'STRAP:multiple sequence alignments '

charite.christo.protein
Interface PredictionFromAminoacidSequence

All Known Subinterfaces:
CoiledCoil_Predictor, SecondaryStructure_Predictor, TransmembraneHelix_Predictor
All Known Implementing Classes:
AbstractPredictionFromAminoacidSequence, CoiledCoil_PredictorRobinson, SecondaryStructure_Jnet, SecondaryStructure_NNPREDICT, SecondaryStructure_Sopma, TransmembraneHelix_DAS, TransmembraneHelix_HMMTOP, TransmembraneHelix_MEMSAT, TransmembraneHelix_ORIENTM, TransmembraneHelix_Phobius, TransmembraneHelix_PRED_TMR, TransmembraneHelix_SOSUI, TransmembraneHelix_SPLIT3, TransmembraneHelix_SPLIT4, TransmembraneHelix_THUMBUP, TransmembraneHelix_TMAP, TransmembraneHelix_TMAP_MULTI, TransmembraneHelix_TMHMM2, TransmembraneHelix_TMPRED, TransmembraneHelix_TOPPRED, TransmembraneHelix_WaveTM

public interface PredictionFromAminoacidSequence

Classes that provide a prediction depending on amino acid setSequences. Some methods send many tasks at once to server. Therefore not just one but an array of sequences. There are methods which make consensus for an alignment. Therefore aligned gapped sequences can be set. STRAP retrieves the result by calling getPrediction().


Method Summary
 void compute()
          Computation is started and may take long time.
 char[][] getPrediction()
          Returns a character for each sequence position.
 void setGappedSequences(java.lang.String[] ss)
          set the sequences.
 

Method Detail

setGappedSequences

void setGappedSequences(java.lang.String[] ss)
set the sequences. Since some prediction methods take an alignment as input we pass several sequences that might be aligned. For example a secondary structure predictore might compute refine the prediction using multiple sequences


compute

void compute()
Computation is started and may take long time.


getPrediction

char[][] getPrediction()
Returns a character for each sequence position. For example 'H' for Helix..


'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, Protein and StrapEvent.'