X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=0ce01efb1d9750a858b5d2ebcb7b266b9b044d9f;hb=34d8b4dc08dcd27c3b5ac3bf7811f709b4db5938;hp=3cc5403106efa65925d59d49281253af5af057a8;hpb=688e59f05f78f52d949f29cd5adc33503d98a147;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 3cc5403..0ce01ef 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -286,6 +286,6 @@
           <td>true</td>
           <td>Show the jalview button on the page. When false, JalviewLite will open immediately.</td>
           </tr>
          </tr>
		  <tr><td>sortByTree</td>
		  <td>true or false (default is false)</td>
		  <td>automatically sort the associated alignment view by the tree when a new tree is opened.</td>
		  </tr>
		  <tr>
		   <td>showTreeBootstraps</td><td>true or false (default is true)</td><td>show or hide branch bootstraps</td>
			</tr>
	<tr><td>showTreeDistances</td><td>true or false (default is true)</td><td>show or hide branch lengths</td></tr>
	<tr><td>showUnlinkedTreeNodes</td><td>true or false (default is false)</td><td>indicate if unassociated nodes should be highlighted in the tree view</td>
	</tr>
          <tr><td>heightScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (<em>since 2.5.1</em>)</td>
          </tr>
-          <tr><td>widthScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
          </tr>
          <tr><td>centrecolumnlabels</td>
          <td>true of false (default is false)</td>
          <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
          <tr><td>showUnconserved</td>
          <td>true of false (default is false)</td>
          <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
          </tr>
          <tr><td>upperCase</td>
          <td><em>bold</em> or other value</td>
          <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
          </tr>
          <tr><td>automaticScrolling</td>
          <td>true of false (default is true)</td>
          <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
          </tr>
          
          <tr><td>showGroupConsensus</td>
          <td>true of false (default is false)</td>
          <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
          </tr>
          
          <tr><td>showGroupConservation</td>
          <td>true of false (default is false)</td>
          <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>showConsensusHistogram</td>
          <td>true of false (default is true)</td>
          <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>showSequenceLogo</td>
          <td>true of false (default is false)</td>
          <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>oninit</td>
          <td><em>after_init()</em></td>
          <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>relaxedidmatch</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>alignpdbfiles</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>externalstructureviewer</td>
          <td><em>true or false (default is false)</em></td>
          <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>
          
          </tr>
          <tr><td>annotationcolour_max</td>
          <td>colour name or RGB hex triplet (default is red)</td>
          <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>annotationcolour_min</td>
          <td>colour name or RGB hex triplet (default is orange)</td>
          <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>jalviewhelpurl</td>
          <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
          <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>resolvetocodebase</td>
          <td>True or False (False)</td>
          <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
          </tr>
          
                  </table>
+          <tr><td>widthScale</td>
          <td>1.0 or greater</td>
          <td>Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (<em>since 2.5.1</em>)</td>
          </tr>
          <tr><td>centrecolumnlabels</td>
          <td>true of false (default is false)</td>
          <td>When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (<em>since 2.4</em>)</td>
          <tr><td>showUnconserved</td>
          <td>true of false (default is false)</td>
          <td>When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (<em>since 2.5</em>)</td>
          </tr>
          <tr><td>upperCase</td>
          <td><em>bold</em> or other value</td>
          <td>Indicate a text style to apply to uppercase sequence symbols. Currently, only <strong>bold</strong> is supported.</td>
          </tr>
          <tr><td>automaticScrolling</td>
          <td>true of false (default is true)</td>
          <td>When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (<em>since 2.6</em>)</td>
          </tr>
          
          <tr><td>showGroupConsensus</td>
          <td>true of false (default is false)</td>
          <td>When true, shows consensus annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
          </tr>
          
          <tr><td>showGroupConservation</td>
          <td>true of false (default is false)</td>
          <td>When true, shows amino-acid property conservation annotation row for any groups on the alignment. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>showConsensusHistogram</td>
          <td>true of false (default is true)</td>
          <td>When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>showSequenceLogo</td>
          <td>true of false (default is false)</td>
          <td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>oninit</td>
          <td><em>after_init()</em></td>
          <td>name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>relaxedidmatch</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>alignpdbfiles</td>
          <td><em>true or false (default is false)</em></td>
          <td>When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>externalstructureviewer</td>
          <td><em>true or false (default is false)</em></td>
          <td>re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (<em>since 2.7</em>)</td>
          
          </tr>
          <tr><td>annotationcolour_max</td>
          <td>colour name or RGB hex triplet (default is red)</td>
          <td>Default colour used for maximum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>annotationcolour_min</td>
          <td>colour name or RGB hex triplet (default is orange)</td>
          <td>Default colour used for minimum value when shading by annotation. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>jalviewhelpurl</td>
          <td>absolute or relative url or javascript function prefixed by <em>javascript:</em> (default is http://www.jalview.org/help.html)</td>
          <td>Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>resolvetocodebase</td>
          <td>True or False (False)</td>
          <td>Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (<em>since 2.7</em>)</td>
          </tr>
          <tr><td>scoreFile</td>
          <td>file</td>
          <td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
          </tr>

          
                  </table>
         <p align="center">&nbsp;</p>
         <!-- InstanceEndEditable --></td>
    </tr>
  </table>
</div>
</body>
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