-/*\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) 2007 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
+{
+ /* (non-Javadoc)
+ * @see java.lang.Object#equals(java.lang.Object)
+ */
+ public boolean equals(MapList obj) {
+ if (obj==this)
+ return true;
+ if (obj!=null && obj.fromRatio==fromRatio && obj.toRatio==toRatio
+ && obj.fromShifts!=null && obj.toShifts!=null) {
+ int i,iSize=fromShifts.size(),j,jSize=obj.fromShifts.size();
+ if (iSize!=jSize)
+ return false;
+ for (i=0,iSize=fromShifts.size(),j=0, jSize=obj.fromShifts.size(); i<iSize;) {
+ int[] mi=(int[]) fromShifts.elementAt(i++);
+ int[] mj=(int[]) obj.fromShifts.elementAt(j++);
+ if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ return false;
+ }
+ iSize=toShifts.size();
+ jSize=obj.toShifts.size();
+ if (iSize!=jSize)
+ return false;
+ for (i=0,j=0; i<iSize;) {
+ int[] mi=(int[]) toShifts.elementAt(i++);
+ int[] mj=(int[]) obj.toShifts.elementAt(j++);
+ if (mi[0]!=mj[0] || mi[1]!=mj[1])
+ return false;
+ }
+ return true;
+ }
+ return false;
+ }
+ 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
+ /**
+ * lowest and highest value in the from Map
+ */
+ int[] fromRange=null;
+ /**
+ * lowest and highest value in the to Map
+ */
+ int[] toRange=null;
+ public int getFromRatio()
+ {
+ return fromRatio;
+ }
+ public int getToRatio()
+ {
+ return toRatio;
+ }
+ public int getFromLowest() {
+ return fromRange[0];
+ }
+ public int getFromHighest() {
+ return fromRange[1];
+ }
+ public int getToLowest() {
+ return toRange[0];
+ }
+ public int getToHighest() {
+ return toRange[1];
+ }
+ private void ensureRange(int[] limits, int pos) {
+ if (limits[0]>pos)
+ limits[0]=pos;
+ if (limits[1]<pos)
+ limits[1]=pos;
+ }
+ public MapList(int from[], int to[], int fromRatio, int toRatio)
+ {
+ fromRange=new int[] { from[0],from[1] };
+ toRange=new int[] { to[0],to[1] };
+
+ fromShifts = new Vector();
+ for (int i=0;i<from.length; i+=2)
+ {
+ ensureRange(fromRange, from[i]);
+ ensureRange(fromRange, from[i+1]);
+
+ fromShifts.addElement(new int[]
+ {from[i], from[i + 1]});
+ }
+ toShifts = new Vector();
+ for (int i=0;i<to.length; i+=2)
+ {
+ ensureRange(toRange, to[i]);
+ ensureRange(toRange, to[i+1]);
+ toShifts.addElement(new int[]
+ {to[i], to[i + 1]});
+ }
+ this.fromRatio=fromRatio;
+ this.toRatio=toRatio;
+ }
+ public MapList(MapList map)
+ {
+ this.fromRange = new int[]
+ { map.fromRange[0], map.fromRange[1] };
+ this.toRange = new int[]
+ { map.toRange[0], map.toRange[1] };
+ this.fromRatio = map.fromRatio;
+ this.toRatio = map.toRatio;
+ if (map.fromShifts != null)
+ {
+ this.fromShifts = new Vector();
+ Enumeration e = map.fromShifts.elements();
+ while (e.hasMoreElements())
+ {
+ int[] el = (int[]) e.nextElement();
+ fromShifts.addElement(new int[]
+ { el[0], el[1] });
+ }
+ }
+ if (map.toShifts != null)
+ {
+ this.toShifts = new Vector();
+ Enumeration e = map.toShifts.elements();
+ while (e.hasMoreElements())
+ {
+ int[] el = (int[]) e.nextElement();
+ toShifts.addElement(new int[]
+ { el[0], el[1] });
+ }
+ }
+ }
+ /**
+ * 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)
+ {
+ int iv=0,ivSize = intVals.size();
+ if (iv>=ivSize)
+ {
+ return null;
+ }
+ int[] intv=(int[]) intVals.elementAt(iv++);
+ int from=intv[0],to=intv[1];
+ if (from > to)
+ {
+ from = intv[1];
+ to=intv[0];
+ }
+ while (iv<ivSize)
+ {
+ intv = (int[]) intVals.elementAt(iv++);
+ 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, direction of mapped symbol in To
+ */
+ 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, direction of mapped symbol in From
+ */
+ 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, pos);
+ if (fromCount==null)
+ {
+ return null;
+ }
+ int fromRemainder=(fromCount[0]-1) % fromRatio;
+ int toCount = 1+(((fromCount[0]-1) / fromRatio) * toRatio);
+ int[] toPos = countToPos(toShifts, 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, toPos[1]};
+ }
+ /**
+ * 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(Vector intVals, int pos)
+ {
+ int count=0,intv[],iv=0,ivSize=intVals.size();
+ while (iv<ivSize)
+ {
+ intv = (int[])intVals.elementAt(iv++);
+ 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(Vector intVals, int pos)
+ {
+ int count = 0, diff = 0, iv=0,ivSize=intVals.size(), intv[] =
+ {
+ 0, 0};
+ while (iv<ivSize)
+ {
+ intv = (int[])intVals.elementAt(iv++);
+ 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);
+ }
+ /**
+ * find series of intervals mapping from start-end in the From map.
+ * @param start position in to map
+ * @param end position in to map
+ * @return series of ranges in from map
+ */
+ public int[] locateInFrom(int start, int end) {
+ // inefficient implementation
+ int fromStart[] = shiftTo(start);
+ int fromEnd[] = shiftTo(end);
+ if (fromStart==null || fromEnd==null)
+ return null;
+ int iv[] = getIntervals(fromShifts, fromStart, fromEnd,fromRatio);
+ return iv;
+ }
+
+ /**
+ * find series of intervals mapping from start-end in the to map.
+ * @param start position in from map
+ * @param end position in from map
+ * @return series of ranges in to map
+ */
+ public int[] locateInTo(int start, int end) {
+ // inefficient implementation
+ int toStart[] = shiftFrom(start);
+ int toEnd[] = shiftFrom(end);
+ if (toStart==null || toEnd==null)
+ return null;
+ int iv[] = getIntervals(toShifts, toStart, toEnd, toRatio);
+ return iv;
+ }
+ /**
+ * like shift - except returns the intervals in the given vector of shifts which were spanned
+ * in traversing fromStart to fromEnd
+ * @param fromShifts2
+ * @param fromStart
+ * @param fromEnd
+ * @param fromRatio2
+ * @return
+ */
+ private int[] getIntervals(Vector fromShifts2, int[] fromStart, int[] fromEnd, int fromRatio2)
+ {
+ // correct for word direction for start and end
+ int startpos = fromStart[0]+fromStart[2]*(fromRatio2-1);
+ int endpos = fromEnd[0]+fromEnd[2]*(fromRatio2-1);
+ int intv=0,intvSize= fromShifts2.size();
+ int iv[],i=0,fs=-1,fe=-1; // containing intervals
+ while (intv<intvSize && (fs==-1 || fe==-1)) {
+ iv = (int[]) fromShifts2.elementAt(intv++);
+ if (iv[0]<=iv[1]) {
+ if (fs==-1 && startpos>=iv[0] && startpos<=iv[1]) {
+ fs = i;
+ }
+ if (fe==-1 && endpos>=iv[0] && endpos<=iv[1]) {
+ fe = i;
+ }
+ } else {
+ if (fs==-1 && startpos<=iv[0] && startpos>=iv[1]) {
+ fs = i;
+ }
+ if (fe==-1 && endpos<=iv[0] && endpos>=iv[1]) {
+ fe = i;
+ }
+ }
+ i++;
+ }
+ if (fs==fe && fe==-1)
+ return null;
+ Vector ranges=new Vector();
+ if (fs<=fe) {
+ intv = fs;
+ i=fs;
+ // truncate initial interval
+ iv = (int[]) fromShifts2.elementAt(intv++);
+ iv = new int[] { iv[0], iv[1]};// clone
+ if (i==fs)
+ iv[0] = startpos;
+ while (i!=fe) {
+ ranges.addElement(iv); // add initial range
+ iv = (int[]) fromShifts2.elementAt(intv++); // get next interval
+ iv = new int[] { iv[0], iv[1]};// clone
+ i++;
+ }
+ if (i==fe)
+ iv[1] = endpos;
+ ranges.addElement(iv); // add only - or final range
+ } else {
+ // walk from end of interval.
+ i=fromShifts2.size()-1;
+ while (i>fs) {
+ i--;
+ }
+ iv = (int[]) fromShifts2.elementAt(i);
+ iv = new int[] { iv[1], iv[0]};// reverse and clone
+ // truncate initial interval
+ if (i==fs)
+ {
+ iv[0] = startpos;
+ }
+ while (i!=fe) {
+ ranges.addElement(iv); // add (truncated) reversed interval
+ iv = (int[]) fromShifts2.elementAt(--i);
+ iv = new int[] { iv[1], iv[0] }; // reverse and clone
+ }
+ if (i==fe) {
+ // interval is already reversed
+ iv[1] = endpos;
+ }
+ ranges.addElement(iv); // add only - or final range
+ }
+ // create array of start end intervals.
+ int[] range = null;
+ if (ranges!=null && ranges.size()>0)
+ {
+ range = new int[ranges.size()*2];
+ intv = 0;
+ intvSize=ranges.size();
+ i=0;
+ while (intv<intvSize)
+ {
+ iv = (int[]) ranges.elementAt(intv);
+ range[i++] = iv[0];
+ range[i++] = iv[1];
+ ranges.setElementAt(null, intv++); // remove
+ }
+ }
+ return range;
+ }
+ /**
+ * test routine. not incremental.
+ * @param ml
+ * @param fromS
+ * @param fromE
+ */
+ 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]+" ("+too[2]+")");
+ System.out.print("\t+--+\t");
+ int[] toofrom=ml.shiftTo(too[0]);
+ if (toofrom != null)
+ {
+ if (toofrom[0]!=from)
+ {
+ System.err.println("Mapping not reflexive:" + from + " " + too[0] +
+ "->" + toofrom[0]);
+ }
+ System.out.println("ShiftTo(" + too[0] + ")==" + toofrom[0] + " % " +
+ toofrom[1]+" ("+toofrom[2]+")");
+ }
+ 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(",");
+ }
+ }
+ //test range function
+ System.out.print("\nTest locateInFrom\n");
+ {
+ int f=mmap[0][2],t=mmap[0][3];
+ while (f<t) {
+ System.out.println("Range "+f+" to "+t);
+ int rng[] = ml.locateInFrom(f,t);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInFrom(t,f);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\n");
+ f++;t--;
+ }
+ }
+ System.out.print("\n");
+ mmap = ml.makeToMap();
+ System.out.println("ToMap : (" + 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");
+ //test range function
+ System.out.print("\nTest locateInTo\n");
+ {
+ int f=mmap[0][2],t=mmap[0][3];
+ while (f<t) {
+ System.out.println("Range "+f+" to "+t);
+ int rng[] = ml.locateInTo(f,t);
+ if (rng!=null) {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ System.out.print("\nReversed\n");
+ rng = ml.locateInTo(t,f);
+ if (rng!=null)
+ {
+ for (int i=0; i<rng.length; i++) {
+ System.out.print(rng[i]+((i%2==0) ? "," : ";"));
+ }
+ }
+ else
+ {
+ System.out.println("No range!");
+ }
+ f++; t--;
+ 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);
+ MapList ml2 = new MapList(new int[] { 1, 60 },
+ new int[] { 1, 20 }, 3, 1);
+ // test internal consistency
+ int to[] = new int[51];
+ MapList.testMap(ml, 1, 60);
+ /*
+ 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 / blobdiff