mspire 0.10.1 → 0.10.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c92ec4a23bf1ecef8abc24269b4e680c8a7ed8bd
-  data.tar.gz: 1016a66f7c99acf348ae1a439c77fd54e91431f6
+  metadata.gz: c5caadb4ca2d21cd1e38f7c1c0cd1c3b0b202a97
+  data.tar.gz: 833962e9730b48a8d4c88558f237c7b780655187
 SHA512:
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-  data.tar.gz: b3161fcf60c22a25b2c736612b7d9798c95185a45b9de97d181c791b6311d58fc73a927540385c908b26a394ca0f5dbe550b646e331da8f0d1f924054a216cb4
+  metadata.gz: 494e529d32f71331b02194356fd5308e30ac43c1c25562d70fb48053fbc4ef576f60e623081dd4d0d71fe4f88df7c08e2e96388b858a40df927f76cacb8789c4
+  data.tar.gz: b00b40b6dd458206035821e34f89ebbecbc12281c63d470862355d3831d88387b28d24ded8971c6d4285e72372b806aeb3e50b153a30e82d999054560cec70f8

data/lib/mspire/mzml/index_list.rb

@@ -63,9 +63,11 @@ module Mspire
               index = Index.new
               index.name = index_n['name'].to_sym
               ids = []
-              index_n.children.map do |offset_n| 
-                index << offset_n.text.to_i 
-                ids << offset_n['idRef']
+              index_n.children.each do |offset_n| 
+                if offset_n.name == 'offset'  # <- pwiz sometimes makes an index with no offsets, in violation of the mzML 1.1 schema--this simple check circumvents their mistake
+                  index << offset_n.text.to_i 
+                  ids << offset_n['idRef']
+                end
               end
               index.ids = ids
               index

data/lib/mspire/mzml/reader.rb

@@ -40,7 +40,7 @@ module Mspire::Mzml::Reader
 
   # returns a hash keyed by :spectrum or :chromatogram that gives the id
   # (aka ref) as a string.
-  def get_default_data_processing_ids(io, index_list, lookback=200)
+  def get_default_data_processing_ids(io, index_list, lookback=300)
     hash = {}
     index_list.each_pair do |name, index|
       io.bookmark do |io|

data/lib/mspire/version.rb

@@ -1,3 +1,3 @@
 module Mspire
-  VERSION = "0.10.1"
+  VERSION = "0.10.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.10.1
+  version: 0.10.2
 platform: ruby
 authors:
 - John T. Prince
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-01 00:00:00.000000000 Z
+date: 2013-10-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri