[biojava] Log of /biojava-live/trunk/biojava3-aa-prop

Revision 9941 - Directory Listing
Modified Fri Nov 30 18:52:08 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9939 - Directory Listing
Modified Fri Nov 30 18:52:01 2012 UTC (5 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.5

Revision 9697 - Directory Listing
Modified Wed Jun 6 05:03:12 2012 UTC (11 months, 2 weeks ago) by andreas

aa-prop module now also gets assembly config

Revision 9696 - Directory Listing
Modified Wed Jun 6 05:02:26 2012 UTC (11 months, 2 weeks ago) by andreas

adding fileSet config

Revision 9645 - Directory Listing
Modified Tue May 22 03:42:41 2012 UTC (12 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9643 - Directory Listing
Modified Tue May 22 03:42:34 2012 UTC (12 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.4

Revision 9638 - Directory Listing
Modified Tue May 15 01:45:30 2012 UTC (12 months, 1 week ago) by kohchuanhock

Revision 9637 - Directory Listing
Modified Tue May 15 01:43:03 2012 UTC (12 months, 1 week ago) by kohchuanhock

Removed line 460-462 of PeptidePropertiesImpl.java which caused getNetCharge of Innovagen to return 0.0 if the net charge excluding the n-terminal and c-terminal are 0.0 regardless of the charge of n-terminal and c-terminal

Revision 9635 - Directory Listing
Modified Sat May 12 00:04:29 2012 UTC (12 months, 1 week ago) by kohchuanhock

Extended getNetCharge to include the ability to find net charge at user given pH point (suggested by Steve Darnell)

Revision 9617 - Directory Listing
Modified Sat Apr 7 14:23:19 2012 UTC (13 months, 2 weeks ago) by kohchuanhock

Fixed the bug of calling getIsoelectricPoint instead of getNetCharge when it should be calling getNetCharge. A careless mistake.

Revision 9590 - Directory Listing
Modified Fri Mar 16 22:28:32 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9588 - Directory Listing
Modified Fri Mar 16 22:28:24 2012 UTC (14 months ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.3

Revision 9503 - Directory Listing
Modified Mon Jan 16 11:38:35 2012 UTC (16 months ago) by rthornton

Simplified boolean expressions.

Revision 9463 - Directory Listing
Modified Wed Nov 23 01:37:32 2011 UTC (17 months, 4 weeks ago) by kohchuanhock

Update test to reflect the new pka values

Revision 9462 - Directory Listing
Modified Wed Nov 23 01:36:10 2011 UTC (17 months, 4 weeks ago) by kohchuanhock

Update to use unique pka values for each of the 20 Amino Acid residues for N-Terminal and C-Terminal

Revision 9452 - Directory Listing
Modified Tue Nov 22 13:04:22 2011 UTC (17 months, 4 weeks ago) by kohchuanhock

Added the testing of NetCharge and Isoelectric Point based on pka values used by ExPASy.

Revision 9451 - Directory Listing
Modified Tue Nov 22 13:04:03 2011 UTC (17 months, 4 weeks ago) by kohchuanhock

Added the computation of NetCharge and Isoelectric Point based on pka values used by ExPASy.

Revision 9449 - Directory Listing
Modified Sun Nov 20 00:32:11 2011 UTC (18 months ago) by kohchuanhock

Comments added for org.biojava3.aaproperties.Constraints.java

Revision 9169 - Directory Listing
Modified Fri Sep 2 15:17:53 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare for next development iteration

Revision 9167 - Directory Listing
Modified Fri Sep 2 15:17:45 2011 UTC (20 months, 2 weeks ago) by andreas

[maven-release-plugin] prepare release biojava-3.0.2

Revision 9133 - Directory Listing
Modified Wed Aug 31 04:29:18 2011 UTC (20 months, 3 weeks ago) by andreas

adding svn:ignore for .profile .project .classpath target .settings files

Revision 9131 - Directory Listing
Modified Wed Aug 31 04:23:49 2011 UTC (20 months, 3 weeks ago) by andreas

minor pom cleanup

Revision 9127 - Directory Listing
Modified Wed Aug 31 04:05:39 2011 UTC (20 months, 3 weeks ago) by andreas

removing files that should not be in svn

Revision 9126 - Directory Listing
Modified Wed Aug 31 04:04:31 2011 UTC (20 months, 3 weeks ago) by andreas

cleaning pom files, removing warnings.

Revision 9073 - Directory Listing
Modified Mon Aug 22 02:55:03 2011 UTC (21 months ago) by kohchuanhock

Shifted Profeat related classes to new packages called aaproperties.profeat and aaproperties.profeat.convertor
Added package-info.java for all packages
Create a test class to test PROFEAT properties
Added documentation in Cookbook on how to use PROFEAT properties API
Update the BioJava community on what is achieved for this Google Summer of Code project

Revision 9064 - Directory Listing
Modified Mon Aug 15 14:42:54 2011 UTC (21 months, 1 week ago) by kohchuanhock

Added dummy id to be allowed in the xml file of AminoAcidComposition. It will be used in future to compute the mass of amino acid instead of based on elements.

Revision 9060 - Directory Listing
Modified Fri Aug 12 22:28:29 2011 UTC (21 months, 1 week ago) by andreas

empty commit to trigger auto-build

Revision 9059 - Directory Listing
Modified Fri Aug 12 22:05:00 2011 UTC (21 months, 1 week ago) by andreas

executable jar is now built during mvn package

Revision 9058 - Directory Listing
Modified Fri Aug 12 22:02:51 2011 UTC (21 months, 1 week ago) by andreas

no need to have a Jar file at this location...

Revision 9057 - Directory Listing
Modified Thu Aug 11 06:59:29 2011 UTC (21 months, 1 week ago) by kohchuanhock

Added SequenceName in the output of AAProperties.jar (in the first column)
Adjusted pom.xml to include AAProperties as part of name but still has jar-with-dependencies in the name

Revision 9056 - Directory Listing
Modified Thu Aug 11 03:39:40 2011 UTC (21 months, 1 week ago) by kohchuanhock

Adjust the configuration of pom.xml to generate a jar file with org.biojava3.aaproperties.CommandPrompt as the main class. However, need to rename it to AAProperties.jar

Revision 9048 - Directory Listing
Modified Tue Aug 2 03:56:43 2011 UTC (21 months, 2 weeks ago) by kohchuanhock

Only consider cases difference for Molecular Weight. Revert all cases consideration for other properties

Revision 9039 - Directory Listing
Modified Wed Jul 27 08:13:06 2011 UTC (21 months, 3 weeks ago) by kohchuanhock

Updated the cookbook on using extended XML file and ModifiedAACompoundSet
Split up the CommandPrompt run to be more "unit" style
Had always assumed that cases are ignored, hence had to change many method to consider case difference
Introduced another class CaseFreeAminoAcidCompoundSet to ignore cases  
By default, set ignore case. If they provide the XML file, then cases will be differentiated
Update the cookbook on Command Prompt

Revision 9037 - Directory Listing
Modified Thu Jul 21 06:00:42 2011 UTC (22 months ago) by kohchuanhock

Improved Help - Tries to mimic "man" in unix.

Revision 9036 - Directory Listing
Modified Thu Jul 21 02:58:33 2011 UTC (22 months ago) by kohchuanhock

Created a new class ModifiedAminoAcidCompoundSet which enables any symbols to be specified in XML file to represent amino acids and modified amino acids.
Added three examples on how to run the tool.
Change output file to optional and default to standard output.
Set default decimal place to 4. Possible to change with -d argument.
Change to use BioJava FASTA reader.
Created CommandPromptTester.java to do testing of CommandPrompt.java

Revision 9035 - Directory Listing
Modified Sun Jul 17 07:33:39 2011 UTC (22 months ago) by kohchuanhock

Created a new class ModifiedAminoAcidCompoundSet which enables any symbols to be specified in XML file to represent amino acids and modified amino acids.

Revision 9034 - Directory Listing
Modified Wed Jul 13 09:40:03 2011 UTC (22 months, 1 week ago) by kohchuanhock

Done up a first draft for command prompt

Revision 9033 - Directory Listing
Modified Fri Jul 8 06:07:54 2011 UTC (22 months, 2 weeks ago) by kohchuanhock

Radio Labeled - Create XML files to show this - Do test cases for them as well
Check the attribute values to ensure that symbols are single character and do not repeat themselves.
Also check to ensure that element/isotope names define are also found in ElementMass XMl file.
Mass and counts are also checked to make sure that they are > 0.

Revision 9031 - Directory Listing
Modified Wed Jul 6 16:15:20 2011 UTC (22 months, 2 weeks ago) by kohchuanhock

Clean up the codes on Computing Molecular Weights
Change the Minimum XML files to more compact
Change the naming of several XML attributes to more intuitive and generic terms

Revision 9030 - Directory Listing
Modified Wed Jul 6 14:33:08 2011 UTC (22 months, 2 weeks ago) by kohchuanhock

Adjust the XML requirements and made attributes as optional if possible
Checked that all Elements and Isotopes used in AminoAcidComposition.xml can be found in ElementMass.xml

Revision 9029 - Directory Listing
Modified Mon Jul 4 09:35:58 2011 UTC (22 months, 2 weeks ago) by kohchuanhock

Work around and made the XML files annotated to requirements.
Use Hydrogen-1 isotope weight

Revision 9028 - Directory Listing
Modified Sun Jul 3 05:48:35 2011 UTC (22 months, 2 weeks ago) by kohchuanhock

Added annotations for AminoAcidComposition.java and Element.java.
Simplified MolecularWeight.xml and ElementMass.xml.

Revision 9027 - Directory Listing
Modified Wed Jun 29 23:46:43 2011 UTC (22 months, 3 weeks ago) by kohchuanhock

Add one more method to enable the creation of aminoacidtable without explicit specification of elementmass.xml
improved the cookbook tester to use the newly added method and combined shortexample 4 with 5

Revision 9025 - Directory Listing
Modified Wed Jun 29 14:29:34 2011 UTC (22 months, 3 weeks ago) by ptroshin

TODO for Ah Fu

Revision 9024 - Directory Listing
Modified Wed Jun 29 14:24:46 2011 UTC (22 months, 3 weeks ago) by ptroshin

Simplified Schema for Compounds

Revision 9023 - Directory Listing
Modified Wed Jun 29 10:06:07 2011 UTC (22 months, 3 weeks ago) by kohchuanhock

Added a new class in test to ensure short examples given in Wiki CookBook are error free.

Revision 9022 - Directory Listing
Modified Wed Jun 29 06:45:46 2011 UTC (22 months, 3 weeks ago) by kohchuanhock

Removed doc folder and its contents

Revision 9021 - Directory Listing
Modified Wed Jun 29 06:44:58 2011 UTC (22 months, 3 weeks ago) by kohchuanhock

Created ValidationEventHandler which allows the xml file to be validated
Validates xml files before they are unmarshal
Added an additional method to auto find a elementMass file in default location
Generated the schema for aminoacidcomposition.xsd
Change the XML file structure such that the element weight is directly recorded instead of computed
Remove all the test cases for the computation of the abundance.
Successfully generated an XML schema for ElementMass.xsd and AminoAcidComposition.xsd
Remove abundance from ElementMass.xml

Revision 9006 - Directory Listing
Modified Tue Jun 21 01:11:29 2011 UTC (23 months ago) by kohchuanhock

Removed Utils.roundToDecimals from PeptidePropertiesImpl.java
Embedded all data from the element information website
Create Test Cases to ensure data are properly embedded
Create new methods to enable the usage of user specified xml file to compute molecular mass
Wrote test cases for these newly created methods

Revision 8997 - Directory Listing
Modified Thu Jun 16 08:11:15 2011 UTC (23 months ago) by kohchuanhock

Implemented the APIs for generation of PROFEAT properties. Also implemented adaptor methods for ease of using the APIs.

Revision 8996 - Directory Listing
Modified Thu Jun 16 07:14:27 2011 UTC (23 months ago) by kohchuanhock

Removed invalid UTF-8 characters

Revision 8995 - Directory Listing
Modified Thu Jun 16 06:57:30 2011 UTC (23 months ago) by andreas

trying to set UTF encoding here, hoping to resolve the cruisecontrol issue

Revision 8994 - Directory Listing
Modified Thu Jun 16 06:39:32 2011 UTC (23 months ago) by kohchuanhock

attempt to remove the characters that could cause the failure in build

Revision 8992 - Directory Listing
Modified Tue Jun 14 05:15:31 2011 UTC (23 months, 1 week ago) by kohchuanhock

Populate two elements based on Peter's Element class. 
Create a ElementTester to test the generated xml and its computed standard atomic weight.
Also created several classes to prepare for the generation of additional physiochemical-related properties.

Revision 8991 - Directory Listing
Modified Mon Jun 13 11:24:57 2011 UTC (23 months, 1 week ago) by ptroshin

One way to model the elements

Revision 8990 - Directory Listing
Modified Sun Jun 12 15:14:32 2011 UTC (23 months, 1 week ago) by kohchuanhock

Create a new package org.biojava3.aaproperties.xml and two new classes IsotopeType and IsotopeTable as an initial effort to learn and utilize JAXB.

Revision 8988 - Directory Listing
Modified Fri Jun 10 01:41:03 2011 UTC (23 months, 1 week ago) by kohchuanhock

Remove all catch NullPointerException in test cases and used expected = NullPointerException.class.
Change all adaptor methods to by default return precise values and only fix their precision for test cases.

Revision 8987 - Directory Listing
Modified Fri Jun 10 01:11:29 2011 UTC (23 months, 1 week ago) by kohchuanhock

Remove the molecularweight.jaxb package as it was done in the wrong way.

Revision 8986 - Directory Listing
Modified Thu Jun 9 14:56:24 2011 UTC (23 months, 1 week ago) by ptroshin

Advice & TODO for Ah Fu

Revision 8985 - Directory Listing
Modified Thu Jun 9 03:05:16 2011 UTC (23 months, 1 week ago) by kohchuanhock

Attempt to use JAXB

Revision 8980 - Directory Listing
Modified Sat Jun 4 12:26:19 2011 UTC (23 months, 2 weeks ago) by kohchuanhock

Added test cases where users gave "bad" input to the properties generating methods. All test cases are successful now.

Revision 8979 - Directory Listing
Modified Sat Jun 4 01:08:11 2011 UTC (23 months, 2 weeks ago) by kohchuanhock

Removed Javadocs from repos

Revision 8978 - Directory Listing
Modified Thu Jun 2 14:53:22 2011 UTC (23 months, 2 weeks ago) by ptroshin

Advice & TODO for Ah Fu

Revision 8977 - Directory Listing
Modified Thu Jun 2 13:57:00 2011 UTC (23 months, 2 weeks ago) by kohchuanhock

Implemented JUnit test cases for all properties. Added an additional property, absorbance. Added several more adaptor methods.

Revision 8974 - Directory Listing
Modified Thu May 26 10:49:47 2011 UTC (23 months, 3 weeks ago) by ptroshin

A few obvious improvements for Constraints class. (Ah Fu see TODO & FIXME)

Revision 8973 - Directory Listing
Modified Thu May 26 10:29:03 2011 UTC (23 months, 3 weeks ago) by ptroshin

Resolving conflict

Revision 8972 - Directory Listing
Modified Thu May 26 10:17:26 2011 UTC (23 months, 3 weeks ago) by ptroshin

More TODOs for Ah Fu

Revision 8971 - Directory Listing
Modified Wed May 25 12:01:42 2011 UTC (23 months, 4 weeks ago) by ptroshin

Add an example test case. Ah Fu to complete

Revision 8970 - Directory Listing
Modified Wed May 25 01:40:27 2011 UTC (23 months, 4 weeks ago) by kohchuanhock

Revision 8966 - Directory Listing
Modified Wed May 25 00:18:51 2011 UTC (23 months, 4 weeks ago) by kohchuanhock

Revision 8962 - Directory Listing
Modified Tue May 24 14:21:35 2011 UTC (23 months, 4 weeks ago) by kohchuanhock

Revision 8960 - Directory Listing
Modified Thu May 19 12:24:13 2011 UTC (2 years ago) by kohchuanhock

Revision 8935 - Directory Listing
Modified Mon May 16 13:37:47 2011 UTC (2 years ago) by ptroshin

More TODO for Ah Fu

Revision 8934 - Directory Listing
Modified Mon May 16 13:03:40 2011 UTC (2 years ago) by kohchuanhock

Revision 8933 - Directory Listing
Modified Thu May 12 15:31:44 2011 UTC (2 years ago) by kohchuanhock

Revision 8932 - Directory Listing
Modified Thu May 12 15:19:48 2011 UTC (2 years ago) by kohchuanhock

Revision 8931 - Directory Listing
Modified Thu May 12 05:57:57 2011 UTC (2 years ago) by kohchuanhock

Revision 8929 - Directory Listing
Modified Tue May 10 11:32:03 2011 UTC (2 years ago) by ptroshin

A one more TODO comments for Ah Fu

Revision 8928 - Directory Listing
Modified Tue May 10 11:19:30 2011 UTC (2 years ago) by ptroshin

A couple of more TODO comments for Ah Fu

Revision 8927 - Directory Listing
Modified Tue May 10 10:58:57 2011 UTC (2 years ago) by ptroshin

Comments on Ah Fu interface for simple AA physico-chemical properties calculations

Revision 8921 - Directory Listing
Modified Mon May 9 22:46:11 2011 UTC (2 years ago) by andreas

adding missing dependency

Revision 8917 - Directory Listing
Modified Mon May 9 12:19:44 2011 UTC (2 years ago) by kohchuanhock

Created an interface class to generate basic physico-chemical properties for protein sequences

Revision 8909 - Directory Listing
Modified Thu May 5 05:11:50 2011 UTC (2 years ago) by kohchuanhock

Revision 8908 - Directory Listing
Modified Thu May 5 05:05:43 2011 UTC (2 years ago) by kohchuanhock
Copied from: biojava-live/trunk/biojava3-protProperties revision 8907

Revision 8907 - Directory Listing
Modified Thu May 5 05:04:57 2011 UTC (2 years ago) by kohchuanhock
Original Path: biojava-live/trunk/biojava3-protProperties

Revision 8902 - Directory Listing
Modified Tue May 3 11:57:57 2011 UTC (2 years ago) by kohchuanhock
Original Path: biojava-live/trunk/biojava3-protProperties

Revision 8901 - Directory Listing
Added Sun May 1 05:58:34 2011 UTC (2 years ago) by kohchuanhock
Original Path: biojava-live/trunk/biojava3-protProperties