X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=aec68ab012a8124176ca7da4fa003bef2dadbc0c;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=69eb1d43e623c421548fc04907b1cbc4d855db46;hpb=e179e97c0330d1981da7383db497caddd8cad232;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 69eb1d4..aec68ab 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -20,8 +20,6 @@ */ package jalview.datamodel; -import jalview.api.DBRefEntryI; - import java.util.List; import java.util.Vector; @@ -219,6 +217,15 @@ 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 + */ + public boolean isProtein(); + + /** * Delete a range of aligned sequence columns, creating a new dataset sequence * if necessary and adjusting start and end positions accordingly. * @@ -233,19 +240,21 @@ 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); @@ -283,11 +292,18 @@ 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 @@ -301,6 +317,14 @@ 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(); @@ -436,20 +460,12 @@ 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 - */ - public void setSourceDBRef(DBRefEntryI dbRef); - - /** - * Get the distinct source database, and accession number from which a - * sequence and its start-end data were derived from. - * - * @return + * @return just the primary references (if any) for this sequence, or an empty + * list */ - public DBRefEntryI getSourceDBRef(); + public List getPrimaryDBRefs(); }