use same default isotopePattern params as in v0.3

removed legacy_interface.py (no longer used by sm-engine)

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)

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"