<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p>
++ <p>
+ <a name="hmmer"><strong>"HMMER" Preferences tab</strong></a>
+ </p>
+ <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+ then you should specify on this screen the location of the installation (the path to the folder
+ containing binary executable programs). Double-click in the input field to open a file browser.</p>
+ <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+ enabled in the Alignment window.</p>
+ <p> </p>
+ <em>Web Services Preferences</em> - documentation for this tab is
+ given in the
+ <a href="../webServices/webServicesPrefs.html">Web Services
+ Preferences section</a>.
+ <p> </p>
</body>
</html>
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
- // report Jalview version
- Cache.loadBuildProperties(true);
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
- {
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
-
- }
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
}
/*
- * configure 'full' SO model if preferences say to, else use the default (SO
- * Lite)
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
++ * configure 'full' SO model
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
package jalview.io;
import jalview.api.FeatureColourI;
+ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GeneLociI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
+ import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2019.06.07 at 02:21:15 PM BST
-// Generated on: 2019.06.06 at 04:31:20 PM BST
++// Generated on: 2019.07.10 at 12:10:00 PM BST
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
import jalview.api.ViewStyleI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
+ import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
git://source.jalview.org / jalview.git / commitdiff