From d46c95ed7285743bfc27e5b08560e7852173ad18 Mon Sep 17 00:00:00 2001
From: Andrew Dowsey <andrew@dowsey.net>
Date: Fri, 12 Jun 2015 18:45:50 +0100
Subject: [PATCH] went back to opening existing smo file as needed to write
 multiple preset scan configs

---
 restoration/restoration.cpp |  2 +-
 seamass/SMOWriter.cpp       | 21 +++++++++++++--------
 seamass/core.cpp            | 17 +++++++++++++++++
 3 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/restoration/restoration.cpp b/restoration/restoration.cpp
index 40d35df..d078da9 100755
--- a/restoration/restoration.cpp
+++ b/restoration/restoration.cpp
@@ -84,7 +84,7 @@ int main(int argc, char *argv[])
 		cout << "<in_file>:  Raw input file in seaMass Input format (smi)" << endl;
 		cout << "            guidelines: Use pwiz-seamass to convert from mzML or vendor format" << endl;
 		cout << "<mz_res>:   MS resolution given as: \"b-splines per Th = 2^mz_res * 60 / 1.0033548378\"" << endl;
-		cout << "            guidelines: between 0 to 2 for ToF, 3 for Orbitrap" << endl;
+		cout << "            guidelines: between 0 to 2 for ToF (e.g. 1 is suitable for 30,000 resolution), 3 for Orbitrap" << endl;
 		cout << "<rt_res>:   LC resolution given as: \"b-splines per minute = 2^rt_res\"" << endl;
 		cout << "            guidelines: around 4" << endl;
 		cout << "<shrink>:   Amount of denoising given as: \"L1 shrinkage = 2^shrinkage\"" << endl;
diff --git a/seamass/SMOWriter.cpp b/seamass/SMOWriter.cpp
index 31ad0c0..6d09369 100755
--- a/seamass/SMOWriter.cpp
+++ b/seamass/SMOWriter.cpp
@@ -28,13 +28,17 @@
 SMOWriter::
 SMOWriter(const string& filename)
 {
-    file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
-    if (file < 0)
-    {
-            // throw exception
-            cerr << "problem opening smo" << endl;
-            throw "problem opening smo";
-    }
+	file = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+	if (file < 0)
+	{
+		file = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+		if (file < 0)
+		{
+			// throw exception
+			cerr << "problem opening smo" << endl;
+			throw "problem opening smo";
+		}
+	}
 }
 
 
@@ -46,7 +50,8 @@ SMOWriter::
     {
         // throw exception
         cerr << "problem closing smo" << endl;
-    }
+		throw "problem closing smo";
+	}
 }
 
 
diff --git a/seamass/core.cpp b/seamass/core.cpp
index fa7a7c4..637d09c 100644
--- a/seamass/core.cpp
+++ b/seamass/core.cpp
@@ -92,6 +92,23 @@ print(ostream& out) const
 ////////////////////////////////////////////////////////////////////////////////
 
 
+double CatmullRomInterpolate(
+	double y0, double y1,
+	double y2, double y3,
+	double mu)
+{
+	double a0, a1, a2, a3, mu2;
+
+	mu2 = mu*mu;
+	a0 = -0.5*y0 + 1.5*y1 - 1.5*y2 + 0.5*y3;
+	a1 = y0 - 2.5*y1 + 2 * y2 - 0.5*y3;
+	a2 = -0.5*y0 + 0.5*y2;
+	a3 = y1;
+
+	return a0*mu*mu2 + a1*mu2 + a2*mu + a3;
+}
+
+
 void bin_mzs_intensities(vector< vector<double> >& mzs,
                          vector< vector<double> >& intensities,
 						 ii instrument_type,