examples/applets.html

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  19
  20 <!-- boiler plate link to alternate demopage -->
  21 <div style="width: 100%">
  22 <div style="width:35%; align:left; float:right;">
  23 <div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
  24 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
  25 </p></div>
  26 </div>
  27 </div>
  28
  29 <!-- content template start -->
  30
  31 <p align="left">
  32 <h2>JalviewLite Button Examples</h2>
  33 Try out JalviewLite by pressing one of the buttons below.<br/>
  34  For more information on how to use the applet in your website, see the <a href="javascript:doSubmit('appletParameters')"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
  35 <p>&nbsp;</p><div align="center">
  36   <p align="center">
  37     <h2>Ferredoxins, chloroplast precursor related UniRef50
  38       cluster</h2>
  39     <br /> (15 sequences x 150 residues)
  40   </p>
  41   <table width="90%">
  42     <tr>
  43       <td width="10%" valign="center">
  44       <applet
  45         code="jalview.bin.JalviewLite" width="140" height="35"
  46         archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
  47         <param name="permissions" value="sandbox"/>
  48         <param name="file" value="uniref50.fa"/>
  49         <param name="treeFile" value="ferredoxin.nw"/>
  50         <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
  51         <param name="sortByTree" value="True"/>
  52         <param name="showSequenceLogo" value="true"/>
  53         <param name="showGroupConsensus" value="true"/>
  54         <param name="showFullId" value="false"/>
  55         <param name="linkLabel_1" value="Uniprot"/>
  56         <param name="linkUrl_1" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  57         <param name="linkLabel_2" value="EMBL-EBI Search"/>
  58         <param name="linkUrl_2" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  59         <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
  60      </applet>
  61 </td>
  62       <td valign="center">User Defined Colours, loads an associated
  63         Newick format tree file which is used to sort the alignment, and
  64         group consensus and sequence logos are shown below the alignment.</td>
  65     </tr>
  66     <tr>
  67       <td width="10%" valign="center"><applet
  68    code="jalview.bin.JalviewLite" width="140" height="35"
  69    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
  70 <param name="permissions" value="sandbox"/>
  71 <param name="file" value="uniref50.fa"/>
  72 <param name="features" value="exampleFeatures.txt"/>
  73 <param name="showFullId" value="false"/>
  74 <param name="windowHeight" value="500"/>
  75 <param name="windowWidth" value="650"/>
  76 <param name="showFeatureSettings" value="true"/>
  77 <param name="wrap" value="true"/>
  78 <param name="showAnnotation" value="false"/>
  79    <param name="linkLabel_1" value="Uniprot"/>
  80    <param name="linkUrl_1"
  81      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  82    <param name="linkLabel_2" value="EMBL-EBI Search"/>
  83    <param name="linkUrl_2"
  84      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  85    <param name="APPLICATION_URL"
  86      value="http://www.jalview.org/services/launchApp"/>
  87 </applet>
  88 </td>
  89       <td valign="center">Displays a features file on the alignment</td>
  90     </tr>
  91     <tr>
  92       <td width="10%" valign="center"><applet
  93    code="jalview.bin.JalviewLite" width="140" height="35"
  94    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
  95 <param name="permissions" value="sandbox"/>
  96 <param name="file" value="uniref50.fa"/>
  97 <param name="showFullId" value="false"/>
  98 <param name="windowHeight" value="500"/>
  99 <param name="windowWidth" value="650"/>
 100 <param name="wrap" value="true"/>
 101 <param name="showAnnotation" value="false"/>
 102 <param name="defaultColour" value="Strand Propensity"/>
 103 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 104    <param name="linkLabel_1" value="Uniprot"/>
 105    <param name="linkUrl_1"
 106      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 107    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 108    <param name="linkUrl_2"
 109      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 110    <param name="APPLICATION_URL"
 111      value="http://www.jalview.org/services/launchApp"/>
 112 </applet>
 113 </td>
 114       <td valign="center">Associates PDB file 1GAQ with sequence
 115         FER1_MAIZE</td>
 116     </tr>
 117     <tr>
 118       <td width="10%" valign="center"><applet
 119    code="jalview.bin.JalviewLite" width="140" height="35"
 120    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
 121 <param name="permissions" value="sandbox"/>
 122 <param name="file" value="jpred_msa.fasta"/>
 123 <param name="jnetfile" value="jpred_msa.seq.concise"/>
 124 <param name="showFullId" value="false"/>
 125 <param name="windowHeight" value="515"/>
 126 <param name="windowWidth" value="650"/>
 127 <param name="showAnnotation" value="true"/>
 128 <param name="defaultColour" value="Clustal"/>
 129    <param name="linkLabel_1" value="Uniprot"/>
 130    <param name="linkUrl_1"
 131      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 132    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 133    <param name="linkUrl_2"
 134      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 135    <param name="APPLICATION_URL"
 136      value="http://www.jalview.org/services/launchApp"/>
 137 </applet>
 138                                                        </td>
 139       <td valign="middle">Displays a Multiple Sequence Alignment
 140         Based JNet Prediction for a Sequence</td>
 141     </tr>
 142   </table>
 143   <p>
 144     <h2>RF00031 RFAM Alignment with per sequence secondary
 145       structure</h2>
 146   </p>
 147   <table width="90%">
 148     <tr>
 149       <td width="10%" valign="center"><applet
 150    code="jalview.bin.JalviewLite" width="140" height="35"
 151    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
 152 <param name="permissions" value="sandbox"/>
 153 <param name="file" value="RF00031_folded.stk"/>
 154 <param name="showFullId" value="false"/>
 155 <param name="windowHeight" value="515"/>
 156 <param name="windowWidth" value="650"/>
 157 <param name="showAnnotation" value="true"/>
 158 <param name="defaultColour" value="Purine/Pyrimidine"/>
 159    <param name="APPLICATION_URL"
 160      value="http://www.jalview.org/services/launchApp"/>
 161 </applet>
 162 </td>
 163       <td valign="center">Displays an RFAM RNA fold family with
 164         secondary structure annotation</td>
 165     </tr>
 166   </table>
 167   <p>
 168     <h2>Linked amino acid and cDNA alignments for homologous proteins</h2>
 169   </p>
 170   <table width="90%">
 171     <tr>
 172       <td width="10%" valign="center">
 173 <applet
 174    code="jalview.bin.JalviewLite" width="140" height="35"
 175    archive="jalviewApplet.jar,JmolApplet-12.2.4.jar,java-json.jar,json_simple-1.1.jar">
 176 <param name="permissions" value="sandbox"/>
 177 <param name="file" value="estrogenReceptorCdna.fa"/>
 178 <param name="file2" value="estrogenReceptorProtein.fa"/>
 179 <param name="enableSplitFrame" value="true"/>
 180 <param name="scaleProteinAsCdna" value="true"/>
 181 <param name="showFullId" value="false"/>
 182 <param name="windowHeight" value="300"/>
 183 <param name="windowWidth" value="800"/>
 184 <param name="showAnnotation" value="true"/>
 185 <param name="showSequenceLogo" value="true"/>
 186 <param name="defaultColour" value="Purine/Pyrimidine"/>
 187    <param name="APPLICATION_URL"
 188      value="http://www.jalview.org/services/launchApp"/>
 189 </applet>
 190 </td>
 191       <td valign="center">Displays a split window view of protein and its related cDNA</td>
 192     </tr>
 193   </table>