/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.util;
* addShift
*
* @param pos
- * start position for shift (in original reference frame)
+ * start position for shift (in original reference frame)
* @param shift
- * length of 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; }
+ * 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
+ * int
* @return int shifted position in To, frameshift in From, direction of mapped
* symbol in To
*/
* inverse of shiftFrom - maps pos in To to a position in From
*
* @param pos
- * (in To)
+ * (in To)
* @return shifted position in From, frameshift in To, direction of mapped
* symbol in From
*/
* find series of intervals mapping from start-end in the From map.
*
* @param start
- * position in to map
+ * position in to map
* @param end
- * position in to map
+ * 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); // needs to be inclusive of end of symbol
- // position
+ // position
if (fromStart == null || fromEnd == null)
return null;
int iv[] = getIntervals(fromShifts, fromStart, fromEnd, fromRatio);
* find series of intervals mapping from start-end in the to map.
*
* @param start
- * position in from map
+ * position in from map
* @param end
- * position in from map
+ * position in from map
* @return series of ranges in to map
*/
public int[] locateInTo(int start, int end)
startpos = fromStart[0]; // first position in fromStart
endpos = fromEnd[0]; // last position in fromEnd
int endindx = (fromRatio2 - 1); // additional positions to get to last
- // position from endpos
+ // position from endpos
int intv = 0, intvSize = fromShifts2.size();
int iv[], i = 0, fs = -1, fe_s = -1, fe = -1; // containing intervals
// search intervals to locate ones containing startpos and count endindx
// positions on from endpos
- while (intv < intvSize && ( fs == -1 || fe == -1))
+ while (intv < intvSize && (fs == -1 || fe == -1))
{
iv = (int[]) fromShifts2.elementAt(intv++);
- if (fe_s>-1)
+ if (fe_s > -1)
{
endpos = iv[0]; // start counting from beginning of interval
endindx--; // inclusive of endpos
if (endpos + endindx <= iv[1])
{
fe = i;
- endpos = endpos + endindx; // end of end token is within this interval
+ endpos = endpos + endindx; // end of end token is within this
+ // interval
}
else
{
- endindx -= iv[1] - endpos; // skip all this interval too
+ endindx -= iv[1] - endpos; // skip all this interval too
}
}
}
if (endpos - endindx >= iv[1])
{
fe = i;
- endpos = endpos - endindx; // end of end token is within this interval
+ endpos = endpos - endindx; // end of end token is within this
+ // interval
}
else
{
- endindx -= endpos-iv[1]; // skip all this interval too
+ endindx -= endpos - iv[1]; // skip all this interval too
}
}
}
* get the 'initial' position of mpos in To
*
* @param mpos
- * position in from
+ * position in from
* @return position of first word in to reference frame
*/
public int getToPosition(int mpos)
* get range of positions in To frame for the mpos word in From
*
* @param mpos
- * position in From
+ * position in From
* @return null or int[] first position in To for mpos, last position in to
* for Mpos
*/
// test internal consistency
int to[] = new int[51];
MapList.testMap(ml, 1, 60);
- MapList mldna = new MapList(new int[] { 2,2,6,8,12,16}, new int[] { 1,3},3,1);
- int[] frm = mldna.locateInFrom(1,1);
- testLocateFrom(mldna, 1,1,new int[] { 2,2,6,7});
- MapList.testMap(mldna, 1,3);
+ MapList mldna = new MapList(new int[]
+ { 2, 2, 6, 8, 12, 16 }, new int[]
+ { 1, 3 }, 3, 1);
+ int[] frm = mldna.locateInFrom(1, 1);
+ testLocateFrom(mldna, 1, 1, new int[]
+ { 2, 2, 6, 7 });
+ MapList.testMap(mldna, 1, 3);
/*
* for (int from=1; from<=51; from++) { int[] too=ml.shiftTo(from); int[]
* toofrom=ml.shiftFrom(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!
+ // working!
}
private static void testLocateFrom(MapList mldna, int i, int j, int[] ks)
{
int[] frm = mldna.locateInFrom(i, j);
- if (frm==ks || java.util.Arrays.equals(frm,ks))
+ if (frm == ks || java.util.Arrays.equals(frm, ks))
{
- System.out.println("Success test locate from "+i+" to "+j);
- } else {
- System.err.println("Failed test locate from "+i+" to "+j);
+ System.out.println("Success test locate from " + i + " to " + j);
+ }
+ else
+ {
+ System.err.println("Failed test locate from " + i + " to " + j);
for (int c = 0; c < frm.length; c++)
{
System.err.print(frm[c] + ((c % 2 == 0) ? "," : ";"));
return new MapList(getToRanges(), getFromRanges(), getToRatio(),
getFromRatio());
}
+
+ /**
+ * test for containment rather than equivalence to another mapping
+ *
+ * @param map
+ * to be tested for containment
+ * @return true if local or mapped range map contains or is contained by this
+ * mapping
+ */
+ public boolean containsEither(boolean local, MapList map)
+ {
+ if (local)
+ {
+ return ((getFromLowest() >= map.getFromLowest() && getFromHighest() <= map
+ .getFromHighest()) || (getFromLowest() <= map.getFromLowest() && getFromHighest() >= map
+ .getFromHighest()));
+ }
+ else
+ {
+ return ((getToLowest() >= map.getToLowest() && getToHighest() <= map
+ .getToHighest()) || (getToLowest() <= map.getToLowest() && getToHighest() >= map
+ .getToHighest()));
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff