-package jalview.datamodel;\r
-\r
-import jalview.util.MapList;\r
-\r
-public class Mapping {\r
- /**\r
- * Contains the\r
- * start-end pairs mapping from \r
- * the associated sequence to the \r
- * sequence in the database \r
- * coordinate system\r
- * it also takes care of step difference between coordinate systems\r
- */\r
- MapList map=null;\r
- /**\r
- * The seuqence that map maps the associated seuqence to (if any).\r
- */\r
- SequenceI to=null;\r
- public Mapping(MapList map) {\r
- super();\r
- this.map = map;\r
- }\r
- /**\r
- * create a new mapping from\r
- * @param exon int[] {start,end,start,end} series on associated sequence\r
- * @param is int[] {start,end,...} ranges on the reference frame being mapped to\r
- * @param i step size on associated sequence\r
- * @param j step size on mapped frame\r
- */\r
- public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)\r
- {\r
- map = new MapList(exon, is, i, j);\r
- }\r
-\r
- /**\r
- * @return the map\r
- */\r
- public MapList getMap() {\r
- return map;\r
- }\r
-\r
- /**\r
- * @param map the map to set\r
- */\r
- public void setMap(MapList map) {\r
- this.map = map;\r
- }\r
- public boolean equals(Mapping other) {\r
- if (other==null)\r
- return false;\r
- if (other==this)\r
- return true;\r
- if ((map!=null && other.map==null) || (map==null && other.map!=null))\r
- return false;\r
- if (map.equals(other.map))\r
- return true;\r
- return false;\r
- }\r
- /**\r
- * get the 'initial' position in the associated\r
- * sequence for a position in the mapped reference frame\r
- * @param mpos\r
- * @return\r
- */\r
- public int getPosition(int mpos) \r
- {\r
- if (map!=null) {\r
- int[] mp = map.shiftTo(mpos);\r
- if (mp!=null)\r
- {\r
- return mp[0];\r
- }\r
- }\r
- return mpos;\r
- }\r
- public int[] getWord(int mpos) {\r
- if (map!=null) {\r
- int[] mp=map.shiftTo(mpos);\r
- if (mp!=null) {\r
- return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)}; \r
- }\r
- }\r
- return null;\r
- }\r
- /**\r
- * width of mapped unit in associated sequence \r
- * \r
- */\r
- public int getWidth() {\r
- if (map!=null) {\r
- return map.getFromRatio();\r
- }\r
- return 1;\r
- }\r
-\r
- /**\r
- * width of unit in mapped reference frame\r
- * @return\r
- */\r
- public int getMappedWidth() {\r
- if (map!=null) {\r
- return map.getToRatio();\r
- }\r
- return 1;\r
- }\r
- /**\r
- * get mapped position in the associated\r
- * reference frame for position pos in the\r
- * associated sequence.\r
- * @param pos\r
- * @return\r
- */\r
- public int getMappedPosition(int pos) {\r
- if (map!=null) {\r
- int[] mp = map.shiftFrom(pos);\r
- if (mp!=null)\r
- {\r
- return mp[0];\r
- }\r
- }\r
- return pos;\r
- }\r
- public int[] getMappedWord(int pos) {\r
- if (map!=null) {\r
- int[] mp = map.shiftFrom(pos);\r
- if (mp!=null)\r
- {\r
- return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};\r
- }\r
- }\r
- return null;\r
- }\r
- /**\r
- * locates the region of feature f in the associated sequence's reference frame \r
- * @param f\r
- * @return one or more features corresponding to f\r
- */\r
- public SequenceFeature[] locateFeature(SequenceFeature f)\r
- {\r
- // this is a stopgap - features broken over exon boundaries will not be\r
- // broken into a collection of feature fragments.\r
- // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence\r
- // need a function like int [] fromrange = map.getRange(from,to)\r
- // need to make subgrouped sequence features.\r
- if (true) {\r
- if (map!=null) {\r
- int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());\r
- SequenceFeature[] vf = new SequenceFeature[frange.length/2];\r
- for (int i=0,v=0;i<frange.length;i+=2) {\r
- vf[v] = new SequenceFeature(f);\r
- vf[v].setBegin(frange[i]);\r
- vf[v].setEnd(frange[i+1]);\r
- if (frange.length>2)\r
- vf[v].setDescription(f.getDescription() +"\nPart "+v);\r
- }\r
- return vf;\r
- }\r
- }\r
- if (false){\r
- int[] word = getWord(f.getBegin());\r
- if (word[0]<word[1]) \r
- {\r
- f.setBegin(word[0]);\r
- } else {\r
- f.setBegin(word[1]);\r
- }\r
- word = getWord(f.getEnd());\r
- if (word[0]>word[1]) \r
- {\r
- f.setEnd(word[0]);\r
- } else {\r
- f.setEnd(word[1]);\r
- }\r
- }\r
- // give up and just return the feature.\r
- return new SequenceFeature[] { f };\r
- }\r
- \r
- /**\r
- * return a series of contigs on the associated sequence corresponding to\r
- * the from,to interval on the mapped reference frame\r
- * @param from\r
- * @param to\r
- * @return\r
- */\r
- public int[] locateRange(int from, int to) {\r
- //TODO\r
- return null;\r
- }\r
- /**\r
- * return a series of contigs on the mapped reference frame corresponding to\r
- * the from,to interval on the associated sequence\r
- * @param from\r
- * @param to\r
- * @return\r
- */\r
- public int[] locateMappedRange(int from, int to) {\r
- //TODO \r
- return null;\r
- }\r
-}\r
+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;i<frange.length;i+=2) {
+ vf[v] = new SequenceFeature(f);
+ vf[v].setBegin(frange[i]);
+ vf[v].setEnd(frange[i+1]);
+ if (frange.length>2)
+ vf[v].setDescription(f.getDescription() +"\nPart "+v);
+ }
+ return vf;
+ }
+ }
+ if (false){
+ int[] word = getWord(f.getBegin());
+ if (word[0]<word[1])
+ {
+ f.setBegin(word[0]);
+ } else {
+ f.setBegin(word[1]);
+ }
+ word = getWord(f.getEnd());
+ 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff