Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/muscleout.cpp b/website/archive/binaries/mac/src/muscle/muscleout.cpp
deleted file mode 100644 (file)
index d4c451c..0000000
--- a/website/archive/binaries/mac/src/muscle/muscleout.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "params.h"\r
-#include "textfile.h"\r
-\r
-static void DoOutput(MSA &msa)\r
-       {\r
-       bool AnyOutput = false;\r
-\r
-// Value options\r
-       if (g_pstrFASTAOutFileName)\r
-               {\r
-               TextFile File(g_pstrFASTAOutFileName, true);\r
-               msa.ToFASTAFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrMSFOutFileName)\r
-               {\r
-               TextFile File(g_pstrMSFOutFileName, true);\r
-               msa.ToMSFFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrClwOutFileName)\r
-               {\r
-               TextFile File(g_pstrClwOutFileName, true);\r
-               msa.ToAlnFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrClwStrictOutFileName)\r
-               {\r
-               g_bClwStrict = true;\r
-               TextFile File(g_pstrClwStrictOutFileName, true);\r
-               msa.ToAlnFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrHTMLOutFileName)\r
-               {\r
-               TextFile File(g_pstrHTMLOutFileName, true);\r
-               msa.ToHTMLFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrPHYIOutFileName)\r
-               {\r
-               TextFile File(g_pstrPHYIOutFileName, true);\r
-               msa.ToPhyInterleavedFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-       if (g_pstrPHYSOutFileName)\r
-               {\r
-               TextFile File(g_pstrPHYSOutFileName, true);\r
-               msa.ToPhySequentialFile(File);\r
-               AnyOutput = true;\r
-               }\r
-\r
-// Flag options, at most one used (because only one -out filename)\r
-       TextFile fileOut(g_pstrOutFileName, true);\r
-       if (g_bFASTA)\r
-               {\r
-               msa.ToFASTAFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-       else if (g_bMSF)\r
-               {\r
-               msa.ToMSFFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-       else if (g_bAln)\r
-               {\r
-               msa.ToAlnFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-       else if (g_bHTML)\r
-               {\r
-               msa.ToHTMLFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-       else if (g_bPHYI)\r
-               {\r
-               msa.ToPhyInterleavedFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-       else if (g_bPHYS)\r
-               {\r
-               msa.ToPhySequentialFile(fileOut);\r
-               AnyOutput = true;\r
-               }\r
-\r
-// If -out option was given but no flags, output as FASTA\r
-       if (!AnyOutput)\r
-               msa.ToFASTAFile(fileOut);\r
-       \r
-       fileOut.Close();\r
-\r
-       if (0 != g_pstrScoreFileName)\r
-               WriteScoreFile(msa);\r
-       }\r
-\r
-void MuscleOutput(MSA &msa)\r
-       {\r
-       MHackEnd(msa);\r
-       if (g_bStable)\r
-               {\r
-               MSA msaStable;\r
-               Stabilize(msa, msaStable);\r
-               msa.Clear();    // save memory\r
-               DoOutput(msaStable);\r
-               }\r
-       else\r
-               DoOutput(msa);\r
-       }\r