Interface | Description | on pressing BUTTON:StrapHotswap#BUT_LAB_Apply |
StrapExtension |
Plugins that can be started and that can react on events in STRAP |
Usually an application frame or application panel is opened. |
ResidueSelection |
Selects residues of proteins. |
A dialog is opened to chose the proteins and the highlighting style. |
SequenceDisSimilarity |
Compares two gapped sequences. Returns a value between 0 and 1 or NaN. |
A Dialog for protein comparison is opened. Specifying the SequenceDisSimilarity requires opening another control panel. |
ProteinProteinDistance |
Assigns float values to tuples of proteins. Is an extendsion of ProteinProteinValue that should return 0.0 for identical proteins and a maximum value for dissimilar proteins. |
A table is created comparing a number of proteins with another set of proteins. Alternatively, a graph is drawn. |
ProteinProteinSimilarity |
Assigns float values to tuples of proteins. Is an extendsion of ProteinProteinValue that should return a high values for identical proteins and low value for dissimilar proteins. |
A table is created comparing a number of proteins with another set of proteins. Alternatively, a graph is drawn. |
SequenceAligner |
Calculates gaps for a given set of proteins. Either it returns an alignment of the entire sequences or a local one. |
The alignment can be probed for a number of proteins and the result can be realized in the alignment or disposed. |
ProteinViewer |
Displays proteins three-dimensionally. A given set of residues can be drawn in different styles. |
A dialog is shown to select the protein to be viewed. |
ProteinParser |
Extracts the data from a protein file and sets the amino acid sequence and other information. |
A protein file selector is shown. When the proteins are loaded all protein parsers are tried until one succeeds. |
ProteinWriter |
These classes require a setProtein and a getText method. In addition the NeedsProteins interface can be implemented to get
protein data in addition to the amino acid sequence. |
Protein files can be written for the selected proteins.. |
AlignmentWriter |
These classes require a setProteins and a getText method. |
An alignment file can be written for the selected proteins.. |
Superimpose3D |
Superimposes one protein (mobile) upon another (reference). |
A 3x3 rotation matrix and an (dx,dy,dz) translation vector is calculated. |
ValueOfAlignPosition |
Assigns float values to sequence alignment positions. |
A profile is plotted along the multiple sequence alignment. |
ValueOfResidue |
Returns a float value for each residue of a protein. |
A profile is plotted along the sequence of the protein. |
ValueOfProtein |
Returns a float value for a given protein. |
The values are charted as bars in the row header of the multiple sequence alignment. |
ProteinsSorter |
ProteinsSorter-objects reorder the proteins by returning a permutation of the series 0, 1, 2, 3 ,4 ... n via the method
of sortProteins(StrapProtein[]). |
A dialog is opened to change the order of the selected proteins. |
TransmembraneHelix_Predictor |
TransmembraneHelix_Predictor objects take the amino acid sequence and predict membrane spanning helices. They return a string with the character 'H' at positions which are likely to be transmembrane helices. SecondaryStructure_Predictor and CoiledCoil_Predictor follow the same principle. |
A dialog is opened to select the prediction method. |
CoiledCoil_Predictor |
as above |
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SecondaryStructure_Predictor |
as above |
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