Directory ISLAND_HOPPING/

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westram 2023-08-05 13:48 Rev.: 19448

* enable + fix warnings in ISLAND_HOPPING.

8 lines of code changed in 2 files:

• ISLAND_HOPPING: Makefile (-3), island_hopping.cxx (+8 -6)

westram 2023-08-05 13:46 Rev.: 19447

* suppression of warnings for source-subtrees:
- comment + warn when suppressed (currently suppressed in GDE)

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2 -3)

westram 2021-09-15 13:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2021-09-15 13:39 Rev.: 18725

* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

5 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+5 -5)

westram 2021-09-15 13:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -3)

westram 2021-09-15 13:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2017-11-28 18:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

33 lines of code changed in 6 files:

• ISLAND_HOPPING: Makefile (+3), align.cxx (+14 -12), i-hopper.cxx (+3 -3), island_hopping.cxx (+2 -2), island_hopping.h (+6 -7), mem.cxx (+5 -4)

westram 2017-01-09 16:10 Rev.: 15529

* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2)

westram 2017-01-04 18:06 Rev.: 15513

* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

2 lines of code changed in 1 file:

• ISLAND_HOPPING: island_hopping.h (+2 -2)

westram 2015-11-05 17:55 Rev.: 14476

* {{{AlignDataAccess}}}:
- use factory function (ensures proper initialization; was missing for SINA interface); removed global
- use callback to get helix-string (only used in island_hopping; optional)
- store alignment-name
- add proper ctor, copy-ctor and op=
* island_hopping
- store helix-string as copy

5 lines of code changed in 1 file:

• ISLAND_HOPPING: island_hopping.h (+5 -4)

westram 2015-11-05 16:57 Rev.: 14475

* fix range definition for islandhopper (i guess it was broken by [8614])

1 lines of code changed in 1 file:

• ISLAND_HOPPING: island_hopping.h (+1 -1)

westram 2015-01-23 15:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2 -2)

westram 2013-10-31 15:18 Rev.: 10997

* use cflags before cxxflags (where locally modified)

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2013-10-30 17:04 Rev.: 10975

* fixed wrong include variables (CC-CXX-mix). Harmless since includes do not differ atm

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2 -2)

westram 2013-10-29 13:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2 -2)

westram 2013-10-29 12:43 Rev.: 10954

- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2013-06-13 14:31 Rev.: 10148

* makedepend changed behavior between 1.0.2 and 1.0.4
- 1.0.4 does generate impossible dependencies (see [10143] for an example)
- force correct behavior by defining SIMPLE_ARB_ASSERT on CLI (when invoking compiler and makedepend)

11 lines of code changed in 2 files:

• ISLAND_HOPPING: Makefile (+10 -7), trnsprob.cxx (+1 -2)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2)

westram 2012-05-24 11:59 Rev.: 8748

- use simpler way to declare attributed static/inline functions

1 lines of code changed in 1 file:

• ISLAND_HOPPING: mem.cxx (+1 -1)

westram 2012-05-11 12:32 Rev.: 8725

* comments cleanup

0 lines of code changed in 1 file:

• ISLAND_HOPPING: island_hopping.cxx (-3)

westram 2012-04-21 12:38 Rev.: 8641

* fixed warnings
- possible uninitialized variables
- DEBUG-mode variables
- ISLAND_HOPPING/Makefile: disabled warnings (i wont touch that module, except for removal)

15 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+15 -2)

westram 2012-04-19 12:54 Rev.: 8614

merge from e4fix [8168] [8169] [8170] [8171] [8178] [8180] [8181] [8182] [8183] [8184] [8185] [8187] [8188] [8189]

* merge similar concepts !UpdateRange and !TargetRange into !PosRange
- moved to CORE
- added !ExplicitRange
- added PosRange::contains()
- able to intersect
- use in
* !AlignParams
* readCompactedSequence()
* !UnalignedBases + !UnalignedBasesList -> !LooseBases
* to handle selection (aka "block") in edit4
* for update interval (draw functions)
* build_probe_match_string
* added !AliChange
- holds sequence before and after alignment
* DRYed code of calc_intervall_displayed_in_rectangle vs calc_update_intervall
* cache sequence length in ED4_orf_terminal
* added test for !UnalignedBasesList (documenting wrong behavior)
* renamed all *.stamp to stamp.*

9 lines of code changed in 2 files:

• ISLAND_HOPPING: Makefile (+2), island_hopping.h (+7 -4)

westram 2012-04-19 09:13 Rev.: 8607

merge from e4fix [8135] [8136] [8137] [8138] [8139] [8140] [8141] [8142] [8143] [8144] [8222]
(this revives the reverted patches [8129] [8130] [8131] [8132]; see [8133])

* fixes
- some free/delete mismatches
- wrong definition of ORF objects (Level was no bit value)
- amino consensus (failed for columns only containing 'C')
* rename
- AA_sequence_term -> orf_term
- ED4_sequence_terminal_basic -> ED4_abstract_sequence_terminal
* cleaned up hierarchy dumps
* tweaked is_terminal()/to_terminal()

0 lines of code changed in 6 files:

• ISLAND_HOPPING: align.cxx (changed), i-hopper.cxx (changed), island_hopping.cxx (changed), mem.cxx (changed), mem.h (changed), trnsprob.cxx (changed)

westram 2012-04-11 13:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

• ISLAND_HOPPING: needs_libs (+1 -1)

westram 2011-12-20 13:29 Rev.: 8309

* moved much code into static scope

(partly reverted by [8310])

6 lines of code changed in 3 files:

• ISLAND_HOPPING: align.cxx (+1 -1), mem.cxx (+1 -1), mem.h (+4 -5)

westram 2011-08-08 01:01 Rev.: 7811

merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

77 lines of code changed in 4 files:

• ISLAND_HOPPING: align.cxx (+37 -37), i-hopper.cxx (+7 -7), mem.cxx (+13 -13), trnsprob.cxx (+20 -20)

westram 2011-06-10 15:50 Rev.: 7623

- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

8 lines of code changed in 2 files:

• ISLAND_HOPPING: Makefile (+1), island_hopping.h (+7 -9)

westram 2011-03-27 22:43 Rev.: 7338

- marked several functions as 'noreturn'

3 lines of code changed in 2 files:

• ISLAND_HOPPING: Makefile (+1), mem.cxx (+2 -1)

westram 2011-02-23 14:37 Rev.: 7183

merges [7084] [7086] [7087] [7088] from refactor
* added CORE lib
- added arb_progress (unused yet)
- moved some code from ARBDB to CORE
* added tests to CORE lib
* generate_all_links.sh
- now tests link targets
- able to replace links (if link stays the same, but target changes)
* fixed perl interface
- link with libCORE
- DRYed LINUX.PL and DARWIN.PL
- added wrapper functionality (ARBDB->CORE). Functions starting with GBC_ are wrappers for code that moved into libCORE (which is NOT xsub'd)

0 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (-3)

westram 2010-09-18 17:20 Rev.: 6866

* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2 -2)

westram 2010-09-09 22:49 Rev.: 6817

- depends for [6816]

2 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+2)

westram 2010-09-09 20:29 Rev.: 6815

* compile ISLAND_HOPPING as C++ (merges [6794])

1699 lines of code changed in 11 files:

• ISLAND_HOPPING: Makefile (+4 -4), align.c (del), align.cxx (new 879), i-hopper.c (del), i-hopper.cxx (new 97), island_hopping.cpp (del), island_hopping.cxx (new 203), mem.c (del), mem.cxx (new 106), trnsprob.c (del), trnsprob.cxx (new 410)

westram 2010-09-09 20:25 Rev.: 6814

* depends updated for [6812] + [6813]

1 lines of code changed in 1 file:

• ISLAND_HOPPING: Makefile (+1)

westram 2010-03-11 11:37 Rev.: 6516

* fixed compile error (assert)
* fixed includes
* added include wrappers
* renamed functions "overloaded" by defines

260 lines of code changed in 12 files:

• ISLAND_HOPPING: Makefile (+8 -5), align.c (+13 -7), defs.h (+16 -1), i-hopper.c (+11 -5), i-hopper.h (+15 -4), island_hopping.cpp (+11 -5), mem.c (new 108), mem.h (new 45), memory.c (del), memory.h (del), trnsprob.c (+16 -6), trnsprob.h (+17)

westram 2010-03-10 18:22 Rev.: 6514

[static checker]
* assertion

4 lines of code changed in 1 file:

• ISLAND_HOPPING: trnsprob.c (+4 -3)

westram 2010-02-17 10:30 Rev.: 6448

- added library dependency declarations

4 lines of code changed in 1 file:

• ISLAND_HOPPING: needs_libs (new 4)

(26 more)