Dear Victor, Thank you for the contribution! Sending a patch is fine, but you can also commit your changes directly to the SVN repository - I gave you the commit permission some time ago. If you need help with using the SVN, contact me.
I just committed your new modules into the SVN, with a few changes on my side. Mainly, I - Updated the code to reflect recent changes in the source tree - Moved the GridMass classes to net.sf.mzmine.modules.rawdatamethods.peakpicking.gridmass package, and renamed the module to GridMass, because it is more specific (there might be more 2D detection modules in the future). - Added copyright notice "Copyright 2006-2014 The MZmine 2 Development Team". This is important for us so we can modify and redistribute the code. Of course, I will include your name to the MZmine website and list you as the author of these modules. - Changed formatting of the code to conform to Java formatting conventions (using automatic formatter in Eclipse), and removed some unused import statements Please try to download the current code from SVN trunk, build a current version of MZmine by running 'mvn package', and let me know if everything works fine. You will notice I changed the GUI to use separate windows instead of a JDesktopPane. This is to allow people to use MZmine on multiple screens, and also to get a rid of the aging MDI interface. There will be more GUI changes in the near future, as I'm planning to make a transition from Swing to JavaFX. I would like to ask you to provide some documentation to your new modules, in the form of HTML help files (please see the help files for other modules, and please follow a similar style). Once the documentation is included, I think we can release MZmine 2.11 including GridMass. Thank you once more! Best regards, Tomas On Sun, Jul 27, 2014 at 8:11 AM, Víctor Manuel Treviño Alvarado <vtrev...@itesm.mx> wrote: > Dear Tomas, > > I´m enclosing the "patch" I just created for GridMass. > Is this the official way to report the GridMass class ? > Please let me know of any issue. > > *** In summary I made the following contributions/modifications: > > (1) Added the GridMass class and its corresponding inclusion in the module > list. > > (2) Added two more optional and experimental classes "AlignScans" and > "ScanSmoothing". These are completely independent of GridMass. > AlignScansModule tries to "align" scans to help reduce noise in following > steps, the input is rawdata and creates a "rawdata" that is aligned. > ScanSmoothing smooths the signal in m/z and time, also the input and output > is rawdata. Unfortunately they are not well documented. But I´m willing to > do so if MZmine team is interested. > > (3) Added a "log" scale mode in the 2D plot. This is quite useful to compare > and reveal high-valued peaks with low-valued peaks. Because of the lack of a > proper "icon", I used the same rainbow icon and is shown below the official > options. The icon should be replaced by an icon expressing "Log()". > > (4) Added a new color palette, (cyan for background, white for medium, > purple for high, and blue for max values) that is particularly useful in log > scale. > > Any issue, please let me know. > > Regards, > vt > > ______________________________________ > Dr. Victor Manuel Treviño Alvarado > Profesor-Investigador, SNI - 1 > Cátedra de Bioinformática > Tecnológico de Monterrey, Campus Monterrey > CITES, 304, Tel. 8888 2045 > Aulas 7-421, Tel. 52-(81) 8358 2000 ext. 4536-103 > http://homepages.mty.itesm.mx/vtrevino > http://www.itesm.mx > > El contenido de este mensaje de datos no se considera oferta, propuesta o > acuerdo, sino hasta que sea confirmado en documento por escrito que > contenga la firma autógrafa del apoderado legal del ITESM. El contenido de > este mensaje de datos es confidencial y se entiende dirigido y para uso > exclusivo del destinatario, por lo que no podrá distribuirse y/o difundirse > por ningún medio sin la previa autorización del emisor original. Si usted no > es el destinatario, se le prohíbe su utilización total o parcial para > cualquier fin. > > The content of this data transmission must not be considered an offer, > proposal, understanding or agreement unless it is confirmed in a document > signed by a legal representative of ITESM. The content of this data > transmission is confidential and is intended to be delivered only to the > addressees. Therefore, it shall not be distributed and/or disclosed through > any means without the authorization of the original sender. If you are not > the addressee, you are forbidden from using it, either totally or partially, > for any purpose. > > On Wed Jul 23, 2014, at 7:44 PM, Tomas Pluskal <plus...@oist.jp> wrote: > > Dear Victor, > ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
