cvs commit: ports/biology Makefile ports/biology/ssaha Makefile distinfo pkg-descr pkg-plist ports/biology/ssaha/files patch-GlobalDefinitions.cpp patch-GlobalDefinitions.h patch-HashTable.cpp patch-HashTableGeneric.cpp patch-HashTablePacked.cpp patch-HashTablePacked.h ...

[Felippe de Meirelles Motta]

lippe       2008-06-21 00:01:57 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/ssaha        Makefile distinfo pkg-descr pkg-plist 
    biology/ssaha/files  patch-GlobalDefinitions.cpp 
                         patch-GlobalDefinitions.h 
                         patch-HashTable.cpp 
                         patch-HashTableGeneric.cpp 
                         patch-HashTablePacked.cpp 
                         patch-HashTablePacked.h 
                         patch-HashTableTranslated.cpp 
                         patch-MatchAligner.cpp 
                         patch-MatchAligner.h patch-MatchStore.h 
                         patch-MatchStoreGapped.h 
                         patch-MatchStoreUngapped.h 
                         patch-QueryManager.cpp 
                         patch-QueryManager.h patch-README 
                         patch-SSAHAMain.cpp patch-SSAHAMain.h 
                         patch-SequenceEncoder.cpp 
                         patch-SequenceReader.cpp 
                         patch-SequenceReader.h 
                         patch-SequenceReaderFasta.cpp 
                         patch-SequenceReaderFasta.h 
                         patch-SequenceReaderFilter.h 
                         patch-SequenceReaderLocal.cpp 
                         patch-SequenceReaderMulti.cpp 
                         patch-SequenceReaderMulti.h 
                         patch-SequenceReaderString.h 
                         patch-makefile 
                         patch-testHashTableNoOverlap.cpp 
                         patch-testQueryManager.cpp 
                         patch-testSequenceReaderFasta.cpp 
  Log:
  SSAHA is a software tool for very fast matching and alignment of DNA
  sequences. It stands for Sequence Search and Alignment by Hashing
  Algorithm. It achieves its fast search speed by converting sequence
  information into a `hash table' data structure, which can then be
  searched very rapidly for matches.
  
  WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/
  
  PR:             ports/124525
  Submitted by:   Fernan Aguero <fernan at iib.unsam.edu.ar>
  Approved by:    gabor (mentor, implicit)
  
  Revision  Changes    Path
  1.102     +1 -0      ports/biology/Makefile
  1.1       +33 -0     ports/biology/ssaha/Makefile (new)
  1.1       +3 -0      ports/biology/ssaha/distinfo (new)
  1.1       +11 -0     ports/biology/ssaha/files/patch-GlobalDefinitions.cpp (new)
  1.1       +82 -0     ports/biology/ssaha/files/patch-GlobalDefinitions.h (new)
  1.1       +20 -0     ports/biology/ssaha/files/patch-HashTable.cpp (new)
  1.1       +48 -0     ports/biology/ssaha/files/patch-HashTableGeneric.cpp (new)
  1.1       +29 -0     ports/biology/ssaha/files/patch-HashTablePacked.cpp (new)
  1.1       +16 -0     ports/biology/ssaha/files/patch-HashTablePacked.h (new)
  1.1       +77 -0     ports/biology/ssaha/files/patch-HashTableTranslated.cpp (new)
  1.1       +94 -0     ports/biology/ssaha/files/patch-MatchAligner.cpp (new)
  1.1       +33 -0     ports/biology/ssaha/files/patch-MatchAligner.h (new)
  1.1       +54 -0     ports/biology/ssaha/files/patch-MatchStore.h (new)
  1.1       +25 -0     ports/biology/ssaha/files/patch-MatchStoreGapped.h (new)
  1.1       +13 -0     ports/biology/ssaha/files/patch-MatchStoreUngapped.h (new)
  1.1       +54 -0     ports/biology/ssaha/files/patch-QueryManager.cpp (new)
  1.1       +19 -0     ports/biology/ssaha/files/patch-QueryManager.h (new)
  1.1       +13 -0     ports/biology/ssaha/files/patch-README (new)
  1.1       +48 -0     ports/biology/ssaha/files/patch-SSAHAMain.cpp (new)
  1.1       +19 -0     ports/biology/ssaha/files/patch-SSAHAMain.h (new)
  1.1       +75 -0     ports/biology/ssaha/files/patch-SequenceEncoder.cpp (new)
  1.1       +20 -0     ports/biology/ssaha/files/patch-SequenceReader.cpp (new)
  1.1       +11 -0     ports/biology/ssaha/files/patch-SequenceReader.h (new)
  1.1       +32 -0     ports/biology/ssaha/files/patch-SequenceReaderFasta.cpp (new)
  1.1       +11 -0     ports/biology/ssaha/files/patch-SequenceReaderFasta.h (new)
  1.1       +20 -0     ports/biology/ssaha/files/patch-SequenceReaderFilter.h (new)
  1.1       +28 -0     ports/biology/ssaha/files/patch-SequenceReaderLocal.cpp (new)
  1.1       +30 -0     ports/biology/ssaha/files/patch-SequenceReaderMulti.cpp (new)
  1.1       +13 -0     ports/biology/ssaha/files/patch-SequenceReaderMulti.h (new)
  1.1       +26 -0     ports/biology/ssaha/files/patch-SequenceReaderString.h (new)
  1.1       +15 -0     ports/biology/ssaha/files/patch-makefile (new)
  1.1       +178 -0    ports/biology/ssaha/files/patch-testHashTableNoOverlap.cpp (new)
  1.1       +20 -0     ports/biology/ssaha/files/patch-testQueryManager.cpp (new)
  1.1       +171 -0    ports/biology/ssaha/files/patch-testSequenceReaderFasta.cpp (new)
  1.1       +11 -0     ports/biology/ssaha/pkg-descr (new)
  1.1       +9 -0      ports/biology/ssaha/pkg-plist (new)