All Classes
| Class | Description |
|---|---|
| AminoAcidParser |
AminoAcidParser
|
| AnalogSequenceException |
AnalogSequenceException
|
| Attachment |
This is a data model for Attachment point on monomer
|
| AttachmentException |
AttachmentException
|
| AttachmentLoader |
loads attachments from a given input stream
|
| Base64 |
A very fast and memory efficient class to encode and decode to and from
BASE64 in full accordance with RFC 2045.<br><br> On Windows XP sp1 with
1.4.2_04 and later ;), this encoder and decoder is about 10 times faster on
small arrays (10 - 1000 bytes) and 2-3 times as fast on larger arrays (10000
- 1000000 bytes) compared to
<code>sun.misc.Encoder()/Decoder()</code>.<br><br>
On byte arrays the encoder is about 20% faster than Jakarta Commons Base64
Codec for encode and about 50% faster for decoding large arrays. This
implementation is about twice as fast on very small arrays (< 30 bytes). If
source/destination is a <code>String</code> this version is about three times
as fast due to the fact that the Commons Codec result has to be recoded to a
<code>String</code> from <code>byte[]</code>, which is very
expensive.<br><br>
This encode/decode algorithm doesn't create any temporary arrays as many
other codecs do, it only allocates the resulting array. This produces less
garbage and it is possible to handle arrays twice as large as algorithms that
create a temporary array. (E.g. Jakarta Commons Codec). It is unknown whether
Sun's <code>sun.misc.Encoder()/Decoder()</code> produce temporary arrays but
since performance is quite low it probably does.<br><br>
The encoder produces the same output as the Sun one except that the Sun's
encoder appends a trailing line separator if the last character isn't a pad.
Unclear why but it only adds to the length and is probably a side effect.
Both are in conformance with RFC 2045 though.<br> Commons codec seem to
always att a trailing line separator.<br><br>
<b>Note!</b> The encode/decode method pairs (types) come in three versions
with the <b>exact</b> same algorithm and thus a lot of code redundancy. This
is to not create any temporary arrays for transcoding to/from different
format types. The methods not used can simply be commented out.<br><br>
There is also a "fast" version of all decode methods that works the same way
as the normal ones, but har a few demands on the decoded input. Normally
though, these fast verions should be used if the source if the input is known
and it hasn't bee tampered with.<br><br>
If you find the code useful or you find a bug, please send me a note at
base64 @ miginfocom . com.
Licence (BSD): ==============
Copyright (c) 2004, Mikael Grev, MiG InfoCom AB. (base64 @ miginfocom . com)
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. Redistributions in binary
form must reproduce the above copyright notice, this list of conditions and
the following disclaimer in the documentation and/or other materials provided
with the distribution. Neither the name of the MiG InfoCom AB nor the names
of its contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
|
| BuilderMolecule |
class to build molecules for the HELMNotation
|
| BuilderMoleculeException |
BuilderMoleculeException
|
| CalculationException |
This is the exception thrown for Invalid Structures
|
| CategorizedMonomer |
CategorizedMonomer used as wrapper class for monomer categorization in the HELMEditor. |
| ChangeObjects |
ChangeObjects, class to provide simple methods to change the HELM2Notation
objects
|
| Chemistry |
Chemistry, singleton class to define which Chemistry-Plugin is used
|
| ChemistryException |
ChemistryException TODO comment me |
| ConnectionNotationException |
ConnectionNotationException
|
| Converter |
Converter
class allowing to convert extended smiles into smiles with atom mapping
|
| DeepCopy | |
| EncoderException |
EncoderException TODO comment me |
| ExtinctionCoefficient |
ExtinctionCoefficient class to calculate the extinction coefficient
|
| ExtinctionCoefficientException |
ExtinctionCoefficientException
|
| FastaFormat |
FastaFormat, class to convert FastaFiles to HELMNotation and vice versa
|
| FastaFormatException |
FastaFormatException
|
| GroupingNotationException |
GroupingNotationException
|
| HELM1FormatException |
HELM1FormatException
|
| HELM1Utils |
HELM1 class to transform a HELM2 into HELM1; this is only possible in the
case of no HELM2 features
|
| HELM2HandledException |
HELM2HandledException
|
| HELM2NotationUtils |
HELM2NotationUtils
|
| ImageGenerationException |
ImageGenerationException
|
| Images |
Image class to generate image generation of monomers and of the helm molecule
|
| InterConnections |
InterConnections, class to save the interconnections of a HELM
|
| MDLUtils |
MDLUtils, class to generate MDL for a HELM molecule.
|
| MethodsMonomerUtils |
MethodsMonomerUtils
|
| MoleculeProperty |
MoleculeInfo
|
| MoleculePropertyCalculator |
MoleculeInformation, class to
|
| MolfileEncoder | |
| Monomer |
This is a data model for Monomer. alternateId is used in polymer notation.
|
| MonomerCache | |
| MonomerException |
This is the exception thrown for Invalid Monomers
|
| MonomerFactory |
This is a factory class to build monomer database from
MonomerDBGZEnconded.xml document
|
| MonomerLoadingException |
This is the exception thrown for errors while loading monomers from source to store.
|
| MonomerParser |
MonomerParser
|
| MonomerStore |
This class represents a store for monomers.
|
| MonomerStoreConfiguration |
Singleton
MonomerStoreConfiguration stores the webservice
configuration, e.g. |
| MonomerWSLoader |
MonomerWSLoader loads monomers from the webservice configured in
MonomerStoreConfiguration. |
| MonomerWSSaver |
MonomerWSSaver saves monomers to the webservice configured in MonomerStoreConfiguration. |
| NotationConstant | |
| NotationException |
This is the exception thrown for Invalid Notations
|
| Nucleotide |
This is a data model class for nucleotide
|
| NucleotideFactory |
This is a factory class to build nucleotide templates
|
| NucleotideLoadingException |
This is the exception thrown for errors while loading nucleotides from source to store.
|
| NucleotideParser |
NucleotideParser
|
| NucleotideWSLoader |
NucleotideWSLoader loads nucleotides from the webservice configured in MonomerStoreConfiguration. |
| NucleotideWSSaver |
NucleotideWSSaver saves nucleotides to the webservice configured in MonomerStoreConfiguration. |
| ParserException |
ParserException
|
| PeptideUtils |
PeptideUtils, class to provide peptide utils
|
| PeptideUtilsException |
PeptideUtilsException
|
| PermutationAndExpansion | |
| PolymerIDsException |
PolymerIDsException
|
| PolymerUtils |
PolymerUtils, class to provide methods for polymer
|
| RgroupStructure |
RgroupStructure
|
| RNAUtils |
RNAUtils, class to provide methods for rna polymer
|
| RNAUtilsException |
RNAUtilsException
|
| SequenceConverter |
SequenceConverter class to convert sequence into the HELM2Notation object and
vice versa
|
| SimpleNotationGroupIterator |
Iterator class for groups within a simple notation string
|
| SiRNANotation |
SiRNANotation, class to generate SirnaNotation
|
| SMILES |
SMILES class to generate SMILES
|
| Validation |
Validation class to validate the whole HELM string
|
| ValidationException |
ValidationException
|
| WebService |
WebService class containing all required methods for the web-service
|
| WSAdapterUtils |
WSAdapterUtils is used to generalize webservice calls. |
| xHelmNotationExporter |
xHELMNotationExporter
|
| xHelmNotationParser |
Class to parse the XHELM XML format
|