X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=72ce22c9fca0880fbba67bc6707e18788daf9858;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=538b791bcac01f78339e1aec5326ac14e2eaa667;hpb=5fc820296bd27badf71036b9d79980277d1dd095;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 538b791..72ce22c 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,9 +20,13 @@ */ package jalview.datamodel; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.MapList; +import jalview.ws.params.InvalidArgumentException; import java.util.BitSet; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -44,6 +48,10 @@ public interface SequenceI extends ASequenceI */ public void setName(String name); + public HiddenMarkovModel getHMM(); + + public void setHMM(HiddenMarkovModel hmm); + /** * Get the display name */ @@ -110,9 +118,11 @@ public interface SequenceI extends ASequenceI * get a range on the sequence as a string * * @param start - * position relative to start of sequence including gaps (from 0) + * (inclusive) position relative to start of sequence including gaps + * (from 0) * @param end - * position relative to start of sequence including gaps (from 0) + * (exclusive) position relative to start of sequence including gaps + * (from 0) * * @return String containing all gap and symbols in specified range */ @@ -192,25 +202,29 @@ public interface SequenceI extends ASequenceI public int findIndex(int pos); /** - * Returns the sequence position for an alignment position. + * Returns the sequence position for an alignment (column) position. If at a + * gap, returns the position of the next residue to the right. If beyond the + * end of the sequence, returns 1 more than the last residue position. * * @param i * column index in alignment (from 0..toColumn */ - public Range findPositions(int fromColum, int toColumn); + public ContiguousI findPositions(int fromColum, int toColumn); /** * Returns an int array where indices correspond to each residue in the @@ -222,6 +236,13 @@ public interface SequenceI extends ASequenceI public int[] gapMap(); /** + * Build a bitset corresponding to sequence gaps + * + * @return a BitSet where set values correspond to gaps in the sequence + */ + public BitSet gapBitset(); + + /** * Returns an int array where indices correspond to each position in sequence * char array and the element value gives the result of findPosition for that * index in the sequence. @@ -340,14 +361,17 @@ public interface SequenceI extends ASequenceI /** * set the array of Database references for the sequence. * + * BH 2019.02.04 changes param to DBModlist + * * @param dbs * @deprecated - use is discouraged since side-effects may occur if DBRefEntry * set are not normalised. + * @throws InvalidArgumentException if the is not one created by Sequence itself */ @Deprecated - public void setDBRefs(DBRefEntry[] dbs); + public void setDBRefs(DBModList dbs); - public DBRefEntry[] getDBRefs(); + public DBModList getDBRefs(); /** * add the given entry to the list of DBRefs for this sequence, or replace a @@ -449,17 +473,6 @@ public interface SequenceI extends ASequenceI public void transferAnnotation(SequenceI entry, Mapping mp); /** - * @param index - * The sequence index in the MSA - */ - public void setIndex(int index); - - /** - * @return The index of the sequence in the alignment - */ - public int getIndex(); - - /** * @return The RNA of the sequence in the alignment */ @@ -497,6 +510,12 @@ public interface SequenceI extends ASequenceI public List getPrimaryDBRefs(); /** + * Answers true if the sequence has annotation for Hidden Markov Model + * information content, else false + */ + boolean hasHMMAnnotation(); + + /** * Returns a (possibly empty) list of sequence features that overlap the given * alignment column range, optionally restricted to one or more specified * feature types. If the range is all gaps, then features which enclose it are @@ -536,20 +555,52 @@ public interface SequenceI extends ASequenceI int replace(char c1, char c2); /** - * Adjusts position and extent of features to allow for cut of the specified - * (inclusive) column range. Returns a list of {originalFeature, - * amendedFeature} for - *
    - *
  • features that have been deleted (as within the cut) - amendedFeature is - * null
    • - *
  • truncated features (as overlapping or spanning the cut)
    • - *
- * Contact features that overlap the cut region are deleted. Contact features - * that enclose the cut region are shortened. + * Answers the GeneLociI, or null if not known + * + * @return + */ + GeneLociI getGeneLoci(); + + /** + * Sets the mapping to gene loci for the sequence + * + * @param speciesId + * @param assemblyId + * @param chromosomeId + * @param map + */ + void setGeneLoci(String speciesId, String assemblyId, + String chromosomeId, MapList map); + + + /** + * Returns the sequence string constructed from the substrings of a sequence + * defined by the int[] ranges provided by an iterator. E.g. the iterator + * could iterate over all visible regions of the alignment + * + * @param it + * the iterator to use + * @return a String corresponding to the sequence + */ + String getSequenceStringFromIterator(Iterator it); + + /** + * Locate the first position in this sequence which is not contained in an + * iterator region. If no such position exists, return 0 + * + * @param it + * iterator over regions + * @return first residue not contained in regions + */ + + public int firstResidueOutsideIterator(Iterator it); + + + /** + * Answers true if this sequence has an associated Hidden Markov Model * - * @param fromColumn - * @param toColumn * @return */ - List adjustFeatures(int fromColumn, int toColumn); + boolean hasHMMProfile(); } +