Feature/silac workflow

README.md

@@ -3,8 +3,11 @@ OpenMS
 
 [![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-blue.svg?style=flat-square)](http://opensource.org/licenses/BSD-3-Clause)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/93e71bad214f46d2a534ec92dbc2efc9)](https://www.codacy.com/app/OpenMS/OpenMS?utm_source=github.com&utm_medium=referral&utm_content=OpenMS/OpenMS&utm_campaign=badger)
-[![Build Status](https://travis-ci.org/OpenMS/OpenMS.svg?branch=develop)](https://travis-ci.org/OpenMS/OpenMS) [![Project Stats](https://www.openhub.net/p/open-ms/widgets/project_thin_badge.gif)](https://www.ohloh.net/p/open-ms) [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/OpenMS/OpenMS?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+[![Build Status](https://travis-ci.org/OpenMS/OpenMS.svg?branch=develop)](https://travis-ci.org/OpenMS/OpenMS)
+[![Project Stats](https://www.openhub.net/p/open-ms/widgets/project_thin_badge.gif)](https://www.ohloh.net/p/open-ms)
+[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/OpenMS/OpenMS?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/openms/README.html)
+[![documentation](https://codedocs.xyz/doxygen/doxygen.svg)](https://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/index.html)
 
 
 <a href="http://www.openms.org/" target="_blank">OpenMS</a> 
@@ -34,8 +37,11 @@ Berlin, and the ETH Zürich.
 
 Features
 --------
-- Core C++ library
-- TOPP Tools, 150+ analysis tools (150+), covering most MS and LC-MS data processing and mining tasks. 
+- Core C++ library under three-clause BSD licence.
+- Python bindings to the C++ API through pyOpenMS.
+- Over 150+ individual analysis tools (TOPP Tools), covering most MS and LC-MS data processing and mining tasks. 
+- Powerful 2D and 3D visualization tools (TOPPView)
+- Support for most MS identification and quantification workflows (label-free, isobaric and stable isotope).
 - Support for all major platforms (Windows [XP, 7, 8, 10], macOS and Linux).
 
 Licence
@@ -49,4 +55,5 @@ The file [AUTHORS](AUTHORS) contains a list of all authors who worked on OpenMS.
 Documentation
 -------------
 Users and developers should start by reading the [OpenMS wiki](https://github.com/OpenMS/OpenMS/wiki) and consult the [current documentation](http://www.openms.de/current_doxygen/).
+Documentation for the Python bindings pyOpenMS can be found on the [pyOpenMS online documentation](https://pyopenms.readthedocs.io).
 

doc/code_examples/Tutorial_Labeled.cpp

@@ -49,12 +49,12 @@ int main(int argc, const char** argv)
   FeatureXMLFile feature_file;
   feature_file.load(tutorial_data_path + "/data/Tutorial_Labeled.featureXML", maps[0]);
   ConsensusMap out;
-  out.getFileDescriptions()[0].filename = "data/Tutorial_Labeled.featureXML";
-  out.getFileDescriptions()[0].size = maps[0].size();
-  out.getFileDescriptions()[0].label = "light";
-  out.getFileDescriptions()[1].filename = "data/Tutorial_Labeled.featureXML";
-  out.getFileDescriptions()[1].size = maps[0].size();
-  out.getFileDescriptions()[1].label = "heavy";
+  out.getColumnHeaders()[0].filename = "data/Tutorial_Labeled.mzML";
+  out.getColumnHeaders()[0].size = maps[0].size();
+  out.getColumnHeaders()[0].label = "light";
+  out.getColumnHeaders()[1].filename = "data/Tutorial_Labeled.mzML";
+  out.getColumnHeaders()[1].size = maps[0].size();
+  out.getColumnHeaders()[1].label = "heavy";
 
   FeatureGroupingAlgorithmLabeled algorithm;
   // ... set parameters

doc/code_examples/Tutorial_Unlabeled.cpp

@@ -51,10 +51,11 @@ int main(int argc, const char** argv)
   feature_file.load(tutorial_data_path + "/data/Tutorial_Unlabeled_2.featureXML", maps[1]);
 
   ConsensusMap out;
-  out.getFileDescriptions()[0].filename = "/data/Tutorial_Unlabeled_1.featureXML";
-  out.getFileDescriptions()[0].size = maps[0].size();
-  out.getFileDescriptions()[1].filename = "/data/Tutorial_Unlabeled_2.featureXML";
-  out.getFileDescriptions()[1].size = maps[1].size();
+  out.getColumnHeaders()[0].filename = "/data/Tutorial_Unlabeled_1.mzML";
+  out.getColumnHeaders()[0].size = maps[0].size();
+  out.getColumnHeaders()[1].filename = "/data/Tutorial_Unlabeled_2.mzML";
+  out.getColumnHeaders()[1].size = maps[1].size();
+
 
   FeatureGroupingAlgorithmUnlabeled algorithm;
   // ... set parameters

doc/doxygen/install/common-cmake-parameters.doxygen

@@ -5,7 +5,7 @@ The most important CMake variables are:
 <table style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;">
   <tr>
     <td valign="top">\c OPENMS_CONTRIB_LIBS</td>
-    <td>Seperate search path for the contrib libraries from github.com/OpenMS/contrib that is internally considered before
+    <td>Separate search path for the contrib libraries from github.com/OpenMS/contrib that is internally considered before
     CMAKE_PREFIX_PATH for searching, linking and adding include directories.</td>
   </tr>
   <tr>

doc/doxygen/install/install-win.doxygen

@@ -117,8 +117,8 @@
     <ol>
       <li>non-commercial:
         <ol>
-          <li>install perl (e.g. Strawberry Perl) and git
-          <li>download <b>Qt5 source</b> via git:
+          <li>install perl (e.g. Strawberry Perl), Python and git
+          <li>download <b>Qt5 source</b> via git or as a source package from the website:
             \code
             git clone git://github.com/qt/qt5 --branch 5.9 qt-5.9
             \endcode
@@ -133,9 +133,10 @@
             \endcode
           <li>if you have multiple versions of VS installed you might need to provide the <tt>-platform</tt> param for the next configure command (e.g., <tt>-platform win32-msvc2012</tt>)
           <li>To save disk space, we use the -prefix switch do install only the required parts of Qt to a new directory of your choice (called <tt>&lt;path-to-qt&gt;</tt>, e.g. <tt>c:/dev/Qt/5.9/</tt>).
-              Check more options and supported compilers here: http://doc.qt.io/qt-5/configure-options.html (especially for developers)
+              Check more options and supported compilers here: http://doc.qt.io/qt-5/configure-options.html (especially for developers). Note that part of Qt requires Python to compile, so its a good idea to add the Python executable to your path
             \code
-            configure -release -nomake example -nomake demos -nomake tests -opensource -confirm-license -prefix <path-to-qt> -platform win32-msvc
+            PATH=%PATH%;C:\Python27\
+            configure -opensource -skip speech -skip location -nomake tests -nomake examples -confirm-license -opengl dynamic -prefix <path-to-qt> -platform win32-msvc 
             \endcode
           <li>
             \code
@@ -276,8 +277,16 @@
   MSBuild.exe <solution.sln> /maxcpucount /target:<target> /p:Configuration=<Config>
   \endcode
 
-  @note Since the call can be a bit lengthy, there is a batch file in <tt>OpenMS/tools/build.bat</tt> and in the root of your build tree (copied there by cmake for convenience), which allows to build the most important targets (TOPP, UTILS, Gui, Tests, Doc) in Release or Debug using very short notation. Call it without arguments to see its usage help text.
+  @note Since the call can be a bit lengthy, there is a batch file in
+  <tt>OpenMS/tools/build.bat</tt> and in the root of your build tree (copied
+  there by cmake for convenience), which allows to build the most important
+  targets (TOPP, UTILS, Gui, Tests, Doc) in Release or Debug using very short
+  notation. Call it without arguments to see its usage help text. For example
+  to build only the OpenMS library in release mode, call
 
+  \code
+  build OpenMS r
+  \endcode
 
 
 */

doc/doxygen/public/UTILS.doxygen

@@ -88,7 +88,8 @@
   <b>Quantitation</b>
   - @subpage UTILS_ERPairFinder - Evaluate pair ratios on enhanced resolution (zoom) scans.
   - @subpage UTILS_FeatureFinderSuperHirn - Find Features using the SuperHirn Algorithm (it can handle centroided or profile data, see .ini file).
-  - @subpage UTILS_MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.
+  - @subpage UTILS_ProteomicsLFQ - A standard Proteomics LFQ pipeline.
+  - @subpage UTILS_MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.  
   - @subpage UTILS_MRMPairFinder - Evaluate labeled pair ratios on MRM features.
   - @subpage UTILS_OpenSwathWorkflow - Complete workflow to run OpenSWATH.
   - @subpage UTILS_SILACWorkflow - Complete workflow to run SILAC analysis.