Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / params.h

diff --git a/website/archive/binaries/mac/src/muscle/params.h b/website/archive/binaries/mac/src/muscle/params.h
new file mode 100644 (file)
index 0000000..aefea32
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/params.h
@@ -0,0 +1,118 @@
+#ifndef params_h\r
+#define params_h\r
+\r
+extern const char *g_pstrInFileName;\r
+extern const char *g_pstrOutFileName;\r
+\r
+extern const char *g_pstrFASTAOutFileName;\r
+extern const char *g_pstrMSFOutFileName;\r
+extern const char *g_pstrClwOutFileName;\r
+extern const char *g_pstrClwStrictOutFileName;\r
+extern const char *g_pstrHTMLOutFileName;\r
+extern const char *g_pstrPHYIOutFileName;\r
+extern const char *g_pstrPHYSOutFileName;\r
+extern const char *g_pstrDistMxFileName1;\r
+extern const char *g_pstrDistMxFileName2;\r
+\r
+extern const char *g_pstrFileName1;\r
+extern const char *g_pstrFileName2;\r
+\r
+extern const char *g_pstrSPFileName;\r
+extern const char *g_pstrMatrixFileName;\r
+\r
+extern const char *g_pstrUseTreeFileName;\r
+extern bool g_bUseTreeNoWarn;\r
+\r
+extern const char *g_pstrComputeWeightsFileName;\r
+extern const char *g_pstrScoreFileName;\r
+\r
+extern SCORE g_scoreGapOpen;\r
+extern SCORE g_scoreCenter;\r
+extern SCORE g_scoreGapExtend;\r
+extern SCORE g_scoreGapAmbig;\r
+\r
+#if    DOUBLE_AFFINE\r
+extern SCORE g_scoreGapOpen2;\r
+extern SCORE g_scoreGapExtend2;\r
+#endif\r
+\r
+extern unsigned g_uSmoothWindowLength;\r
+extern unsigned g_uAnchorSpacing;\r
+extern unsigned g_uMaxTreeRefineIters;\r
+\r
+extern unsigned g_uMinDiagLength;\r
+extern unsigned g_uMaxDiagBreak;\r
+extern unsigned g_uDiagMargin;\r
+\r
+extern unsigned g_uRefineWindow;\r
+extern unsigned g_uWindowFrom;\r
+extern unsigned g_uWindowTo;\r
+extern unsigned g_uSaveWindow;\r
+extern unsigned g_uWindowOffset;\r
+\r
+extern unsigned g_uMaxSubFamCount;\r
+\r
+extern unsigned g_uHydrophobicRunLength;\r
+extern float g_dHydroFactor;\r
+\r
+extern float g_dSmoothScoreCeil;\r
+extern float g_dMinBestColScore;\r
+extern float g_dMinSmoothScore;\r
+extern float g_dSUEFF;\r
+\r
+extern bool g_bPrecompiledCenter;\r
+extern bool g_bNormalizeCounts;\r
+extern bool g_bDiags1;\r
+extern bool g_bDiags2;\r
+extern bool g_bDiags;\r
+extern bool g_bAnchors;\r
+extern bool g_bCatchExceptions;\r
+\r
+extern bool g_bMSF;\r
+extern bool g_bAln;\r
+extern bool g_bClwStrict;\r
+extern bool g_bHTML;\r
+extern bool g_bPHYI;\r
+extern bool g_bPHYS;\r
+\r
+extern bool g_bQuiet;\r
+extern bool g_bVerbose;\r
+extern bool g_bRefine;\r
+extern bool g_bRefineW;\r
+extern bool g_bRefineX;\r
+extern bool g_bLow;\r
+extern bool g_bSW;\r
+extern bool g_bClusterOnly;\r
+extern bool g_bProfile;\r
+extern bool g_bProfDB;\r
+extern bool g_bPPScore;\r
+extern bool g_bBrenner;\r
+extern bool g_bDimer;\r
+extern bool g_bVersion;\r
+extern bool g_bStable;\r
+extern bool g_bFASTA;\r
+extern bool g_bPAS;\r
+extern bool g_bTomHydro;\r
+extern bool g_bMakeTree;\r
+\r
+extern PPSCORE g_PPScore;\r
+extern OBJSCORE g_ObjScore;\r
+\r
+extern DISTANCE g_Distance1;\r
+extern CLUSTER g_Cluster1;\r
+extern ROOT g_Root1;\r
+extern SEQWEIGHT g_SeqWeight1;\r
+\r
+extern DISTANCE g_Distance2;\r
+extern CLUSTER g_Cluster2;\r
+extern ROOT g_Root2;\r
+extern SEQWEIGHT g_SeqWeight2;\r
+\r
+extern unsigned g_uMaxIters;\r
+extern unsigned long g_ulMaxSecs;\r
+extern unsigned g_uMaxMB;\r
+\r
+extern SEQTYPE g_SeqType;\r
+extern TERMGAPS g_TermGaps;\r
+\r
+#endif // params_h\r