Dear Tomas, > 1) minimumTimeSpan and maximumTimeSpan parameters - why not use a > RangeParameter for this?
You are right !, I changed this. > > 2) mzTolerance parameter - here you should definitely use > MZToleranceParameter type, instead of DoubleParameter > This will take some time because of the implications of considering the possibility of using the ppm value. At the initial stages of GridMass, I used the raw m/z to speed up my tests and development (the concept of gridmass evolved two or three times until the shape it has now). Then, the grid is estimated by the m/z tolerance, so if the ppm is used, this will generate changes in the way the grid is built. So, although I agree this definitively should be as MZToleranceParameter, by now, I will leave it as it is, then in four weeks time or so, I will re-do this (I have one grant to write by Aug 18th, classes start next week where I run two of them, and have to deliver one paper revision ASAP). > 3) showDebug parameter - why not use a ComboParameter for selecting the debug > level (No debug/Basic Information/etc) > I updated this. > Two more general questions: > > 4) GridMass performs smoothing of the raw data. Wouldn't it make sense to > implement this smoothing as a standalone module in MZmine? Such smoothing > might be useful also for other peak detection methods, not only for GridMass. > In the original patch I sent you, I included two more classes. One was precisely the smoothing one, the other was an "aligning" method. Nevertheless, the smoothing works nice for continuous data but I don´t know whether it may be useful for centroided data. It also needs documentation. I can do some work here but again, in 4 weeks time. > 5) What is the motivation behind the ignoreTimes parameter? As you said in > the manual, the same function can be achieved using the crop filter, or not? Two reasons: (1) Speed, (2) Flexibility. The ignoretimes help you to avoid to cropping all files, this is indeed a lot faster than cropping. But more importantly, it may help to avoid regions within the chromatographic area in combination with edges instead of only the edges. For example if your gradient generated an artefact in the middle of region, then you may need to run two analyses, one for each side (using crop). If you use the ignoretimes, you don´t need to do this at all, just feed the time ranges of the artefact. I cannot use a timerange parameter since this can be a list of ranges, so I used string instead and parse it to obtain time ranges. I´ll send you the "patch" in a further mail. 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 Mon Aug 4, 2014, at 7:23 PM, Tomas Pluskal <plus...@oist.jp> wrote: > Dear Victor, > > Thanks a lot! I checked your description in the manual and I think it is very > good. You can use the same description for the html help. > > I have a few additional comments to the way how GridMass sets its parameters: > > 1) minimumTimeSpan and maximumTimeSpan parameters - why not use a > RangeParameter for this? > > 2) mzTolerance parameter - here you should definitely use > MZToleranceParameter type, instead of DoubleParameter > > 3) showDebug parameter - why not use a ComboParameter for selecting the debug > level (No debug/Basic Information/etc) > > Two more general questions: > > 4) GridMass performs smoothing of the raw data. Wouldn't it make sense to > implement this smoothing as a standalone module in MZmine? Such smoothing > might be useful also for other peak detection methods, not only for GridMass. > > 5) What is the motivation behind the ignoreTimes parameter? As you said in > the manual, the same function can be achieved using the crop filter, or not? > > Best regards, > > Tomas > > > > On Aug 5, 2014, at 3:17, Víctor Manuel Treviño Alvarado <vtrev...@itesm.mx> > wrote: > >> Dear Tomas, >> >> I´m on the process to update MZmine to check GridMass within the official >> release. Please give me some days for this. >> >> About the html documentation you asked for, I just updated the manual, >> please check it out and tell me if it is right to then build a html alike. >> >> 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 Sun Jul 27, 2014, at 4:42 AM, Tomas Pluskal <plus...@oist.jp> wrote: >> >>> 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, >>>> >> > > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > WWW: https://groups.oist.jp/g0 > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. 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