O2Plib library for Open2Dprot

Welcome To O2Plib

http://open2dprot.sourceforge.net/O2Plib and
http://www.lecb.ncifcrf.gov/Open2Dprot/O2Plib/


Note: This pre-alpha level software is under construction and will change. 
Not all functionality described is fully implemented or fully debugged.    
This documentation will undergo revision as the program develops.

Introduction

O2Plib is a Java common library for use with Open2Dprot project available from the open2dprot.sourceforge.net server. The common library makes it easier to interface the various applications in the Open2Dprot analysis pipeline since it enforces the consistency of conventions including the XML data exchange formats.

The library is automatically downloaded ( O2Plib.jar) with the Open2Dprot application programs when you download any of them to your computer. All of the programs will also download the new version of O2Plib.jar if you update the application program from the server (see particular application for details).

Design of the O2Plib library

The library is divided into subdirectories by function. It currently contains the following directories:

db database objects and their readers and writers
- DbAccession.java - read, write and access accession sample database
- DbBaseSpot.java - base spot feature object
- DbBoundary.java - spot boundary manipulation
- DbLM.java - read, write and access paired sample landmark spots database
- DbPairSamples.java - read, write and access paired sample instance
- DbPspot.java - duplet spot-pair feature object extends DbBaseSpot
- DbSample.java - read, write and access sample spot list instance
- DbSpot.java - spot feature object extends DbBaseSpot
- LMset.java - landmark set object for a (Rsample,Sample) pair
- CSD - Composite Samples Database objects
  - CSD.java - CSD top-level database instance object
  - CSDglb.java - instance variables
  - CSDacc.java - accession object
  - CSDannotation.java - CSD annotation
  - CSDcache.java - CSD cache manageer
  - CSDcal.java - calibration object
  - CSDcond.java - named condition object list of samples
  - CSDexpr.java - expression across samples object
  - CSDexprList.java - named list of expression objects
  - CSDfilterState.java - data filter object
  - CSDio.java - CSD I/O object
  - CSDlimits.java - limits object
  - CSDlistInterface.java - Java interface for some list classes
  - CSDlms.java - landmark sets object
  - CSDnorm.java - normalization object
  - CSDRmap.java - Rspot map object
  - CSDRspot.java - Rspot set object
  - CSDRspotList.java - named list of Rspots obvject
  - CSDsizes.java - manage sizes
  - CSDtotals.java - manage CSD totals
- xml - XML loader
  - PipeLineDefault - load pipeline module
  - XmlLoader - XML loader using .xsd schemas
gui popup gui objects
- MenuSupport.java - pull-down menu MenuItem and CheckboxMenuItem support
- PopupDialogQuery.java - popup dialog window
- PopupFileDialog.java - popup file-dialog window
- PopupHTMLbrowser.java - popup Web browser window
- PopupNameListSelectorDialog.java - popup name-list checkbox edit window
- PopupOptions.java - popup command-line switch list edit options window
- PopupTableEditDialog.java - popup Table object editing window
- PopupTextFieldDialog.java - popup text field dialog window
- PopupYesNoDialogBox.java - popup yes/no/cancel confirmation window
image image objects and their readers and writers
- DrawOverlays.java - draw overlays for us with ScrollableImage
- DrawPix.java - draw text into pixel array image
- PixReader.java - read picture image file into picture object
- PixWriter.java - write picture image file from picture object
- PpxLoader.java - read PPX (old GELLAB-II) format image file
- Roi.java - Region Of Interest (ROI) object
- RoiList.java - list of ROIs
- ScrollableImage.java - to support zoom images
- TiffPixelLoader.java - read TIFF format image file
- WinDump.java - make printable window string of pixel array image
- WriteGifEncoder.java - write GIF image from pixel array image
io file, URL readers and writers
- FileIO.java - file reader and writer
misc utility functions
- CalibrateOD.java - calibrate grayscale to OD or other units
- ParamHash.java - get parameters from a hash table
- Sort.java - sort package
- Switches.java - support for command-line switch parsing
- Util.java - miscellaneous utility functions
table spread-sheet type (row X column) table objects
- SimpleTable.java - base class for table objects
- Table.java - table objects

Javadoc API documentation for the O2Plib library

See the javadoc documentation for more details on the library API.

Source code for the O2Plib library

The source code is available on either the Open2Dprot CVS server; view individual files in the CVS browser server; or complete checkpointed version on the Files mirror.

Please contact us with suggestions and comments. If you make interesting changes in the source code, please send us a copy and describe your changes so we can merge them in the released version.