[v1] Log of /trunk/c++/include/objects/seqalign/Dense

Revision 86313 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Apr 29 12:27:17 2019 UTC (5 years ago) by badrazat
File length: 8100 byte(s)
Diff to previous 76684

revert r585406

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Modified Mon Feb 27 16:18:20 2017 UTC (7 years, 2 months ago) by astashya
File length: 8100 byte(s)
Diff to previous 52540

Addressing compiler warning (extra ;)

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Modified Thu Jan 5 17:03:37 2012 UTC (12 years, 3 months ago) by vasilche
File length: 8101 byte(s)
Diff to previous 52311

Reimplemented pre-read member hooks as objects instead of function pointers. JIRA: CXX-2848

Revision 52311 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Dec 15 19:24:57 2011 UTC (12 years, 4 months ago) by vasilche
File length: 7871 byte(s)
Diff to previous 51019

Added vector reserve in pre-read hooks for Seq-table and Dense-seg. JIRA: CXX-2848

Revision 51019 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Aug 25 16:03:09 2011 UTC (12 years, 8 months ago) by boukn
File length: 7666 byte(s)
Diff to previous 48918

JIRA: GP-1607: Added OrderAdjacentGaps(), so that
  functionally identical Denseg's with adjacent gaps
  can be put into a consistant order, so they will
  not only be functionally identical but also
  Equals() identical.

Revision 48918 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 9 17:35:23 2011 UTC (13 years, 1 month ago) by grichenk
File length: 7549 byte(s)
Diff to previous 47385

CDense_seg:FillUnaligned() made const.

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Modified Mon Oct 4 15:26:24 2010 UTC (13 years, 6 months ago) by grichenk
File length: 7543 byte(s)
Diff to previous 47246

Added CreateRowSeq_loc(). JIRA CXX-1774

Revision 47246 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 23 12:14:41 2010 UTC (13 years, 7 months ago) by vasilche
File length: 7457 byte(s)
Diff to previous 47158

Implemented various methods for sparse alignments. JIRA: CXX-1904

Revision 47158 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Sep 16 15:50:29 2010 UTC (13 years, 7 months ago) by vasilche
File length: 7340 byte(s)
Diff to previous 46697

Implemented CheckNumRows() for sparsed alignments. JIRA: CXX-1904

Revision 46697 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Aug 2 16:36:25 2010 UTC (13 years, 8 months ago) by vasilche
File length: 7727 byte(s)
Diff to previous 46567

Added setters for global hooks. JIRA: CXX-688

Revision 46567 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jul 20 18:24:15 2010 UTC (13 years, 9 months ago) by vasilche
File length: 7397 byte(s)
Diff to previous 33815

Added read hooks to reduce memory used by Dense-seg. JIRA: CXX-688

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Modified Fri May 4 17:18:18 2007 UTC (16 years, 11 months ago) by kazimird
File length: 6409 byte(s)
Diff to previous 33208

Fixed svn properties in trunk/c++.

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Modified Thu Mar 29 16:53:02 2007 UTC (17 years, 1 month ago) by jcherry
File length: 6409 byte(s)
Diff to previous 33149

Added CDense_seg::RemovePureGapSegs()

Revision 33149 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 26 15:22:50 2007 UTC (17 years, 1 month ago) by jcherry
File length: 6033 byte(s)
Diff to previous 32839

Added CDense_seg::ExtractRows

Revision 32839 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Mar 5 20:41:55 2007 UTC (17 years, 1 month ago) by kazimird
File length: 5670 byte(s)
Diff to previous 31868

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

Revision 31868 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Jan 3 15:52:31 2007 UTC (17 years, 3 months ago) by todorov
File length: 7602 byte(s)
Diff to previous 31003

Allow negative offsets in OffsetRow

Revision 31003 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Nov 13 16:54:15 2006 UTC (17 years, 5 months ago) by grichenk
File length: 7510 byte(s)
Diff to previous 30797

Fixed comments and default value.

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Modified Thu Oct 26 19:11:02 2006 UTC (17 years, 6 months ago) by todorov
File length: 7406 byte(s)
Diff to previous 28665

Added comment for the deprecated RempaToLoc.

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Modified Tue Jun 6 22:44:47 2006 UTC (17 years, 10 months ago) by todorov
File length: 7268 byte(s)
Diff to previous 27255

Added OffsetRow method.
Marked RemapToLoc for deprecation.

Revision 27255 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 15 15:49:04 2006 UTC (18 years, 1 month ago) by dicuccio
File length: 7133 byte(s)
Diff to previous 25396

Added TrimEndGaps()

Revision 25396 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 22 18:47:37 2005 UTC (18 years, 5 months ago) by dicuccio
File length: 6990 byte(s)
Diff to previous 25393

Restore default parameter for Assign()

Revision 25393 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 22 18:15:06 2005 UTC (18 years, 5 months ago) by dicuccio
File length: 6871 byte(s)
Diff to previous 20631

Added Assign()

Revision 20631 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Wed Mar 2 14:58:58 2005 UTC (19 years, 2 months ago) by dicuccio
File length: 6707 byte(s)
Diff to previous 18405

Added CDense_seg::Compact(): merges abutting segments where appropriate

Revision 18405 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Oct 21 01:38:12 2004 UTC (19 years, 6 months ago) by kapustin
File length: 6479 byte(s)
Diff to previous 16508

+FromTranscript

Revision 16508 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu Jul 1 20:35:59 2004 UTC (19 years, 10 months ago) by todorov
File length: 6169 byte(s)
Diff to previous 16455

+ FillUnaligned()

Revision 16455 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Jun 29 18:42:59 2004 UTC (19 years, 10 months ago) by johnson
File length: 5944 byte(s)
Diff to previous 16144

+ExtractSlice

Revision 16144 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Mon Jun 14 22:09:03 2004 UTC (19 years, 10 months ago) by johnson
File length: 5652 byte(s)
Diff to previous 15428

Added GetSeqStrand method (analogous to GetSeq_id)

Revision 15428 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Thu May 6 18:23:54 2004 UTC (19 years, 11 months ago) by todorov
File length: 5431 byte(s)
Diff to previous 14886

+ optional ignore_strand param to RemapToLoc

Revision 14886 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Fri Apr 9 14:31:35 2004 UTC (20 years ago) by dicuccio
File length: 5240 byte(s)
Diff to previous 14885

Back out previous commit - don't automatically set bit 1 and 2 in Set()

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Modified Fri Apr 9 14:26:46 2004 UTC (20 years ago) by dicuccio
File length: 5118 byte(s)
Diff to previous 11923

FIxed bug in SetWidths(): use the correct bit to indicate set state

Revision 11923 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Nov 4 14:46:16 2003 UTC (20 years, 5 months ago) by todorov
File length: 5000 byte(s)
Diff to previous 11046

+RemapToLoc

Revision 11046 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Sep 16 15:31:59 2003 UTC (20 years, 7 months ago) by todorov
File length: 4791 byte(s)
Diff to previous 10663

Added validation methods. Added seq range methods

Revision 10663 - (view) (download) (as text) (annotate) - [select for diffs]
Modified Tue Aug 26 20:28:38 2003 UTC (20 years, 8 months ago) by johnson
File length: 3813 byte(s)
Diff to previous 10441

added 'SwapRows' method

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Modified Thu Aug 14 19:52:53 2003 UTC (20 years, 8 months ago) by todorov
File length: 3644 byte(s)
Diff to previous 10424

Added m_Widths to support nuc2prot aligns

Revision 10424 - (view) (download) (as text) (annotate) - [select for diffs]
Added Wed Aug 13 18:12:03 2003 UTC (20 years, 8 months ago) by johnson
File length: 2729 byte(s)

added 'Reverse' method

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Log of /trunk/c++/include/objects/seqalign/Dense_seg.hpp