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Analyzed 12 minutes ago. based on code collected 1 day ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Nov 06, 2025 — Nov 06, 2026 Showing page 193 of 243 Search / Filter on:
Improved Help - Tries to mimic "man" in unix.	Chuan Hock Koh	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago
Created a new class ModifiedAminoAcidCompoundSet which enables any symbols to be specified in XML file to represent amino acids and modified amino acids.	Chuan Hock Koh	More...				over 15 years ago
Done up a first draft for command prompt	Chuan Hock Koh	More...				over 15 years ago
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.	Chuan Hock Koh	More...				over 15 years ago
Contributing new framework for loading amino acid substitution matrices from the AAINDEX database.	Andreas Prlic	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago
Work around and made the XML files annotated to requirements. Use Hydrogen-1 isotope weight	Chuan Hock Koh	More...				over 15 years ago
Added annotations for AminoAcidComposition.java and Element.java. Simplified MolecularWeight.xml and ElementMass.xml.	Chuan Hock Koh	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago
adding check if no domains can be found for a PDB id to avoid nullpointerexception	Andreas Prlic	More...				over 15 years ago
TODO for Ah Fu	Peter Troshin	More...				over 15 years ago
Simplified Schema for Compounds	Peter Troshin	More...				over 15 years ago
Added a new class in test to ensure short examples given in Wiki CookBook are error free.	Chuan Hock Koh	More...				over 15 years ago
Removed doc folder and its contents	Chuan Hock Koh	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago
some more refinements	Andreas Prlic	More...				over 15 years ago
some more refinements	Andreas Prlic	More...				over 15 years ago
more display options	Andreas Prlic	More...				over 15 years ago
moved a utility method from DisplayAFP to AFPAlignmentDisplay	Andreas Prlic	More...				over 15 years ago
moved a utility method from DisplayAFP to AFPAlignmentDisplay	Andreas Prlic	More...				over 15 years ago
nicer website display and fixing an issue where the PDB residue ranges were one line off	Andreas Prlic	More...				over 15 years ago
now allowing outside user to specify alternative ptm_list.xml	Andreas Prlic	More...				over 15 years ago
now allowing outside user to specify alternative ptm_list.xml	Andreas Prlic	More...				over 15 years ago
new method for accessing jmolscript for alignment blocks	Andreas Prlic	More...				over 15 years ago
now using ScopDatabase interface	Andreas Prlic	More...				over 15 years ago
better javadoc	Andreas Prlic	More...				over 15 years ago
fixing typo in method name	Andreas Prlic	More...				over 15 years ago
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	Chuan Hock Koh	More...				over 15 years ago

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