minor change to output of main method for testing file IO
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groovy from stdin
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memory usage information and flag to indicate if warning dialog boxes should be raised when problems occur.
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add methods to read from current position of existing fileParse object.
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ensure mark is set before identification is started.
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FileParse object can be re-used to read different files concatenated together
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flag to indicate if errors are raised as warning dialog boxes or not.
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explicitly allow access to showMemoryUsage flag in myDesktopPane
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javadoc
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groovy scripts can be read from stdin
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reinstated proper case insensitive searching for both upper and lower case
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timings and memory usage for reading in a file
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more efficient parsing of large files, do not create sequence features from GR annotation positions with '.'
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ensured that seqeunce feature shift takes into account start position difference w.r.t. db seqeunce
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new method to get map of sequence positions corresponding to alignment columns
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fix regex for annotation subtype to use non-whitespace presence rather than word boundary tokens
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javadoc and main method for testing file input routines
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javadoc
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draft of 2.4 features in feature list
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added groovy documentation to contents
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jalview memory monitor instructions added
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desktop tools menu updated
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groovy and das fetching stuff in command line argument list
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documentation for groovy console and basic groovy scripting support
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added groovy argument for launching a groovy script from the command line
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memory monitor, garbage collection and changed menu item for groovy console opening
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