--- /dev/null
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.util;\r
+\r
+import java.util.*;\r
+\r
+/**\r
+ * MapList\r
+ * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range\r
+ * Use at your own risk!\r
+ * TODO: efficient implementation of private posMap method\r
+ * TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery)\r
+ * TODO: optimize to use int[][] arrays rather than vectors.\r
+ */\r
+public class MapList\r
+{\r
+ public Vector fromShifts;\r
+ public Vector toShifts;\r
+ int fromRatio; // number of steps in fromShifts to one toRatio unit\r
+ int toRatio; // number of steps in toShifts to one fromRatio\r
+ public MapList(int from[], int to[], int fromRatio, int toRatio)\r
+ {\r
+ fromShifts = new Vector();\r
+ for (int i=0;i<from.length; i+=2)\r
+ fromShifts.add(new int[] { from[i], from[i+1]});\r
+ toShifts = new Vector();\r
+ for (int i=0;i<to.length; i+=2)\r
+ toShifts.add(new int[] { to[i], to[i+1]});\r
+ this.fromRatio=fromRatio;\r
+ this.toRatio=toRatio;\r
+ }\r
+ /**\r
+ * get all mapped positions from 'from' to 'to'\r
+ * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}\r
+ */\r
+ public int[][] makeFromMap() {\r
+ return posMap(fromShifts, fromRatio, toShifts, toRatio);\r
+ }\r
+ /**\r
+ * get all mapped positions from 'to' to 'from'\r
+ * @return int[to position]=position mapped in from\r
+ */\r
+ public int[][] makeToMap() {\r
+ return posMap(toShifts,toRatio, fromShifts, fromRatio);\r
+ }\r
+ /**\r
+ * construct an int map for intervals in intVals\r
+ * @param intVals\r
+ * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position\r
+ */\r
+ private int[][] posMap(Vector intVals, int ratio, Vector toIntVals, int toRatio) {\r
+ Iterator iv = intVals.iterator();\r
+ if (!iv.hasNext())\r
+ return null;\r
+ int[] intv=(int[]) iv.next();\r
+ int from=intv[0],to=intv[1];\r
+ if (from>to) {\r
+ from = intv[1];\r
+ to=intv[0];\r
+ }\r
+ while (iv.hasNext()) {\r
+ intv = (int[]) iv.next();\r
+ if (intv[0]<from)\r
+ from=intv[0];\r
+ if (intv[1]<from)\r
+ from=intv[1];\r
+ if (intv[0]>to)\r
+ to=intv[0];\r
+ if (intv[1]>to)\r
+ to=intv[1];\r
+ }\r
+ int tF=0,tT=0;\r
+ int mp[][] = new int[to-from+2][];\r
+ for (int i=0;i<mp.length; i++) {\r
+ int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);\r
+ if (m!=null) {\r
+ if (i==0) {\r
+ tF=tT=m[0];\r
+ } else {\r
+ if (m[0]<tF) {\r
+ tF=m[0];\r
+ }\r
+ if (m[0]>tT) {\r
+ tT=m[0];\r
+ }\r
+ }\r
+ }\r
+ mp[i] = m;\r
+ }\r
+ int[][] map=new int[][] { new int[]{from, to, tF, tT}, new int[to-from+2]};\r
+\r
+ map[0][2] = tF;\r
+ map[0][3] = tT;\r
+ \r
+ for (int i=0;i<mp.length; i++) {\r
+ if (mp[i]!=null) {\r
+ map[1][i] = mp[i][0]-tF;\r
+ } else {\r
+ map[1][i] = -1; // indicates an out of range mapping\r
+ }\r
+ }\r
+ return map;\r
+ }\r
+ /**\r
+ * addShift\r
+ * @param pos start position for shift (in original reference frame)\r
+ * @param shift length of shift\r
+ *\r
+ public void addShift(int pos, int shift)\r
+ {\r
+ int sidx = 0;\r
+ int[] rshift=null;\r
+ while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)\r
+ sidx++;\r
+ if (sidx==shifts.size())\r
+ shifts.insertElementAt(new int[] { pos, shift}, sidx);\r
+ else\r
+ rshift[1]+=shift;\r
+ }\r
+*/\r
+ /**\r
+ * shift from pos to To(pos)\r
+ *\r
+ * @param pos int\r
+ * @return int shifted position in To, frameshift in From\r
+ */\r
+ public int[] shiftFrom(int pos)\r
+ {\r
+ return shift(pos, fromShifts, fromRatio, toShifts, toRatio);\r
+ }\r
+\r
+ /**\r
+ * inverse of shiftFrom - maps pos in To to a position in From\r
+ * @param pos (in To)\r
+ * @return shifted position in From, frameshift in To\r
+ */\r
+ public int[] shiftTo(int pos) {\r
+ return shift(pos, toShifts, toRatio, fromShifts, fromRatio);\r
+ }\r
+ /**\r
+ * \r
+ * @param fromShifts\r
+ * @param fromRatio\r
+ * @param toShifts\r
+ * @param toRatio\r
+ * @return\r
+ */\r
+ private int[] shift(int pos, Vector fromShifts, int fromRatio, Vector toShifts, int toRatio) {\r
+ int[] fromCount = countPos(fromShifts.iterator(), pos);\r
+ if (fromCount==null)\r
+ return null;\r
+ int fromRemainder=(fromCount[0]-1) % fromRatio;\r
+ int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);\r
+ int[] toPos = countToPos(toShifts.iterator(), toCount);\r
+ if (toPos==null)\r
+ return null; // throw new Error("Bad Mapping!");\r
+ //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);\r
+ return new int[] {toPos[0], fromRemainder};\r
+ }\r
+ /**\r
+ * count how many positions pos is along the series of intervals.\r
+ * @param intVals\r
+ * @param pos\r
+ * @return number of positions or null if pos is not within intervals\r
+ */\r
+ private int[] countPos(Iterator intVals, int pos) {\r
+ int count=0,intv[];\r
+ while (intVals.hasNext()) {\r
+ intv = (int[])intVals.next();\r
+ if (intv[0] <= intv[1]) {\r
+ if (pos>=intv[0] && pos<=intv[1]) {\r
+ return new int[] { count+pos-intv[0]+1, +1 };\r
+ } else {\r
+ count+=intv[1]-intv[0]+1;\r
+ }\r
+ } else {\r
+ if (pos>=intv[1] && pos<=intv[0]) {\r
+ return new int[] { count+intv[0]-pos+1, -1 };\r
+ } else {\r
+ count+=intv[0]-intv[1]+1;\r
+ }\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+ /**\r
+ * count out pos positions into a series of intervals and return the position\r
+ * @param intVals\r
+ * @param pos\r
+ * @return position pos in interval set\r
+ */\r
+ private int[] countToPos(Iterator intVals, int pos) {\r
+ int count=0,diff=0,intv[]={0,0};\r
+ while (intVals.hasNext()) {\r
+ intv = (int[])intVals.next();\r
+ diff = intv[1]-intv[0];\r
+ if (diff>=0) {\r
+ if (pos<=count+1+diff) {\r
+ return new int[] { pos-count-1+intv[0],+1 };\r
+ } else {\r
+ count+=1+diff;\r
+ }\r
+ } else {\r
+ if (pos<=count+1-diff) {\r
+ return new int[] { intv[0]-(pos-count-1),-1 };\r
+ } else {\r
+ count+=1-diff;\r
+ }\r
+ }\r
+ }\r
+ return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);\r
+ }\r
+ public static void testMap(MapList ml, int fromS,int fromE) {\r
+ for (int from=1; from<=25; from++) {\r
+ int[] too=ml.shiftFrom(from);\r
+ System.out.print("ShiftFrom("+from+")==");\r
+ if (too==null)\r
+ System.out.print("NaN\n");\r
+ else {\r
+ System.out.print(too[0]+" % "+too[1]);\r
+ System.out.print("\t+--+\t");\r
+ int[] toofrom=ml.shiftTo(too[0]);\r
+ if (toofrom!=null)\r
+ System.out.println("ShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);\r
+ else\r
+ System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");\r
+ }\r
+ }\r
+ int mmap[][] = ml.makeFromMap();\r
+ System.out.println("FromMap : ("+mmap[0][0]+" "+mmap[0][1]+" "+mmap[0][2]+" "+mmap[0][3]+" ");\r
+ for (int i=1;i<=mmap[1].length; i++) {\r
+ if (mmap[1][i-1]==-1) {\r
+ System.out.print(i+"=XXX");\r
+ \r
+ } else {\r
+ System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));\r
+ }\r
+ if (i % 20==0)\r
+ System.out.print("\n");\r
+ else\r
+ System.out.print(",");\r
+ }\r
+ System.out.print("\n");\r
+ }\r
+ public static void main(String argv[]) {\r
+ MapList ml=new MapList(new int[] { 1,5,10,15,25,20}, \r
+ new int[] { 51,1}, 1, 3);\r
+ MapList ml1=new MapList(new int[] { 1,3,17,4}, \r
+ new int[] { 51,1}, 1, 3);\r
+ \r
+ // test internal consistency\r
+ int to[] = new int[51];\r
+ MapList.testMap(ml, 1, 25);\r
+ /*\r
+ for (int from=1; from<=51; from++) {\r
+ int[] too=ml.shiftTo(from);\r
+ int[] toofrom=ml.shiftFrom(too[0]);\r
+ System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);\r
+ }*/\r
+ System.out.print("Success?\n"); // if we get here - something must be working!\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / commitdiff