Log of /trunk/c++/include/objtools/alnmgr/aln_user_options.hpp

---

Revision 53721 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Apr 12 15:23:21 2012 UTC (12 years, 2 months ago) by grichenk
File length: 7062 byte(s)
Diff to previous 53306

More doxygen comments for alignment manager. JIRA CXX-2301

---

Revision 53306 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 7 19:44:47 2012 UTC (12 years, 3 months ago) by grichenk
File length: 7598 byte(s)
Diff to previous 51796

Added fIgnoreInsertions option. Fixed processing of std-segs. Fixed sequence translation in CSparseAln. JIRA CXX-3010, CXX-2607

---

Revision 51796 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 2 16:25:43 2011 UTC (12 years, 7 months ago) by grichenk
File length: 7531 byte(s)
Diff to previous 40809

Added a new flag to CAlnUserOptions allowing to use the first row as the anchor. JIRA CXX-2623

---

Revision 40809 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 22 18:27:41 2009 UTC (15 years, 4 months ago) by todorov
File length: 7329 byte(s)
Diff to previous 39383

Better comments.

---

Revision 39383 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Sep 22 19:24:34 2008 UTC (15 years, 8 months ago) by todorov
File length: 7116 byte(s)
Diff to previous 37574

BuildAln now creates a pseudo alignment sequence (a dummy reference
sequence expressed in alignment coordinates) by default.
Alternatively (as a user option), the anchor sequence can be used for
this purpose (which was the design until this point).

---

Revision 37574 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Apr 16 22:47:38 2008 UTC (16 years, 2 months ago) by todorov
File length: 6377 byte(s)
Diff to previous 36543

Rewrote the greedy algorithms to support for mixed
strands rows and translocations.  Introduced an option to skip sorting
input alignments by score to allow for user-defined order.

---

Revision 36543 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 10 21:53:49 2008 UTC (16 years, 5 months ago) by todorov
File length: 5530 byte(s)
Diff to previous 36539

Keep "objects::CBioseq_Handle m_Anchor" until dependencies are fully resolved.

---

Revision 36539 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jan 10 21:45:06 2008 UTC (16 years, 5 months ago) by todorov
File length: 5532 byte(s)
Diff to previous 34859

Allow the user to choose an anchor.

---

Revision 34859 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 2 19:53:17 2007 UTC (16 years, 10 months ago) by todorov
File length: 5311 byte(s)
Diff to previous 33815

Fixed a m_MergeAlgo vs m_MergeOption conflict; initialize all vars in the ctor

---

Revision 33815 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri May 4 17:18:18 2007 UTC (17 years, 1 month ago) by kazimird
File length: 5306 byte(s)
Diff to previous 32839

Fixed svn properties in trunk/c++.

---

Revision 32839 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 5 20:41:55 2007 UTC (17 years, 3 months ago) by kazimird
File length: 5306 byte(s)
Diff to previous 32809

CVS $Log$ keyword clean-up: everything except "internal".

---

Revision 32809 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Mar 1 23:18:01 2007 UTC (17 years, 3 months ago) by yazhuk
File length: 6023 byte(s)
Diff to previous 32338

Corrected selection broadcasting to work properly with Selecton Inspector; reorganized commands - eliminated redundant; open views for every object in plugin reply; added accelerators; refactoring;

---

Revision 32338 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 31 00:19:09 2007 UTC (17 years, 4 months ago) by todorov
File length: 6013 byte(s)
Diff to previous 31988

Optional filtering based on diagonal direction.

---

Revision 31988 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jan 9 19:56:57 2007 UTC (17 years, 5 months ago) by yazhuk
File length: 5617 byte(s)
Diff to previous 31557

Fixed a warning, changed the default value for m_Extension

---

Revision 31557 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Dec 11 20:43:42 2006 UTC (17 years, 6 months ago) by yazhuk
File length: 5512 byte(s)
Diff to previous 31487

Extended CAlnUserOptions.

---

Revision 31487 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Dec 6 20:09:43 2006 UTC (17 years, 6 months ago) by todorov
File length: 4317 byte(s)
Diff to previous 31401

MergeOptions => MergeAlgo

---

Revision 31401 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Dec 1 21:24:09 2006 UTC (17 years, 6 months ago) by todorov
File length: 4243 byte(s)
Diff to previous 31399

- NCBI_XALNMGR_EXPORT

---

Revision 31399 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Dec 1 17:54:05 2006 UTC (17 years, 6 months ago) by todorov
File length: 4192 byte(s)
Diff to previous 31251

+ NCBI_XALNMGR_EXPORT

---

Revision 31251 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Nov 22 00:46:16 2006 UTC (17 years, 6 months ago) by todorov
File length: 4101 byte(s)
Diff to previous 31135

Fixed the flags and options.

---

Revision 31135 - (view) (download) (as text) (annotate) - [select for diffs]
Added Fri Nov 17 05:35:11 2006 UTC (17 years, 6 months ago) by todorov
File length: 3634 byte(s)

Initial revision.