examples/formComplete.html

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   5 <TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
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  60     <tr>
  61       <td background="../jalview.gif">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
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  70             <tr>
  71               <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
  72             </tr>
  73             <tr>
  74               <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
  75             </tr>
  76             <tr>
  77               <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
  78             </tr>
  79             <tr>
  80               <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
  81                 Version</a></td>
  82             </tr>
  83             <tr>
  84               <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
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  86             <tr>
  87               <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
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  93               <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
  94                 history</a></td>
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  96             <tr>
  97               <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
  98                 Code</a></td>
  99             </tr>
 100                         <tr>
 101               <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
 102             </tr>
 103                         <tr>
 104               <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
 105             </tr>
 106             <tr>
 107               <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
 108                 Mailing List</a></td>
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 112             href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
 113             class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
 114             bug reports to the discussion list.</em></td>
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 124         <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
 125           <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
 126         </div>
 127         </td>
 128       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
 129                 <p>&nbsp;</p>
 130                 Click the Javascript buttons below to interact with the Applet
 131                 instance on the page.<br>
 132                 View the source in your browser to see how it has been done.<br>
 133                 The applet's public API methods are <a href="#api">listed below</a>
 134                 the following example.<br>
 135                 <applet code="jalview.bin.JalviewLite" width="140" height="35"
 136                         archive="jalviewApplet.jar" name="Jalview">
 137                         <param name="file" value="plantfdx.fa">
 138                         <param name="features" value="plantfdx.features">
 139                         <param name="wrap" value="true">
 140                         <param name="showAnnotation" value="false">
 141                         <param name="windowHeight" value="500">
 142                         <param name="windowWidth" value="650">
 143                         <param name="showFullId" value="false">
 144                         <param name="RGB" value="F2F2FF">
 145                         <param name="linkLabel_1" value="SRS">
 146                         <param name="linkUrl_1"
 147                                 value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
 148                         <param name="linkLabel_2" value="Uniprot">
 149                         <param name="linkUrl_2"
 150                                 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 151                         <param name="hidefeaturegroups" value="uniprot" />
 152                         <param name="showbutton" value="false" />
 153                 </applet>
 154                 <form name="exampleForm"><br>
 155                 <br>
 156                 <center><strong>Using the Jalview Applet for Input
 157                 to an HTML Form</strong></center>
 158                 <div align="center"><input type="button"
 159                         onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
 160                         value="Fill Form from Jalview" /> <br>
 161                 <br>
 162                 <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
 163                 </form>
 164                 <center><strong>Make a new View and Get and Set
 165                 Group Display List</strong></center>
 166                 <form name="groupForm">
 167                 <div align="center"><input type="button"
 168                         onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
 169                         value="Get groups" /> <input type="button"
 170                         onClick="document.applets.Jalview.newView()" value="new View" /> <br>
 171                 <textarea name="groups" cols="55" rows="9"></textarea> <br>
 172                 <input type="button"
 173                         onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
 174                         value="Display groups" /> <input type="button"
 175                         onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
 176                         value="Hide groups" /></div>
 177                 </form>
 178                 <p><a name="api" /> Since Jalview 2.5, the public methods listed
 179                 below are available to be called via Javascript.</p>
 180                 <p>Unfortunately Javascript - Java communication is not possible
 181                 using Internet Explorer or Opera on Macs. Please use Safari or
 182                 Firefox.</p>
 183                 <p>If more than one Jalview window is open, Jalview returns the
 184                 alignment in the active window, unless you provide an AlignFrame
 185                 object reference.</p>
 186                 <p>The alignment output format can be either Fasta, PFAM, Clustal,
 187                 MSF, PIR, or BLC.</p>
 188                 <p>When referring to the Jalview applet in javascript, you must
 189                 either give Jalview a name in the applet tag or use the applets index.</p>
 190
 191                 <pre>//get list of IDs of selected sequences
 192 public String getSelectedSequences()
 193
 194 // list of IDs of selected sequences terminated by sep or, if sep is null, '&#172;' (&amp;#172;)
 195 public String getSelectedSequences(sep)
 196
 197 // get selected sequences as alignment as format with or without start-end suffix
 198 public String getSelectedSequencesAsAlignment(String format, boolean suffix)
 199
 200 // get selected sequences as alignment from given view as format with or without start-end suffix
 201 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix)
 202
 203 // get alignment as format
 204 public String getAlignment(String format)
 205
 206 // get alignment as format with jalview
 207 // start-end sequence suffix appended
 208 public String getAlignment(String format, String suffix)
 209
 210 // get alignment displayed in alf as format
 211 public String getAlignmentFrom(AlignFrame alf, String format)
 212
 213 // get alignment displayed in alf as format
 214 // with jalview start-end sequence suffix appended
 215 public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
 216
 217 // add the given features or annotation to the current alignment
 218 public void loadAnnotation(String annotation)
 219
 220 // add the given features or annotation to the given alignment view
 221 public void loadAnnotationFrom(AlignFrame alf, String annotation)
 222
 223 // get the sequence features in the given format (Jalview or GFF)
 224 public String getFeatures(String format)
 225
 226 // get the sequence features in alf in the given format (Jalview or GFF)
 227 public String getFeaturesFrom(AlignFrame alf, String format)
 228
 229 // get current alignment's annotation as an annotation file
 230 public String getAnnotation()
 231
 232 // get alignment view alf's annotation as an annotation file
 233 public String getAnnotationFrom(AlignFrame alf)
 234
 235 // create a new view and return the alignFrame instance
 236 public AlignFrame newView()
 237
 238 // create a new view named name and return the alignFrame instance
 239 public AlignFrame newView(String name)
 240
 241 // create a new view on alf and return the alignFrame instance
 242 public AlignFrame newViewFrom(AlignFrame alf)
 243
 244 // create a new view named name on alf
 245 // and return the alignFrame instance
 246 public AlignFrame newViewFrom(AlignFrame alf, String name)
 247
 248 // load a new alignment
 249 public AlignFrame loadAlignment(String text, String title)
 250
 251 // return separator separated list of feature groups
 252 // on the current alignment
 253 public String getFeatureGroups()
 254
 255 // return separator separated list of feature groups on alf
 256 public String getFeatureGroupsOn(AlignFrame alf)
 257
 258 // return separator separated list of feature groups
 259 // either visible or hidden
 260 public String getFeatureGroupsOfState(boolean state)
 261
 262 // return separator separated list of feature groups
 263 // either visible or hidden on alf
 264 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state)
 265
 266 // set the separator separated list of feature groups as
 267 // visible or hidden on the current alignment
 268 public void setFeatureGroupState(String groupList, boolean state)
 269
 270 // set the separator separated list of feature groups
 271 // as visible or hidden on alf
 272 public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state)
 273
 274 // helper functions
 275
 276 // convert list to a separator separated array
 277 public String arrayToSeparatorList(String[] list)
 278
 279 // get a string array from a list
 280 public String[] separatorListToArray(String list)
 281
 282 // get the current separator
 283 public String getSeparator()
 284
 285 // set the current separator
 286 public void setSeparator(String)
 287
 288 //// JalviewLite global state methods and fields
 289
 290 // return the build date as a string
 291 public static String getBuildDate()
 292
 293 // return the JalviewLite version as a string
 294 public static String getVersion()
 295
 296 // debug flag - controls output to standard out
 297 public static boolean debug
 298
 299 </pre> <!-- InstanceEndEditable --></td>
 300     </tr>
 301   </table>
 302 </div>
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