From a878db688154da91ca7cc75a90c75d39bd193b3c Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 17 Apr 2007 11:02:43 +0000 Subject: [PATCH] copy constructor and ascii type change. --- src/jalview/datamodel/Mapping.java | 428 +++++++++++++++++++----------------- 1 file changed, 227 insertions(+), 201 deletions(-) diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java index 4daf7d4..705cb15 100644 --- a/src/jalview/datamodel/Mapping.java +++ b/src/jalview/datamodel/Mapping.java @@ -1,201 +1,227 @@ -package jalview.datamodel; - -import jalview.util.MapList; - -public class Mapping { - /** - * Contains the - * start-end pairs mapping from - * the associated sequence to the - * sequence in the database - * coordinate system - * it also takes care of step difference between coordinate systems - */ - MapList map=null; - /** - * The seuqence that map maps the associated seuqence to (if any). - */ - SequenceI to=null; - public Mapping(MapList map) { - super(); - this.map = map; - } - /** - * create a new mapping from - * @param exon int[] {start,end,start,end} series on associated sequence - * @param is int[] {start,end,...} ranges on the reference frame being mapped to - * @param i step size on associated sequence - * @param j step size on mapped frame - */ - public Mapping(SequenceI to, int[] exon, int[] is, int i, int j) - { - map = new MapList(exon, is, i, j); - } - - /** - * @return the map - */ - public MapList getMap() { - return map; - } - - /** - * @param map the map to set - */ - public void setMap(MapList map) { - this.map = map; - } - public boolean equals(Mapping other) { - if (other==null) - return false; - if (other==this) - return true; - if ((map!=null && other.map==null) || (map==null && other.map!=null)) - return false; - if (map.equals(other.map)) - return true; - return false; - } - /** - * get the 'initial' position in the associated - * sequence for a position in the mapped reference frame - * @param mpos - * @return - */ - public int getPosition(int mpos) - { - if (map!=null) { - int[] mp = map.shiftTo(mpos); - if (mp!=null) - { - return mp[0]; - } - } - return mpos; - } - public int[] getWord(int mpos) { - if (map!=null) { - int[] mp=map.shiftTo(mpos); - if (mp!=null) { - return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; - } - } - return null; - } - /** - * width of mapped unit in associated sequence - * - */ - public int getWidth() { - if (map!=null) { - return map.getFromRatio(); - } - return 1; - } - - /** - * width of unit in mapped reference frame - * @return - */ - public int getMappedWidth() { - if (map!=null) { - return map.getToRatio(); - } - return 1; - } - /** - * get mapped position in the associated - * reference frame for position pos in the - * associated sequence. - * @param pos - * @return - */ - public int getMappedPosition(int pos) { - if (map!=null) { - int[] mp = map.shiftFrom(pos); - if (mp!=null) - { - return mp[0]; - } - } - return pos; - } - public int[] getMappedWord(int pos) { - if (map!=null) { - int[] mp = map.shiftFrom(pos); - if (mp!=null) - { - return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)}; - } - } - return null; - } - /** - * locates the region of feature f in the associated sequence's reference frame - * @param f - * @return one or more features corresponding to f - */ - public SequenceFeature[] locateFeature(SequenceFeature f) - { - // this is a stopgap - features broken over exon boundaries will not be - // broken into a collection of feature fragments. - // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence - // need a function like int [] fromrange = map.getRange(from,to) - // need to make subgrouped sequence features. - if (true) { - if (map!=null) { - int[] frange = map.locateInFrom(f.getBegin(), f.getEnd()); - SequenceFeature[] vf = new SequenceFeature[frange.length/2]; - for (int i=0,v=0;i2) - vf[v].setDescription(f.getDescription() +"\nPart "+v); - } - return vf; - } - } - if (false){ - int[] word = getWord(f.getBegin()); - if (word[0]word[1]) - { - f.setEnd(word[0]); - } else { - f.setEnd(word[1]); - } - } - // give up and just return the feature. - return new SequenceFeature[] { f }; - } - - /** - * return a series of contigs on the associated sequence corresponding to - * the from,to interval on the mapped reference frame - * @param from - * @param to - * @return - */ - public int[] locateRange(int from, int to) { - //TODO - return null; - } - /** - * return a series of contigs on the mapped reference frame corresponding to - * the from,to interval on the associated sequence - * @param from - * @param to - * @return - */ - public int[] locateMappedRange(int from, int to) { - //TODO - return null; - } -} +package jalview.datamodel; + +import jalview.util.MapList; + +public class Mapping { + /** + * Contains the + * start-end pairs mapping from + * the associated sequence to the + * sequence in the database + * coordinate system + * it also takes care of step difference between coordinate systems + */ + MapList map=null; + /** + * The seuqence that map maps the associated seuqence to (if any). + */ + SequenceI to=null; + public Mapping(MapList map) { + super(); + this.map = map; + } + public Mapping(SequenceI to, MapList map) { + this(map); + this.to = to; + } + /** + * create a new mapping from + * @param to the sequence being mapped + * @param exon int[] {start,end,start,end} series on associated sequence + * @param is int[] {start,end,...} ranges on the reference frame being mapped to + * @param i step size on associated sequence + * @param j step size on mapped frame + */ + public Mapping(SequenceI to, int[] exon, int[] is, int i, int j) + { + this(to, new MapList(exon, is, i, j)); + } + /** + * create a duplicate (and independent) mapping object with + * the same reference to any SequenceI being mapped to. + * @param map2 + */ + public Mapping(Mapping map2) + { + if (map2!=this && map2!=null) { + if (map2.map!=null) + { + map=new MapList(map2.map); + } + to = map2.to; + } + } + /** + * @return the map + */ + public MapList getMap() { + return map; + } + + /** + * @param map the map to set + */ + public void setMap(MapList map) { + this.map = map; + } + /** + * Equals that compares both the to references and MapList mappings. + * @param other + * @return + */ + public boolean equals(Mapping other) { + if (other==null) + return false; + if (other==this) + return true; + if (other.to!=to) + return false; + if ((map!=null && other.map==null) || (map==null && other.map!=null)) + return false; + if (map.equals(other.map)) + return true; + return false; + } + /** + * get the 'initial' position in the associated + * sequence for a position in the mapped reference frame + * @param mpos + * @return + */ + public int getPosition(int mpos) + { + if (map!=null) { + int[] mp = map.shiftTo(mpos); + if (mp!=null) + { + return mp[0]; + } + } + return mpos; + } + public int[] getWord(int mpos) { + if (map!=null) { + int[] mp=map.shiftTo(mpos); + if (mp!=null) { + return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; + } + } + return null; + } + /** + * width of mapped unit in associated sequence + * + */ + public int getWidth() { + if (map!=null) { + return map.getFromRatio(); + } + return 1; + } + + /** + * width of unit in mapped reference frame + * @return + */ + public int getMappedWidth() { + if (map!=null) { + return map.getToRatio(); + } + return 1; + } + /** + * get mapped position in the associated + * reference frame for position pos in the + * associated sequence. + * @param pos + * @return + */ + public int getMappedPosition(int pos) { + if (map!=null) { + int[] mp = map.shiftFrom(pos); + if (mp!=null) + { + return mp[0]; + } + } + return pos; + } + public int[] getMappedWord(int pos) { + if (map!=null) { + int[] mp = map.shiftFrom(pos); + if (mp!=null) + { + return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)}; + } + } + return null; + } + /** + * locates the region of feature f in the associated sequence's reference frame + * @param f + * @return one or more features corresponding to f + */ + public SequenceFeature[] locateFeature(SequenceFeature f) + { + // this is a stopgap - features broken over exon boundaries will not be + // broken into a collection of feature fragments. + // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence + // need a function like int [] fromrange = map.getRange(from,to) + // need to make subgrouped sequence features. + if (true) { + if (map!=null) { + int[] frange = map.locateInFrom(f.getBegin(), f.getEnd()); + SequenceFeature[] vf = new SequenceFeature[frange.length/2]; + for (int i=0,v=0;i2) + vf[v].setDescription(f.getDescription() +"\nPart "+v); + } + return vf; + } + } + if (false){ + int[] word = getWord(f.getBegin()); + if (word[0]word[1]) + { + f.setEnd(word[0]); + } else { + f.setEnd(word[1]); + } + } + // give up and just return the feature. + return new SequenceFeature[] { f }; + } + + /** + * return a series of contigs on the associated sequence corresponding to + * the from,to interval on the mapped reference frame + * @param from + * @param to + * @return + */ + public int[] locateRange(int from, int to) { + //TODO + return null; + } + /** + * return a series of contigs on the mapped reference frame corresponding to + * the from,to interval on the associated sequence + * @param from + * @param to + * @return + */ + public int[] locateMappedRange(int from, int to) { + //TODO + return null; + } +} -- 1.7.10.2