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[proteowizard-commit] SF.net SVN: proteowizard:[490] trunk/pwiz
|
From: <dke...@us...> - 2008-11-25 22:18:36
|
Revision: 490
http://proteowizard.svn.sourceforge.net/proteowizard/?rev=490&view=rev
Author: dkessner
Date: 2008-11-25 22:18:26 +0000 (Tue, 25 Nov 2008)
Log Message:
-----------
added sld file handling stuff
Modified Paths:
--------------
trunk/pwiz/Jamroot.jam
trunk/pwiz/pwiz_tools/Jamfile.jam
Added Paths:
-----------
trunk/pwiz/pwiz_tools/sld/
trunk/pwiz/pwiz_tools/sld/Jamfile.jam
trunk/pwiz/pwiz_tools/sld/short_dump.cpp
trunk/pwiz/pwiz_tools/sld/sld.cpp
trunk/pwiz/pwiz_tools/sld/sld.hpp
trunk/pwiz/pwiz_tools/sld/sldout.cpp
trunk/pwiz/pwiz_tools/sld/test/
trunk/pwiz/pwiz_tools/sld/test/chosen_14.csv
trunk/pwiz/pwiz_tools/sld/test/chosen_14.sld
trunk/pwiz/pwiz_tools/sld/test/chosen_14.txt
trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.csv
trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.sld
trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.txt
trunk/pwiz/pwiz_tools/sld/test/chosen_205.csv
trunk/pwiz/pwiz_tools/sld/test/chosen_205.sld
trunk/pwiz/pwiz_tools/sld/test/chosen_205.txt
trunk/pwiz/pwiz_tools/sld/test/chosen_205_exported.csv
trunk/pwiz/pwiz_tools/sld/test/test_sldout
Modified: trunk/pwiz/Jamroot.jam
===================================================================
--- trunk/pwiz/Jamroot.jam 2008-11-25 20:16:22 UTC (rev 489)
+++ trunk/pwiz/Jamroot.jam 2008-11-25 22:18:26 UTC (rev 490)
@@ -135,6 +135,7 @@
install executables
: pwiz_tools/commandline
+ pwiz_tools/sld//sldout
pwiz/examples
: <install-type>EXE
<toolset>gcc,<variant>release:<location>build/gcc-release
@@ -148,6 +149,7 @@
install libraries
: pwiz_tools/commandline
+ pwiz_tools/sld//sldout
pwiz/examples
: <install-type>LIB
<install-dependencies>on
Modified: trunk/pwiz/pwiz_tools/Jamfile.jam
===================================================================
--- trunk/pwiz/pwiz_tools/Jamfile.jam 2008-11-25 20:16:22 UTC (rev 489)
+++ trunk/pwiz/pwiz_tools/Jamfile.jam 2008-11-25 22:18:26 UTC (rev 490)
@@ -22,4 +22,5 @@
build-project commandline ;
-build-project SeeMS ;
\ No newline at end of file
+build-project SeeMS ;
+build-project sld ;
Added: trunk/pwiz/pwiz_tools/sld/Jamfile.jam
===================================================================
--- trunk/pwiz/pwiz_tools/sld/Jamfile.jam (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/Jamfile.jam 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,36 @@
+#
+# Jamfile (pwiz_tools/sld)
+#
+#
+# Original author: Darren Kessner <Dar...@cs...>
+#
+# Copyright 2008 Spielberg Family Center for Applied Proteomics
+# Cedars-Sinai Medical Center, Los Angeles, California 90048
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+
+exe sldout
+ : sldout.cpp sld.cpp
+ ;
+
+exe short_dump
+ : short_dump.cpp
+ ;
+
+
+install test : short_dump sldout : <location>test ;
+explicit test ;
+
+
Property changes on: trunk/pwiz/pwiz_tools/sld/Jamfile.jam
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/pwiz/pwiz_tools/sld/short_dump.cpp
===================================================================
--- trunk/pwiz/pwiz_tools/sld/short_dump.cpp (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/short_dump.cpp 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,60 @@
+//
+// short_dump.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include <iostream>
+#include <fstream>
+
+
+using namespace std;
+
+
+int main(int argc, char* argv[])
+{
+ if (argc < 2)
+ {
+ cout << "Usage: short_dump filename\n";
+ return 1;
+ }
+
+ const char* filename = argv[1];
+ ifstream is(filename);
+
+ while (is)
+ {
+ // read 2 bytes at a time
+ short x = 0;
+ is.read((char*)&x, sizeof(short));
+ if (!is) break;
+
+ // print characters if printable, /0 if 0, value otherwise
+ if (x>=' ' && x<='~')
+ cout << (char)x;
+ else if (x==0)
+ cout << "\\0 <pos " << is.tellg() << " 0x" << hex << is.tellg() << dec << ">\n";
+ else
+ cout << "<int " << dec << x << " 0x" << hex << x << dec << ">\n";
+ }
+
+ return 0;
+}
+
Added: trunk/pwiz/pwiz_tools/sld/sld.cpp
===================================================================
--- trunk/pwiz/pwiz_tools/sld/sld.cpp (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/sld.cpp 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,354 @@
+//
+// sld.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include "sld.hpp"
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <stdexcept>
+
+
+using namespace std;
+
+
+namespace pwiz {
+namespace sld {
+
+
+char check_short_size[((int)sizeof(short)-2)==0];
+
+
+template <typename value_type>
+value_type readValue(istream& is)
+{
+ value_type result = 0;
+ is.read((char*)&result, sizeof(result));
+ return result;
+}
+
+
+string readString(istream& is)
+{
+ // read length-encoded unicode string
+
+ // 32-bit length
+ int length = readValue<int>(is);
+ if (length > 1024) throw runtime_error("[readString()] String too long?");
+
+ string result;
+ result.resize(length);
+
+ // unicode string
+ for (int i=0; i<length; i++)
+ {
+ short c;
+ is.read((char*)&c, sizeof(short));
+ result[i] = (char)c;
+ }
+
+ return result;
+}
+
+
+string readString0(istream& is)
+{
+ // read zero-terminated unicode string
+
+ string result;
+
+ while (short s=readValue<short>(is))
+ result.push_back((char)s);
+
+ return result;
+}
+
+
+Record readRecord(istream& is)
+{
+ Record result;
+
+ result.one = readValue<int>(is);
+ result.sampleType = readValue<int>(is);
+ result.unknown1 = readValue<int>(is);
+ result.unknown2 = readValue<int>(is);
+ result.unknown3 = readValue<int>(is);
+ result.injectionVolume = readValue<double>(is);
+ result.sampleWeight = readValue<double>(is);
+ result.sampleVolume = readValue<double>(is);
+ result.istdCorrectionAmount = readValue<double>(is);
+ result.dilFactor = readValue<double>(is);
+ result.unknown4 = readValue<int>(is);
+
+ for (int i=0; i<Record::StringCount; i++)
+ result.strings[i] = readString(is);
+
+ return result;
+}
+
+
+Record::Record()
+: one(0), sampleType(0),
+ unknown1(0), unknown2(0), unknown3(0),
+ injectionVolume(0), sampleWeight(0), sampleVolume(0),
+ istdCorrectionAmount(0), dilFactor(0), unknown4(0),
+ strings(StringCount)
+{}
+
+
+const char* stringLabelText_[Record::StringCount] =
+{
+ "Sample Name",
+ "Sample ID",
+ "Comment",
+ "L1",
+ "L2",
+ "L3",
+ "L4",
+ "L5",
+ "Instrument Method",
+ "Process Method",
+ "File Name",
+ "Path",
+ "Position",
+ "Unknown",
+ "Unknown",
+ "Unknown",
+ "Unknown"
+};
+
+
+string stringLabelText(int index, const vector<string>* userLabels = 0)
+{
+ if (index<0 || index>=Record::StringCount)
+ throw runtime_error("[sld::stringLabelText()] Bad index.");
+
+ string result = stringLabelText_[index];
+
+ // special handling of user-defined labels
+ const int indexUserLabelsBegin = 3;
+ const int indexUserLabelsEnd = indexUserLabelsBegin + File::userLabelCount_;
+ if (userLabels &&
+ (int)userLabels->size()==File::userLabelCount_ &&
+ index >= indexUserLabelsBegin &&
+ index < indexUserLabelsEnd)
+ result += " " + userLabels->at(index-indexUserLabelsBegin);
+
+ return result;
+}
+
+
+const char* sampleTypeText(int sampleType)
+{
+ switch (sampleType)
+ {
+ case 0:
+ return "Unknown";
+ case 1:
+ return "Blank";
+ case 2:
+ return "QC";
+ case 5:
+ return "Std Bracket";
+ default:
+ return "I don't know";
+ }
+}
+
+
+const char* labelSampleType_ = "Sample Type";
+const char* labelInjectionVolume_ = "Inj Vol";
+const char* labelSampleWeight_ = "Sample Wt";
+const char* labelSampleVolume_ = "Sample Vol";
+const char* labelISTDCorrectionAmount_ = "ISTD Amt";
+const char* labelDilFactor_ = "Dil Factor";
+
+
+void Record::writeText(ostream& os, const vector<string>* userLabels) const
+{
+ os << "one: " << one << endl;
+ os << labelSampleType_ << ": " << sampleTypeText(sampleType) << endl;
+ os << "unknown1: " << unknown1 << endl;
+ os << "unknown2: " << unknown2 << endl;
+ os << "unknown3: " << unknown3 << endl;
+ os << labelInjectionVolume_ << ": " << injectionVolume << endl;
+ os << labelSampleWeight_ << ": " << sampleWeight << endl;
+ os << labelSampleVolume_ << ": " << sampleVolume << endl;
+ os << labelISTDCorrectionAmount_ << ": " << istdCorrectionAmount << endl;
+ os << labelDilFactor_ << ": " << dilFactor << endl;
+ os << "unknown4: " << unknown4 << endl;
+
+ for (int i=0; i<Record::StringCount; i++)
+ os << stringLabelText(i, userLabels) << ": " << strings[i] << endl;
+}
+
+
+void Record::writeCSVLabels(ostream& os, const vector<string>* userLabels)
+{
+ os << labelSampleType_ << ","
+ << stringLabelText(Filename) << ","
+ << stringLabelText(SampleID) << ","
+ << stringLabelText(Path) << ","
+ << stringLabelText(InstrumentMethod) << ","
+ << stringLabelText(ProcessMethod) << ","
+ << stringLabelText(Position) << ","
+ << labelInjectionVolume_ << ","
+ << "Level,"
+ << stringLabelText(Comment) << ","
+ << labelDilFactor_ << ","
+ << stringLabelText(L1, userLabels) << ","
+ << stringLabelText(L2, userLabels) << ","
+ << stringLabelText(L3, userLabels) << ","
+ << stringLabelText(L4, userLabels) << ","
+ << stringLabelText(L5, userLabels) << ","
+ << labelISTDCorrectionAmount_ << ","
+ << labelSampleVolume_ << ","
+ << labelSampleWeight_ << ","
+ << stringLabelText(SampleName) << ","
+ << "Calibration File,"
+ << endl;
+}
+
+
+void Record::writeCSV(std::ostream& os) const
+{
+ os << fixed << setprecision(3)
+ << sampleTypeText(sampleType) << ","
+ << strings[Filename] << ","
+ << strings[SampleID] << ","
+ << strings[Path] << ","
+ << strings[InstrumentMethod] << ","
+ << strings[ProcessMethod] << ","
+ << strings[Position] << ","
+ << injectionVolume << ","
+ << "," // Level
+ << strings[Comment] << ","
+ << dilFactor << ","
+ << strings[L1] << ","
+ << strings[L2] << ","
+ << strings[L3] << ","
+ << strings[L4] << ","
+ << strings[L5] << ","
+ << istdCorrectionAmount << ","
+ << sampleVolume << ","
+ << sampleWeight << ","
+ << strings[SampleName] << ","
+ << "," // Calibration File
+ << endl;
+}
+
+
+enum XcaliburVersion
+{
+ XcaliburVersion_1_4,
+ XcaliburVersion_2_0,
+ XcaliburVersion_2_0_5
+};
+
+
+XcaliburVersion interpretVersion(short versionNumber)
+{
+ switch (versionNumber)
+ {
+ case 0x39:
+ return XcaliburVersion_1_4;
+ case 0x3e:
+ return XcaliburVersion_2_0;
+ case 0x3f:
+ return XcaliburVersion_2_0_5;
+ default:
+ throw runtime_error("Invalid version number. Tell Darren.");
+ }
+}
+
+
+File::File(const string& filename)
+: userLabels(userLabelCount_)
+{
+ ifstream is(filename.c_str(), ios::binary);
+ if (!is)
+ throw runtime_error("Unable to read file " + filename);
+
+ short magic = readValue<short>(is);
+ if (magic != (short)0xa101)
+ throw runtime_error("Bad format: Magic number not found!");
+
+ string finnigan = readString0(is);
+ if (finnigan != "Finnigan")
+ throw runtime_error("Bad format: Finnigan not found!");
+
+ is.seekg(36);
+ short versionNumber = readValue<short>(is);
+ XcaliburVersion version = interpretVersion(versionNumber);
+
+ const int headSize = 1452;
+ is.seekg(headSize);
+
+ string unknown1 = readString(is);
+ for (int i=0; i<userLabelCount_; i++)
+ userLabels[i] = readString(is);
+ string unknown2 = readString(is);
+
+ if (version >= XcaliburVersion_2_0)
+ is.seekg(60, ios::cur);
+
+ int recordCount = readValue<int>(is);
+ readValue<int>(is); // unknown int value
+
+ for (int i=0; i<recordCount; i++)
+ {
+ records.push_back(readRecord(is));
+ if (version >= XcaliburVersion_2_0)
+ is.seekg(60, ios::cur);
+ }
+}
+
+
+void File::writeText(ostream& os) const
+{
+ for (int i=0; i<File::userLabelCount_; i++)
+ os << "User Label " << i << ": " << userLabels[i] << endl;
+
+ os << "Record count: " << records.size() << "\n\n";
+
+ for (unsigned int i=0; i<records.size(); i++)
+ {
+ os << "Record #" << i+1 << endl;
+ records[i].writeText(os, &userLabels);
+ os << endl;
+ }
+}
+
+
+void File::writeCSV(ostream& os) const
+{
+ Record::writeCSVLabels(os, &userLabels);
+
+ for (vector<Record>::const_iterator it=records.begin(); it!=records.end(); ++it)
+ it->writeCSV(os);
+}
+
+
+} // namespace sld
+} // namespace pwiz
+
+
Added: trunk/pwiz/pwiz_tools/sld/sld.hpp
===================================================================
--- trunk/pwiz/pwiz_tools/sld/sld.hpp (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/sld.hpp 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,111 @@
+//
+// sld.hpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#ifndef _SLD_HPP_
+#define _SLD_HPP_
+
+
+#include <vector>
+#include <string>
+#include <iosfwd>
+
+
+namespace pwiz {
+namespace sld {
+
+
+struct Record
+{
+ Record();
+
+ // 64 byte header
+
+ int one; // always 1?
+ int sampleType;
+ int unknown1;
+ int unknown2;
+ int unknown3;
+ double injectionVolume;
+ double sampleWeight;
+ double sampleVolume;
+ double istdCorrectionAmount;
+ double dilFactor;
+ int unknown4;
+
+ // 17 strings
+
+ enum StringIndex
+ {
+ SampleName,
+ SampleID,
+ Comment,
+ L1,
+ L2,
+ L3,
+ L4,
+ L5,
+ InstrumentMethod,
+ ProcessMethod,
+ Filename,
+ Path,
+ Position,
+ Unknown1,
+ Unknown2,
+ Unknown3,
+ Unknown4,
+ StringCount
+ };
+
+ std::vector<std::string> strings;
+
+ // output functions
+
+ void writeText(std::ostream& os, const std::vector<std::string>* userLabels = 0) const;
+ static void writeCSVLabels(std::ostream& os, const std::vector<std::string>* userLabels = 0);
+ void writeCSV(std::ostream& os) const;
+};
+
+
+struct File
+{
+ File(const std::string& filename);
+
+ // user-defined labels
+ static const int userLabelCount_ = 5;
+ std::vector<std::string> userLabels;
+
+ // records
+ std::vector<Record> records;
+
+ // output functions
+ void writeText(std::ostream& os) const;
+ void writeCSV(std::ostream& os) const;
+};
+
+
+} // namespace sld
+} // namespace pwiz
+
+
+#endif // _SLD_HPP_
+
Added: trunk/pwiz/pwiz_tools/sld/sldout.cpp
===================================================================
--- trunk/pwiz/pwiz_tools/sld/sldout.cpp (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/sldout.cpp 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,62 @@
+//
+// sldout.cpp
+//
+//
+// Original author: Darren Kessner <Dar...@cs...>
+//
+// Copyright 2008 Spielberg Family Center for Applied Proteomics
+// Cedars-Sinai Medical Center, Los Angeles, California 90048
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+
+#include "sld.hpp"
+#include <iostream>
+#include <stdexcept>
+
+
+using namespace std;
+
+
+int main(int argc, char* argv[])
+{
+ try
+ {
+ if (argc < 3) throw runtime_error("Usage: sldout [csv|txt] filename.sld");
+ const string& outputType = argv[1];
+ const string& filename = argv[2];
+
+ const pwiz::sld::File file(filename);
+
+ if (outputType == "csv")
+ file.writeCSV(cout);
+ else if (outputType == "txt")
+ file.writeText(cout);
+ else
+ throw runtime_error("Output type must be \"csv\" or \"txt\".");
+
+ return 0;
+ }
+ catch (exception& e)
+ {
+ cout << e.what() << endl;
+ }
+ catch (...)
+ {
+ cout << "Unknown exception.\n";
+ }
+
+ return 1;
+}
+
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14.csv
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_14.csv (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_14.csv 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,21 @@
+Sample Type,File Name,Sample ID,Path,Instrument Method,Process Method,Position,Inj Vol,Level,Comment,Dil Factor,L1 Heading1,L2 Heading2,L3 Heading3,L4 Heading4,L5 Heading5,ISTD Amt,Sample Vol,Sample Wt,Sample Name,Calibration File,
+Unknown,data01,id1,C:\Xcalibur\Data,instmeth1,procmeth2,pos1,10.000,,comment1,0.000,1head1,1head2,1head3,1head4,1head5,0.000,0.000,0.000,name1,,
+Blank,data02,id2,C:\Xcalibur\Data,instmeth2,procmeth2,pos2,11.000,,comment2,0.000,2head1,2head2,2head3,2head4,2head5,0.000,0.000,0.000,name2,,
+QC,data03,id3,C:\Xcalibur\Data,instmeth3,procmeth2,pos2,12.000,,comment3,0.000,3head1,3head2,3head3,3head4,3head5,0.000,0.000,0.000,name3,,
+Std Bracket,data04,id4,C:\Xcalibur\Data,instmeth4,procmeth2,pos2,13.000,,comment4,0.000,4head1,4head2,4head3,4head4,4head5,0.000,0.000,0.000,name4,,
+Unknown,data01,id5,C:\Xcalibur\Data,instmeth1,procmeth2,pos1,10.000,,comment1,0.000,1head1,1head2,1head3,1head4,1head5,1.000,0.000,0.000,name1,,
+Blank,data02,id6,C:\Xcalibur\Data,instmeth2,procmeth2,pos2,11.000,,comment2,0.000,2head1,2head2,2head3,2head4,2head5,2.000,0.000,0.000,name2,,
+QC,data03,id7,C:\Xcalibur\Data,instmeth3,procmeth2,pos2,12.000,,comment3,0.000,3head1,3head2,3head3,3head4,3head5,3.000,0.000,0.000,name3,,
+Std Bracket,data04,id8,C:\Xcalibur\Data,instmeth4,procmeth2,pos2,13.000,,comment4,0.000,4head1,4head2,4head3,4head4,4head5,4.000,0.000,0.000,name4,,
+Unknown,data01,id9,C:\Xcalibur\Data,instmeth1,procmeth2,pos1,10.000,,comment1,0.000,1head1,1head2,1head3,1head4,1head5,0.000,5.000,0.000,name1,,
+Blank,data02,id10,C:\Xcalibur\Data,instmeth2,procmeth2,pos2,11.000,,comment2,0.000,2head1,2head2,2head3,2head4,2head5,0.000,6.000,0.000,name2,,
+QC,data03,id11,C:\Xcalibur\Data,instmeth3,procmeth2,pos2,12.000,,comment3,0.000,3head1,3head2,3head3,3head4,3head5,0.000,7.000,0.000,name3,,
+Std Bracket,data04,id12,C:\Xcalibur\Data,instmeth4,procmeth2,pos2,13.000,,comment4,0.000,4head1,4head2,4head3,4head4,4head5,0.000,8.000,0.000,name4,,
+Unknown,data01,id13,C:\Xcalibur\Data,instmeth1,procmeth2,pos1,10.000,,comment1,0.000,1head1,1head2,1head3,1head4,1head5,0.000,0.000,1.000,name1,,
+Blank,data02,id14,C:\Xcalibur\Data,instmeth2,procmeth2,pos2,11.000,,comment2,0.000,2head1,2head2,2head3,2head4,2head5,0.000,0.000,2.000,name2,,
+QC,data03,id15,C:\Xcalibur\Data,instmeth3,procmeth2,pos2,12.000,,comment3,0.000,3head1,3head2,3head3,3head4,3head5,0.000,0.000,3.000,name3,,
+Std Bracket,data04,id16,C:\Xcalibur\Data,instmeth4,procmeth2,pos2,13.000,,comment4,0.000,4head1,4head2,4head3,4head4,4head5,0.000,0.000,4.000,name4,,
+Unknown,data01,id1,C:\Xcalibur\Data,instmeth1,procmeth2,pos1,10.000,,comment1,1.000,1head1,1head2,1head3,1head4,1head5,0.000,0.000,0.000,name1,,
+Blank,data02,id2,C:\Xcalibur\Data,instmeth2,procmeth2,pos2,11.000,,comment2,2.000,2head1,2head2,2head3,2head4,2head5,0.000,0.000,0.000,name2,,
+QC,data03,id3,C:\Xcalibur\Data,instmeth3,procmeth2,pos2,12.000,,comment3,3.000,3head1,3head2,3head3,3head4,3head5,0.000,0.000,0.000,name3,,
+Std Bracket,data04,id4,C:\Xcalibur\Data,instmeth4,procmeth2,pos2,13.000,,comment4,4.000,4head1,4head2,4head3,4head4,4head5,0.000,0.000,0.000,name4,,
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14.sld
===================================================================
(Binary files differ)
Property changes on: trunk/pwiz/pwiz_tools/sld/test/chosen_14.sld
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14.txt
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_14.txt (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_14.txt 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,607 @@
+User Label 0: Heading1
+User Label 1: Heading2
+User Label 2: Heading3
+User Label 3: Heading4
+User Label 4: Heading5
+Record count: 20
+
+Record #1
+one: 1
+Sample Type: Unknown
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+unknown2: 0
+unknown3: 0
+Inj Vol: 10
+Sample Wt: 0
+Sample Vol: 0
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+Dil Factor: 0
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+Comment: comment1
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+L2 Heading2: 1head2
+L3 Heading3: 1head3
+L4 Heading4: 1head4
+L5 Heading5: 1head5
+Instrument Method: instmeth1
+Process Method: procmeth2
+File Name: data01
+Path: C:\Xcalibur\Data
+Position: pos1
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
+Record #2
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+Sample Type: Blank
+unknown1: 0
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+Inj Vol: 11
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+L4 Heading4: 2head4
+L5 Heading5: 2head5
+Instrument Method: instmeth2
+Process Method: procmeth2
+File Name: data02
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+Position: pos2
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
+Record #3
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+Sample Type: QC
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+Unknown:
+Unknown:
+Unknown:
+
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+Sample Type: Std Bracket
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+Unknown:
+Unknown:
+
+Record #5
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+Unknown:
+Unknown:
+Unknown:
+
+Record #6
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+Record #10
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+Process Method: procmeth2
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+Position: pos2
+Unknown:
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+
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.csv
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.csv (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.csv 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,9 @@
+Sample Type,File Name,Sample ID,Path,Instrument Method,Process Method,Position,Inj Vol,Level,Comment,Dil Factor,L1 Study,L2 Client,L3 Laboratory,L4 Company,L5 Phone,ISTD Amt,Sample Vol,Sample Wt,Sample Name,Calibration File,
+Unknown,data01,1,C:\Xcalibur\Data,,,1,1.234,,,1.000,,,,,,0.000,0.000,0.000,,,
+Unknown,data02,1,C:\Xcalibur\Data,,,1,999.000,,,1.000,,,,,,0.000,0.000,0.000,,,
+Unknown,data03,1,C:\Xcalibur\Data,,,1,10.400,,,1.000,,,,,,0.000,0.000,0.000,,,
+Unknown,data04,1,C:\Xcalibur\Data,,,1,10.400,,,0.000,,,,,,0.000,0.000,0.000,,,
+Unknown,data05,1,C:\Xcalibur\Data,,,1,0.000,,,10.435,,,,,,0.000,0.000,0.000,,,
+Unknown,data06,1,C:\Xcalibur\Data,,,1,0.000,,,0.000,,,laboratory,,phone,1.234,0.000,0.000,,,
+Unknown,data07,1,C:\Xcalibur\Data,,,1,0.000,,,0.000,,,laboratory,,phone,0.000,1.234,0.000,,,
+Unknown,data08,1,C:\Xcalibur\Data,,,1,0.000,,,0.000,,,laboratory,,phone,0.000,0.000,1.234,,,
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.sld
===================================================================
(Binary files differ)
Property changes on: trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.sld
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.txt
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.txt (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_14_b.txt 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,247 @@
+User Label 0: Study
+User Label 1: Client
+User Label 2: Laboratory
+User Label 3: Company
+User Label 4: Phone
+Record count: 8
+
+Record #1
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+Sample Type: Unknown
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+Inj Vol: 1.234
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+L5 Phone:
+Instrument Method:
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+Path: C:\Xcalibur\Data
+Position: 1
+Unknown:
+Unknown:
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+
+Record #2
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+Unknown:
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+Unknown:
+
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+Process Method:
+File Name: data07
+Path: C:\Xcalibur\Data
+Position: 1
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
+Record #8
+one: 1
+Sample Type: Unknown
+unknown1: 0
+unknown2: 0
+unknown3: 0
+Inj Vol: 0
+Sample Wt: 1.2345
+Sample Vol: 0
+ISTD Amt: 0
+Dil Factor: 0
+unknown4: 0
+Sample Name:
+Sample ID: 1
+Comment:
+L1 Study:
+L2 Client:
+L3 Laboratory: laboratory
+L4 Company:
+L5 Phone: phone
+Instrument Method:
+Process Method:
+File Name: data08
+Path: C:\Xcalibur\Data
+Position: 1
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_205.csv
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_205.csv (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_205.csv 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,4 @@
+Sample Type,File Name,Sample ID,Path,Instrument Method,Process Method,Position,Inj Vol,Level,Comment,Dil Factor,L1 Study,L2 Client,L3 Laboratory,L4 Company,L5 Phone,ISTD Amt,Sample Vol,Sample Wt,Sample Name,Calibration File,
+Unknown,filename1,sampleID1,path1,instmeth1,procmeth,pos1,1.000,,comment1,10.000,study1,client1,lab1,company1,phone1,20.000,30.000,40.000,sampleName1,,
+Blank,filename2,sampleID2,path2,instmeth2,procmeth,pos2,2.000,,comment2,11.000,study2,client2,lab2,company2,phone2,21.000,31.000,41.000,sampleName2,,
+QC,filename3,sampleID3,path3,instmeth3,procmeth,pos3,3.000,,comment3,12.000,study3,client3,lab3,company3,phone3,22.000,32.000,42.000,sampleName3,,
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_205.sld
===================================================================
(Binary files differ)
Property changes on: trunk/pwiz/pwiz_tools/sld/test/chosen_205.sld
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_205.txt
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_205.txt (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_205.txt 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,97 @@
+User Label 0: Study
+User Label 1: Client
+User Label 2: Laboratory
+User Label 3: Company
+User Label 4: Phone
+Record count: 3
+
+Record #1
+one: 1
+Sample Type: Unknown
+unknown1: 0
+unknown2: 0
+unknown3: 0
+Inj Vol: 1
+Sample Wt: 40
+Sample Vol: 30
+ISTD Amt: 20
+Dil Factor: 10
+unknown4: 0
+Sample Name: sampleName1
+Sample ID: sampleID1
+Comment: comment1
+L1 Study: study1
+L2 Client: client1
+L3 Laboratory: lab1
+L4 Company: company1
+L5 Phone: phone1
+Instrument Method: instmeth1
+Process Method: procmeth
+File Name: filename1
+Path: path1
+Position: pos1
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
+Record #2
+one: 1
+Sample Type: Blank
+unknown1: 0
+unknown2: 0
+unknown3: 0
+Inj Vol: 2
+Sample Wt: 41
+Sample Vol: 31
+ISTD Amt: 21
+Dil Factor: 11
+unknown4: 0
+Sample Name: sampleName2
+Sample ID: sampleID2
+Comment: comment2
+L1 Study: study2
+L2 Client: client2
+L3 Laboratory: lab2
+L4 Company: company2
+L5 Phone: phone2
+Instrument Method: instmeth2
+Process Method: procmeth
+File Name: filename2
+Path: path2
+Position: pos2
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
+Record #3
+one: 1
+Sample Type: QC
+unknown1: 0
+unknown2: 0
+unknown3: 0
+Inj Vol: 3
+Sample Wt: 42
+Sample Vol: 32
+ISTD Amt: 22
+Dil Factor: 12
+unknown4: 0
+Sample Name: sampleName3
+Sample ID: sampleID3
+Comment: comment3
+L1 Study: study3
+L2 Client: client3
+L3 Laboratory: lab3
+L4 Company: company3
+L5 Phone: phone3
+Instrument Method: instmeth3
+Process Method: procmeth
+File Name: filename3
+Path: path3
+Position: pos3
+Unknown:
+Unknown:
+Unknown:
+Unknown:
+
Added: trunk/pwiz/pwiz_tools/sld/test/chosen_205_exported.csv
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/chosen_205_exported.csv (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/chosen_205_exported.csv 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,5 @@
+Bracket Type=4
+Sample Type,File Name,Path,Instrument Method,Position,Inj Vol,Sample Name,Comment,Process Method,L5 Phone,L2 Client,L4 Company,Dil Factor,ISTD Amt,L3 Laboratory,Level,Sample ID,Sample Vol,Sample Wt,L1 Study,Calibration File,
+Unknown,filename1,path1,instmeth1,pos1,1.000,sampleName1,comment1,procmeth,phone1,client1,company1,10.000,20.000,lab1,,sampleID1,30.000,40.000,study1,,
+Blank,filename2,path2,instmeth2,pos2,2.000,sampleName2,comment2,procmeth,phone2,client2,company2,11.000,21.000,lab2,,sampleID2,31.000,41.000,study2,,
+QC,filename3,path3,instmeth3,pos3,3.000,sampleName3,comment3,procmeth,phone3,client3,company3,12.000,22.000,lab3,,sampleID3,32.000,42.000,study3,,
Added: trunk/pwiz/pwiz_tools/sld/test/test_sldout
===================================================================
--- trunk/pwiz/pwiz_tools/sld/test/test_sldout (rev 0)
+++ trunk/pwiz/pwiz_tools/sld/test/test_sldout 2008-11-25 22:18:26 UTC (rev 490)
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+sldout csv chosen_14.sld | diff chosen_14.csv -
+sldout txt chosen_14.sld | diff chosen_14.txt -
+
+sldout csv chosen_14_b.sld | diff chosen_14_b.csv -
+sldout txt chosen_14_b.sld | diff chosen_14_b.txt -
+
+sldout csv chosen_205.sld | diff chosen_205.csv -
+sldout txt chosen_205.sld | diff chosen_205.txt -
+
Property changes on: trunk/pwiz/pwiz_tools/sld/test/test_sldout
___________________________________________________________________
Added: svn:executable
+ *
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