What's New in Laj

2005-Dec-14

• Laj is now compiled with version 1.3.1 of Sun's SDK. For best results, please use Java 1.3 or higher to run it.
• Users who have a one-button mouse can get crosshairs by using the Shift key.
• If an attempted zoom is beyond the maximum resolution, Laj will show an error message instead of treating the drag as a click.
• Thousands are always separated with commas in the ruler panel (for consistency with Lat, in which the default locale's number format caused problems on some systems).
• The File - Save feature now uses the "new" version of blastz's lav alignment format (see 2002-Feb-5 below), for better compatibility with downstream tools. (Note that the m{} stanzas produced by Laj are just placeholders containing dummy values.)
• Minor aesthetic tweaks.

2004-Mar-5

• Bug fix: switched to a new mechanism for keyboard shortcuts, so they don't interfere with mouse clicks on the menu bar.
• Bug fix: don't crash when file contains no alignments; display warning message instead.
• Fix usage message to show full command syntax instead of our local wrapper script shortcut.
• The laj.jar file is now executable, so on some systems you may be able to run it by typing its name or double-clicking on it.
• A new Help - Keys menu item lists the keyboard shortcuts, since that dialog no longer pops up on unassigned keys.
• "Installing the Java Plug-in" and other docs have been updated.
• Minor tweaks in appearance and behavior.
• Alternative demo page uses browser's default Java instead of Sun's plugin.

2002-Jul-17

• New options to override the sequence files named in the alignment file, by either specifying a different file name, specifying the URL of a "sequence dispenser" script, or instructing Laj to omit the text view and not read sequences at all.
• New options to limit the region displayed (i.e., the maximum unzoom).
• New option to open the Laj applet window immediately, instead of displaying a button for the user to click on.
• All input files can now be supplied in compressed GZIP format.
• Stand-alone mode uses a new file chooser dialog that requests all file names at once, and has Browse buttons.
• Keyboard shortcuts for menu bar controls are now available.
• The "About" message includes more information, and is now also accessible in stand-alone mode.
• Bug fix: avoid error message when the user clicks on the annotation panel's background.
• Various minor improvements in appearance and behavior.
• Updated and clarified documentation.

2002-Feb-8

• Laj no longer requires alignment files to use the same second sequence file throughout, in order to accommodate whole-genome alignments.

2002-Feb-5

• Laj can now handle the latest output format from the blastz alignment program, which features "factored-out" d{}, s{}, and h{} stanzas to save space. There are also new m{} and x{} stanzas, which are ignored by Laj.
• Bug fix: single-word labels in underlay files now work properly.
• Bug fix: unknown gene direction '|' is allowed in exons files.

2001-Sep-12

• Improved memory management allows Laj and Lat to handle sequence files containing many contigs.
• Bug fixes: "summary" lines in annotation files are now skipped properly, and so are comments within or following URLs.
• If multiple URLs, etc. are encountered in a single annotation, a warning is displayed and only the first one is used.

2001-Jun-26

• Handle the new file formats for repeats, color underlays, and hyperlinked annotations that are already in use by PipMaker and PipTools, including user-defined annotation types.
• In the labeled underlay format, the "dummy" item is no longer needed.
• Misc. minor improvements to the documentation.