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Commits on Jun 6, 2012

• aa-prop module now also gets assembly config

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Commits on May 15, 2012

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• 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…

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Commits on May 12, 2012

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

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Commits on Apr 7, 2012

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

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Commits on Jan 16, 2012

• Simplified boolean expressions.

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Commits on Nov 23, 2011

• Update test to reflect the new pka values

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

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Commits on Nov 22, 2011

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

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  kohchuanhock

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

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  kohchuanhock

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Commits on Nov 20, 2011

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

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  kohchuanhock

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Commits on Aug 22, 2011

• Shifted Profeat related classes to new packages called aaproperties.profeat and aaproperties.profeat.convertor

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  kohchuanhock

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Commits on Aug 15, 2011

• 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.

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  kohchuanhock

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Commits on Aug 12, 2011

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

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Commits on Aug 11, 2011

• Added SequenceName in the output of AAProperties.jar (in the first column)

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  kohchuanhock

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• 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

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Commits on Aug 2, 2011

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

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  kohchuanhock

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Commits on Jul 27, 2011

• Updated the cookbook on using extended XML file and ModifiedAACompoundSet

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  kohchuanhock

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Commits on Jul 21, 2011

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

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  kohchuanhock

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

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  kohchuanhock

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Commits on Jul 17, 2011

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

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  kohchuanhock

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Commits on Jul 13, 2011

• Done up a first draft for command prompt

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Commits on Jul 8, 2011

• Radio Labeled - Create XML files to show this - Do test cases for them as well

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  kohchuanhock

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Commits on Jul 6, 2011

• Clean up the codes on Computing Molecular Weights

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  kohchuanhock

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• Adjust the XML requirements and made attributes as optional if possible

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  kohchuanhock

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Commits on Jul 4, 2011

• Work around and made the XML files annotated to requirements.

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  kohchuanhock

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Commits on Jul 3, 2011

• Added annotations for AminoAcidComposition.java and Element.java.

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  kohchuanhock

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Commits on Jun 29, 2011

• Add one more method to enable the creation of aminoacidtable without explicit specification of elementmass.xml

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  kohchuanhock

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• Simplified Schema for Compounds

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

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  kohchuanhock

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• Created ValidationEventHandler which allows the xml file to be validated

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  kohchuanhock

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Commits on Jun 21, 2011

• Removed Utils.roundToDecimals from PeptidePropertiesImpl.java

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  kohchuanhock

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Commits on Jun 16, 2011

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

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  kohchuanhock

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• Removed invalid UTF-8 characters

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  kohchuanhock

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

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  kohchuanhock

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