X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0267f45b5fdba865e0be04dedc7e4b137f336b1f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f628699dee035546020be7c2d4c014efbd6ab8d9;hpb=2755c8765d39da0da2be087b301d47fc153d9236;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index f628699..0267f45 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -493,7 +493,9 @@ public class Sequence implements SequenceI public char[] getSequence(int start, int end) { if (start < 0) + { start = 0; + } // JBPNote - left to user to pad the result here (TODO:Decide on this // policy) if (start >= sequence.length) @@ -512,16 +514,7 @@ public class Sequence implements SequenceI return reply; } - /** - * make a new Sequence object from start to end (including gaps) over this - * seqeunce - * - * @param start - * int - * @param end - * int - * @return SequenceI - */ + @Override public SequenceI getSubSequence(int start, int end) { if (start < 0) @@ -621,14 +614,7 @@ public class Sequence implements SequenceI } } - /** - * Returns the sequence position for an alignment position - * - * @param i - * column index in alignment (from 1) - * - * @return residue number for residue (left of and) nearest ith column - */ + @Override public int findPosition(int i) { int j = 0; @@ -675,11 +661,7 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#findPositionMap() - */ + @Override public int[] findPositionMap() { int map[] = new int[sequence.length]; @@ -699,11 +681,43 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deleteChars(int, int) - */ + @Override + public List getInsertions() + { + ArrayList map = new ArrayList(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + if (jalview.util.Comparison.isGap(sequence[j])) + { + if (lastj == -1) + { + lastj = j; + } + } + else + { + if (lastj != -1) + { + map.add(new int[] + { lastj, j - 1 }); + lastj = -1; + } + } + j++; + } + if (lastj != -1) + { + map.add(new int[] + { lastj, j - 1 }); + lastj = -1; + } + return map; + } + + @Override public void deleteChars(int i, int j) { int newstart = start, newend = end; @@ -782,16 +796,7 @@ public class Sequence implements SequenceI sequence = tmp; } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * @param c - * DOCUMENT ME! - * @param chop - * DOCUMENT ME! - */ + @Override public void insertCharAt(int i, int length, char c) { char[] tmp = new char[sequence.length + length]; @@ -821,26 +826,31 @@ public class Sequence implements SequenceI sequence = tmp; } + @Override public void insertCharAt(int i, char c) { insertCharAt(i, 1, c); } + @Override public String getVamsasId() { return vamsasId; } + @Override public void setVamsasId(String id) { vamsasId = id; } + @Override public void setDBRef(DBRefEntry[] dbref) { dbrefs = dbref; } + @Override public DBRefEntry[] getDBRef() { if (dbrefs == null && datasetSequence != null @@ -851,6 +861,7 @@ public class Sequence implements SequenceI return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { if (dbrefs == null) @@ -883,32 +894,33 @@ public class Sequence implements SequenceI dbrefs = temp; } + @Override public void setDatasetSequence(SequenceI seq) { datasetSequence = seq; } + @Override public SequenceI getDatasetSequence() { return datasetSequence; } + @Override public AlignmentAnnotation[] getAnnotation() { - if (annotation == null) - { - return null; - } + return annotation == null ? null : annotation + .toArray(new AlignmentAnnotation[annotation.size()]); + } - AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()]; - for (int r = 0; r < ret.length; r++) - { - ret[r] = annotation.elementAt(r); - } - return ret; + @Override + public boolean hasAnnotation(AlignmentAnnotation ann) + { + return annotation == null ? false : annotation.contains(ann); } + @Override public void addAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation == null) @@ -928,7 +940,9 @@ public class Sequence implements SequenceI { this.annotation.removeElement(annotation); if (this.annotation.size() == 0) + { this.annotation = null; + } } } @@ -952,11 +966,7 @@ public class Sequence implements SequenceI return true; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deriveSequence() - */ + @Override public SequenceI deriveSequence() { SequenceI seq = new Sequence(this); @@ -1040,16 +1050,14 @@ public class Sequence implements SequenceI for (int i = 0; i < annotations.length; i++) { if (annotations[i] != null) + { addAlignmentAnnotation(annotations[i]); + } } } } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String) - */ + @Override public AlignmentAnnotation[] getAnnotation(String label) { if (annotation == null || annotation.size() == 0) @@ -1082,33 +1090,7 @@ public class Sequence implements SequenceI return anns; } - /** - * Returns a list of any annotations on the sequence that match the given - * calcId (source) and label (type). Null values do not match. - * - * @param calcId - * @param label - * @return - */ @Override - public List getAlignmentAnnotations(String calcId, - String label) - { - List result = new ArrayList(); - if (annotation != null) - { - for (AlignmentAnnotation ann : annotation) - { - if (ann.calcId != null && ann.calcId.equals(calcId) - && ann.label != null && ann.label.equals(label)) - { - result.add(ann); - } - } - } - return result; - } - public boolean updatePDBIds() { if (datasetSequence != null) @@ -1162,13 +1144,7 @@ public class Sequence implements SequenceI return false; } - /* - * (non-Javadoc) - * - * @see - * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, - * jalview.datamodel.Mapping) - */ + @Override public void transferAnnotation(SequenceI entry, Mapping mp) { if (datasetSequence != null) @@ -1264,4 +1240,21 @@ public class Sequence implements SequenceI return rna; } + @Override + public List getAlignmentAnnotations(String calcId, + String label) + { + List result = new ArrayList(); + if (this.annotation != null) { + for (AlignmentAnnotation ann : annotation) { + if (ann.calcId != null && ann.calcId.equals(calcId) + && ann.label != null && ann.label.equals(label)) + { + result.add(ann); + } + } + } + return result; + } + }