DTASelect version log information
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This page contains recent CVS revisions of the DTASelect code. It is intended for those advanced users who want to know more about the features and bug fixes released in each version. Not all revisions on this list have been deployed; many of them are simply internal development versions.
Note: the oldest (last) revision on the list corresponds to DTASelect2.0.1, released in July 2006. Earlier versions are not listed.
revision 2.0.23
date: 2008/01/12 01:16:53; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.23: bug fixed in OUT file reader. Same bug was fixed for the SQT file reader in version 2.0.21.
revision 2.0.22
date: 2008/01/11 22:44:24; author: cociorva; state: Exp; lines: +1 -1
Fixed a bug that made the statistics package only work with SQT files (didn't work with OUT files). Version number is now 2.0.22.
revision 2.0.21
date: 2007/12/09 23:49:46; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.21: bug fixed in the SQT file reader. Previously, when a sequence was present in the same protein in multiple places, each place was counted as a new peptide match. This has been corrected: only one peptide match is now counted by DTASelect in such an instance.
revision 2.0.20
date: 2007/10/05 19:40:16; author: cociorva; state: Exp; lines: +5 -5
Version 2.0.20: enzymatic cleavage can now be specified to be different from tryptic. Enzyme numbers 1 (tryptic, default), 2 (lys-C) and 3 (aspN) are supported, together with intact protein (no digest, 99). Users can also specify any cleavage conditions with the --before and --after options (for example, "--after KR" is the same as tryptic digest, while "--before D" is the same as AspN digest). Note: the "DetermineMissedTryptic" function has not been updated, and it still counts missed tryptic sites (rather than missed cleavage sites). This will be fixed in a future release.
revision 2.0.19
date: 2007/09/27 00:35:46; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.19: DTASelect.params info is now printed in the output header.
revision 2.0.18
date: 2007/09/26 22:39:44; author: cociorva; state: Exp; lines: +1 -1
Added "Reverse_sp" option for OMSSA, to be compatible with earlier changes. Version number is now DTASelect2.0.18.
revision 2.0.17
date: 2007/08/13 23:10:21; author: cociorva; state: Exp; lines: +3 -3
More OMSSA options added. Attention: the sqt file filter is no longer "*.sqt", but rather "qt". This is to accomodate "*.oqt", "*.tqt", and "*.mqt" files from OMSSA, XTANDEM, and Mascot respectively. This change can potentially create problems when random files with the "qt" extensions are encountered.
Still to be addressed: the OMSSA filters are turned on with the "--omssa" flag, while the column headers are controlled by the "qt" file header. This can potentially create problems.
Version number is now 2.0.17.
revision 2.0.16
date: 2007/06/27 16:45:12; author: cociorva; state: Exp; lines: +1 -1
Column headers fixed for ProLuCID, and also new headers introduced for OMSSA.
revision 2.0.15
date: 2007/05/24 22:32:59; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.15: fixes bug introduced in 2.0.14. Version2.0.14 is not a production version, and should not be used.
revision 2.0.14
date: 2007/05/24 22:01:29; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.14: DTAFile now has a ScanNumber field. This will be used in the future.
revision 2.0.13
date: 2007/05/24 21:46:59; author: cociorva; state: Exp; lines: +1 -1
Fixed a bug in LDAConfidence.java, where the == operator was used for string comparison (potentially very dangerous bug, although in this particular case, it had no harmful effect).
revision 2.0.12
date: 2007/05/15 21:07:00; author: cociorva; state: Exp; lines: +1 -1
Major change: the --trypstat and --modstat options now work differently. The discriminant analysis is first done on the full data set of a given charge state, and the linear coefficients are computed. Then the confidence values are computed for different tryptic and modification values, using the SAME coefficients. This makes the discriminant analysis much more robust, as the data sets are larger. Note: version number is now 2.0.12.
revision 2.0.11
date: 2007/05/14 05:32:48; author: cociorva; state: Exp; lines: +6 -10
Finished the charge state extension for double digit charge states (in v2.0.10, it only worked in the first run). Version number is now 2.0.11.
revision 2.0.10
date: 2007/05/08 22:16:48; author: cociorva; state: Exp; lines: +1 -1
MaxChargeState changed to 16. Version number is now 2.0.10.
revision 2.0.9
date: 2007/04/19 22:34:31; author: cociorva; state: Exp; lines: +1 -1
Charge state statistics option is now included. Previously, charges +3 and above were lumped together. Now, the user specifies the maximum charge state for statistics (default = 3). Version number changed to 2.0.9.
revision 2.0.8
date: 2007/02/22 23:57:15; author: cociorva; state: Exp; lines: +1 -1
Ambiguous ID flag now set to "false" by default.
revision 2.0.7
date: 2007/02/09 21:12:16; author: cociorva; state: Exp; lines: +1 -1
Bug fixed for "-Sic" and "-Sec" options.
revision 2.0.6
date: 2006/11/09 19:52:17; author: cociorva; state: Exp; lines: +13 -5
Fixed a bug that created problems when the "--copy" option was used in conjunction with ProLuCID. The bug fix is just for the "--copy" option, and it doesn't affect how the rest of the program treats ProLuCID output. Version number is now 2.0.6.
revision 2.0.5
date: 2006/09/20 23:12:54; author: cociorva; state: Exp; lines: +1 -1
Fixed a bug that crashed the program in the event that a sequence was incomplete. The bug was in the DetermineTryptic method. Version number is now 2.0.5.
revision 2.0.4
date: 2006/09/18 22:12:18; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.4: a bug is the calculation of missed tryptic sites has now been fixed.
revision 2.0.3
date: 2006/08/17 20:11:39; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.3 has minimum XCorr set to 1 (change made earlier in SelectCriteria.java).
revision 2.0.2
date: 2006/07/13 20:14:00; author: cociorva; state: Exp; lines: +1 -1
Version 2.0.2: --hidedecoy option now inhibits the appearance of the false positive info at the bottom.
revision 2.0.1
date: 2006/07/13 19:13:41; author: cociorva; state: Exp; lines: +1 -1
Version name is now 2.0.1. This will be tagged.
