* PURPOSE. See the GNU General Public License for more details.\r
* \r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
---!>\r
-<head><title>Groovy Shell</title></head>\r
-<body>\r
-<p><strong>The Groovy Shell</strong></p>\r
-<p><a href="http://groovy.codehaus.org/">Groovy</a> is an "<em>agile and dynamic \r
-language for the Java platform</em>". The groovy scripting language makes it \r
-extremely easy to programmatically interact with Java programs, in much the same \r
-way that Javascript is used to generate and interact with applets and other \r
-objects on the page.</p>\r
-<p><strong><em>Getting Groovy...</em></strong><br>\r
-Jalview Groovy support is only possible if the core groovy \r
-jars which include the GroovyShell are present on the CLASSPATH \r
-when Jalview is started.</p><p>The jars are obtained from the \r
-<em>embedded</em> directory within the <a \r
-href="http://dist.codehaus.org/groovy/distributions">groovy \r
-distribution</a>. The easiest way of adding them to the \r
-Jalview classpath is to download and build jalview from \r
-it's source distribution, and then add the groovy-all-*.jar \r
-to the lib directory whose path is given in the java.ext.dirs property.</p>\r
-<p><strong>Opening Jalview's Groovy Console</strong><br>If groovy is available, then the \r
-<strong>Tools→Groovy Console...</strong> menu entry will be available \r
-from the Jalview Desktop's drop-down menu. Selecting this will open the\r
-<a href="http://groovy.codehaus.org/Groovy+Console">Groovy Console</a> which \r
-allows you to interactively execute Groovy scripts within the Jalview run-time environment.</p>\r
-<p><strong>Executing groovy scripts on Jalview startup</strong><br>\r
-The -groovy <script> option on the <a href="commandline.html"/>\r
-Jalview command line</a> will execute the contents of \r
-<script>. <script> may be a file, or alternatively if it is "STDIN" \r
-then the standard input will be used.</p>\r
-<p><strong>Access to Jalview's functions from Groovy Scripts</strong><br>\r
-There is as yet no properly defined scripting interface to Jalview, but all the\r
-public methods of the jalview class hierarchy can be called from Groovy scripts. \r
-The access point for this is the <strong>Jalview</strong> object defined in\r
-the groovy environent which corresponds to the <pre>jalview.gui.Desktop</pre> object which\r
-manages all the Jalview windows.</p> \r
-Here's an example to get you started:<br>\r
-<ul><li>Getting the title, alignment and first sequence from the current alignFrame<br>\r
-<pre>\r
-def alf = Jalview.getAlignframes();\r
-print alf[0].getTitle();\r
-def alignment = alf[0].viewport.alignment;\r
-def seq = alignment.getSequenceAt(0);\r
-</pre>\r
-</li>\r
-</ul>\r
-</p>\r
-\r
-<p> </p>\r
-</body>\r
-</html>\r
+-->\r
git://source.jalview.org / jalview.git / blobdiff