From 18cc2b96897a1ab1635c47e2b902233e54c36a34 Mon Sep 17 00:00:00 2001
From: Artem Tarasov <artem.tarasov@embl.de>
Date: Mon, 21 Aug 2017 10:59:29 +0200
Subject: [PATCH] use same default isotopePattern params as in v0.3

removed legacy_interface.py (no longer used by sm-engine)
---
 cpyMSpec/legacy_interface.py | 36 ------------------------------------
 cpyMSpec/spectrum.py         | 14 ++++++++++++--
 cpyMSpec/utils.py            |  2 +-
 ims-cpp                      |  2 +-
 4 files changed, 14 insertions(+), 40 deletions(-)
 delete mode 100644 cpyMSpec/legacy_interface.py

diff --git a/cpyMSpec/legacy_interface.py b/cpyMSpec/legacy_interface.py
deleted file mode 100644
index 4e5abea..0000000
--- a/cpyMSpec/legacy_interface.py
+++ /dev/null
@@ -1,36 +0,0 @@
-from cpyMSpec import isotopePattern, InstrumentModel, ProfileSpectrum
-
-# layer of compatibility with the original pyMSpec.pyisocalc module
-
-from pyMSpec.pyisocalc import pyisocalc
-from pyMSpec.mass_spectrum import MassSpectrum
-
-import numpy as np
-
-def complete_isodist(sf, sigma=0.001, cutoff_perc=0.1, charge=None, pts_per_mz=10000, **kwargs):
-    if charge is None:
-        charge = sf.charge()
-
-    cutoff = cutoff_perc / 100.0
-    fwhm = sigma * 2.3548200450309493  # the exact ratio is 2 \sqrt{2 \log 2}
-    abs_charge = max(1, abs(charge))
-    p = isotopePattern(str(sf), 0.9999)
-    p.addCharge(charge)
-
-    mz = min(p.masses) / abs_charge
-    resolution = mz / fwhm
-
-    mzs = np.arange(min(p.masses) / abs_charge - 1,
-                    max(p.masses) / abs_charge + 1, 1.0/pts_per_mz)
-    instr = InstrumentModel('tof', resolution)
-    intensities = np.asarray(p.envelope(instr)(mzs * abs_charge))
-    intensities *= 100.0 / intensities.max()
-
-    ms = MassSpectrum()
-    ms.add_spectrum(mzs, intensities)
-
-    p = ProfileSpectrum(mzs, intensities).centroids(5)
-    p.removeIntensitiesBelow(cutoff)
-    p.sortByMass()
-    ms.add_centroids(p.masses, np.array(p.intensities) * 100)
-    return ms
diff --git a/cpyMSpec/spectrum.py b/cpyMSpec/spectrum.py
index 2743f43..af6a519 100644
--- a/cpyMSpec/spectrum.py
+++ b/cpyMSpec/spectrum.py
@@ -298,14 +298,24 @@ def trimmed(self, n_peaks):
     def removeIntensitiesBelow(self, min_intensity):
         ims.spectrum_trim_intensity(self.ptr, min_intensity)
 
-def isotopePattern(sum_formula, desired_prob=0.99999):
+def isotopePattern(sum_formula, threshold=1e-4, rel_threshold=True, desired_prob=0.99999):
     """
     Calculates isotopic peaks for a sum formula.
 
     :param sum_formula: text representation of an atomic composition
     :type sum_formula: str
+    :param threshold: minimum peak abundance; if nonzero, desired_prob parameter is ignored
+    :type threshold: float
+    :param rel_threshold: if True, threshold is relative to the highest peak, otherwise it is a probability
+    :type rel_threshold: bool
     :param desired_prob: total probability covered by the result
     :type desired_prob: float
     """
-    s = ims.spectrum_new_from_sf(sum_formula.encode('ascii'), desired_prob)
+    assert threshold >= 0 and threshold < 1
+    assert desired_prob > 0 and desired_prob <= 1
+
+    if threshold > 0:
+        s = ims.spectrum_new_from_sf_thr(sum_formula.encode('ascii'), threshold, rel_threshold)
+    else:
+        s = ims.spectrum_new_from_sf(sum_formula.encode('ascii'), desired_prob)
     return _new_spectrum(TheoreticalSpectrum, s)
diff --git a/cpyMSpec/utils.py b/cpyMSpec/utils.py
index 821ef48..297d8b5 100644
--- a/cpyMSpec/utils.py
+++ b/cpyMSpec/utils.py
@@ -17,4 +17,4 @@ def init_ffi():
 def load_shared_lib(ffi):
     return ffi.dlopen(full_filename(shared_lib("ms_cffi")))
 
-VERSION = "0.4.0"
+VERSION = "0.4.1"
diff --git a/ims-cpp b/ims-cpp
index 840dc49..0aec99f 160000
--- a/ims-cpp
+++ b/ims-cpp
@@ -1 +1 @@
-Subproject commit 840dc490c3d551c8ad580f21479398d43b222f53
+Subproject commit 0aec99f937ce0519aee3d86ae9dfc97f918d8c33