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MassPlusPlus: Commit

Mass++ ソースリポジトリ


Commit MetaInfo

Revisionc144399f4dbd9facbe24400908c2095677cb18ec (tree)
Time2015-07-16 11:15:28
AuthorSatoshi Tanaka
CommiterSatoshi Tanaka

Log Message

added OpenMS plug-in

Change Summary

Incremental Difference

diff -r 501b14f9e83d -r c144399f4dbd build/msvs/opt/tandem/bin/default_input.xml
--- a/build/msvs/opt/tandem/bin/default_input.xml Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/opt/tandem/bin/default_input.xml Thu Jul 16 11:15:28 2015 +0900
@@ -1,180 +1,180 @@
1-<?xml version="1.0"?>
2-<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?>
3-<bioml>
4-<note>list path parameters</note>
5- <note type="input" label="list path, default parameters">default_input.xml</note>
6- <note>This value is ignored when it is present in the default parameter
7- list path.</note>
8- <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
9-
10-<note>spectrum parameters</note>
11- <note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
12- <note type="input" label="spectrum, parent monoisotopic mass error plus">100</note>
13- <note type="input" label="spectrum, parent monoisotopic mass error minus">100</note>
14- <note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
15- <note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
16- <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
17- <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
18- <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
19- <note type="input" label="spectrum, fragment mass type">monoisotopic</note>
20- <note>values are monoisotopic|average </note>
21-
22-<note>spectrum conditioning parameters</note>
23- <note type="input" label="spectrum, dynamic range">100.0</note>
24- <note>The peaks read in are normalized so that the most intense peak
25- is set to the dynamic range value. All peaks with values of less that
26- 1, using this normalization, are not used. This normalization has the
27- overall effect of setting a threshold value for peak intensities.</note>
28- <note type="input" label="spectrum, total peaks">50</note>
29- <note>If this value is 0, it is ignored. If it is greater than zero (lets say 50),
30- then the number of peaks in the spectrum with be limited to the 50 most intense
31- peaks in the spectrum. X! tandem does not do any peak finding: it only
32- limits the peaks used by this parameter, and the dynamic range parameter.</note>
33- <note type="input" label="spectrum, maximum parent charge">4</note>
34- <note type="input" label="spectrum, use noise suppression">yes</note>
35- <note type="input" label="spectrum, minimum parent m+h">500.0</note>
36- <note type="input" label="spectrum, minimum fragment mz">150.0</note>
37- <note type="input" label="spectrum, minimum peaks">15</note>
38- <note type="input" label="spectrum, threads">1</note>
39- <note type="input" label="spectrum, sequence batch size">1000</note>
40-
41-<note>residue modification parameters</note>
42- <note type="input" label="residue, modification mass"></note>
43- <note>The format of this parameter is m@X, where m is the modfication
44- mass in Daltons and X is the appropriate residue to modify. Lists of
45- modifications are separated by commas. For example, to modify M and C
46- with the addition of 16.0 Daltons, the parameter line would be
47- +16.0@M,+16.0@C
48- Positive and negative values are allowed.
49- </note>
50- <note type="input" label="residue, potential modification mass"></note>
51- <note>The format of this parameter is the same as the format
52- for residue, modification mass (see above).</note>
53- <note type="input" label="residue, potential modification motif"></note>
54- <note>The format of this parameter is similar to residue, modification mass,
55- with the addition of a modified PROSITE notation sequence motif specification.
56- For example, a value of 80@[ST!]PX[KR] indicates a modification
57- of either S or T when followed by P, and residue and the a K or an R.
58- A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it
59- is NOT followed by a P, then either an S or a T, NOT followed by a P.
60- Positive and negative values are allowed.
61- </note>
62-
63-<note>protein parameters</note>
64- <note type="input" label="protein, taxon">other mammals</note>
65- <note>This value is interpreted using the information in taxonomy.xml.</note>
66- <note type="input" label="protein, cleavage site">[RK]|{P}</note>
67- <note>this setting corresponds to the enzyme trypsin. The first characters
68- in brackets represent residues N-terminal to the bond - the '|' pipe -
69- and the second set of characters represent residues C-terminal to the
70- bond. The characters must be in square brackets (denoting that only
71- these residues are allowed for a cleavage) or french brackets (denoting
72- that these residues cannot be in that position). Use UPPERCASE characters.
73- To denote cleavage at any residue, use [X]|[X] and reset the
74- scoring, maximum missed cleavage site parameter (see below) to something like 50.
75- </note>
76- <note type="input" label="protein, modified residue mass file"></note>
77- <note type="input" label="protein, cleavage C-terminal mass change">+17.002735</note>
78- <note type="input" label="protein, cleavage N-terminal mass change">+1.007825</note>
79- <note type="input" label="protein, N-terminal residue modification mass">0.0</note>
80- <note type="input" label="protein, C-terminal residue modification mass">0.0</note>
81- <note type="input" label="protein, homolog management">no</note>
82- <note>if yes, an upper limit is set on the number of homologues kept for a particular spectrum</note>
83-
84-<note>model refinement parameters</note>
85- <note type="input" label="refine">yes</note>
86- <note type="input" label="refine, modification mass"></note>
87- <note type="input" label="refine, sequence path"></note>
88- <note type="input" label="refine, tic percent">20</note>
89- <note type="input" label="refine, spectrum synthesis">yes</note>
90- <note type="input" label="refine, maximum valid expectation value">100</note>
91- <note type="input" label="refine, potential N-terminus modifications"></note>
92- <note type="input" label="refine, potential C-terminus modifications"></note>
93- <note type="input" label="refine, unanticipated cleavage">yes</note>
94- <note type="input" label="refine, potential modification mass"></note>
95- <note type="input" label="refine, point mutations">no</note>
96- <note type="input" label="refine, use potential modifications for full refinement">no</note>
97- <note type="input" label="refine, point mutations">no</note>
98- <note type="input" label="refine, potential modification motif"></note>
99- <note>The format of this parameter is similar to residue, modification mass,
100- with the addition of a modified PROSITE notation sequence motif specification.
101- For example, a value of 80@[ST!]PX[KR] indicates a modification
102- of either S or T when followed by P, and residue and the a K or an R.
103- A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it
104- is NOT followed by a P, then either an S or a T, NOT followed by a P.
105- Positive and negative values are allowed.
106- </note>
107-
108-<note>scoring parameters</note>
109- <note type="input" label="scoring, minimum ion count">4</note>
110- <note type="input" label="scoring, maximum missed cleavage sites">1</note>
111- <note type="input" label="scoring, x ions">no</note>
112- <note type="input" label="scoring, y ions">yes</note>
113- <note type="input" label="scoring, z ions">no</note>
114- <note type="input" label="scoring, a ions">no</note>
115- <note type="input" label="scoring, b ions">yes</note>
116- <note type="input" label="scoring, c ions">no</note>
117- <note type="input" label="scoring, cyclic permutation">no</note>
118- <note>if yes, cyclic peptide sequence permutation is used to pad the scoring histograms</note>
119- <note type="input" label="scoring, include reverse">no</note>
120- <note>if yes, then reversed sequences are searched at the same time as forward sequences</note>
121- <note type="input" label="scoring, cyclic permutation">no</note>
122- <note type="input" label="scoring, include reverse">no</note>
123-
124-<note>output parameters</note>
125- <note type="input" label="output, log path"></note>
126- <note type="input" label="output, message">testing 1 2 3</note>
127- <note type="input" label="output, one sequence copy">no</note>
128- <note type="input" label="output, sequence path"></note>
129- <note type="input" label="output, path">output.xml</note>
130- <note type="input" label="output, sort results by">protein</note>
131- <note>values = protein|spectrum (spectrum is the default)</note>
132- <note type="input" label="output, path hashing">yes</note>
133- <note>values = yes|no</note>
134- <note type="input" label="output, xsl path">tandem-style.xsl</note>
135- <note type="input" label="output, parameters">yes</note>
136- <note>values = yes|no</note>
137- <note type="input" label="output, performance">yes</note>
138- <note>values = yes|no</note>
139- <note type="input" label="output, spectra">yes</note>
140- <note>values = yes|no</note>
141- <note type="input" label="output, histograms">yes</note>
142- <note>values = yes|no</note>
143- <note type="input" label="output, proteins">yes</note>
144- <note>values = yes|no</note>
145- <note type="input" label="output, sequences">yes</note>
146- <note>values = yes|no</note>
147- <note type="input" label="output, one sequence copy">no</note>
148- <note>values = yes|no, set to yes to produce only one copy of each protein sequence in the output xml</note>
149- <note type="input" label="output, results">valid</note>
150- <note>values = all|valid|stochastic</note>
151- <note type="input" label="output, maximum valid expectation value">expectation value</note>
152- <note>value is used in the valid|stochastic setting of output, results</note>
153- <note type="input" label="output, histogram column width">30</note>
154- <note>values any integer greater than 0. Setting this to '1' makes cutting and pasting histograms
155- into spread sheet programs easier.</note>
156-<note type="description">ADDITIONAL EXPLANATIONS</note>
157- <note type="description">Each one of the parameters for X! tandem is entered as a labeled note
158- node. In the current version of X!, keep those note nodes
159- on a single line.
160- </note>
161- <note type="description">The presence of the type 'input' is necessary if a note is to be considered
162- an input parameter.
163- </note>
164- <note type="description">Any of the parameters that are paths to files may require alteration for a
165- particular installation. Full path names usually cause the least trouble,
166- but there is no reason not to use relative path names, if that is the
167- most convenient.
168- </note>
169- <note type="description">Any parameter values set in the 'list path, default parameters' file are
170- reset by entries in the normal input file, if they are present. Otherwise,
171- the default set is used.
172- </note>
173- <note type="description">The 'list path, taxonomy information' file must exist.
174- </note>
175- <note type="description">The directory containing the 'output, path' file must exist: it will not be created.
176- </note>
177- <note type="description">The 'output, xsl path' is optional: it is only of use if a good XSLT style sheet exists.
178- </note>
179-
180-</bioml>
1+<?xml version="1.0"?>
2+<?xml-stylesheet type="text/xsl" href="tandem-input-style.xsl"?>
3+<bioml>
4+<note>list path parameters</note>
5+ <note type="input" label="list path, default parameters">default_input.xml</note>
6+ <note>This value is ignored when it is present in the default parameter
7+ list path.</note>
8+ <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
9+
10+<note>spectrum parameters</note>
11+ <note type="input" label="spectrum, fragment monoisotopic mass error">0.4</note>
12+ <note type="input" label="spectrum, parent monoisotopic mass error plus">100</note>
13+ <note type="input" label="spectrum, parent monoisotopic mass error minus">100</note>
14+ <note type="input" label="spectrum, parent monoisotopic mass isotope error">yes</note>
15+ <note type="input" label="spectrum, fragment monoisotopic mass error units">Daltons</note>
16+ <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
17+ <note type="input" label="spectrum, parent monoisotopic mass error units">ppm</note>
18+ <note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
19+ <note type="input" label="spectrum, fragment mass type">monoisotopic</note>
20+ <note>values are monoisotopic|average </note>
21+
22+<note>spectrum conditioning parameters</note>
23+ <note type="input" label="spectrum, dynamic range">100.0</note>
24+ <note>The peaks read in are normalized so that the most intense peak
25+ is set to the dynamic range value. All peaks with values of less that
26+ 1, using this normalization, are not used. This normalization has the
27+ overall effect of setting a threshold value for peak intensities.</note>
28+ <note type="input" label="spectrum, total peaks">50</note>
29+ <note>If this value is 0, it is ignored. If it is greater than zero (lets say 50),
30+ then the number of peaks in the spectrum with be limited to the 50 most intense
31+ peaks in the spectrum. X! tandem does not do any peak finding: it only
32+ limits the peaks used by this parameter, and the dynamic range parameter.</note>
33+ <note type="input" label="spectrum, maximum parent charge">4</note>
34+ <note type="input" label="spectrum, use noise suppression">yes</note>
35+ <note type="input" label="spectrum, minimum parent m+h">500.0</note>
36+ <note type="input" label="spectrum, minimum fragment mz">150.0</note>
37+ <note type="input" label="spectrum, minimum peaks">15</note>
38+ <note type="input" label="spectrum, threads">1</note>
39+ <note type="input" label="spectrum, sequence batch size">1000</note>
40+
41+<note>residue modification parameters</note>
42+ <note type="input" label="residue, modification mass"></note>
43+ <note>The format of this parameter is m@X, where m is the modfication
44+ mass in Daltons and X is the appropriate residue to modify. Lists of
45+ modifications are separated by commas. For example, to modify M and C
46+ with the addition of 16.0 Daltons, the parameter line would be
47+ +16.0@M,+16.0@C
48+ Positive and negative values are allowed.
49+ </note>
50+ <note type="input" label="residue, potential modification mass"></note>
51+ <note>The format of this parameter is the same as the format
52+ for residue, modification mass (see above).</note>
53+ <note type="input" label="residue, potential modification motif"></note>
54+ <note>The format of this parameter is similar to residue, modification mass,
55+ with the addition of a modified PROSITE notation sequence motif specification.
56+ For example, a value of 80@[ST!]PX[KR] indicates a modification
57+ of either S or T when followed by P, and residue and the a K or an R.
58+ A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it
59+ is NOT followed by a P, then either an S or a T, NOT followed by a P.
60+ Positive and negative values are allowed.
61+ </note>
62+
63+<note>protein parameters</note>
64+ <note type="input" label="protein, taxon">other mammals</note>
65+ <note>This value is interpreted using the information in taxonomy.xml.</note>
66+ <note type="input" label="protein, cleavage site">[RK]|{P}</note>
67+ <note>this setting corresponds to the enzyme trypsin. The first characters
68+ in brackets represent residues N-terminal to the bond - the '|' pipe -
69+ and the second set of characters represent residues C-terminal to the
70+ bond. The characters must be in square brackets (denoting that only
71+ these residues are allowed for a cleavage) or french brackets (denoting
72+ that these residues cannot be in that position). Use UPPERCASE characters.
73+ To denote cleavage at any residue, use [X]|[X] and reset the
74+ scoring, maximum missed cleavage site parameter (see below) to something like 50.
75+ </note>
76+ <note type="input" label="protein, modified residue mass file"></note>
77+ <note type="input" label="protein, cleavage C-terminal mass change">+17.002735</note>
78+ <note type="input" label="protein, cleavage N-terminal mass change">+1.007825</note>
79+ <note type="input" label="protein, N-terminal residue modification mass">0.0</note>
80+ <note type="input" label="protein, C-terminal residue modification mass">0.0</note>
81+ <note type="input" label="protein, homolog management">no</note>
82+ <note>if yes, an upper limit is set on the number of homologues kept for a particular spectrum</note>
83+
84+<note>model refinement parameters</note>
85+ <note type="input" label="refine">yes</note>
86+ <note type="input" label="refine, modification mass"></note>
87+ <note type="input" label="refine, sequence path"></note>
88+ <note type="input" label="refine, tic percent">20</note>
89+ <note type="input" label="refine, spectrum synthesis">yes</note>
90+ <note type="input" label="refine, maximum valid expectation value">100</note>
91+ <note type="input" label="refine, potential N-terminus modifications"></note>
92+ <note type="input" label="refine, potential C-terminus modifications"></note>
93+ <note type="input" label="refine, unanticipated cleavage">yes</note>
94+ <note type="input" label="refine, potential modification mass"></note>
95+ <note type="input" label="refine, point mutations">no</note>
96+ <note type="input" label="refine, use potential modifications for full refinement">no</note>
97+ <note type="input" label="refine, point mutations">no</note>
98+ <note type="input" label="refine, potential modification motif"></note>
99+ <note>The format of this parameter is similar to residue, modification mass,
100+ with the addition of a modified PROSITE notation sequence motif specification.
101+ For example, a value of 80@[ST!]PX[KR] indicates a modification
102+ of either S or T when followed by P, and residue and the a K or an R.
103+ A value of 204@N!{P}[ST]{P} indicates a modification of N by 204, if it
104+ is NOT followed by a P, then either an S or a T, NOT followed by a P.
105+ Positive and negative values are allowed.
106+ </note>
107+
108+<note>scoring parameters</note>
109+ <note type="input" label="scoring, minimum ion count">4</note>
110+ <note type="input" label="scoring, maximum missed cleavage sites">1</note>
111+ <note type="input" label="scoring, x ions">no</note>
112+ <note type="input" label="scoring, y ions">yes</note>
113+ <note type="input" label="scoring, z ions">no</note>
114+ <note type="input" label="scoring, a ions">no</note>
115+ <note type="input" label="scoring, b ions">yes</note>
116+ <note type="input" label="scoring, c ions">no</note>
117+ <note type="input" label="scoring, cyclic permutation">no</note>
118+ <note>if yes, cyclic peptide sequence permutation is used to pad the scoring histograms</note>
119+ <note type="input" label="scoring, include reverse">no</note>
120+ <note>if yes, then reversed sequences are searched at the same time as forward sequences</note>
121+ <note type="input" label="scoring, cyclic permutation">no</note>
122+ <note type="input" label="scoring, include reverse">no</note>
123+
124+<note>output parameters</note>
125+ <note type="input" label="output, log path"></note>
126+ <note type="input" label="output, message">testing 1 2 3</note>
127+ <note type="input" label="output, one sequence copy">no</note>
128+ <note type="input" label="output, sequence path"></note>
129+ <note type="input" label="output, path">output.xml</note>
130+ <note type="input" label="output, sort results by">protein</note>
131+ <note>values = protein|spectrum (spectrum is the default)</note>
132+ <note type="input" label="output, path hashing">yes</note>
133+ <note>values = yes|no</note>
134+ <note type="input" label="output, xsl path">tandem-style.xsl</note>
135+ <note type="input" label="output, parameters">yes</note>
136+ <note>values = yes|no</note>
137+ <note type="input" label="output, performance">yes</note>
138+ <note>values = yes|no</note>
139+ <note type="input" label="output, spectra">yes</note>
140+ <note>values = yes|no</note>
141+ <note type="input" label="output, histograms">yes</note>
142+ <note>values = yes|no</note>
143+ <note type="input" label="output, proteins">yes</note>
144+ <note>values = yes|no</note>
145+ <note type="input" label="output, sequences">yes</note>
146+ <note>values = yes|no</note>
147+ <note type="input" label="output, one sequence copy">no</note>
148+ <note>values = yes|no, set to yes to produce only one copy of each protein sequence in the output xml</note>
149+ <note type="input" label="output, results">valid</note>
150+ <note>values = all|valid|stochastic</note>
151+ <note type="input" label="output, maximum valid expectation value">expectation value</note>
152+ <note>value is used in the valid|stochastic setting of output, results</note>
153+ <note type="input" label="output, histogram column width">30</note>
154+ <note>values any integer greater than 0. Setting this to '1' makes cutting and pasting histograms
155+ into spread sheet programs easier.</note>
156+<note type="description">ADDITIONAL EXPLANATIONS</note>
157+ <note type="description">Each one of the parameters for X! tandem is entered as a labeled note
158+ node. In the current version of X!, keep those note nodes
159+ on a single line.
160+ </note>
161+ <note type="description">The presence of the type 'input' is necessary if a note is to be considered
162+ an input parameter.
163+ </note>
164+ <note type="description">Any of the parameters that are paths to files may require alteration for a
165+ particular installation. Full path names usually cause the least trouble,
166+ but there is no reason not to use relative path names, if that is the
167+ most convenient.
168+ </note>
169+ <note type="description">Any parameter values set in the 'list path, default parameters' file are
170+ reset by entries in the normal input file, if they are present. Otherwise,
171+ the default set is used.
172+ </note>
173+ <note type="description">The 'list path, taxonomy information' file must exist.
174+ </note>
175+ <note type="description">The directory containing the 'output, path' file must exist: it will not be created.
176+ </note>
177+ <note type="description">The 'output, xsl path' is optional: it is only of use if a good XSLT style sheet exists.
178+ </note>
179+
180+</bioml>
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/opt/tandem/bin/input.xml
--- a/build/msvs/opt/tandem/bin/input.xml Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/opt/tandem/bin/input.xml Thu Jul 16 11:15:28 2015 +0900
@@ -1,22 +1,22 @@
1-<?xml version="1.0"?>
2-<bioml>
3- <note>
4- Each one of the parameters for x! tandem is entered as a labeled note node.
5- Any of the entries in the default_input.xml file can be over-ridden by
6- adding a corresponding entry to this file. This file represents a minimum
7- input file, with only entries for the default settings, the output file
8- and the input spectra file name.
9- See the taxonomy.xml file for a description of how FASTA sequence list
10- files are linked to a taxon name.
11- </note>
12-
13- <note type="input" label="list path, default parameters">default_input.xml</note>
14- <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
15-
16- <note type="input" label="protein, taxon">yeast</note>
17-
18- <note type="input" label="spectrum, path">test_spectra.mgf</note>
19-
20- <note type="input" label="output, path">output.xml</note>
21- <note type="input" label="output, results">valid</note>
22-</bioml>
1+<?xml version="1.0"?>
2+<bioml>
3+ <note>
4+ Each one of the parameters for x! tandem is entered as a labeled note node.
5+ Any of the entries in the default_input.xml file can be over-ridden by
6+ adding a corresponding entry to this file. This file represents a minimum
7+ input file, with only entries for the default settings, the output file
8+ and the input spectra file name.
9+ See the taxonomy.xml file for a description of how FASTA sequence list
10+ files are linked to a taxon name.
11+ </note>
12+
13+ <note type="input" label="list path, default parameters">default_input.xml</note>
14+ <note type="input" label="list path, taxonomy information">taxonomy.xml</note>
15+
16+ <note type="input" label="protein, taxon">yeast</note>
17+
18+ <note type="input" label="spectrum, path">test_spectra.mgf</note>
19+
20+ <note type="input" label="output, path">output.xml</note>
21+ <note type="input" label="output, results">valid</note>
22+</bioml>
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/opt/tandem/bin/tandem-style.xsl
--- a/build/msvs/opt/tandem/bin/tandem-style.xsl Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/opt/tandem/bin/tandem-style.xsl Thu Jul 16 11:15:28 2015 +0900
@@ -181,15 +181,6 @@
181181 <DIV id="{generate-id()}" STYLE="display:none" class="k">
182182 <xsl:apply-templates select="GAML:trace" />
183183 </DIV>
184-
185- <!-- 2015.6.9 added by Masaki Murase to display peaklist title header -->
186- <xsl:if test="contains(@label,'fragment ion mass spectrum')">
187- <div id="peaklist_title">
188- mgf title: <xsl:value-of select="note" />
189- </div>
190- </xsl:if>
191-
192-
193184 </xsl:if>
194185 </xsl:template>
195186
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/opt/tandem/bin/taxonomy.xml
--- a/build/msvs/opt/tandem/bin/taxonomy.xml Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/opt/tandem/bin/taxonomy.xml Thu Jul 16 11:15:28 2015 +0900
@@ -1,8 +1,8 @@
1-<?xml version="1.0"?>
2-<bioml label="x! taxon-to-file matching list">
3- <taxon label="yeast">
4- <file format="peptide" URL="../fasta/scd.fasta.pro" />
5- <file format="peptide" URL="../fasta/scd_1.fasta.pro" />
6- <file format="peptide" URL="../fasta/crap.fasta.pro" />
7- </taxon>
8-</bioml>
1+<?xml version="1.0"?>
2+<bioml label="x! taxon-to-file matching list">
3+ <taxon label="yeast">
4+ <file format="peptide" URL="../fasta/scd.fasta.pro" />
5+ <file format="peptide" URL="../fasta/scd_1.fasta.pro" />
6+ <file format="peptide" URL="../fasta/crap.fasta.pro" />
7+ </taxon>
8+</bioml>
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/solutions/common-plugin-analyze/OpenMSPlugin/OpenMSPlugin.vcxproj
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build/msvs/solutions/common-plugin-analyze/OpenMSPlugin/OpenMSPlugin.vcxproj Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,212 @@
1+<?xml version="1.0" encoding="utf-8"?>
2+<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3+ <ItemGroup Label="ProjectConfigurations">
4+ <ProjectConfiguration Include="Debug|Win32">
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6+ <Platform>Win32</Platform>
7+ </ProjectConfiguration>
8+ <ProjectConfiguration Include="Debug|x64">
9+ <Configuration>Debug</Configuration>
10+ <Platform>x64</Platform>
11+ </ProjectConfiguration>
12+ <ProjectConfiguration Include="Release|Win32">
13+ <Configuration>Release</Configuration>
14+ <Platform>Win32</Platform>
15+ </ProjectConfiguration>
16+ <ProjectConfiguration Include="Release|x64">
17+ <Configuration>Release</Configuration>
18+ <Platform>x64</Platform>
19+ </ProjectConfiguration>
20+ </ItemGroup>
21+ <PropertyGroup Label="Globals">
22+ <ProjectGuid>{CB76A555-263B-44C4-9F84-345F701BFA7B}</ProjectGuid>
23+ <RootNamespace>OpenMSPlugin</RootNamespace>
24+ <Keyword>Win32Proj</Keyword>
25+ </PropertyGroup>
26+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
27+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
28+ <ConfigurationType>DynamicLibrary</ConfigurationType>
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32+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
33+ <ConfigurationType>DynamicLibrary</ConfigurationType>
34+ <CharacterSet>MultiByte</CharacterSet>
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36+ </PropertyGroup>
37+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
38+ <ConfigurationType>DynamicLibrary</ConfigurationType>
39+ <CharacterSet>MultiByte</CharacterSet>
40+ </PropertyGroup>
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42+ <ConfigurationType>DynamicLibrary</ConfigurationType>
43+ <CharacterSet>MultiByte</CharacterSet>
44+ </PropertyGroup>
45+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
46+ <ImportGroup Label="ExtensionSettings">
47+ </ImportGroup>
48+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
49+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
50+ </ImportGroup>
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52+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
53+ </ImportGroup>
54+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
55+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
56+ </ImportGroup>
57+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
58+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
59+ </ImportGroup>
60+ <PropertyGroup Label="UserMacros" />
61+ <PropertyGroup>
62+ <_ProjectFileVersion>10.0.30319.1</_ProjectFileVersion>
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67+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Platform)-$(Configuration)\</IntDir>
68+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Platform)-$(Configuration)\</IntDir>
69+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(Platform)-$(Configuration)\</IntDir>
70+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(Platform)-$(Configuration)\</IntDir>
71+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
72+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
73+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
74+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
75+ <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Parallel-Release|x64 '">false</LinkIncremental>
76+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)</TargetName>
77+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)</TargetName>
78+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)</TargetName>
79+ <TargetName Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)</TargetName>
80+ <LibraryPath Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(LibraryPath)</LibraryPath>
81+ <LibraryPath Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(VCInstallDir)lib;$(VCInstallDir)atlmfc\lib;$(WindowsSdkDir)lib;$(FrameworkSDKDir)\lib</LibraryPath>
82+ </PropertyGroup>
83+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
84+ <ClCompile>
85+ <Optimization>Disabled</Optimization>
86+ <AdditionalIncludeDirectories>$(SolutionDir)..\..\..\..\include;$(SolutionDir)..\..\contrib\common\$(Platform)\boost\include;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib\msw;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\include;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\include;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
87+ <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;OPENMSPLUGIN_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
88+ <MinimalRebuild>true</MinimalRebuild>
89+ <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
90+ <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
91+ <PrecompiledHeader>
92+ </PrecompiledHeader>
93+ <WarningLevel>Level3</WarningLevel>
94+ <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
95+ <MultiProcessorCompilation>
96+ </MultiProcessorCompilation>
97+ </ClCompile>
98+ <Link>
99+ <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
100+ <AdditionalLibraryDirectories>$(SolutionDir)..\..\..\..\lib\msvs\$(Platform)-$(Configuration);$(SolutionDir)..\..\contrib\common\$(Platform)\boost\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
101+ <ModuleDefinitionFile>$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\$(ProjectName).def</ModuleDefinitionFile>
102+ <GenerateDebugInformation>true</GenerateDebugInformation>
103+ <SubSystem>Windows</SubSystem>
104+ <TargetMachine>MachineX86</TargetMachine>
105+ </Link>
106+ <PostBuildEvent>
107+ <Command>mkdir $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
108+copy $(TargetPath) $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
109+copy $(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\*.xml $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)</Command>
110+ </PostBuildEvent>
111+ </ItemDefinitionGroup>
112+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
113+ <ClCompile>
114+ <Optimization>Disabled</Optimization>
115+ <AdditionalIncludeDirectories>$(SolutionDir)..\..\..\..\include;$(SolutionDir)..\..\contrib\common\$(Platform)\boost\include;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib\msw;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\include;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\include;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
116+ <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;LOCALMAXIMUMLABELINGPLUGIN_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
117+ <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
118+ <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
119+ <PrecompiledHeader>
120+ </PrecompiledHeader>
121+ <WarningLevel>Level3</WarningLevel>
122+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
123+ </ClCompile>
124+ <Link>
125+ <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
126+ <AdditionalLibraryDirectories>$(SolutionDir)..\..\..\..\lib\msvs\$(Platform)-$(Configuration);$(SolutionDir)..\..\contrib\common\$(Platform)\boost\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
127+ <ModuleDefinitionFile>$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\$(ProjectName).def</ModuleDefinitionFile>
128+ <GenerateDebugInformation>true</GenerateDebugInformation>
129+ <SubSystem>Windows</SubSystem>
130+ </Link>
131+ <PostBuildEvent>
132+ <Command>mkdir $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
133+copy $(TargetPath) $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
134+copy $(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\*.xml $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)</Command>
135+ </PostBuildEvent>
136+ </ItemDefinitionGroup>
137+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
138+ <ClCompile>
139+ <Optimization>MaxSpeed</Optimization>
140+ <IntrinsicFunctions>true</IntrinsicFunctions>
141+ <AdditionalIncludeDirectories>$(SolutionDir)..\..\..\..\include;$(SolutionDir)..\..\contrib\common\$(Platform)\boost\include;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib\msw;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\include;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\include;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
142+ <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;LOCALMAXIMUMLABELINGPLUGIN_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
143+ <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
144+ <FunctionLevelLinking>true</FunctionLevelLinking>
145+ <PrecompiledHeader>
146+ </PrecompiledHeader>
147+ <WarningLevel>Level3</WarningLevel>
148+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
149+ </ClCompile>
150+ <Link>
151+ <AdditionalLibraryDirectories>$(SolutionDir)..\..\..\..\lib\msvs\$(Platform)-$(Configuration);$(SolutionDir)..\..\contrib\common\$(Platform)\boost\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
152+ <ModuleDefinitionFile>$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\$(ProjectName).def</ModuleDefinitionFile>
153+ <GenerateDebugInformation>true</GenerateDebugInformation>
154+ <SubSystem>Windows</SubSystem>
155+ <OptimizeReferences>true</OptimizeReferences>
156+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
157+ <TargetMachine>MachineX86</TargetMachine>
158+ </Link>
159+ <PostBuildEvent>
160+ <Command>mkdir $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
161+copy $(TargetPath) $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
162+copy $(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\*.xml $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)</Command>
163+ </PostBuildEvent>
164+ </ItemDefinitionGroup>
165+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
166+ <ClCompile>
167+ <Optimization>MaxSpeed</Optimization>
168+ <IntrinsicFunctions>true</IntrinsicFunctions>
169+ <AdditionalIncludeDirectories>$(SolutionDir)..\..\..\..\include;$(SolutionDir)..\..\contrib\common\$(Platform)\boost\include;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\include;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib\msw;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\include;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\include;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
170+ <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;LOCALMAXIMUMLABELINGPLUGIN_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
171+ <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
172+ <FunctionLevelLinking>true</FunctionLevelLinking>
173+ <PrecompiledHeader>
174+ </PrecompiledHeader>
175+ <WarningLevel>Level3</WarningLevel>
176+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
177+ </ClCompile>
178+ <Link>
179+ <AdditionalLibraryDirectories>$(SolutionDir)..\..\..\..\lib\msvs\$(Platform)-$(Configuration);$(SolutionDir)..\..\contrib\common\$(Platform)\boost\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\cairo\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\wxWidgets\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\xerces-c\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\zlib\lib;$(SolutionDir)..\..\contrib\common\$(Platform)\Java\include;$(SolutionDir)..\..\contrib\common\$(Platform)\gtest\lib;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
180+ <ModuleDefinitionFile>$(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\$(ProjectName).def</ModuleDefinitionFile>
181+ <GenerateDebugInformation>true</GenerateDebugInformation>
182+ <SubSystem>Windows</SubSystem>
183+ <OptimizeReferences>true</OptimizeReferences>
184+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
185+ </Link>
186+ <PostBuildEvent>
187+ <Command>mkdir $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
188+copy $(TargetPath) $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)
189+copy $(SolutionDir)..\..\..\..\src\$(SolutionName)\$(ProjectName)\*.xml $(SolutionDir)..\..\stage\$(Platform)-$(Configuration)\plugins\$(ProjectName)</Command>
190+ </PostBuildEvent>
191+ </ItemDefinitionGroup>
192+ <ItemGroup>
193+ <ClCompile Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\OpenMS.cpp" />
194+ <ClCompile Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\OpenMSFunctions.cpp" />
195+ </ItemGroup>
196+ <ItemGroup>
197+ <None Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\OpenMSPlugin.def" />
198+ <None Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\options.xml" />
199+ <None Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\plugin.xml">
200+ <SubType>Designer</SubType>
201+ </None>
202+ <None Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\settings.xml" />
203+ </ItemGroup>
204+ <ItemGroup>
205+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\OpenMS.h" />
206+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\OpenMSFunctions.h" />
207+ <ClInclude Include="..\..\..\..\..\src\common-plugin-analyze\OpenMSPlugin\stdafx.h" />
208+ </ItemGroup>
209+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
210+ <ImportGroup Label="ExtensionTargets">
211+ </ImportGroup>
212+</Project>
\ No newline at end of file
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln
--- a/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/solutions/common-plugin-analyze/common-plugin-analyze.sln Thu Jul 16 11:15:28 2015 +0900
@@ -1,6 +1,6 @@
11 
22 Microsoft Visual Studio Solution File, Format Version 11.00
3-# Visual Studio 2010
3+# Visual C++ Express 2010
44 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "IdentificationPlugin", "IdentificationPlugin\IdentificationPlugin.vcxproj", "{EDA8473A-1B86-456D-91A3-DC91983624AE}"
55 EndProject
66 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "XTandemSearchPlugin", "XTandemSearchPlugin\XTandemSearchPlugin.vcxproj", "{2A1EEE74-0158-4068-A53C-B76789CFCE17}"
@@ -67,6 +67,8 @@
6767 EndProject
6868 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MascotPMFForLCMSPlugin", "MascotPMFForLCMSPlugin\MascotPMFForLCMSPlugin.vcxproj", "{84090F00-9281-4844-A1A8-B46C907F3684}"
6969 EndProject
70+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "OpenMSPlugin", "OpenMSPlugin\OpenMSPlugin.vcxproj", "{CB76A555-263B-44C4-9F84-345F701BFA7B}"
71+EndProject
7072 Global
7173 GlobalSection(SolutionConfigurationPlatforms) = preSolution
7274 Debug|Win32 = Debug|Win32
@@ -601,6 +603,18 @@
601603 {84090F00-9281-4844-A1A8-B46C907F3684}.Release|Win32.Build.0 = Release|Win32
602604 {84090F00-9281-4844-A1A8-B46C907F3684}.Release|x64.ActiveCfg = Release|x64
603605 {84090F00-9281-4844-A1A8-B46C907F3684}.Release|x64.Build.0 = Release|x64
606+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Debug|Win32.ActiveCfg = Debug|Win32
607+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Debug|Win32.Build.0 = Debug|Win32
608+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Debug|x64.ActiveCfg = Debug|Win32
609+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Debug|Win32.ActiveCfg = Debug|Win32
610+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Debug|Win32.Build.0 = Debug|Win32
611+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Debug|x64.ActiveCfg = Debug|Win32
612+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Release|Win32.ActiveCfg = Release|Win32
613+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Release|Win32.Build.0 = Release|Win32
614+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Parallel-Release|x64.ActiveCfg = Release|Win32
615+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Release|Win32.ActiveCfg = Release|Win32
616+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Release|Win32.Build.0 = Release|Win32
617+ {CB76A555-263B-44C4-9F84-345F701BFA7B}.Release|x64.ActiveCfg = Release|Win32
604618 EndGlobalSection
605619 GlobalSection(SolutionProperties) = preSolution
606620 HideSolutionNode = FALSE
diff -r 501b14f9e83d -r c144399f4dbd build/msvs/solutions/common-plugin-operation/OperationLogPlugin/operations.h
--- a/build/msvs/solutions/common-plugin-operation/OperationLogPlugin/operations.h Fri Jun 12 00:16:08 2015 +0900
+++ b/build/msvs/solutions/common-plugin-operation/OperationLogPlugin/operations.h Thu Jul 16 11:15:28 2015 +0900
@@ -8,7 +8,7 @@
88 using namespace System::Security::Permissions;
99 [assembly:SecurityPermissionAttribute(SecurityAction::RequestMinimum, SkipVerification=false)];
1010 //
11-// このソース コードは xsd によって自動生成されました。Version=4.0.30319.1 です。
11+// This source code was auto-generated by xsd, Version=4.0.30319.1.
1212 //
1313 using namespace System;
1414 ref class NewDataSet;
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/OpenMS.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/OpenMS.cpp Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,388 @@
1+/**
2+ * @file OpenMS.cpp
3+ * @brief implements of OpenMS class
4+ *
5+ * @author S.Tanaka
6+ * @date 2015.07.01
7+ *
8+ * Copyright(C) 2015 Mass++ All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "OpenMS.h"
14+
15+#include <windows.h>
16+
17+
18+using namespace kome::thirdparty::openms;
19+
20+
21+#include <crtdbg.h>
22+#ifdef _DEBUG
23+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
24+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
25+#endif // _DEBUG
26+
27+
28+
29+// constructor
30+OpenMS::OpenMS( kome::objects::SettingParameterValues* params ) {
31+ m_params = params;
32+}
33+
34+// destructor
35+OpenMS::~OpenMS() {
36+}
37+
38+// wavelet peak detection
39+void OpenMS::wavelet (
40+ kome::core::XYData& xyData,
41+ kome::objects::Peaks& peaks
42+) {
43+ // tmp dir
44+ std::string tmpDir = getTmpDir();
45+
46+ // parameters
47+ double sn = m_params->getDoubleValue( "sn", 1.0 );
48+ double width = m_params->getDoubleValue( "width", 0.15 );
49+ bool estimate = m_params->getBoolValue( "estimate", false );
50+
51+ addParameter( "", "signal_to_noise", FMT( "%f", sn ).c_str(), "double" );
52+ addParameter( "", "peak_width", FMT( "%f", width ).c_str(), "double" );
53+ addParameter( "", "estimate_peak_width", ( estimate ? "true" : "false" ), "string" );
54+
55+ // files
56+ std::string dataDta2d = getpath( tmpDir.c_str(), "data.dta2d" );
57+ std::string dataMzml = getpath( tmpDir.c_str(), "data.mzML" );
58+ std::string peaksMzml = getpath( tmpDir.c_str(), "peaks.mzML" );
59+ std::string peaksDta2d = getpath( tmpDir.c_str(), "peaks.dta2d" );
60+ std::string ini = getpath( tmpDir.c_str(), "params.ini" );
61+
62+ // run mzml
63+ writeDta2d( dataDta2d.c_str(), xyData );
64+
65+ std::string command = getCommandPath( "FileConverter.exe" );
66+ command = FMT(
67+ "%s -in \"%s\" -out \"%s\"",
68+ command.c_str(),
69+ dataDta2d.c_str(),
70+ dataMzml.c_str()
71+ );
72+ if( !createProcess( command.c_str() ) ) {
73+ return;
74+ }
75+
76+ writeIniFile( ini.c_str(), "PeakPickerWavelet" );
77+ command = getCommandPath( "PeakPickerWavelet.exe" );
78+ command = FMT(
79+ "%s -in \"%s\" -out \"%s\" -ini \"%s\"",
80+ command.c_str(),
81+ dataMzml.c_str(),
82+ peaksMzml.c_str(),
83+ ini.c_str()
84+ );
85+ if( !createProcess( command.c_str() ) ) {
86+ return;
87+ }
88+
89+ command = getCommandPath( "FileConverter.exe" );
90+ command = FMT(
91+ "%s -in \"%s\" -out \"%s\"",
92+ command.c_str(),
93+ peaksMzml.c_str(),
94+ peaksDta2d.c_str()
95+ );
96+ if( !createProcess( command.c_str() ) ) {
97+ return;
98+ }
99+
100+ readDta2d( peaksDta2d.c_str(), peaks );
101+}
102+
103+// high resolution peak detection
104+void OpenMS::hires (
105+ kome::core::XYData& xyData,
106+ kome::objects::Peaks& peaks
107+) {
108+ // tmp dir
109+ std::string tmpDir = getTmpDir();
110+
111+ // parameters
112+ double sn = m_params->getDoubleValue( "sn", 1.0 );
113+ double len = m_params->getDoubleValue( "len", 200.0 );
114+ int bin = m_params->getIntValue( "cnt", 30 );
115+ int minElms = m_params->getIntValue( "min", 10 );
116+
117+ addParameter( "", "signal_to_noise", FMT( "%f", sn ).c_str(), "double" );
118+ addParameter( "", "ms_levels", "[1,2]", "int" );
119+ addParameter( "SignalToNoise", "win_len", FMT( "%f", len ).c_str(), "double" );
120+ addParameter( "SignalToNoise", "bin_count", FMT( "%d", bin ).c_str(), "int" );
121+ addParameter( "SignalToNoise", "min_required_elements", FMT( "%d", minElms ).c_str(), "int" );
122+
123+ // files
124+ std::string dataDta2d = getpath( tmpDir.c_str(), "data.dta2d" );
125+ std::string dataMzml = getpath( tmpDir.c_str(), "data.mzML" );
126+ std::string peaksMzml = getpath( tmpDir.c_str(), "peaks.mzML" );
127+ std::string peaksDta2d = getpath( tmpDir.c_str(), "peaks.dta2d" );
128+ std::string ini = getpath( tmpDir.c_str(), "params.ini" );
129+
130+ // run mzml
131+ writeDta2d( dataDta2d.c_str(), xyData );
132+
133+ std::string command = getCommandPath( "FileConverter.exe" );
134+ command = FMT(
135+ "%s -in \"%s\" -out \"%s\"",
136+ command.c_str(),
137+ dataDta2d.c_str(),
138+ dataMzml.c_str()
139+ );
140+ if( !createProcess( command.c_str() ) ) {
141+ return;
142+ }
143+
144+ writeIniFile( ini.c_str(), "PeakPickerHiRes" );
145+ command = getCommandPath( "PeakPickerHiRes.exe" );
146+ command = FMT(
147+ "%s -in \"%s\" -out \"%s\" -ini \"%s\"",
148+ command.c_str(),
149+ dataMzml.c_str(),
150+ peaksMzml.c_str(),
151+ ini.c_str()
152+ );
153+ if( !createProcess( command.c_str() ) ) {
154+ return;
155+ }
156+
157+ command = getCommandPath( "FileConverter.exe" );
158+ command = FMT(
159+ "%s -in \"%s\" -out \"%s\"",
160+ command.c_str(),
161+ peaksMzml.c_str(),
162+ peaksDta2d.c_str()
163+ );
164+ if( !createProcess( command.c_str() ) ) {
165+ return;
166+ }
167+
168+ readDta2d( peaksDta2d.c_str(), peaks );
169+}
170+
171+
172+// temporary directory
173+const char* OpenMS::getTmpDir() {
174+ if( m_tmpDir.empty() ) {
175+ // open ms folder
176+ kome::core::MsppManager& msppMgr = kome::core::MsppManager::getInstance();
177+ std::string dir = msppMgr.getTmpDir();
178+ dir = getpath( dir.c_str(), "openms" );
179+ if( !fileexists( dir.c_str() ) ) {
180+ makedirectory( dir.c_str() );
181+ }
182+
183+ // tmp dir
184+ m_tmpDir = getpath( dir.c_str(), FMT( "%lld", getcurrenttime() ).c_str() );
185+ makedirectory( m_tmpDir.c_str() );
186+ }
187+
188+ return m_tmpDir.c_str();
189+}
190+
191+// add parameter
192+void OpenMS::addParameter( const char* sec, const char* name, const char* value, const char* type ) {
193+ m_iniParameters.resize( m_iniParameters.size() + 1 );
194+ m_iniParameters.back().section = NVL( sec, "" );
195+ m_iniParameters.back().name = NVL( name, "" );
196+ m_iniParameters.back().value = NVL( value, "" );
197+ m_iniParameters.back().type = NVL( type, "" );
198+}
199+
200+// write ini file
201+void OpenMS::writeIniFile( const char* path, const char* name ) {
202+ // open
203+ FILE* fp = fileopen( path, "w" );
204+ if( fp == NULL ) {
205+ return;
206+ }
207+
208+ // write
209+ fprintf( fp, "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n" );
210+ fprintf( fp, "<PARAMETERS version=\"1.6.2\" xsi:noNamespaceSchemaLocation=\"http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\n" );
211+ fprintf( fp, " <NODE name=\"%s\">\n", name );
212+ fprintf( fp, " <ITEM name=\"version\" value=\"2.0.0\" type=\"string\" />\n" );
213+ fprintf( fp, " <NODE name=\"1\">\n" );
214+ fprintf( fp, " <ITEM name=\"in\" value=\"\" type=\"input-file\" />\n" );
215+ fprintf( fp, " <ITEM name=\"out\" value=\"\" type=\"output-file\" />\n" );
216+
217+ fprintf( fp, " <NODE name=\"algorithm\">\n" );
218+
219+ std::string currentSec = "";
220+ for( unsigned int i = 0; i < m_iniParameters.size(); i++ ) {
221+ std::string s = m_iniParameters[ i ].section;
222+ std::string n = m_iniParameters[ i ].name;
223+ std::string v = m_iniParameters[ i ].value;
224+ std::string t = m_iniParameters[ i ].type;
225+
226+ std::vector< std::string > values;
227+ stringtoken( v.c_str(), ", []", values );
228+
229+ if( currentSec.compare( s ) != 0 ) {
230+ if( currentSec.empty() ) {
231+ fprintf( fp, " <NODE name=\"%s\">\n", s.c_str() );
232+ }
233+ else {
234+ fprintf( fp, " </NODE>\n" );
235+ }
236+ currentSec = s;
237+ }
238+
239+ int indent = ( currentSec.empty() ? 8 : 10 );
240+
241+ for( int j = 0; j < indent; j++ ) {
242+ fprintf( fp, " " );
243+ }
244+
245+ if( values.size() > 1 ) {
246+ fprintf( fp, "<ITEMLIST name=\"%s\" type=\"%s\">\n", n.c_str(), t.c_str() );
247+ for( unsigned int j = 0; j < values.size(); j++ ) {
248+ for( int k = 0; k < indent + 2; k++ ) {
249+ fprintf( fp, " " );
250+ }
251+ fprintf( fp, "<LISTITEM value=\"%s\" />\n", values[ i ].c_str() );
252+ }
253+ for( int k = 0; k < indent; k++ ) {
254+ fprintf( fp, " " );
255+ }
256+ fprintf( fp, "</ITEMLIST>\n" );
257+ }
258+ else {
259+ fprintf(
260+ fp,
261+ "<ITEM name=\"%s\" value=\"%s\" type=\"%s\" />\n",
262+ n.c_str(),
263+ v.c_str(),
264+ t.c_str()
265+ );
266+ }
267+ }
268+ if( !currentSec.empty() ) {
269+ fprintf( fp, " </NODE>\n" );
270+ }
271+ fprintf( fp, " </NODE>\n" );
272+ fprintf( fp, " </NODE>\n" );
273+ fprintf( fp, " </NODE>\n" );
274+ fprintf( fp, "</PARAMETERS>\n" );
275+
276+ // close
277+ fflush( fp );
278+ fclose( fp );
279+}
280+
281+// gets the command path
282+std::string OpenMS::getCommandPath( const char* commandName ) {
283+ // return value
284+ std::string path = NVL( commandName, "" );
285+
286+ // ini
287+ kome::core::MsppManager& msppMgr = kome::core::MsppManager::getInstance();
288+ kome::core::IniFile* ini = msppMgr.getIniFile();
289+ if( ini == NULL ) {
290+ return path;
291+ }
292+
293+ std::string dir = trimstring( ini->getString( "OpenMS", "OPENMS_HOME", "" ) );
294+ if( dir.compare( "none" ) == 0 ) {
295+ dir = "";
296+ }
297+ if( !dir.empty() ) {
298+ path = getpath( dir.c_str(), path.c_str() );
299+ }
300+ path = FMT( "\"%s\"", path.c_str() );
301+
302+ return path;
303+}
304+
305+// write data
306+void OpenMS::writeDta2d( const char* path, kome::core::XYData& xyData ) {
307+ // open
308+ FILE* fp = fileopen( path, "w" );
309+ if( fp == NULL ) {
310+ return;
311+ }
312+
313+ // write
314+ fprintf( fp, "#SEC\tMZ\tINT\n" );
315+
316+ for( unsigned int i = 0; i < xyData.getLength(); i++ ) {
317+ fprintf( fp, "%f\t%f\t%f\n", 1.0, xyData.getX( i ), xyData.getY( i ) );
318+ }
319+
320+ // close
321+ fflush( fp );
322+ fclose( fp );
323+}
324+
325+
326+// read data
327+void OpenMS::readDta2d( const char* path, kome::core::XYData& xyData ) {
328+ // open
329+ FILE* fp = fileopen( path, "r" );
330+ if( fp == NULL ) {
331+ return;
332+ }
333+
334+ // read
335+ char line[ 4096 ];
336+ while( fgets( line, 4096, fp ) != NULL ) {
337+ double rt = 0.0;
338+ double mz = 0.0;
339+ double intensity = 0.0;
340+
341+ if( sscanf( line, "%lf %lf %lf", &rt, &mz, &intensity ) > 0 ) {
342+ if( rt > 0.0 && mz > 0.0 && intensity > 0.0 ) {
343+ xyData.addPoint( mz, intensity );
344+ }
345+ }
346+ }
347+
348+ // close
349+ fclose( fp );
350+}
351+
352+// creates process
353+bool OpenMS::createProcess( const char* command ) {
354+ STARTUPINFO si = { sizeof( STARTUPINFO ) };
355+ PROCESS_INFORMATION pi = {};
356+ size_t szLine =strlen( command ) + 1;
357+ char *pLine = new char[ szLine ];
358+ bool bSuccess = false;
359+
360+ sprintf( pLine, "%s", command );
361+
362+ if (CreateProcess( NULL, pLine, NULL, NULL, FALSE, CREATE_NO_WINDOW, NULL, getTmpDir(), &si, &pi))
363+ {
364+ // Wait until child process exits.
365+ DWORD r = WaitForSingleObject( pi.hProcess, INFINITE );
366+ if( r == WAIT_FAILED ) {
367+ LOG_ERROR( FMT( "Process Failed" ) );
368+ }
369+ else if( r == WAIT_ABANDONED ) {
370+ LOG_ERROR( FMT( "Process Abandoned" ) );
371+ }
372+ else if( r == WAIT_TIMEOUT ) {
373+ LOG_ERROR( FMT( "Process Timeout" ) );
374+ }
375+ else if( r == WAIT_OBJECT_0 ) {
376+ bSuccess = true;
377+ }
378+ else {
379+ LOG_ERROR( FMT( "Process Error (code=%d)", r ) );
380+ }
381+ }
382+ if ( (char *)NULL != pLine )
383+ {
384+ delete[] pLine;
385+ }
386+
387+ return bSuccess;
388+}
\ No newline at end of file
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/OpenMS.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/OpenMS.h Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,139 @@
1+/**
2+ * @file OpenMS.h
3+ * @brief interfaces of OpenMS class
4+ *
5+ * @author S.Tanaka
6+ * @date 2015.07.01
7+ *
8+ * Copyright(C) 2015 Mass++ All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_THIRDPARTY_OPENMS_H__
13+#define __KOME_THIRDPARTY_OPENMS_H__
14+
15+
16+namespace kome {
17+ namespace thirdparty {
18+ namespace openms {
19+ /**
20+ * @class OpenMS
21+ * @brief local peak detect class
22+ */
23+ class OpenMS {
24+ public:
25+ /**
26+ * @fn OpenMS( kome::objects::SettingParameterValues* params );
27+ * @brief constructor
28+ * @param[in] params parameters
29+ */
30+ OpenMS( kome::objects::SettingParameterValues* params );
31+
32+ /**
33+ * @fn virtual ~OpenMS()
34+ * @brief destructor
35+ */
36+ virtual ~OpenMS();
37+
38+ protected:
39+ /** parameters */
40+ kome::objects::SettingParameterValues* m_params;
41+
42+ /** temporary directory */
43+ std::string m_tmpDir;
44+
45+ /**
46+ * @struct ParamInfo
47+ * @brief parameter information
48+ */
49+ struct ParamInfo {
50+ std::string section;
51+ std::string name;
52+ std::string value;
53+ std::string type;
54+ };
55+
56+ /** parameters */
57+ std::vector< ParamInfo > m_iniParameters;
58+
59+ public:
60+ /**
61+ * @fn void wavelet( kome::core::XYData& xyData, kome::objects::Peaks& peaks )
62+ * @brief detects peaks by wavelet
63+ * @param xyData data points
64+ * @param peaks peak object to store peak data
65+ */
66+ void wavelet( kome::core::XYData& xyData, kome::objects::Peaks& peaks );
67+
68+ /**
69+ * @fn void hires( kome::core::XYData& xyData, kome::objects::Peaks& peaks )
70+ * @brief detects peaks by high resolution
71+ * @param xyData data points
72+ * @param peaks peak object to store peak data
73+ */
74+ void hires( kome::core::XYData& xyData, kome::objects::Peaks& peaks );
75+
76+ protected:
77+ /**
78+ * @fn const char* getTmpDir();
79+ * @brief gets the temporary directory
80+ * @return temporary directory
81+ */
82+ const char* getTmpDir();
83+
84+ /**
85+ * @fn void addParameter( const char* sec, const char* name, const char* value, const char* type )
86+ * @brief adds parameter
87+ * @param[in] sec section
88+ * @param[in] name parameter name
89+ * @param[in] value parameter value
90+ * @param[in] type parameter type
91+ */
92+ void addParameter( const char* sec, const char* name, const char* value, const char* type );
93+
94+ /**
95+ * @fn void writeIniFile( const char* path, const char* name )
96+ * @brief writes ini file
97+ * @param[in] path ini file path
98+ * @param[in] name program name
99+ */
100+ void writeIniFile( const char* path, const char* name );
101+
102+ /**
103+ * @fn std::string getCommandPath( const char* commandName );
104+ * @brief gets the command path
105+ * @param[in] commandName command name
106+ * @return command path
107+ */
108+ std::string getCommandPath( const char* commandName );
109+
110+ /**
111+ * @fn void writeDta2d( const char* path, kome::core::XYData& xyData );
112+ * @brief writes dta2d file
113+ * @param[in] path file path
114+ * @param[in] xyData xy data
115+ */
116+ void writeDta2d( const char* path, kome::core::XYData& xyData );
117+
118+ /**
119+ * @fn
120+ * @brief reads dta2d file
121+ * @param[in] path file path
122+ * @param[out] xyData the object to store data
123+ */
124+ void readDta2d( const char* path, kome::core::XYData& xyData );
125+
126+ /**
127+ * @fn bool createProcess( const char* command );
128+ * @brief creates process
129+ * @param[in] command command line
130+ * @return If true, the process was finished successfully.
131+ */
132+ bool createProcess( const char* command );
133+ };
134+ }
135+ }
136+}
137+
138+
139+#endif // __KOME_THIRDPARTY_OPENMS_H__
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/OpenMSFunctions.cpp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/OpenMSFunctions.cpp Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,81 @@
1+/**
2+ * @file OpenMSFunctions.cpp
3+ * @brief implements of OpenMS plug-in functions
4+ *
5+ * @author S.Tanaka
6+ * @date 2015.07.01
7+ *
8+ * Copyright(C) 2015 Mass++ All rights reserved.
9+ */
10+
11+
12+#include "stdafx.h"
13+#include "OpenMSFunctions.h"
14+
15+#include "OpenMS.h"
16+
17+
18+using namespace kome::thirdparty::openms;
19+
20+
21+#include <crtdbg.h>
22+#ifdef _DEBUG
23+ #define new new( _NORMAL_BLOCK, __FILE__, __LINE__ )
24+ #define malloc( s ) _malloc_dbg( s, _NORMAL_BLOCK, __FILE__, __LINE__ )
25+#endif // _DEBUG
26+
27+
28+
29+// detect peaks
30+kome::objects::Variant detectPeaksByWavelet( kome::objects::Parameters* params ) {
31+ // return value
32+ kome::objects::Variant ret;
33+
34+ // get xy data object
35+ kome::core::XYData* xyData = kome::plugin::PluginCallTool::getXYData( params );
36+ if( xyData == NULL ) {
37+ return ret;
38+ }
39+
40+ // get peaks object
41+ kome::objects::Peaks* peaks = kome::plugin::PluginCallTool::getPeaks( params );
42+ if( peaks == NULL ) {
43+ return ret;
44+ }
45+
46+ // parameters
47+ kome::objects::SettingParameterValues* settings = kome::plugin::PluginCallTool::getSettingValues( params );
48+
49+ // peak detection
50+ OpenMS oms( settings );
51+ oms.wavelet( *xyData, *peaks );
52+
53+ return ret;
54+}
55+
56+// detect peaks
57+kome::objects::Variant detectPeaksByHiRes( kome::objects::Parameters* params ) {
58+ // return value
59+ kome::objects::Variant ret;
60+
61+ // get xy data object
62+ kome::core::XYData* xyData = kome::plugin::PluginCallTool::getXYData( params );
63+ if( xyData == NULL ) {
64+ return ret;
65+ }
66+
67+ // get peaks object
68+ kome::objects::Peaks* peaks = kome::plugin::PluginCallTool::getPeaks( params );
69+ if( peaks == NULL ) {
70+ return ret;
71+ }
72+
73+ // parameters
74+ kome::objects::SettingParameterValues* settings = kome::plugin::PluginCallTool::getSettingValues( params );
75+
76+ // peak detection
77+ OpenMS oms( settings );
78+ oms.hires( *xyData, *peaks );
79+
80+ return ret;
81+}
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/OpenMSFunctions.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/OpenMSFunctions.h Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,40 @@
1+/**
2+ * @file OpenMSFunctions.h
3+ * @brief interfaces of OpenMS plug-in functions
4+ *
5+ * @author S.Tanaka
6+ * @date 2015.07.01
7+ *
8+ * Copyright(C) 2015 Mass++ All rights reserved.
9+ */
10+
11+#ifndef __KOME_THIRDPARTY_OPENMS_FUNCTIONS_H__
12+#define __KOME_THIRDPARTY_OPENMS_FUNCTIONS_H__
13+
14+
15+#ifdef __unix
16+ extern "C" {
17+#endif // __unix
18+
19+
20+/**
21+ * @fn kome::objects::Variant detectPeaksByWavelet( kome::objects::Parameters* params )
22+ * @brief detects peaks by local peak picking algorithm
23+ * @return return value. (This value has no meanings.)
24+ */
25+kome::objects::Variant detectPeaksByWavelet( kome::objects::Parameters* params );
26+
27+/**
28+ * @fn kome::objects::Variant detectPeaksByHiRes( kome::objects::Parameters* params )
29+ * @brief detects peaks by local peak picking algorithm
30+ * @return return value. (This value has no meanings.)
31+ */
32+kome::objects::Variant detectPeaksByHiRes( kome::objects::Parameters* params );
33+
34+
35+#ifdef __unix
36+ }
37+#endif // __unix
38+
39+
40+#endif // __KOME_THIRDPARTY_OPENMS_FUNCTIONS_H__
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/OpenMSPlugin.def
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/OpenMSPlugin.def Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,3 @@
1+EXPORTS
2+ detectPeaksByWavelet
3+ detectPeaksByHiRes
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/options.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/options.xml Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,33 @@
1+<?xml version="1.0"?>
2+
3+<settings
4+ xmlns="http://xml.first-ms3d.jp/masspp/settings"
5+ xsi:schemaLocation="http://xml.first-ms3d.jp/masspp/settings http://first-ms3d.jp/development/masspp-settings110.xsd"
6+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
7+ <chapters>
8+ <chapter id="0">Thirdparty</chapter>
9+ </chapters>
10+ <values>
11+ <value id="0" type="dir" required="false" />
12+ </values>
13+ <params>
14+ <param id="0" value="0">
15+ <param-name>dir</param-name>
16+ <param-section>OpenMS</param-section>
17+ <param-key>OPENMS_HOME</param-key>
18+ </param>
19+ </params>
20+ <pages>
21+ <page chapter="0" common="true">
22+ <page-name>common</page-name>
23+ <page-title>OpenMS</page-title>
24+ <forms>
25+ <form id="0" param="0">
26+ <form-title>OpenMS Home</form-title>
27+ <form-desc>Set the OpenMS home directory.</form-desc>
28+ </form>
29+ </forms>
30+ </page>
31+ </pages>
32+</settings>
33+
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/plugin.xml Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,105 @@
1+<?xml version="1.0"?>
2+
3+<plugin
4+ xmlns="http://xml.first-ms3d.jp/masspp/plugin"
5+ xsi:schemaLocation="http://xml.first-ms3d.jp/masspp/plugin http://first-ms3d.jp/development/masspp-plugin110.xsd"
6+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
7+ <name>Simple Peak Detect</name>
8+ <version>1.00</version>
9+ <provider>Mass++</provider>
10+ <link>OpenMSPlugin</link>
11+ <function>
12+ <call type="spec_peak_picking">
13+ <call-name>wavelet</call-name>
14+ <call-function>detectPeaksByWavelet</call-function>
15+ <params>
16+ <params>
17+ <param>
18+ <param-name>long name</param-name>
19+ <param-value>Wavelet Peak Detection (OpenMS)</param-value>
20+ </param>
21+ <param>
22+ <param-name>short name</param-name>
23+ <param-value>wavelet</param-value>
24+ </param>
25+ <param>
26+ <param-name>page</param-name>
27+ <param-value>wavelet</param-value>
28+ </param>
29+ <param>
30+ <param-name>desc</param-name>
31+ <param-value>detect peaks by wavelet algorithm contained in OpenMS.</param-value>
32+ </param>
33+ </params>
34+ </params>
35+ <call-description>detect spectrum peaks</call-description>
36+ </call>
37+ <call type="spec_peak_picking">
38+ <call-name>hires</call-name>
39+ <call-function>detectPeaksByHiRes</call-function>
40+ <params>
41+ <params>
42+ <param>
43+ <param-name>long name</param-name>
44+ <param-value>High Resolution Peak Detection (OpenMS)</param-value>
45+ </param>
46+ <param>
47+ <param-name>short name</param-name>
48+ <param-value>highres</param-value>
49+ </param>
50+ <param>
51+ <param-name>page</param-name>
52+ <param-value>hires</param-value>
53+ </param>
54+ <param>
55+ <param-name>desc</param-name>
56+ <param-value>detect peaks by high resolution algorithm contained in OpenMS.</param-value>
57+ </param>
58+ </params>
59+ </params>
60+ <call-description>detect spectrum peaks</call-description>
61+ </call>
62+ </function>
63+ <components>
64+ <component>
65+ <component-name>peaks</component-name>
66+ <component-desc>Local Maximum Peak Detector</component-desc>
67+ <component-calls>
68+ <component-call>detectSpecPeaks</component-call>
69+ <component-call>detectChromPeaks</component-call>
70+ </component-calls>
71+ </component>
72+ </components>
73+ <packages>
74+ <package>
75+ <package-name>Identification</package-name>
76+ <package-components>
77+ <package-component>peaks</package-component>
78+ </package-components>
79+ </package>
80+ <package>
81+ <package-name>Quantitation</package-name>
82+ <package-components>
83+ <package-component>peaks</package-component>
84+ </package-components>
85+ </package>
86+ <package>
87+ <package-name>Data Processing</package-name>
88+ <package-components>
89+ <package-component>peaks</package-component>
90+ </package-components>
91+ </package>
92+ <package>
93+ <package-name>Viewer</package-name>
94+ <package-components>
95+ <package-component>peaks</package-component>
96+ </package-components>
97+ </package>
98+ </packages>
99+ <settings>
100+ <settings-file>options.xml</settings-file>
101+ </settings>
102+ <parameters>
103+ <parameters-file>settings.xml</parameters-file>
104+ </parameters>
105+</plugin>
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/settings.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/settings.xml Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,82 @@
1+<?xml version="1.0"?>
2+
3+<settings
4+ xmlns="http://xml.first-ms3d.jp/masspp/settings"
5+ xsi:schemaLocation="http://xml.first-ms3d.jp/masspp/settings http://first-ms3d.jp/development/masspp-settings110.xsd"
6+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
7+ <values>
8+ <value id="0" type="double" default="1.0" minInclusive="0.0" required="true" />
9+ <value id="1" type="double" default="0.15" minInclusive="0.0" required="true" />
10+ <value id="2" type="bool" default="false" required="true" />
11+ <value id="3" type="double" default="200.0" minInclusive="1.0" required="true" />
12+ <value id="4" type="int" default="30" minInclusive="3" required="true" />
13+ <value id="5" type="int" default="10" minInclusive="1" required="true" />
14+ </values>
15+ <params>
16+ <param id="0" value="0">
17+ <param-name>sn</param-name>
18+ <param-section>OpenMS</param-section>
19+ <param-key>SIGNAL_TO_NOISE</param-key>
20+ </param>
21+ <param id="1" value="1">
22+ <param-name>width</param-name>
23+ <param-section>OpenMS</param-section>
24+ <param-key>PEAK_WIDTH</param-key>
25+ </param>
26+ <param id="2" value="2">
27+ <param-name>estimate</param-name>
28+ <param-section>OpenMS</param-section>
29+ <param-key>ESTIMATE_PEAK_WIDTH</param-key>
30+ </param>
31+ <param id="3" value="3">
32+ <param-name>len</param-name>
33+ <param-section>OpenMS</param-section>
34+ <param-key>WINDOW_LENGTH</param-key>
35+ </param>
36+ <param id="4" value="4">
37+ <param-name>cnt</param-name>
38+ <param-section>OpenMS</param-section>
39+ <param-key>BIN_COUNT</param-key>
40+ </param>
41+ <param id="5" value="5">
42+ <param-name>min</param-name>
43+ <param-section>OpenMS</param-section>
44+ <param-key>MIN_ELEMENTS</param-key>
45+ </param>
46+ </params>
47+ <pages>
48+ <page common="false">
49+ <page-name>wavelet</page-name>
50+ <page-title>Wavelet Peak Detection (OpenMS)</page-title>
51+ <forms>
52+ <form id="0" param="0">
53+ <form-title>S/N</form-title>
54+ </form>
55+ <form id="1" param="1">
56+ <form-title>Peak Width</form-title>
57+ </form>
58+ <form id="2" param="2">
59+ <form-title>Estimate Peak Width</form-title>
60+ </form>
61+ </forms>
62+ </page>
63+ <page common="false">
64+ <page-name>hires</page-name>
65+ <page-title>High Resolution Peak Detection (OpenMS)</page-title>
66+ <forms>
67+ <form id="0" param="0">
68+ <form-title>S/N</form-title>
69+ </form>
70+ <form id="3" param="3">
71+ <form-title>Window Length</form-title>
72+ </form>
73+ <form id="4" param="4">
74+ <form-title>Bin Count</form-title>
75+ </form>
76+ <form id="5" param="5">
77+ <form-title>Min. Required Elements</form-title>
78+ </form>
79+ </forms>
80+ </page>
81+ </pages>
82+</settings>
diff -r 501b14f9e83d -r c144399f4dbd src/common-plugin-analyze/OpenMSPlugin/stdafx.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/src/common-plugin-analyze/OpenMSPlugin/stdafx.h Thu Jul 16 11:15:28 2015 +0900
@@ -0,0 +1,76 @@
1+/**
2+ * @file stdafx.h
3+ * @brief common header file
4+ *
5+ * @author S.Tanaka
6+ * @date 2015.07.01
7+ *
8+ * Copyright(C) 2015 Mass++ All rights reserved.
9+ */
10+
11+
12+#ifndef __KOME_THIRDPARTY_OPENMS_STD_AFX_H__
13+#define __KOME_THIRDPARTY_OPENMS_STD_AFX_H__
14+
15+//
16+// namespace
17+//
18+
19+/// kome project namespace
20+namespace kome {
21+ /// peak detect namespace
22+ namespace thirdparty {
23+ /// Local Maximum Labeling plug-in namespace
24+ namespace openms {
25+ }
26+ }
27+}
28+
29+
30+//
31+// macros
32+//
33+
34+#define WXUSINGDLL
35+
36+
37+//
38+// message
39+//
40+
41+#ifdef _MSC_VER
42+ #pragma warning( disable:4190 )
43+ #pragma warning( disable:4244 )
44+ #pragma warning( disable:4251 )
45+ #pragma warning( disable:4267 )
46+ #pragma warning( disable:4561 )
47+ #pragma warning( disable:4793 )
48+ #pragma warning( disable:4819 )
49+ #pragma warning( disable:4996 )
50+#endif // _MSC_VER
51+
52+
53+//
54+// libraries
55+//
56+
57+#ifdef _MSC_VER
58+ #pragma comment( lib, "CoreFunctions" )
59+ #pragma comment( lib, "CoreToolkits" )
60+ #pragma comment( lib, "DataObjects" )
61+ #pragma comment( lib, "PluginTools" )
62+#endif // _MSC_VER
63+
64+
65+
66+//
67+// includes
68+//
69+
70+#include "kome/CoreFunctions.h"
71+#include "kome/CoreToolkits.h"
72+#include "kome/DataObjects.h"
73+#include "kome/PluginTools.h"
74+
75+
76+#endif // __KOME_THIRDPARTY_OPENMS_STD_AFX_H__
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