X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=38be37f1f72af433fc3605e8f80ce7c0d12d1996;hb=88694463a2aea303694231603b61970f72a5a259;hp=355e27102970e4ae7f9e174d477b5bdc70d48d30;hpb=63c08febd1f76249b308628611857b9698baaf8d;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 355e271..38be37f 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,8 +20,9 @@ */ package jalview.datamodel; -import jalview.api.DBRefEntryI; +import jalview.datamodel.features.SequenceFeaturesI; +import java.util.BitSet; import java.util.List; import java.util.Vector; @@ -176,7 +177,7 @@ public interface SequenceI extends ASequenceI public String getDescription(); /** - * Return the alignment column for a sequence position + * Return the alignment column (from 1..) for a sequence position * * @param pos * lying from start to end @@ -191,16 +192,41 @@ 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 position. * * @param i * column index in alignment (from 0.. + * Example: + * >Seq/8-13 + * ABC--DE-F + * findPositions(1, 4) returns Range(9, 9) // B only + * findPositions(3, 4) returns null // all gaps + * findPositions(2, 6) returns Range(10, 12) // CDE + * findPositions(3, 7) returns Range(11,12) // DE + * + * + * @param fromCol + * first aligned column position (base 0, inclusive) + * @param toCol + * last aligned column position (base 0, inclusive) + * + * @return + */ + public Range findPositions(int fromCol, int toCol); + + /** * Returns an int array where indices correspond to each residue in the * sequence and the element value gives its position in the alignment * @@ -219,8 +245,11 @@ public interface SequenceI extends ASequenceI public int[] findPositionMap(); /** + * Answers true if the sequence is composed of amino acid characters. Note + * that implementations may use heuristic methods which are not guaranteed to + * give the biologically 'right' answer. * - * @return true if sequence is composed of amino acid characters + * @return */ public boolean isProtein(); @@ -239,39 +268,47 @@ public interface SequenceI extends ASequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * alignment column number * @param c - * DOCUMENT ME! + * character to insert */ public void insertCharAt(int i, char c); /** - * DOCUMENT ME! + * insert given character at alignment column position * * @param position - * DOCUMENT ME! + * alignment column number + * @param count + * length of insert * @param ch - * DOCUMENT ME! + * character to insert */ public void insertCharAt(int position, int count, char ch); /** - * Gets array holding sequence features associated with this sequence. The - * array may be held by the sequence's dataset sequence if that is defined. + * 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 */ - public SequenceFeature[] getSequenceFeatures(); + public List getSequenceFeatures(); + + /** + * Answers the object holding features for the sequence + * + * @return + */ + SequenceFeaturesI getFeatures(); /** - * Replaces the array of sequence features associated with this sequence with - * a new array reference. If this sequence has a dataset sequence, then this - * method will update the dataset sequence's feature array + * Replaces the sequence features associated with this sequence with the given + * features. If this sequence has a dataset sequence, then this method will + * update the dataset sequence's features instead. * * @param features - * New array of sequence features */ - public void setSequenceFeatures(SequenceFeature[] features); + public void setSequenceFeatures(List features); /** * DOCUMENT ME! @@ -289,11 +326,18 @@ public interface SequenceI extends ASequenceI public Vector getAllPDBEntries(); /** - * add entry to the vector of PDBIds, if it isn't in the list already + * Adds the entry to the *normalised* list of PDBIds. + * + * If a PDBEntry is passed with the same entry.getID() string as one already + * in the list, or one is added that appears to be the same but has a chain ID + * appended, then the existing PDBEntry will be updated with the new + * attributes instead, unless the entries have distinct chain codes or + * associated structure files. * * @param entry + * @return true if the entry was added, false if updated */ - public void addPDBId(PDBEntry entry); + public boolean addPDBId(PDBEntry entry); /** * update the list of PDBEntrys to include any DBRefEntrys citing structural @@ -307,6 +351,14 @@ public interface SequenceI extends ASequenceI public void setVamsasId(String id); + /** + * set the array of Database references for the sequence. + * + * @param dbs + * @deprecated - use is discouraged since side-effects may occur if DBRefEntry + * set are not normalised. + */ + @Deprecated public void setDBRefs(DBRefEntry[] dbs); public DBRefEntry[] getDBRefs(); @@ -319,7 +371,14 @@ public interface SequenceI extends ASequenceI */ public void addDBRef(DBRefEntry entry); - public void addSequenceFeature(SequenceFeature sf); + /** + * Adds the given sequence feature and returns true, or returns false if it is + * already present on the sequence, or if the feature type is null. + * + * @param sf + * @return + */ + public boolean addSequenceFeature(SequenceFeature sf); public void deleteFeature(SequenceFeature sf); @@ -442,20 +501,38 @@ public interface SequenceI extends ASequenceI public PDBEntry getPDBEntry(String pdbId); /** - * Set the distinct source database, and accession number from which a - * sequence and its start-end data were derived from. This is very important - * for SIFTS mappings and must be set prior to performing SIFTS mapping. + * Get all primary database/accessions for this sequence's data. These + * DBRefEntry are expected to resolve to a valid record in the associated + * external database, either directly or via a provided 1:1 Mapping. * - * @param dbRef - * the source dbRef for the sequence + * @return just the primary references (if any) for this sequence, or an empty + * list */ - public void setSourceDBRef(DBRefEntryI dbRef); + public List getPrimaryDBRefs(); /** - * Get the distinct source database, and accession number from which a - * sequence and its start-end data were derived from. + * Returns a (possibly empty) list of sequence features that overlap the range + * from-to (inclusive), optionally restricted to one or more specified feature + * types * + * @param from + * @param to + * @param types * @return */ - public DBRefEntryI getSourceDBRef(); + List findFeatures(int from, int to, String... types); + + /** + * Method to call to indicate that the sequence (characters or alignment/gaps) + * has been modified. Provided to allow any cursors on residue/column + * positions to be invalidated. + */ + void sequenceChanged(); + + /** + * + * @return BitSet corresponding to index [0,length) where Comparison.isGap() + * returns true. + */ + BitSet getInsertionsAsBits(); }