X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMapList.java;h=8ff640b582b417f46353d282c47b22f61c942a89;hb=9b3219d225131af5a165553f206ebf8da304ee23;hp=26416599e95984a587291851a08c814200afe1d6;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java index 2641659..8ff640b 100644 --- a/src/jalview/util/MapList.java +++ b/src/jalview/util/MapList.java @@ -41,12 +41,12 @@ public class MapList /* * Subregions (base 1) described as { [start1, end1], [start2, end2], ...} */ - private List fromShifts = new ArrayList(); + private List fromShifts; /* * Same format as fromShifts, for the 'mapped to' sequence */ - private List toShifts = new ArrayList(); + private List toShifts; /* * number of steps in fromShifts to one toRatio unit @@ -73,6 +73,15 @@ public class MapList private int toHighest; /** + * Constructor + */ + public MapList() + { + fromShifts = new ArrayList(); + toShifts = new ArrayList(); + } + + /** * Two MapList objects are equal if they are the same object, or they both * have populated shift ranges and all values are the same. */ @@ -180,7 +189,8 @@ public class MapList } /** - * Constructor. + * Constructor given from and to ranges as [start1, end1, start2, end2,...]. + * If any end is equal to the next start, the ranges will be merged. * * @param from * contiguous regions as [start1, end1, start2, end2, ...] @@ -193,27 +203,47 @@ public class MapList */ public MapList(int from[], int to[], int fromRatio, int toRatio) { + this(); this.fromRatio = fromRatio; this.toRatio = toRatio; fromLowest = from[0]; fromHighest = from[1]; + int added = 0; + for (int i = 0; i < from.length; i += 2) { fromLowest = Math.min(fromLowest, from[i]); fromHighest = Math.max(fromHighest, from[i + 1]); - - fromShifts.add(new int[] - { from[i], from[i + 1] }); + if (added > 0 && from[i] == fromShifts.get(added - 1)[1]) + { + /* + * this range starts where the last ended - just extend it + */ + fromShifts.get(added - 1)[1] = from[i + 1]; + } + else + { + fromShifts.add(new int[] { from[i], from[i + 1] }); + added++; + } } toLowest = to[0]; toHighest = to[1]; + added = 0; for (int i = 0; i < to.length; i += 2) { toLowest = Math.min(toLowest, to[i]); toHighest = Math.max(toHighest, to[i + 1]); - toShifts.add(new int[] - { to[i], to[i + 1] }); + if (added > 0 && to[i] == toShifts.get(added - 1)[1]) + { + toShifts.get(added - 1)[1] = to[i + 1]; + } + else + { + toShifts.add(new int[] { to[i], to[i + 1] }); + added++; + } } } @@ -224,6 +254,7 @@ public class MapList */ public MapList(MapList map) { + this(); // TODO not used - remove? this.fromLowest = map.fromLowest; this.fromHighest = map.fromHighest; @@ -236,16 +267,14 @@ public class MapList { for (int[] r : map.fromShifts) { - fromShifts.add(new int[] - { r[0], r[1] }); + fromShifts.add(new int[] { r[0], r[1] }); } } if (map.toShifts != null) { for (int[] r : map.toShifts) { - toShifts.add(new int[] - { r[0], r[1] }); + toShifts.add(new int[] { r[0], r[1] }); } } } @@ -258,9 +287,10 @@ public class MapList * @param fromRatio * @param toRatio */ - public MapList(List fromRange, List toRange, - int fromRatio, int toRatio) + public MapList(List fromRange, List toRange, int fromRatio, + int toRatio) { + this(); this.fromShifts = fromRange; this.toShifts = toRange; this.fromRatio = fromRatio; @@ -268,7 +298,8 @@ public class MapList fromLowest = Integer.MAX_VALUE; fromHighest = 0; - for (int[] range : fromRange) { + for (int[] range : fromRange) + { fromLowest = Math.min(fromLowest, range[0]); fromHighest = Math.max(fromHighest, range[1]); } @@ -313,8 +344,7 @@ public class MapList * returning mapped position */ private int[][] posMap(List shiftTo, int ratio, - List shiftFrom, - int toRatio) + List shiftFrom, int toRatio) { // TODO not used - remove?? int iv = 0, ivSize = shiftTo.size(); @@ -374,9 +404,8 @@ public class MapList } mp[i] = m; } - int[][] map = new int[][] - { new int[] - { from, to, tF, tT }, new int[to - from + 2] }; + int[][] map = new int[][] { new int[] { from, to, tF, tT }, + new int[to - from + 2] }; map[0][2] = tF; map[0][3] = tT; @@ -461,8 +490,7 @@ public class MapList return null; // throw new Error("Bad Mapping!"); } // System.out.println(fromCount[0]+" "+fromCount[1]+" "+toCount); - return new int[] - { toPos[0], fromRemainder, toPos[1] }; + return new int[] { toPos[0], fromRemainder, toPos[1] }; } /** @@ -482,8 +510,7 @@ public class MapList { if (pos >= intv[0] && pos <= intv[1]) { - return new int[] - { count + pos - intv[0] + 1, +1 }; + return new int[] { count + pos - intv[0] + 1, +1 }; } else { @@ -494,8 +521,7 @@ public class MapList { if (pos >= intv[1] && pos <= intv[0]) { - return new int[] - { count + intv[0] - pos + 1, -1 }; + return new int[] { count + intv[0] - pos + 1, -1 }; } else { @@ -516,8 +542,7 @@ public class MapList protected static int[] countToPos(List shiftFrom, int pos) { int count = 0, diff = 0, iv = 0, ivSize = shiftFrom.size(); - int[] intv = - { 0, 0 }; + int[] intv = { 0, 0 }; while (iv < ivSize) { intv = shiftFrom.get(iv++); @@ -526,8 +551,7 @@ public class MapList { if (pos <= count + 1 + diff) { - return new int[] - { pos - count - 1 + intv[0], +1 }; + return new int[] { pos - count - 1 + intv[0], +1 }; } else { @@ -538,8 +562,7 @@ public class MapList { if (pos <= count + 1 - diff) { - return new int[] - { intv[0] - (pos - count - 1), -1 }; + return new int[] { intv[0] - (pos - count - 1), -1 }; } else { @@ -597,8 +620,7 @@ public class MapList * region to final position of ending region inclusive */ protected static int[] getIntervals(List shiftFrom, - int[] fromStart, - int[] fromEnd, int fromRatio2) + int[] fromStart, int[] fromEnd, int fromRatio2) { if (fromStart == null || fromEnd == null) { @@ -688,8 +710,7 @@ public class MapList i = fs; // truncate initial interval iv = shiftFrom.get(intv++); - iv = new int[] - { iv[0], iv[1] };// clone + iv = new int[] { iv[0], iv[1] };// clone if (i == fs) { iv[0] = startpos; @@ -698,8 +719,7 @@ public class MapList { ranges.add(iv); // add initial range iv = shiftFrom.get(intv++); // get next interval - iv = new int[] - { iv[0], iv[1] };// clone + iv = new int[] { iv[0], iv[1] };// clone i++; } if (i == fe) @@ -717,8 +737,7 @@ public class MapList i--; } iv = shiftFrom.get(i); - iv = new int[] - { iv[1], iv[0] };// reverse and clone + iv = new int[] { iv[1], iv[0] };// reverse and clone // truncate initial interval if (i == fs) { @@ -728,8 +747,7 @@ public class MapList { // fix apparent logic bug when fe==-1 ranges.add(iv); // add (truncated) reversed interval iv = shiftFrom.get(i); - iv = new int[] - { iv[1], iv[0] }; // reverse and clone + iv = new int[] { iv[1], iv[0] }; // reverse and clone } if (i == fe) { @@ -788,8 +806,7 @@ public class MapList int[] mp = shiftTo(mpos); if (mp != null) { - return new int[] - { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) }; + return new int[] { mp[0], mp[0] + mp[2] * (getFromRatio() - 1) }; } return null; } @@ -818,8 +835,7 @@ public class MapList int[] mp = shiftFrom(pos); if (mp != null) { - return new int[] - { mp[0], mp[0] + mp[2] * (getToRatio() - 1) }; + return new int[] { mp[0], mp[0] + mp[2] * (getToRatio() - 1) }; } return null; } @@ -859,4 +875,26 @@ public class MapList .getToHighest())); } } + + /** + * String representation - for debugging, not guaranteed not to change + */ + @Override + public String toString() + { + StringBuilder sb = new StringBuilder(64); + sb.append("From (").append(fromRatio).append(":").append(toRatio) + .append(") ["); + for (int[] shift : fromShifts) + { + sb.append(" ").append(Arrays.toString(shift)); + } + sb.append(" ] To ["); + for (int[] shift : toShifts) + { + sb.append(" ").append(Arrays.toString(shift)); + } + sb.append(" ]"); + return sb.toString(); + } }