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