permissions" value="sandbox"/>
  45         <param name="file" value="uniref50.fa"/>
  46         <param name="treeFile" value="ferredoxin.nw"/>
  47         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
  48         <param name="sortByTree" value="True"/>
  49         <param name="showSequenceLogo" value="true"/>
  50         <param name="showGroupConsensus" value="true"/>
  51         <param name="showFullId" value="false"/>
  52         <param name="linkLabel_1" value="Uniprot"/>
  53         <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  54         <param name="linkLabel_2" value="EMBL-EBI Search"/>
  55         <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  56         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
  57      </applet>
  58 </td>
  59       <td valign="center">User Defined Colours, loads an associated
  60         Newick format tree file which is used to sort the alignment, and
  61         group consensus and sequence logos are shown below the alignment.</td>
  62     </tr>
  63     <tr>
  64       <td width="10%" valign="center"><applet
  65    code="jalview.bin.JalviewLite" width="140" height="35"
  66    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
  67 <param name="permissions" value="sandbox"/>
  68 <param name="file" value="uniref50.fa"/>
  69 <param name="features" value="exampleFeatures.txt"/>
  70 <param name="showFullId" value="false"/>
  71 <param name="windowHeight" value="500"/>
  72 <param name="windowWidth" value="650"/>
  73 <param name="showFeatureSettings" value="true"/>
  74 <param name="wrap" value="true"/>
  75 <param name="showAnnotation" value="false"/>
  76    <param name="linkLabel_1" value="Uniprot"/>
  77    <param name="linkUrl_1"
  78      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  79    <param name="linkLabel_2" value="EMBL-EBI Search"/>
  80    <param name="linkUrl_2"
  81      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  82    <param name="APPLICATION_URL"
  83      value="http://www.jalview.org/services/launchApp"/>
  84 </applet>
  85 </td>
  86       <td valign="center">Displays a features file on the alignment</td>
  87     </tr>
  88     <tr>
  89       <td width="10%" valign="center"><applet
  90    code="jalview.bin.JalviewLite" width="140" height="35"
  91    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
  92 <param name="permissions" value="sandbox"/>
  93 <param name="file" value="uniref50.fa"/>
  94 <param name="showFullId" value="false"/>
  95 <param name="windowHeight" value="500"/>
  96 <param name="windowWidth" value="650"/>
  97 <param name="wrap" value="true"/>
  98 <param name="debug" value="true"/>
  99 <param name="showAnnotation" value="false"/>
 100 <param name="defaultColour" value="Strand Propensity"/>
 101 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 102    <param name="linkLabel_1" value="Uniprot"/>
 103    <param name="linkUrl_1"
 104      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 105    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 106    <param name="linkUrl_2"
 107      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 108    <param name="APPLICATION_URL"
 109      value="http://www.jalview.org/services/launchApp"/>
 110 </applet>
 111 </td>
 112       <td valign="center">Associates PDB file 1GAQ with sequence
 113         FER1_MAIZE</td>
 114     </tr>
 115     <tr>
 116       <td width="10%" valign="center"><applet
 117    code="jalview.bin.JalviewLite" width="140" height="35"
 118    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 119 <param name="permissions" value="sandbox"/>
 120 <param name="file" value="jpred_msa.fasta"/>
 121 <param name="jnetfile" value="jpred_msa.seq.concise"/>
 122 <param name="showFullId" value="false"/>
 123 <param name="windowHeight" value="515"/>
 124 <param name="windowWidth" value="650"/>
 125 <param name="showAnnotation" value="true"/>
 126 <param name="defaultColour" value="Clustal"/>
 127    <param name="linkLabel_1" value="Uniprot"/>
 128    <param name="linkUrl_1"
 129      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 130    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 131    <param name="linkUrl_2"
 132      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 133    <param name="APPLICATION_URL"
 134      value="http://www.jalview.org/services/launchApp"/>
 135 </applet>
 136                                                        </td>
 137       <td valign="middle">Displays a Multiple Sequence Alignment
 138         Based JNet Prediction for a Sequence</td>
 139     </tr>
 140   </table>
 141   <p>
 142     <h2>RF00031 RFAM Alignment with per sequence secondary
 143       structure</h2>
 144   </p>
 145   <table width="90%">
 146     <tr>
 147       <td width="10%" valign="center"><applet
 148    code="jalview.bin.JalviewLite" width="140" height="35"
 149    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 150 <param name="permissions" value="sandbox"/>
 151 <param name="file" value="RF00031_folded.stk"/>
 152 <param name="showFullId" value="false"/>
 153 <param name="windowHeight" value="515"/>
 154 <param name="windowWidth" value="650"/>
 155 <param name="showAnnotation" value="true"/>
 156 <param name="defaultColour" value="Purine/Pyrimidine"/>
 157    <param name="APPLICATION_URL"
 158      value="http://www.jalview.org/services/launchApp"/>
 159 </applet>
 160 </td>
 161       <td valign="center">Displays an RFAM RNA fold family with
 162         secondary structure annotation</td>
 163     </tr>
 164   </table>
 165   <p>
 166     <h2>Linked Protein and cDNA alignments for a family of Steroid Receptors</h2>
 167   </p>
 168   <table width="90%">
 169     <tr>
 170       <td width="10%" valign="center">
 171 <applet
 172    code="jalview.bin.JalviewLite" width="140" height="35"
 173    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 174 <param name="permissions" value="sandbox"/>
 175 <param name="file2" value="estrogenReceptorCdna_frag.fa"/>
 176 <param name="file" value="estrogenReceptorProtein_frag.fa"/>
 177 <param name="enableSplitFrame" value="true"/>
 178 <param name="scaleProteinAsCdna" value="true"/>
 179 <param name="showFullId" value="false"/>
 180 <param name="windowHeight" value="300"/>
 181 <param name="windowWidth" value="800"/>
 182 <param name="showAnnotation" value="true"/>
 183 <param name="showSequenceLogo" value="true"/>
 184 <param name="defaultColourNuc" value="Purine/Pyrimidine"/>
 185 <param name="defaultColourProt" value="Clustal"/>
 186    <param name="APPLICATION_URL"
 187      value="http://www.jalview.org/services/launchApp"/>
 188 </applet>
 189 </td>
 190       <td valign="center">Displays a split window view showing aligned protein
 191         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
 192         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
 193         via the Jalview Desktop).<br />Data retrieved from Uniprot and
 194         ENA, after Thornton, Need and Crews, <a
 195         href="http://dx.doi.org/10.1126/science.1086185">Science 19
 196           September 2003: 301 (5640), 1714-1717</a>
 197       </td>
 198     </tr>
 199   </table>