December 2013 - Pharo-dev - lists.pharo.org

Re: [Pharo-dev] Relation tower is coming for Roassal

by Tudor Girba

Hi HernÃ¡n, The input should be independent from the visualization engine. Roassal offers you a way of transforming your objects into a visualization and it should not be responsible for the input formats. Cheers, Doru On Thu, Dec 26, 2013 at 9:28 PM, HernÃ¡n Morales Durand < hernan.morales(a)gmail.com> wrote: > Hi Alexandre and Ricardo, > > I am glad to see your advances in Roassal visualization! > I wonder which input formats do you plan to support? > > Your relation tower can be used to visualize the crossover percentages > between haplotype blocks. For example, here are some Haplotypes drawings > from Haploview (http://en.wikipedia.org/wiki/Haploview) which may > interest you: > > > http://www.jnsbm.org/viewimage.asp?img=JNatScBiolMed_2012_3_2_139_101887_f1… > from this paper > http://www.jnsbm.org/temp/JNatScBiolMed32139-5367486_145434.pdf > > http://www.mailund.dk/wp-content/uploads/2010/04/haplotypes.png > > http://www.mailund.dk/wp-content/uploads/2010/04/journal.pone_.0010207.g005… > > I can send you the exported haplotypes from a study if you are interested. > It contains 131 blocks which is somewhat big to attach to this list. The > only problem I see is that a parser is needed to parse the Haplotype text > output file, although the format should not be difficult to parse. > > Cheers, > > HernÃ¡n > > > > > > > > 2013/12/17 Alexandre Bergel <alexandre.bergel(a)me.com> > >> Hi! >> >> A new builder for Roassal is comingâ¦ The goal of Relation tower is to >> easily visualize relations between group of elements. We had the >> inspiration from the following website http://peoplemov.in/#! >> >> Here are some screenshots: >> >> https://www.facebook.com/media/set/?set=a.559114290841839.1073741837.340543… >> >> If you like these screenshots, then you know where the like button is :-) >> >> We will have this visualization on the web, thanks to our smooth and nice >> Pharo2Amber migration process. >> >> Any idea on how to extend/apply Relation tower? Any set of data you want >> us to play with? Your data? >> Feedback are very welcome! >> >> Cheers, >> Ricardo & Alexandre >> >> -- >> _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: >> Alexandre Bergel http://www.bergel.eu >> ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;. >> >> >> > -- www.tudorgirba.com "Every thing has its own flow"

Dec. 26, 2013

Re: [Pharo-dev] Relation tower is coming for Roassal

by HernÃ¡n Morales Durand

Hi Alexandre and Ricardo, I am glad to see your advances in Roassal visualization! I wonder which input formats do you plan to support? Your relation tower can be used to visualize the crossover percentages between haplotype blocks. For example, here are some Haplotypes drawings from Haploview (http://en.wikipedia.org/wiki/Haploview) which may interest you: http://www.jnsbm.org/viewimage.asp?img=JNatScBiolMed_2012_3_2_139_101887_f1… from this paper http://www.jnsbm.org/temp/JNatScBiolMed32139-5367486_145434.pdf http://www.mailund.dk/wp-content/uploads/2010/04/haplotypes.png http://www.mailund.dk/wp-content/uploads/2010/04/journal.pone_.0010207.g005… I can send you the exported haplotypes from a study if you are interested. It contains 131 blocks which is somewhat big to attach to this list. The only problem I see is that a parser is needed to parse the Haplotype text output file, although the format should not be difficult to parse. Cheers, HernÃ¡n 2013/12/17 Alexandre Bergel <alexandre.bergel(a)me.com> > Hi! > > A new builder for Roassal is comingâ¦ The goal of Relation tower is to > easily visualize relations between group of elements. We had the > inspiration from the following website http://peoplemov.in/#! > > Here are some screenshots: > > https://www.facebook.com/media/set/?set=a.559114290841839.1073741837.340543… > > If you like these screenshots, then you know where the like button is :-) > > We will have this visualization on the web, thanks to our smooth and nice > Pharo2Amber migration process. > > Any idea on how to extend/apply Relation tower? Any set of data you want > us to play with? Your data? > Feedback are very welcome! > > Cheers, > Ricardo & Alexandre > > -- > _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: > Alexandre Bergel http://www.bergel.eu > ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;. > > >

Dec. 26, 2013

Re: [Pharo-dev] Nautilus: tab key change focus

by Juraj Kubelka

Hi Thierry, thank you. Actually I have started with an issue with package filter input. When it has a focus, there is no way to change a focus with key press. Like tab, or down arrow key, or anything. And I also find out the tab order is strange. When package list has focus, tab change focus to the filter. I think it should change to class list. For some reasons it is possible to escape the filter input by pressing shift+tab, but not by pressing tab. So I wanted to try to change the âtab" order. Thanks, Jura El 26-12-2013, a las 16:34, GOUBIER Thierry <thierry.goubier(a)cea.fr> escribiÃ³: > Hi Jura, > > it's implemented at the Morphic level; it follow the chain of owners / submorphs and should correctly tab to all morphs in the window, except when going through text fields which will catch the tab for themselves (but Ctrl+tab should work). > > To change the order, you may have a look at the order in which the morphs are added to the window. > > Another thing which may be of interest to you, Spec has the necessary code to override the default Morphic tab navigation and force an application defined order. > > What is the issue you are facing ? > > Thierry > ________________________________________ > De : Pharo-dev [pharo-dev-bounces(a)lists.pharo.org] de la part de Juraj Kubelka [juraj.kubelka(a)gmail.com] > Date d'envoi : jeudi 26 dÃ©cembre 2013 17:09 > Ã : Pharo Development List > Objet : [Pharo-dev] Nautilus: tab key change focus > > Hi, > > Can someone give me any glue how tab-key-order and handling works in Nautilus? I am trying to fix the tab order in Nautilus but I do not see how it is implemented. > > Thanks, > Jura >

Dec. 26, 2013

Re: [Pharo-dev] Nautilus: tab key change focus

by GOUBIER Thierry

Hi Jura, it's implemented at the Morphic level; it follow the chain of owners / submorphs and should correctly tab to all morphs in the window, except when going through text fields which will catch the tab for themselves (but Ctrl+tab should work). To change the order, you may have a look at the order in which the morphs are added to the window. Another thing which may be of interest to you, Spec has the necessary code to override the default Morphic tab navigation and force an application defined order. What is the issue you are facing ? Thierry ________________________________________ De : Pharo-dev [pharo-dev-bounces(a)lists.pharo.org] de la part de Juraj Kubelka [juraj.kubelka(a)gmail.com] Date d'envoi : jeudi 26 dÃ©cembre 2013 17:09 Ã : Pharo Development List Objet : [Pharo-dev] Nautilus: tab key change focus Hi, Can someone give me any glue how tab-key-order and handling works in Nautilus? I am trying to fix the tab order in Nautilus but I do not see how it is implemented. Thanks, Jura

Dec. 26, 2013

Re: [Pharo-dev] Merry Christmas!

by Serge Stinckwich

Crash on my mac OS X ! Cheers, On Thu, Dec 26, 2013 at 7:26 PM, milton mamani <akevalion(a)gmail.com> wrote: > Merry Christmas and happy new year to everyone!. > > [image: ImÃ¡genes integradas 1] > > This is another script: > > .=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= > | view body head > b1 b2 b3 > eye1 eye2 nose smile > cravat lhand rhand > sphere cone cylinder | > > cylinder := [ :m | | e | > e := R3CylinderShape element. > e on: m. > e ]. > > cone := [ :m | | e | > e := R3ConeShape element. > e on: m. > e. ]. > > sphere := [ :m | |e | > e := R3IcoSphereShape element. > e on: m. > e shape color: Color white. > e shape recursionLevel: 3. > e ]. > > view := R3View new. > body := sphere value: 'body'. > head := sphere value: 'Merry Christmas and Happy new year!!! > > From all of us at ObjectProfile'"'head'". > head addInteraction: R3TooltipPopup. > > b1 := sphere value: '1'. > b2 := sphere value: '2'. > b3 := sphere value: '3'. > > eye1 := sphere value: 'o'. > nose := cone value: 'j'. > eye2 := sphere value: 'o'. > > cravat := sphere value: 'cravat'. > lhand := cylinder value: 'left hand'. > rhand := cylinder value: 'right hand'. > > body shape size: 1.5. > head translateTo: (R3Vector3 x: 0 y: 1 z: 0). > > { b1. b2. b3 } do: [ :b | b shape color: Color yellow; size: 0.15 ]. > b1 translateTo: (R3Vector3 x: 0 y: 0.5 z: 0.5). > b2 translateTo: (R3Vector3 x: 0 y: 0.25 z: 0.66). > b3 translateTo: (R3Vector3 x: 0 y: 0.0 z: 0.71). > > { eye1. eye2 } do: [ :e | e shape color: Color black; size: 0.15 ]. > eye1 translateTo: (R3Vector3 x: -0.2 y: 1.1 z: 0.44). > eye2 translateTo: (R3Vector3 x: 0.2 y: 1.1 z: 0.44). > > nose shape color: Color orange; size: 0.15; height: 0.5. > nose translateTo: (R3Vector3 x: 0 y: 0.9 z: 0.7); > orientation: (R3Matrix3 xrot: 90 degreesToRadians ). > > smile := R3BezierLineShape new > elementFrom: (R3Vector3 x: -0.2 y: 0.85 z: 0.45) > control: (R3Vector3 x: 0 y: 0.7 z:0.43 ) > to: (R3Vector3 x: 0.2 y: 0.85 z: 0.45). > smile shape color: Color black. > > cravat shape color: Color blue; height: 0.2. > cravat translateTo: (R3Vector3 x: 0 y: 0.6 z: 0). > > { lhand. rhand } do: [ :h | h shape color: Color brown; size: 0.1; height: > 1 ]. > lhand translateTo: (R3Vector3 x: -0.9 y: 0.7 z: 0); > orientation: (R3Matrix3 zrot:45 degreesToRadians). > rhand translateTo: (R3Vector3 x: 0.9 y: 0.7 z: 0); > orientation: (R3Matrix3 zrot: -45 degreesToRadians). > view lightingModel: R3MultipassPerPixelLighting new. > view addAll: > { body. head. > b1. b2. b3. > eye1. eye2. nose. smile. > cravat. lhand. rhand. > }. > view addInteraction: R3MKControl. > view setRoassal2DView: (ROView new). > view openWithOverlay. > .=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= > > Milton > > > 2013/12/25 Tudor Girba <tudor(a)tudorgirba.com> > >> Fun! >> >> Merry Christmas! >> >> Doru >> >> >> On Wed, Dec 25, 2013 at 12:29 PM, Alexandre Bergel < >> alexandre.bergel(a)me.com> wrote: >> >>> Oh!! Well spotted! >>> >>> Alexandre >>> >>> > Le 25-12-2013 Ã 11:25, Sven Van Caekenberghe <sven(a)stfx.eu> a Ã©crit : >>> > >>> > People keep on forgetting that you can write this load expression much >>> more elegantly: >>> > >>> > === >>> > Gofer new smalltalkhubUser: 'ronsaldo' project: 'roassal3d'; >>> configuration; loadDevelopment. >>> > === >>> >>> >> >> >> -- >> www.tudorgirba.com >> >> "Every thing has its own flow" >> > > -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

Dec. 26, 2013

Re: [Pharo-dev] Merry Christmas!

by milton mamani

Merry Christmas and happy new year to everyone!. [image: ImÃ¡genes integradas 1] This is another script: .=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= | view body head b1 b2 b3 eye1 eye2 nose smile cravat lhand rhand sphere cone cylinder | cylinder := [ :m | | e | e := R3CylinderShape element. e on: m. e ]. cone := [ :m | | e | e := R3ConeShape element. e on: m. e. ]. sphere := [ :m | |e | e := R3IcoSphereShape element. e on: m. e shape color: Color white. e shape recursionLevel: 3. e ]. view := R3View new. body := sphere value: 'body'. head := sphere value: 'Merry Christmas and Happy new year!!! >From all of us at ObjectProfile'"'head'". head addInteraction: R3TooltipPopup. b1 := sphere value: '1'. b2 := sphere value: '2'. b3 := sphere value: '3'. eye1 := sphere value: 'o'. nose := cone value: 'j'. eye2 := sphere value: 'o'. cravat := sphere value: 'cravat'. lhand := cylinder value: 'left hand'. rhand := cylinder value: 'right hand'. body shape size: 1.5. head translateTo: (R3Vector3 x: 0 y: 1 z: 0). { b1. b2. b3 } do: [ :b | b shape color: Color yellow; size: 0.15 ]. b1 translateTo: (R3Vector3 x: 0 y: 0.5 z: 0.5). b2 translateTo: (R3Vector3 x: 0 y: 0.25 z: 0.66). b3 translateTo: (R3Vector3 x: 0 y: 0.0 z: 0.71). { eye1. eye2 } do: [ :e | e shape color: Color black; size: 0.15 ]. eye1 translateTo: (R3Vector3 x: -0.2 y: 1.1 z: 0.44). eye2 translateTo: (R3Vector3 x: 0.2 y: 1.1 z: 0.44). nose shape color: Color orange; size: 0.15; height: 0.5. nose translateTo: (R3Vector3 x: 0 y: 0.9 z: 0.7); orientation: (R3Matrix3 xrot: 90 degreesToRadians ). smile := R3BezierLineShape new elementFrom: (R3Vector3 x: -0.2 y: 0.85 z: 0.45) control: (R3Vector3 x: 0 y: 0.7 z:0.43 ) to: (R3Vector3 x: 0.2 y: 0.85 z: 0.45). smile shape color: Color black. cravat shape color: Color blue; height: 0.2. cravat translateTo: (R3Vector3 x: 0 y: 0.6 z: 0). { lhand. rhand } do: [ :h | h shape color: Color brown; size: 0.1; height: 1 ]. lhand translateTo: (R3Vector3 x: -0.9 y: 0.7 z: 0); orientation: (R3Matrix3 zrot:45 degreesToRadians). rhand translateTo: (R3Vector3 x: 0.9 y: 0.7 z: 0); orientation: (R3Matrix3 zrot: -45 degreesToRadians). view lightingModel: R3MultipassPerPixelLighting new. view addAll: { body. head. b1. b2. b3. eye1. eye2. nose. smile. cravat. lhand. rhand. }. view addInteraction: R3MKControl. view setRoassal2DView: (ROView new). view openWithOverlay. .=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.=.= Milton 2013/12/25 Tudor Girba <tudor(a)tudorgirba.com> > Fun! > > Merry Christmas! > > Doru > > > On Wed, Dec 25, 2013 at 12:29 PM, Alexandre Bergel < > alexandre.bergel(a)me.com> wrote: > >> Oh!! Well spotted! >> >> Alexandre >> >> > Le 25-12-2013 Ã 11:25, Sven Van Caekenberghe <sven(a)stfx.eu> a Ã©crit : >> > >> > People keep on forgetting that you can write this load expression much >> more elegantly: >> > >> > === >> > Gofer new smalltalkhubUser: 'ronsaldo' project: 'roassal3d'; >> configuration; loadDevelopment. >> > === >> >> > > > -- > www.tudorgirba.com > > "Every thing has its own flow" >

Dec. 26, 2013

Re: [Pharo-dev] [OT]: Looking for Bill Schwab

by Sean P. DeNigris

Ben Coman wrote > It would seem there is unfortunate news. > http://www.legacy.com/obituaries/gainesville/obituary.aspx?pid=159883187 Thank you. It's a bit shocking that it happened a year ago. I figured he was off hacking and would come back to show us something cool :) I will miss his valuable contributions and unique perspectives... ----- Cheers, Sean -- View this message in context: http://forum.world.st/OT-Looking-for-Bill-Schwab-tp4732479p4732550.html Sent from the Pharo Smalltalk Developers mailing list archive at Nabble.com.

Dec. 26, 2013

[pharo-project/pharo-core] c6adb0: 30663

by GitHub

Branch: refs/heads/3.0 Home: https://github.com/pharo-project/pharo-core Commit: c6adb033b0a42acbfe45195541a3de56f5814a9b https://github.com/pharo-project/pharo-core/commit/c6adb033b0a42acbfe451955… Author: Jenkins Build Server <board(a)pharo-project.org> Date: 2013-12-26 (Thu, 26 Dec 2013) Changed paths: A FileSystem-Core.package/FileSystemPermission.class/instance/comparing/%3C=.st A FileSystem-Core.package/FileSystemPermission.class/instance/comparing/%3E.st A FileSystem-Core.package/FileSystemPermission.class/instance/comparing/%3E=.st A FileSystem-Core.package/FileSystemPermission.class/instance/private/posixPermission.st R Nautilus.package/PackageTreeNautilusUI.class/instance/menus behavior/fullBrowse.st A Nautilus.package/PackageTreeNautilusUI.class/instance/private dispatch/fullBrowseFromPackage_.st A Nautilus.package/PackageTreeNautilusUI.class/instance/private dispatch/fullBrowseFromTag_.st M NautilusCommon.package/NautilusHistoryEntry.class/instance/protocol/applyTo_.st A ScriptLoader30.package/ScriptLoader.class/instance/pharo - scripts/script316.st A ScriptLoader30.package/ScriptLoader.class/instance/pharo - updates/update30663.st M ScriptLoader30.package/ScriptLoader.class/instance/public/commentForCurrentUpdate.st A Spec-MorphicAdapters.package/MorphicWindowAdapter.class/instance/widget API/okToChange.st M Spec-Tools.package/MessageBrowser.class/instance/initialization/initialize.st Log Message: ----------- 30663 12510 NautilusHistory entry for class methods loads instance methods https://pharo.fogbugz.com/f/cases/12510 12502 FileList MNU FileSystemPermission>><= https://pharo.fogbugz.com/f/cases/12502 12429 MessageBrowser loses changes https://pharo.fogbugz.com/f/cases/12429 12451 Error on Browse Full in Nautilus from class in group view https://pharo.fogbugz.com/f/cases/12451 http://files.pharo.org/image/30/30663.zip

Dec. 26, 2013

[pharo-project/pharo-core]

by GitHub

Branch: refs/tags/30663 Home: https://github.com/pharo-project/pharo-core

Dec. 26, 2013

MessageBrowser doesn't play well with RGCommentDefinition as search results

by Nicolai Hess

Hi, I am about to file in a whole bunch of issues regarding MessageBrowser. All are related to search result of the kind RGCommentDefinition. These are collected by SystemNavigation or doing a search: "class comments with it" or "method source with it". Most of you may not recognize these bugs, as the typically "senders of it", "implementors of it" search results doesn't suffer from these. (and doing search "class comments with it" isn't used that often from all, I think) But for newcomers searching strings through "method source with it" is an handy task for exploring the image. And this search mixes search results of RGCommentDefinition and RGMethodDefinition. And it is annoying for newcomers to stumble of not working buttons/menus without realizing that there is actually a difference in the search results. These bugs are: In MessageBrowser, search results of kind RGCommentDefinition - have no working context menu - use syntax highlighting for a class comment text - can not be changed (raising an error on accept) - Browse button opens the Systembrowser but it does not show the comment text, but the class definition - Senders button opens a MessageBrowser for selectors containing the symbol #Comment - Implementors button searches for implementors of a "Comment" selector (no search results) - Version button raises an error - switch source formatter to "Byte Code" or "Time stamp" raises an error I would add all issues under one parent issue (MessageBrowser doesn't play well with RGCommentDefinition) I don't consider all issues as "must fix", some are real bugs (all that raising an error) and some are more like enhancements (useless syntax highlight for comment text) But I would like to fix them all and maybe even all at once. What do you think? All for Pharo3, none for Pharo3, split them by bugfixes for 3 and "nice to have" for 4? Nicolai

Dec. 26, 2013