mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Attempt binary conversion of newlines if UTF conversion fails.
This commit is contained in:
John Chilton
@@ -139,26 +139,52 @@ def convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix="gxupload",
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"""
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fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
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i = 0
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with io.open(fd, mode="wt", encoding='utf-8') as fp:
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with io.open(fname, encoding='utf-8') as fi:
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partial_line = False
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while True:
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line = fi.readline(block_size)
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if not line:
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if partial_line:
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fp.write(u"\n")
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try:
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with io.open(fd, mode="wt", encoding='utf-8') as fp:
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with io.open(fname, encoding='utf-8') as fi:
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partial_line = False
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while True:
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line = fi.readline(block_size)
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if not line:
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if partial_line:
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fp.write(u"\n")
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i += 1
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break
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if line[-1] == u"\n":
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partial_line = False
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fp.write(line)
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i += 1
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break
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continue
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if line[-1] == u"\n":
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partial_line = False
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# We have a block... maybe at the end of the file.
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partial_line = True
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fp.write(line)
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i += 1
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continue
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except UnicodeDecodeError:
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fd, temp_name = tempfile.mkstemp(prefix=tmp_prefix, dir=tmp_dir)
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i = 0
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with io.open(fd, mode="wb") as fp:
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with io.open(fname, mode="rb") as fi:
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partial_line = False
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while True:
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line = fi.readline(block_size)
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if not line:
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if partial_line:
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fp.write(b"\n")
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i += 1
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break
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# We have a block... maybe at the end of the file.
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partial_line = True
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fp.write(line)
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strip_line = line.rstrip(b"\r\n")
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if len(strip_line) != len(line):
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partial_line = False
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fp.write(strip_line)
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fp.write(b"\n")
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i += 1
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continue
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# We have a block... maybe at the end of the file.
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partial_line = True
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fp.write(line)
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if in_place:
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shutil.move(temp_name, fname)
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@@ -0,0 +1,380 @@
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<?xml version="1.0" encoding="ISO-8859-1"?>
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<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
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<cvList count="4">
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<cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
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<cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
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<cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
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<cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
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</cvList>
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<fileDescription>
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<fileContent>
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<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
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<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
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<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
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<cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
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</fileContent>
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<sourceFileList count="1">
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<sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
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<cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
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<cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
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<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
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</sourceFile>
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</sourceFileList>
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<contact>
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<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
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<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
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<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
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<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
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</contact>
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</fileDescription>
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<referenceableParamGroupList count="4">
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<referenceableParamGroup id="mzArray">
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
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<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
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</referenceableParamGroup>
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<referenceableParamGroup id="intensityArray">
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<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
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<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
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<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
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<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
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</referenceableParamGroup>
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<referenceableParamGroup id="scan1">
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<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
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<cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
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</referenceableParamGroup>
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<referenceableParamGroup id="spectrum1">
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<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
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<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
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<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
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<cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
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</referenceableParamGroup>
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</referenceableParamGroupList>
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<sampleList count="1">
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<sample id="sample1" name="Sample1">
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<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
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</sample>
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</sampleList>
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<softwareList count="2">
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<software id="Xcalibur" version="2.2">
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<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
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</software>
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<software id="TMC" version="1.1 beta">
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<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
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</software>
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</softwareList>
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<scanSettingsList count="1">
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<scanSettings id="scansettings1">
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<cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/>
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<cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/>
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<cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/>
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<cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/>
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<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/>
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<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/>
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<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size (x)" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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</scanSettings>
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</scanSettingsList>
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<instrumentConfigurationList count="1">
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<instrumentConfiguration id="LTQFTUltra0">
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<cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/>
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<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
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<componentList count="3">
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<source order="1">
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<cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization"/>
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<cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet"/>
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<cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10.0"/>
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<cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10.0"/>
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<cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10.0"/>
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<cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10.0"/>
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<cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50.0"/>
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<cvParam cvRef="MS" accession="MS:1000850" name="gas laser"/>
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<cvParam cvRef="MS" accession="MS:1000836" name="dried droplet MALDI matrix preparation"/>
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<cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10.0"/>
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<cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
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</source>
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<analyzer order="2">
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<cvParam cvRef="MS" accession="MS:1000264" name="ion trap"/>
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<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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</analyzer>
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<detector order="3">
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<cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/>
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<cvParam cvRef="MS" accession="MS:1000120" name="transient recorder"/>
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</detector>
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||||
</componentList>
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<softwareRef ref="Xcalibur"/>
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</instrumentConfiguration>
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</instrumentConfigurationList>
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<dataProcessingList count="2">
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||||
<dataProcessing id="XcaliburProcessing">
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||||
<processingMethod softwareRef="Xcalibur" order="1">
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<cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal"/>
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||||
</processingMethod>
|
||||
</dataProcessing>
|
||||
<dataProcessing id="TMCConversion">
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||||
<processingMethod softwareRef="TMC" order="2">
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||||
<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
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||||
</processingMethod>
|
||||
</dataProcessing>
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||||
</dataProcessingList>
|
||||
<run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
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||||
<spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
|
||||
<spectrum id="Scan=1" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="0">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="121.85039039868471"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=3" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="2">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="161.8091904482675"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=4" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="3">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="200.9633277092539"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=5" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="4">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="135.30584173158496"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=6" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="5">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="108.39597418421639"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=7" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="6">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="127.84664447846832"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
</spectrumList>
|
||||
</run>
|
||||
</mzML>
|
||||
@@ -0,0 +1,380 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<mzML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
|
||||
<cvList count="4">
|
||||
<cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
|
||||
<cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
|
||||
<cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
|
||||
<cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
|
||||
</cvList>
|
||||
<fileDescription>
|
||||
<fileContent>
|
||||
<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
|
||||
</fileContent>
|
||||
<sourceFileList count="1">
|
||||
<sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
|
||||
<cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
|
||||
</sourceFile>
|
||||
</sourceFileList>
|
||||
<contact>
|
||||
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
|
||||
</contact>
|
||||
</fileDescription>
|
||||
<referenceableParamGroupList count="4">
|
||||
<referenceableParamGroup id="mzArray">
|
||||
<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
|
||||
</referenceableParamGroup>
|
||||
<referenceableParamGroup id="intensityArray">
|
||||
<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
|
||||
</referenceableParamGroup>
|
||||
<referenceableParamGroup id="scan1">
|
||||
<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
|
||||
</referenceableParamGroup>
|
||||
<referenceableParamGroup id="spectrum1">
|
||||
<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
|
||||
</referenceableParamGroup>
|
||||
</referenceableParamGroupList>
|
||||
<sampleList count="1">
|
||||
<sample id="sample1" name="Sample1">
|
||||
<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
|
||||
</sample>
|
||||
</sampleList>
|
||||
<softwareList count="2">
|
||||
<software id="Xcalibur" version="2.2">
|
||||
<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
|
||||
</software>
|
||||
<software id="TMC" version="1.1 beta">
|
||||
<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
|
||||
</software>
|
||||
</softwareList>
|
||||
<scanSettingsList count="1">
|
||||
<scanSettings id="scansettings1">
|
||||
<cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size (x)" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
|
||||
</scanSettings>
|
||||
</scanSettingsList>
|
||||
<instrumentConfigurationList count="1">
|
||||
<instrumentConfiguration id="LTQFTUltra0">
|
||||
<cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
|
||||
<componentList count="3">
|
||||
<source order="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000846" name="pulse energy" value="10.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000847" name="pulse duration" value="10.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000848" name="attenuation" value="50.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000850" name="gas laser"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000836" name="dried droplet MALDI matrix preparation"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10.0"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
|
||||
</source>
|
||||
<analyzer order="2">
|
||||
<cvParam cvRef="MS" accession="MS:1000264" name="ion trap"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
|
||||
</analyzer>
|
||||
<detector order="3">
|
||||
<cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000120" name="transient recorder"/>
|
||||
</detector>
|
||||
</componentList>
|
||||
<softwareRef ref="Xcalibur"/>
|
||||
</instrumentConfiguration>
|
||||
</instrumentConfigurationList>
|
||||
<dataProcessingList count="2">
|
||||
<dataProcessing id="XcaliburProcessing">
|
||||
<processingMethod softwareRef="Xcalibur" order="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal"/>
|
||||
</processingMethod>
|
||||
</dataProcessing>
|
||||
<dataProcessing id="TMCConversion">
|
||||
<processingMethod softwareRef="TMC" order="2">
|
||||
<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
|
||||
</processingMethod>
|
||||
</dataProcessing>
|
||||
</dataProcessingList>
|
||||
<run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
|
||||
<spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
|
||||
<spectrum id="Scan=1" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="0">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="121.85039039868471"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="33612"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=2" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="1">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="182.31835420101888"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="67208"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="100804"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=3" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="2">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="161.8091904482675"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="134400"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="167996"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=4" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="3">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="200.9633277092539"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="201592"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=5" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="4">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="135.30584173158496"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=6" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="5">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="108.39597418421639"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=7" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="6">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="127.84664447846832"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="436764"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=8" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="7">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="168.27018147522492"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="470360"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="503956"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
<spectrum id="Scan=9" defaultArrayLength="0" dataProcessingRef="XcaliburProcessing" sourceFileRef="sf1" index="8">
|
||||
<referenceableParamGroupRef ref="spectrum1"/>
|
||||
<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="243.5395066031077"/>
|
||||
<scanList count="1">
|
||||
<cvParam cvRef="MS" accession="MS:1000795" name="no combination"/>
|
||||
<scan instrumentConfigurationRef="LTQFTUltra0">
|
||||
<referenceableParamGroupRef ref="scan1"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>
|
||||
</scan>
|
||||
</scanList>
|
||||
<binaryDataArrayList count="2">
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="mzArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
<binaryDataArray encodedLength="0">
|
||||
<referenceableParamGroupRef ref="intensityArray"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148"/>
|
||||
<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596"/>
|
||||
<binary />
|
||||
</binaryDataArray>
|
||||
</binaryDataArrayList>
|
||||
</spectrum>
|
||||
</spectrumList>
|
||||
</run>
|
||||
</mzML>
|
||||
@@ -1,6 +1,11 @@
|
||||
import tempfile
|
||||
|
||||
from galaxy.datatypes.sniff import convert_newlines_sep2tabs, sep2tabs
|
||||
from galaxy.datatypes.sniff import (
|
||||
convert_newlines,
|
||||
convert_newlines_sep2tabs,
|
||||
get_test_fname,
|
||||
sep2tabs,
|
||||
)
|
||||
|
||||
|
||||
def assert_converts_to_1234_sep2tabs(content, line_ending="\n"):
|
||||
@@ -23,6 +28,13 @@ def assert_converts_to_1234_convert_sep2tabs(content, expected='1\t2\n3\t4\n', l
|
||||
assert expected == open(tf.name).read()
|
||||
|
||||
|
||||
def test_convert_newlines_non_utf():
|
||||
fname = get_test_fname("dosimzml")
|
||||
rval = convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir(), in_place=False)
|
||||
new_file = rval[1]
|
||||
assert open(new_file, "rb").read() == open(get_test_fname("1.imzml"), "rb").read()
|
||||
|
||||
|
||||
def test_sep2tabs():
|
||||
assert_converts_to_1234_sep2tabs("1 2\n3 4\n")
|
||||
assert_converts_to_1234_sep2tabs("1 2\n3 4\n")
|
||||
|
||||
Reference in New Issue
Block a user