X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=30ba7589392f96708b7416016e87bf3ed4e13a47;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8376047444fb4cff5840e33e4ec2d7c036f44554;hpb=03496bf88fc1bec3ce628ac79ce69440ce244007;p=jalview.git diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java index 8376047..30ba758 100755 --- a/src/jalview/datamodel/SequenceI.java +++ b/src/jalview/datamodel/SequenceI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -26,12 +26,13 @@ import java.util.Vector; import fr.orsay.lri.varna.models.rna.RNA; /** - * DOCUMENT ME! + * Methods for manipulating a sequence, its metadata and related annotation in + * an alignment or dataset. * * @author $author$ * @version $Revision$ */ -public interface SequenceI +public interface SequenceI extends ASequenceI { /** * Set the display name for the sequence @@ -134,12 +135,13 @@ public interface SequenceI public char[] getSequence(int start, int end); /** - * create a new sequence object from start to end of this sequence + * create a new sequence object with a subsequence of this one but sharing the + * same dataset sequence * * @param start - * int index for start position + * int index for start position (base 0, inclusive) * @param end - * int index for end position + * int index for end position (base 0, exclusive) * * @return SequenceI * @note implementations may use getSequence to get the sequence data @@ -147,12 +149,12 @@ public interface SequenceI public SequenceI getSubSequence(int start, int end); /** - * DOCUMENT ME! + * get the i'th character in this sequence's local reference frame (ie from + * 0-number of characters lying from start-end) * * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * index + * @return character or ' ' */ public char getCharAt(int i); @@ -172,8 +174,7 @@ public interface SequenceI public String getDescription(); /** - * Return the alignment column for a sequence position * Return the alignment - * position for a sequence position + * Return the alignment column for a sequence position * * @param pos * lying from start to end @@ -220,9 +221,9 @@ public interface SequenceI * if necessary and adjusting start and end positions accordingly. * * @param i - * first column in range to delete + * first column in range to delete (inclusive) * @param j - * last column in range to delete + * last column in range to delete (exclusive) */ public void deleteChars(int i, int j); @@ -239,12 +240,12 @@ public interface SequenceI /** * DOCUMENT ME! * - * @param i + * @param position * DOCUMENT ME! - * @param c + * @param ch * DOCUMENT ME! */ - public void insertCharAt(int i, int length, char c); + public void insertCharAt(int position, int count, char ch); /** * DOCUMENT ME! @@ -267,14 +268,14 @@ public interface SequenceI * @param id * DOCUMENT ME! */ - public void setPDBId(Vector ids); + public void setPDBId(Vector ids); /** - * DOCUMENT ME! + * Returns a list * * @return DOCUMENT ME! */ - public Vector getPDBId(); + public Vector getAllPDBEntries(); /** * add entry to the vector of PDBIds, if it isn't in the list already @@ -315,8 +316,22 @@ public interface SequenceI public SequenceI getDatasetSequence(); + /** + * Returns a new array containing this sequence's annotations, or null. + */ public AlignmentAnnotation[] getAnnotation(); + /** + * Returns true if this sequence has the given annotation (by object + * identity). + */ + public boolean hasAnnotation(AlignmentAnnotation ann); + + /** + * Add the given annotation, if not already added, and set its sequence ref to + * be this sequence. Does nothing if this sequence's annotations already + * include this annotation (by identical object reference). + */ public void addAlignmentAnnotation(AlignmentAnnotation annotation); public void removeAlignmentAnnotation(AlignmentAnnotation annotation); @@ -345,12 +360,11 @@ public interface SequenceI public AlignmentAnnotation[] getAnnotation(String label); /** - * Return a list of any annotations which match the given calcId (source) and - * label (type). Null values do not match. + * Returns a (possibly empty) list of any annotations that match on given + * calcId (source) and label (type). Null values do not match. * * @param calcId * @param label - * @return */ public List getAlignmentAnnotations(String calcId, String label); @@ -369,8 +383,8 @@ public interface SequenceI /** * Transfer any database references or annotation from entry under a sequence * mapping.
- * Note: DOES NOT transfer sequence associated alignment - * annotation
+ * Note: DOES NOT transfer sequence associated alignment annotation + *
* * @param entry * @param mp @@ -401,4 +415,18 @@ public interface SequenceI */ public void setRNA(RNA rna); + /** + * + * @return list of insertions (gap characters) in sequence + */ + public List getInsertions(); + + /** + * Given a pdbId String, return the equivalent PDBEntry if available in the + * given sequence + * + * @param pdbId + * @return + */ + public PDBEntry getPDBEntry(String pdbId); }