Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / profile.cpp

diff --git a/website/archive/binaries/mac/src/muscle/profile.cpp b/website/archive/binaries/mac/src/muscle/profile.cpp
deleted file mode 100644 (file)
index f02b381..0000000
--- a/website/archive/binaries/mac/src/muscle/profile.cpp
+++ /dev/null
@@ -1,147 +0,0 @@
-#include "muscle.h"\r
-#include "textfile.h"\r
-#include "msa.h"\r
-#include "tree.h"\r
-#include "profile.h"\r
-#include "objscore.h"\r
-\r
-bool TreeNeededForWeighting(SEQWEIGHT s)\r
-       {\r
-       switch (s)\r
-               {\r
-       case SEQWEIGHT_ClustalW:\r
-       case SEQWEIGHT_ThreeWay:\r
-               return true;\r
-       default:\r
-               return false;\r
-               }\r
-       }\r
-\r
-static ProfPos *ProfileFromMSALocal(MSA &msa, Tree &tree)\r
-       {\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               msa.SetSeqId(uSeqIndex, uSeqIndex);\r
-\r
-       if (TreeNeededForWeighting(g_SeqWeight2))\r
-               {\r
-               TreeFromMSA(msa, tree, g_Cluster2, g_Distance2, g_Root1);\r
-               SetMuscleTree(tree);\r
-               }\r
-       return ProfileFromMSA(msa);\r
-       }\r
-\r
-void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut)\r
-       {\r
-       //ALPHA Alpha = ALPHA_Undefined;\r
-       //switch (g_SeqType)\r
-       //      {\r
-       //case SEQTYPE_Auto:\r
-       //      Alpha = msa1.GuessAlpha();\r
-       //      break;\r
-\r
-       //case SEQTYPE_Protein:\r
-       //      Alpha = ALPHA_Amino;\r
-       //      break;\r
-\r
-       //case SEQTYPE_DNA:\r
-       //      Alpha = ALPHA_DNA;\r
-       //      break;\r
-\r
-       //case SEQTYPE_RNA:\r
-       //      Alpha = ALPHA_RNA;\r
-       //      break;\r
-\r
-       //default:\r
-       //      Quit("Invalid SeqType");\r
-       //      }\r
-       //SetAlpha(Alpha);\r
-\r
-       //msa1.FixAlpha();\r
-       //msa2.FixAlpha();\r
-\r
-       unsigned uLength1;\r
-       unsigned uLength2;\r
-\r
-       uLength1 = msa1.GetColCount();\r
-       uLength2 = msa2.GetColCount();\r
-\r
-       Tree tree1;\r
-       Tree tree2;\r
-       ProfPos *Prof1 = ProfileFromMSALocal(msa1, tree1);\r
-       ProfPos *Prof2 = ProfileFromMSALocal(msa2, tree2);\r
-\r
-       PWPath Path;\r
-       ProfPos *ProfOut;\r
-       unsigned uLengthOut;\r
-       Progress("Aligning profiles");\r
-       AlignTwoProfs(Prof1, uLength1, 1.0, Prof2, uLength2, 1.0, Path, &ProfOut, &uLengthOut);\r
-\r
-       Progress("Building output");\r
-       AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);\r
-       }\r
-\r
-// Do profile-profile alignment\r
-void Profile()\r
-       {\r
-       if (0 == g_pstrFileName1 || 0 == g_pstrFileName2)\r
-               Quit("-profile needs -in1 and -in2");\r
-\r
-       SetSeqWeightMethod(g_SeqWeight1);\r
-\r
-       TextFile file1(g_pstrFileName1);\r
-       TextFile file2(g_pstrFileName2);\r
-\r
-       MSA msa1;\r
-       MSA msa2;\r
-       MSA msaOut;\r
-\r
-       Progress("Reading %s", g_pstrFileName1);\r
-       msa1.FromFile(file1);\r
-       Progress("%u seqs %u cols", msa1.GetSeqCount(), msa1.GetColCount());\r
-\r
-       Progress("Reading %s", g_pstrFileName2);\r
-       msa2.FromFile(file2);\r
-       Progress("%u seqs %u cols", msa2.GetSeqCount(), msa2.GetColCount());\r
-\r
-       ALPHA Alpha = ALPHA_Undefined;\r
-       switch (g_SeqType)\r
-               {\r
-       case SEQTYPE_Auto:\r
-               Alpha = msa1.GuessAlpha();\r
-               break;\r
-\r
-       case SEQTYPE_Protein:\r
-               Alpha = ALPHA_Amino;\r
-               break;\r
-\r
-       case SEQTYPE_DNA:\r
-               Alpha = ALPHA_DNA;\r
-               break;\r
-\r
-       case SEQTYPE_RNA:\r
-               Alpha = ALPHA_RNA;\r
-               break;\r
-\r
-       default:\r
-               Quit("Invalid seq type");\r
-               }\r
-       SetAlpha(Alpha);\r
-\r
-       msa1.FixAlpha();\r
-       msa2.FixAlpha();\r
-\r
-       SetPPScore();\r
-       if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha)\r
-               SetPPScore(PPSCORE_SPN);\r
-\r
-       const unsigned uSeqCount1 = msa1.GetSeqCount();\r
-       const unsigned uSeqCount2 = msa2.GetSeqCount();\r
-       const unsigned uSumSeqCount = uSeqCount1 + uSeqCount2;\r
-       MSA::SetIdCount(uSumSeqCount);\r
-\r
-       ProfileProfile(msa1, msa2, msaOut);\r
-\r
-       Progress("Writing output");\r
-       MuscleOutput(msaOut);\r
-       }\r