Opened 15 years ago

Closed 15 years ago

Last modified 10 years ago

#363 closed (fixed)

A GUI for selecting search parameters for X!Tandem searches.

Reported by: Fredrik Levander Owned by: olle
Milestone: Proteios 2.3 Keywords:
Cc: Gregory Vincic

Description

Refs #362. Generate a GUI for editing search parameters for X! Tandem.

Change History (25)

comment:1 Changed 15 years ago by Gregory Vincic

Cc: Gregory Vincic added
priority: majorminor
severity: 164
Status: newassigned

comment:2 Changed 15 years ago by Gregory Vincic

Owner: changed from Gregory Vincic to olle
Status: assignednew

comment:3 Changed 15 years ago by olle

Status: newassigned

Ticket accepted.

comment:4 Changed 15 years ago by Gregory Vincic

Milestone: Proteios 2.2Proteios 2.3

comment:5 Changed 15 years ago by olle

Traceability note: Related to Ticket #362 (Run X! Tandem from Proteios).

Previous tickets on importing results from X!Tandem searches are Ticket #129 (Implement X!Tandem Search Results import) and #234 (Enable parsing of pluggable score types for X! Tandem import).

comment:6 Changed 15 years ago by olle

(In [2656]) Refs #362. Refs #363. Api/core updated with new core classes to support X!Tandem parameter storage in file items:

  1. New class/file core/XTandemParameterSetStorage.java with

data class/file core/data/XTandemParameterSetStorageData.java in api/core/ added for storing X!Tandem parameter data in a related parameter file item in X!Tandem input XML file format.

  1. Classes/files core/Item.java and core/Install.java in

api/core/ updated with the new XTandemParameterSetStorage item.

  1. New class/file io/XTandemParameterSet.java in api/core/

with instance variables and public accessor methods for fields corresponding to variables in an X!Tandem input XML file.

  1. New interface/file io/XTandemParameterFileUtilInterface.java

in api/core for obtaining an XTandemParameterSet.

  1. New class/file io/XTandemParameterFileUtil.java

in api/core/ with public methods for importing data from an X!Tandem input XML file to an XTandemParameterSet, and exporting an XTandemParameterSet to an X!Tandem input XML file.

  1. Class/file io/XMLCrudeWriterImpl.java in api/core/

updated with new convenience methods for writing XML tags used when writing an X!Tandem input XML file.

  1. New class/file props/XTandemParameterFileNameReader.java

in api/core/ added to read the name of the parameter file item related to an XTandemParameterSetStorage item.

comment:7 Changed 15 years ago by olle

(In [2657]) Refs #362. Refs #363. Added new source directory action/xTandemInput in client/servlet/ for action classes/files related to X!Tandem parameter set creation and editing, as well as performing X!Tandem searches from Proteios.

comment:8 Changed 15 years ago by olle

(In [2658]) Refs #362. Refs #363. Added two new XSL files for X!Tandem input XML files and output XML files, www/tandem-input-style.xsl and www/tandem-style.xsl in client/servlet/, respectively.

comment:9 Changed 15 years ago by olle

(In [2659]) Refs #362. Refs #363. Class/file core/XTandemParameterSetStorage.java in api/core/ updated with new public method XTandemParameterSet fetchXTandemParameterSet() for fetching X!Tandem parameter data from a related parameter file item in X!Tandem input XML file format. Together with public method void save(XTandemParameterSet xTandemParameterSet) this method makes it possible to store and retrieve an X!Tandem parameter set using the XTandemParameterSetStorage core class, without referencing the related parameter file item directly.

comment:10 Changed 15 years ago by olle

(In [2660]) Refs #362. Refs #363. Configuration and template files for X!Tandem search added:

  1. X!Tandem search properties template file

conf/xtandem.properties.in in client/servlet/ added. Intended to be copied to an X!Tandem search properties file conf/xtandem.properties, which is updated with correct settings.

  1. New class/file XTandemPropertiesFile.java in client/servlet/

added. It loads xtandem.properties file and gives access to the settings in the latter.

  1. X!Tandem search default parameter set file

conf/xtandem_default_input.xml added. It is based on file bin/default_input.xml from unpacked archive file downloaded from url ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-08-02-01-1.tar.gz.

  1. Outermost ant build file build.xml updated to copy

configuration/settings files conf/xtandem.properties and conf/xtandem_default_input.xml in client/servlet/ to distribution directory www/WEB-INF/classes/.

comment:11 Changed 15 years ago by olle

(In [2661]) Refs #362. Refs #363. Refs #287. First revision of X!Tandem search in Proteios via web interface to GPM web site.

  1. Class/file gui/table/TableFactory.java in client/servlet/

updated in public method void useColumnsFromClass() by obtaining parameter file for XTandemParameterSetStorage item.

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new methods related to forms for X!Tandem search:

  1. Private method Select<VString> newStringSelectBox(VString validParam, List<String> optionList, String selected).
  2. Private method Select<VString> newStringSelectBox2(VString validParam, List<Option> optionList, String selected).
  3. Public method Form getNewXTandemParameterSetStorageForm(XTandemParameterSetStorage xTandemParameterSetStorage).
  4. Public method Form getXTandemParameterSetForm(XTandemParameterSet xTandemParameterSet).
  1. Class/file action/read/ViewLeft.java in client/servlet/ updated

by adding node for viewing XTandemParameterSetStorage items.

  1. New core extension class/file

action/file/UseSpectrumFileForXTandemSearchExtension.java in client/servlet/ added, for creating X!Tandem search jobs for selected spectrum files.

  1. New action classes/files added to action/xTandemInput/ in

client/servlet/ for creating, viewing, and editing X!Tandem parameter sets and starting X!Tandem search jobs from them:

  1. AddXTandemParameterSetStorage.java.
  2. ListXTandemParameterSetStorage.java.
  3. NewXTandemParameterSetStorage.java.
  4. SaveXTandemParameterSetStorage.java.
  5. SearchXTandem.java.
  6. SelectXTandemParameterFileStep1a.java.
  7. SelectXTandemParameterFileStep1b.java.
  8. ViewActiveXTandemParameterFile.java.
  9. ViewActiveXTandemParameterSetStorage.java.
  10. ViewXTandemParameterFile.java.
  11. ViewXTandemParameterSetStorage.java.
  1. New plugin class/file plugins/SearchXTandemPlugin.java in plugin/

for executing an X!Tandem search via web interface and trying to upload the output XML file into Proteios.

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

comment:12 Changed 15 years ago by olle

(In [2662]) Refs #362. Refs #363. X!Tandem search default parameter set file conf/xtandem_default_input.xml in client/servlet/ updated by removal of white space characters at end of lines, in order to simplify comparison of the default file with exported X!Tandem parameter files.

comment:13 Changed 15 years ago by olle

(In [2663]) Refs #362. Refs #363. Class/file io/XTandemParameterFileUtil.java in api/core/ updated in public method void exportXTandemParameterSet(XTandemParameterSet xTandemParameterSet) by adding one extra level of indentation to lines inside an XML "note" tag with type equal to "description", as well as to the XML "note" end tag if it directly follows the XML "note" start tag with type equal to "description". These changes are intended to increase similarity to the format used in the X!Tandem default input XML file obtained from unpacked archive file downloaded from url ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-08-02-01-1.tar.gz.

comment:14 Changed 15 years ago by olle

(In [2664]) Refs #362. Refs #363. X!Tandem search default parameter set file conf/xtandem_default_input.xml in client/servlet/ updated by adding extra indentation of first line of comment XML "note" tag explaining parameters in previous XML "note" tag, since this convention is used elsewhere in the file.

comment:15 Changed 15 years ago by olle

(In [2665]) Refs #362. Refs #363. X!Tandem search default parameter set file conf/xtandem_default_input.xml in client/servlet/ updated by moving XML "note" tag of type "input" with label "protein, cleavage N-terminal mass change" before corresponding tag for the C-terminal, since at other places in the file a tag related to the N-terminal comes before the tag related to the C-terminal. This change is intended to simplify manual inspection of the file, but if strong reasons are found to keep the original tag order, the change may be reverted. Currently public method void exportXTandemParameterSet(XTandemParameterSet xTandemParameterSet) in class/file io/XTandemParameterFileUtil.java in api/core/ follows the convention of writing N-terminal tags before C-terminal.

comment:16 Changed 15 years ago by olle

(In [2666]) Refs #362. Refs #363. X!Tandem search default parameter set file conf/xtandem_default_input.xml in client/servlet/ updated by removing duplicate XML "note" tags of type "input" with labels "refine, point mutations", "scoring, cyclic permutation", "scoring, include reverse", and "output, one sequence copy".

comment:17 Changed 15 years ago by olle

(In [2667]) Refs #362. Refs #363. Class/file io/XTandemParameterFileUtil.java in api/core/ updated in public method void exportXTandemParameterSet(XTandemParameterSet xTandemParameterSet) by moving XML "note" tag of type "input" with label "output, path" to location after XML "note" tag of type "input" with label "output, sequence path". This change is intended to increase similarity to the format used in the X!Tandem default input XML file obtained from unpacked archive file downloaded from url ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-08-02-01-1.tar.gz.

comment:18 Changed 15 years ago by olle

(In [2677]) Refs #362. Refs #363. Refs #287. X!Tandem search updated for use of locally installed search engine (currently for test purposes only).

  1. Class/file se/lu/thep/waf/Event.java in api/waf/ updated by

addition of new public method String fetchTempDirPath() for obtaining the path to directory for temporary files from configuration parameter value.

  1. Class/file/

action/xTandemInput/ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated in public method void runMe() by setting value of valid parameter SearchXTandem.VSAVEXTANDEMPARAMETERSETFLAG to "true" for commented-out action link to perform X!Tandem search using locally installed search engine, and some other minor changes.

  1. Class/file action/xTandemInput/SearchXTandem.java in

client/servlet/ updated in protected method void runMe():

  1. Path to directory for temporary files obtained by calling

getEvent().fetchTempDirPath().

  1. Use of search engine via web interface is set as default.
  2. Bug fixed when creating output path when more than one spectrum

file are used (previously only the first search result was stored in a result file correctly named using the output path base name).

  1. Spectrum path is now created using the directory for temporary

files.

  1. Class/file plugins/SearchXTandemPlugin.java in plugin/ updated in

private method void xTandemSearchLocal(...) by saving a copy of the spectrum file item in the directory for temporary files. Description of imported result file updated to correspond to description of imported result file when performing X!Tandem search via web interface. Obsolete private method void saveTemporaryFile(java.io.File inFile, java.io.File tmpFile) removed, as it is replaced by polymorphic private method void saveTemporaryFile(File inFile, java.io.File tmpFile).

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

comment:19 Changed 15 years ago by olle

The Proteios SE Manual wiki page updated with link to new X!Tandem Search Engine Interface wiki page.

comment:20 Changed 15 years ago by olle

Resolution: fixed
Status: assignedclosed

Ticket closed as the requested functionality has been added. This initial version may be used to test if the functionality is adequate for normal use. If it is to be updated, this ticket may be reopened, or a new ticket created.

comment:21 Changed 14 years ago by olle

(In [2835]) Refs #458. Refs #362. Refs #363. Support added for inspecting and editing new X!Tandem search parameters related to scoring algorithm:

  1. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java

in client/servlet/ updated:

  1. New valid parameters added corresponding to X!Tandem settings

"spectrum, use conditioning" and "scoring, algorithm".

  1. Public method XTandemParameterSet fetchCurrentXTandemParameterSet()

updated by retrieving the values corresponding to X!Tandem settings "spectrum, use conditioning" and "scoring, algorithm" from valid parameters.

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated

in public method Form getXTandemParameterSetForm(...) by adding select box for inspecting and setting the value corresponding to "scoring, algorithm". Default value is an empty string, which is displayed as option "native" in the select box.

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

comment:22 Changed 14 years ago by olle

(In [2906]) Refs #481. Refs #362. Refs #363. Refs #287. First revision of support for "Save As..." functionality when editing an X!Tandem Parameter Set:

  1. Class/file action/xTandemInput/SearchXTandem.java in

client/servlet/ updated with new valid parameter VBoolean VSAVEASXTANDEMPARAMETERSETFLAG.

  1. Class/file

action/xTandemInput/ViewActiveXTandemParameterSetStorage.java in client/servlet/ updated in public method void runMe() to add "Save As..." button coupled to action link to SaveXTandemParameterSetStorage.class, and setting value of added parameter VBoolean VSAVEASXTANDEMPARAMETERSETFLAG to true.

  1. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java

in client/servlet/ updated in protected method void runMe() with support for "Save As..." functionality. It calls new public FormFactory? method Form getSaveAsXTandemParameterSetStorageForm( XTandemParameterSetStorage xTandemParameterSetStorage, XTandemParameterSet xTandemParameterSet) to obtain a form for setting properties for a new X!Tandem parameter set tot store the data in.

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated

with new public method Form getSaveAsXTandemParameterSetStorageForm( XTandemParameterSetStorage xTandemParameterSetStorage, XTandemParameterSet xTandemParameterSet) for getting a form for setting properties for a new X!Tandem parameter set tot store the data in. Also new convenience methods public Fieldset addXTandemParameterSetToFieldset( XTandemParameterSet xTandemParameterSet, Fieldset fs, boolean fieldsHidden, boolean fieldsDisabled) etc. for storing values of X!Tandem parameters in hidden fields coupled to valid parameters.

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new entries for various string keys.

comment:23 Changed 14 years ago by Fredrik Levander

(In [3053]) Refs #363. Allowing longer string for modifications, to allow multiple modifications to be entered

comment:24 Changed 13 years ago by olle

(In [3303]) Refs #564. Refs #363. Listing of X!Tandem parameter set storage items updated to display the item selection check box column, making it possible to share a search parameter set to the active project:

  1. Class/file action/xTandemInput/ListXTandemParameterSetStorage.java

in client/servlet/ updated in public method void runMe() to display the item selection check box column.

  1. Class/file action/execute/ShareToProject.java in client/servlet/

updated in protected method void runMe() when sharing an X!Tandem parameter set storage item to to also share the related parameter file item with the same access rights.

comment:25 Changed 10 years ago by olle

(In [4366]) Refs #787. Refs #362. Refs #363. When a new X!Tandem search parameter set is created, the corresponding parameter file is set to file type FileType.XTANDEM_PARAMETERS:

  1. Class/file action/xTandemInput/AddXTandemParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save".
  1. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save As...".
Note: See TracTickets for help on using tickets.