X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=5cddadef481b3c29ebfbf8611d76b0a406dd29e2;hb=13f232d8ecdc2665be8239a4049022127ea8399e;hp=f49039cfe66e76b8f5c2ea6116aa1a1c19ee1a22;hpb=b5aea33b1a9dcb1831ef681342be55c8929cf080;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index f49039c..5cddade 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -21,8 +21,10 @@ package jalview.datamodel; import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.MapList; import java.util.BitSet; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -44,6 +46,10 @@ public interface SequenceI extends ASequenceI */ public void setName(String name); + public HiddenMarkovModel getHMM(); + + public void setHMM(HiddenMarkovModel hmm); + /** * Get the display name */ @@ -110,18 +116,20 @@ 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 */ public String getSequenceAsString(int start, int end); /** - * Get the sequence as a character array + * Answers a copy of the sequence as a character array * - * @return seqeunce and any gaps + * @return */ public char[] getSequence(); @@ -192,17 +200,31 @@ 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 ContiguousI findPositions(int fromColum, int toColumn); + + /** * Returns an int array where indices correspond to each residue in the * sequence and the element value gives its position in the alignment * @@ -212,6 +234,13 @@ 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. @@ -266,7 +295,7 @@ public interface SequenceI extends ASequenceI * Answers a list of all sequence features associated with this sequence. The * list may be held by the sequence's dataset sequence if that is defined. * - * @return hard reference to array + * @return */ public List getSequenceFeatures(); @@ -439,17 +468,6 @@ 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 */ @@ -487,6 +505,12 @@ 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 @@ -515,4 +539,60 @@ public interface SequenceI extends ASequenceI * returns true. */ BitSet getInsertionsAsBits(); + + /** + * Replaces every occurrence of c1 in the sequence with c2 and returns the + * number of characters changed + * + * @param c1 + * @param c2 + */ + int replace(char c1, char c2); + + /** + * 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 + */ + int firstResidueOutsideIterator(Iterator it); + + /** + * Answers true if this sequence has an associated Hidden Markov Model + * + * @return + */ + boolean hasHMMProfile(); }