2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.util;
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25 * Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range
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26 * Use at your own risk!
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27 * TODO: efficient implementation of private posMap method
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28 * TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery)
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29 * TODO: optimize to use int[][] arrays rather than vectors.
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31 public class MapList
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33 public Vector fromShifts;
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34 public Vector toShifts;
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35 int fromRatio; // number of steps in fromShifts to one toRatio unit
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36 int toRatio; // number of steps in toShifts to one fromRatio
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37 public MapList(int from[], int to[], int fromRatio, int toRatio)
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39 fromShifts = new Vector();
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40 for (int i=0;i<from.length; i+=2)
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41 fromShifts.add(new int[] { from[i], from[i+1]});
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42 toShifts = new Vector();
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43 for (int i=0;i<to.length; i+=2)
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44 toShifts.add(new int[] { to[i], to[i+1]});
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45 this.fromRatio=fromRatio;
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46 this.toRatio=toRatio;
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49 * get all mapped positions from 'from' to 'to'
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50 * @return int[][] { int[] { fromStart, fromFinish, toStart, toFinish }, int [fromFinish-fromStart+2] { toStart..toFinish mappings}}
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52 public int[][] makeFromMap() {
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53 return posMap(fromShifts, fromRatio, toShifts, toRatio);
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56 * get all mapped positions from 'to' to 'from'
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57 * @return int[to position]=position mapped in from
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59 public int[][] makeToMap() {
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60 return posMap(toShifts,toRatio, fromShifts, fromRatio);
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63 * construct an int map for intervals in intVals
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65 * @return int[] { from, to pos in range }, int[range.to-range.from+1] returning mapped position
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67 private int[][] posMap(Vector intVals, int ratio, Vector toIntVals, int toRatio) {
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68 Iterator iv = intVals.iterator();
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71 int[] intv=(int[]) iv.next();
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72 int from=intv[0],to=intv[1];
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77 while (iv.hasNext()) {
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78 intv = (int[]) iv.next();
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89 int mp[][] = new int[to-from+2][];
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90 for (int i=0;i<mp.length; i++) {
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91 int[] m = shift(i+from,intVals,ratio,toIntVals, toRatio);
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106 int[][] map=new int[][] { new int[]{from, to, tF, tT}, new int[to-from+2]};
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111 for (int i=0;i<mp.length; i++) {
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113 map[1][i] = mp[i][0]-tF;
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115 map[1][i] = -1; // indicates an out of range mapping
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122 * @param pos start position for shift (in original reference frame)
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123 * @param shift length of shift
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125 public void addShift(int pos, int shift)
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129 while (sidx<shifts.size() && (rshift=(int[]) shifts.elementAt(sidx))[0]<pos)
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131 if (sidx==shifts.size())
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132 shifts.insertElementAt(new int[] { pos, shift}, sidx);
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138 * shift from pos to To(pos)
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141 * @return int shifted position in To, frameshift in From
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143 public int[] shiftFrom(int pos)
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145 return shift(pos, fromShifts, fromRatio, toShifts, toRatio);
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149 * inverse of shiftFrom - maps pos in To to a position in From
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150 * @param pos (in To)
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151 * @return shifted position in From, frameshift in To
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153 public int[] shiftTo(int pos) {
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154 return shift(pos, toShifts, toRatio, fromShifts, fromRatio);
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158 * @param fromShifts
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164 private int[] shift(int pos, Vector fromShifts, int fromRatio, Vector toShifts, int toRatio) {
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165 int[] fromCount = countPos(fromShifts.iterator(), pos);
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166 if (fromCount==null)
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168 int fromRemainder=(fromCount[0]-1) % fromRatio;
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169 int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
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170 int[] toPos = countToPos(toShifts.iterator(), toCount);
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172 return null; // throw new Error("Bad Mapping!");
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173 //System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount);
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174 return new int[] {toPos[0], fromRemainder};
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177 * count how many positions pos is along the series of intervals.
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180 * @return number of positions or null if pos is not within intervals
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182 private int[] countPos(Iterator intVals, int pos) {
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183 int count=0,intv[];
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184 while (intVals.hasNext()) {
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185 intv = (int[])intVals.next();
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186 if (intv[0] <= intv[1]) {
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187 if (pos>=intv[0] && pos<=intv[1]) {
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188 return new int[] { count+pos-intv[0]+1, +1 };
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190 count+=intv[1]-intv[0]+1;
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193 if (pos>=intv[1] && pos<=intv[0]) {
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194 return new int[] { count+intv[0]-pos+1, -1 };
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196 count+=intv[0]-intv[1]+1;
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203 * count out pos positions into a series of intervals and return the position
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206 * @return position pos in interval set
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208 private int[] countToPos(Iterator intVals, int pos) {
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209 int count=0,diff=0,intv[]={0,0};
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210 while (intVals.hasNext()) {
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211 intv = (int[])intVals.next();
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212 diff = intv[1]-intv[0];
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214 if (pos<=count+1+diff) {
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215 return new int[] { pos-count-1+intv[0],+1 };
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220 if (pos<=count+1-diff) {
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221 return new int[] { intv[0]-(pos-count-1),-1 };
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227 return null;//(diff<0) ? (intv[1]-1) : (intv[0]+1);
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229 public static void testMap(MapList ml, int fromS,int fromE) {
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230 for (int from=1; from<=25; from++) {
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231 int[] too=ml.shiftFrom(from);
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232 System.out.print("ShiftFrom("+from+")==");
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234 System.out.print("NaN\n");
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236 System.out.print(too[0]+" % "+too[1]);
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237 System.out.print("\t+--+\t");
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238 int[] toofrom=ml.shiftTo(too[0]);
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240 System.out.println("ShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
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242 System.out.println("ShiftTo("+too[0]+")=="+"NaN! - not Bijective Mapping!");
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245 int mmap[][] = ml.makeFromMap();
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246 System.out.println("FromMap : ("+mmap[0][0]+" "+mmap[0][1]+" "+mmap[0][2]+" "+mmap[0][3]+" ");
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247 for (int i=1;i<=mmap[1].length; i++) {
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248 if (mmap[1][i-1]==-1) {
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249 System.out.print(i+"=XXX");
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252 System.out.print(i+"="+(mmap[0][2]+mmap[1][i-1]));
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255 System.out.print("\n");
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257 System.out.print(",");
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259 System.out.print("\n");
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261 public static void main(String argv[]) {
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262 MapList ml=new MapList(new int[] { 1,5,10,15,25,20},
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263 new int[] { 51,1}, 1, 3);
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264 MapList ml1=new MapList(new int[] { 1,3,17,4},
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265 new int[] { 51,1}, 1, 3);
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267 // test internal consistency
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268 int to[] = new int[51];
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269 MapList.testMap(ml, 1, 25);
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271 for (int from=1; from<=51; from++) {
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272 int[] too=ml.shiftTo(from);
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273 int[] toofrom=ml.shiftFrom(too[0]);
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274 System.out.println("ShiftFrom("+from+")=="+too[0]+" % "+too[1]+"\t+-+\tShiftTo("+too[0]+")=="+toofrom[0]+" % "+toofrom[1]);
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276 System.out.print("Success?\n"); // if we get here - something must be working!
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