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[jabaws.git] / website / archive / binaries / mac / src / muscle / seqvect.cpp
diff --git a/website/archive/binaries/mac/src/muscle/seqvect.cpp b/website/archive/binaries/mac/src/muscle/seqvect.cpp
deleted file mode 100644 (file)
index 52b46fc..0000000
--- a/website/archive/binaries/mac/src/muscle/seqvect.cpp
+++ /dev/null
@@ -1,290 +0,0 @@
-#include "muscle.h"\r
-#include "seqvect.h"\r
-#include "textfile.h"\r
-#include "msa.h"\r
-\r
-const size_t MAX_FASTA_LINE = 16000;\r
-\r
-SeqVect::~SeqVect()\r
-       {\r
-       Clear();\r
-       }\r
-\r
-void SeqVect::Clear()\r
-       {\r
-       for (size_t n = 0; n < size(); ++n)\r
-               delete (*this)[n];\r
-       }\r
-\r
-void SeqVect::ToFASTAFile(TextFile &File) const\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->ToFASTAFile(File);\r
-               }\r
-       }\r
-\r
-void SeqVect::FromFASTAFile(TextFile &File)\r
-       {\r
-       Clear();\r
-\r
-       FILE *f = File.GetStdioFile();\r
-       for (;;)\r
-               {\r
-               char *Label;\r
-               unsigned uLength;\r
-               char *SeqData = GetFastaSeq(f, &uLength, &Label);\r
-               if (0 == SeqData)\r
-                       return;\r
-               Seq *ptrSeq = new Seq;\r
-\r
-               for (unsigned i = 0; i < uLength; ++i)\r
-                       {\r
-                       char c = SeqData[i];\r
-                       ptrSeq->push_back(c);\r
-                       }\r
-\r
-               ptrSeq->SetName(Label);\r
-               push_back(ptrSeq);\r
-\r
-               delete[] SeqData;\r
-               delete[] Label;\r
-               }\r
-       }\r
-\r
-void SeqVect::PadToMSA(MSA &msa)\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       if (0 == uSeqCount)\r
-               {\r
-               msa.Clear();\r
-               return;\r
-               }\r
-\r
-       unsigned uLongestSeqLength = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               unsigned uColCount = ptrSeq->Length();\r
-               if (uColCount > uLongestSeqLength)\r
-                       uLongestSeqLength = uColCount;\r
-               }\r
-       msa.SetSize(uSeqCount, uLongestSeqLength);\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               msa.SetSeqName(uSeqIndex, ptrSeq->GetName());\r
-               unsigned uColCount = ptrSeq->Length();\r
-               unsigned uColIndex;\r
-               for (uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-                       {\r
-                       char c = ptrSeq->at(uColIndex);\r
-                       msa.SetChar(uSeqIndex, uColIndex, c);\r
-                       }\r
-               while (uColIndex < uLongestSeqLength)\r
-                       msa.SetChar(uSeqIndex, uColIndex++, '.');\r
-               }\r
-       }\r
-\r
-void SeqVect::Copy(const SeqVect &rhs)\r
-       {\r
-       clear();\r
-       unsigned uSeqCount = rhs.Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = rhs.at(uSeqIndex);\r
-               Seq *ptrSeqCopy = new Seq;\r
-               ptrSeqCopy->Copy(*ptrSeq);\r
-               push_back(ptrSeqCopy);\r
-               }\r
-       }\r
-\r
-void SeqVect::StripGaps()\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->StripGaps();\r
-               }\r
-       }\r
-\r
-void SeqVect::StripGapsAndWhitespace()\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->StripGapsAndWhitespace();\r
-               }\r
-       }\r
-\r
-void SeqVect::ToUpper()\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->ToUpper();\r
-               }\r
-       }\r
-\r
-bool SeqVect::FindName(const char *ptrName, unsigned *ptruIndex) const\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               const Seq *ptrSeq = at(uSeqIndex);\r
-               if (0 == stricmp(ptrSeq->GetName(), ptrName))\r
-                       {\r
-                       *ptruIndex = uSeqIndex;\r
-                       return true;\r
-                       }\r
-               }\r
-       return false;\r
-       }\r
-\r
-void SeqVect::AppendSeq(const Seq &s)\r
-       {\r
-       Seq *ptrSeqCopy = new Seq;\r
-       ptrSeqCopy->Copy(s);\r
-       push_back(ptrSeqCopy);\r
-       }\r
-\r
-void SeqVect::LogMe() const\r
-       {\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               const Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->LogMe();\r
-               }\r
-       }\r
-\r
-const char *SeqVect::GetSeqName(unsigned uSeqIndex) const\r
-       {\r
-       assert(uSeqIndex < size());\r
-       const Seq *ptrSeq = at(uSeqIndex);\r
-       return ptrSeq->GetName();\r
-       }\r
-\r
-unsigned SeqVect::GetSeqId(unsigned uSeqIndex) const\r
-       {\r
-       assert(uSeqIndex < size());\r
-       const Seq *ptrSeq = at(uSeqIndex);\r
-       return ptrSeq->GetId();\r
-       }\r
-\r
-unsigned SeqVect::GetSeqIdFromName(const char *Name) const\r
-       {\r
-       const unsigned uSeqCount = GetSeqCount();\r
-       for (unsigned i = 0; i < uSeqCount; ++i)\r
-               {\r
-               if (!strcmp(Name, GetSeqName(i)))\r
-                       return GetSeqId(i);\r
-               }\r
-       Quit("SeqVect::GetSeqIdFromName(%s): not found", Name);\r
-       return 0;\r
-       }\r
-\r
-Seq &SeqVect::GetSeqById(unsigned uId)\r
-       {\r
-       const unsigned uSeqCount = GetSeqCount();\r
-       for (unsigned i = 0; i < uSeqCount; ++i)\r
-               {\r
-               if (GetSeqId(i) == uId)\r
-                       return GetSeq(i);\r
-               }\r
-       Quit("SeqVect::GetSeqIdByUd(%d): not found", uId);\r
-       return (Seq &) *((Seq *) 0);\r
-       }\r
-\r
-unsigned SeqVect::GetSeqLength(unsigned uSeqIndex) const\r
-       {\r
-       assert(uSeqIndex < size());\r
-       const Seq *ptrSeq = at(uSeqIndex);\r
-       return ptrSeq->Length();\r
-       }\r
-\r
-Seq &SeqVect::GetSeq(unsigned uSeqIndex)\r
-       {\r
-       assert(uSeqIndex < size());\r
-       return *at(uSeqIndex);\r
-       }\r
-\r
-const Seq &SeqVect::GetSeq(unsigned uSeqIndex) const\r
-       {\r
-       assert(uSeqIndex < size());\r
-       return *at(uSeqIndex);\r
-       }\r
-\r
-void SeqVect::SetSeqId(unsigned uSeqIndex, unsigned uId)\r
-       {\r
-       assert(uSeqIndex < size());\r
-       Seq *ptrSeq = at(uSeqIndex);\r
-       return ptrSeq->SetId(uId);\r
-       }\r
-\r
-ALPHA SeqVect::GuessAlpha() const\r
-       {\r
-// If at least MIN_NUCLEO_PCT of the first CHAR_COUNT non-gap\r
-// letters belong to the nucleotide alphabet, guess nucleo.\r
-// Otherwise amino.\r
-       const unsigned CHAR_COUNT = 100;\r
-       const unsigned MIN_NUCLEO_PCT = 95;\r
-\r
-       const unsigned uSeqCount = GetSeqCount();\r
-       if (0 == uSeqCount)\r
-               return ALPHA_Amino;\r
-\r
-       unsigned uSeqIndex = 0;\r
-       unsigned uPos = 0;\r
-       unsigned uSeqLength = GetSeqLength(0);\r
-       unsigned uDNACount = 0;\r
-       unsigned uRNACount = 0;\r
-       unsigned uTotal = 0;\r
-       const Seq *ptrSeq = &GetSeq(0);\r
-       for (;;)\r
-               {\r
-               while (uPos >= uSeqLength)\r
-                       {\r
-                       ++uSeqIndex;\r
-                       if (uSeqIndex >= uSeqCount)\r
-                               break;\r
-                       ptrSeq = &GetSeq(uSeqIndex);\r
-                       uSeqLength = ptrSeq->Length();\r
-                       uPos = 0;\r
-                       }\r
-               if (uSeqIndex >= uSeqCount)\r
-                       break;\r
-               char c = ptrSeq->at(uPos++);\r
-               if (IsGapChar(c))\r
-                       continue;\r
-               if (IsDNA(c))\r
-                       ++uDNACount;\r
-               if (IsRNA(c))\r
-                       ++uRNACount;\r
-               ++uTotal;\r
-               if (uTotal >= CHAR_COUNT)\r
-                       break;\r
-               }\r
-       if (uTotal != 0 && ((uDNACount*100)/uTotal) >= MIN_NUCLEO_PCT)\r
-               return ALPHA_DNA;\r
-       if (uTotal != 0 && ((uRNACount*100)/uTotal) >= MIN_NUCLEO_PCT)\r
-               return ALPHA_RNA;\r
-       return ALPHA_Amino;\r
-       }\r
-\r
-void SeqVect::FixAlpha()\r
-       {\r
-       ClearInvalidLetterWarning();\r
-       unsigned uSeqCount = Length();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq *ptrSeq = at(uSeqIndex);\r
-               ptrSeq->FixAlpha();\r
-               }\r
-       ReportInvalidLetters();\r
-       }\r