+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import jalview.util.MapList;
-public class Mapping {
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Vector;
+
+public class Mapping
+{
/**
- * Contains the
- * start-end pairs mapping from
- * the associated sequence to the
- * sequence in the database
- * coordinate system
- * it also takes care of step difference between coordinate systems
+ * An iterator that serves the aligned codon positions (with their protein
+ * products).
+ *
+ * @author gmcarstairs
+ *
*/
- MapList map=null;
+ public class AlignedCodonIterator implements Iterator<AlignedCodon>
+ {
+ /*
+ * The gap character used in the aligned sequence
+ */
+ private final char gap;
+
+ /*
+ * The characters of the aligned sequence e.g. "-cGT-ACgTG-"
+ */
+ private final char[] alignedSeq;
+
+ /*
+ * the sequence start residue
+ */
+ private int start;
+
+ /*
+ * Next position (base 0) in the aligned sequence
+ */
+ private int alignedColumn = 0;
+
+ /*
+ * Count of bases up to and including alignedColumn position
+ */
+ private int alignedBases = 0;
+
+ /*
+ * [start, end] from ranges (base 1)
+ */
+ private Iterator<int[]> fromRanges;
+
+ /*
+ * [start, end] to ranges (base 1)
+ */
+ private Iterator<int[]> toRanges;
+
+ /*
+ * The current [start, end] (base 1) from range
+ */
+ private int[] currentFromRange = null;
+
+ /*
+ * The current [start, end] (base 1) to range
+ */
+ private int[] currentToRange = null;
+
+ /*
+ * The next 'from' position (base 1) to process
+ */
+ private int fromPosition = 0;
+
+ /*
+ * The next 'to' position (base 1) to process
+ */
+ private int toPosition = 0;
+
+ /**
+ * Constructor
+ *
+ * @param seq
+ * the aligned sequence
+ * @param gapChar
+ */
+ public AlignedCodonIterator(SequenceI seq, char gapChar)
+ {
+ this.alignedSeq = seq.getSequence();
+ this.start = seq.getStart();
+ this.gap = gapChar;
+ fromRanges = map.getFromRanges().iterator();
+ toRanges = map.getToRanges().iterator();
+ if (fromRanges.hasNext())
+ {
+ currentFromRange = fromRanges.next();
+ fromPosition = currentFromRange[0];
+ }
+ if (toRanges.hasNext())
+ {
+ currentToRange = toRanges.next();
+ toPosition = currentToRange[0];
+ }
+ }
+
+ /**
+ * Returns true unless we have already traversed the whole mapping.
+ */
+ @Override
+ public boolean hasNext()
+ {
+ if (fromRanges.hasNext())
+ {
+ return true;
+ }
+ if (currentFromRange == null || fromPosition >= currentFromRange[1])
+ {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the next codon's aligned positions, and translated value.
+ *
+ * @throws NoSuchElementException
+ * if hasNext() would have returned false
+ * @throws IncompleteCodonException
+ * if not enough mapped bases are left to make up a codon
+ */
+ @Override
+ public AlignedCodon next() throws IncompleteCodonException
+ {
+ if (!hasNext())
+ {
+ throw new NoSuchElementException();
+ }
+
+ int[] codon = getNextCodon();
+ int[] alignedCodon = getAlignedCodon(codon);
+
+ String peptide = getPeptide();
+ return new AlignedCodon(alignedCodon[0], alignedCodon[1],
+ alignedCodon[2], peptide);
+ }
+
+ /**
+ * Retrieve the translation as the 'mapped to' position in the mapped to
+ * sequence.
+ *
+ * @return
+ */
+ private String getPeptide()
+ {
+ // TODO should ideally handle toRatio other than 1 as well...
+ // i.e. code like getNextCodon()
+ if (toPosition <= currentToRange[1])
+ {
+ SequenceI seq = Mapping.this.to;
+ char pep = seq.getSequence()[toPosition - seq.getStart()];
+ toPosition++;
+ return String.valueOf(pep);
+ }
+ if (!toRanges.hasNext())
+ {
+ throw new NoSuchElementException("Ran out of peptide at position "
+ + toPosition);
+ }
+ currentToRange = toRanges.next();
+ toPosition = currentToRange[0];
+ return getPeptide();
+ }
+
+ /**
+ * Get the (base 1) dataset positions for the next codon in the mapping.
+ *
+ * @throws IncompleteCodonException
+ * if less than 3 remaining bases are mapped
+ */
+ private int[] getNextCodon()
+ {
+ int[] codon = new int[3];
+ int codonbase = 0;
+
+ while (codonbase < 3)
+ {
+ if (fromPosition <= currentFromRange[1])
+ {
+ /*
+ * Add next position from the current start-end range
+ */
+ codon[codonbase++] = fromPosition++;
+ }
+ else
+ {
+ /*
+ * Move to the next range - if there is one
+ */
+ if (!fromRanges.hasNext())
+ {
+ throw new IncompleteCodonException();
+ }
+ currentFromRange = fromRanges.next();
+ fromPosition = currentFromRange[0];
+ }
+ }
+ return codon;
+ }
+
+ /**
+ * Get the aligned column positions (base 0) for the given sequence
+ * positions (base 1), by counting ungapped characters in the aligned
+ * sequence.
+ *
+ * @param codon
+ * @return
+ */
+ private int[] getAlignedCodon(int[] codon)
+ {
+ int[] aligned = new int[codon.length];
+ for (int i = 0; i < codon.length; i++)
+ {
+ aligned[i] = getAlignedColumn(codon[i]);
+ }
+ return aligned;
+ }
+
+ /**
+ * Get the aligned column position (base 0) for the given sequence position
+ * (base 1).
+ *
+ * @param sequencePos
+ * @return
+ */
+ private int getAlignedColumn(int sequencePos)
+ {
+ /*
+ * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
+ */
+ int truePos = sequencePos - (start - 1);
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
+ {
+ if (alignedSeq[alignedColumn++] != gap)
+ {
+ alignedBases++;
+ }
+ }
+ return alignedColumn - 1;
+ }
+
+ @Override
+ public void remove()
+ {
+ // ignore
+ }
+
+ }
+
+ /**
+ * Contains the start-end pairs mapping from the associated sequence to the
+ * sequence in the database coordinate system. It also takes care of step
+ * difference between coordinate systems.
+ */
+ MapList map = null;
+
/**
- * The seuqence that map maps the associated seuqence to (if any).
+ * The sequence that map maps the associated sequence to (if any).
*/
- SequenceI to=null;
- public Mapping(MapList map) {
+ SequenceI to = null;
+
+ public Mapping(MapList map)
+ {
super();
this.map = map;
}
- public Mapping(SequenceI to, MapList map) {
+
+ public Mapping(SequenceI to, MapList map)
+ {
this(map);
this.to = to;
}
+
/**
* create a new mapping from
- * @param to the sequence being mapped
- * @param exon int[] {start,end,start,end} series on associated sequence
- * @param is int[] {start,end,...} ranges on the reference frame being mapped to
- * @param i step size on associated sequence
- * @param j step size on mapped frame
+ *
+ * @param to
+ * the sequence being mapped
+ * @param exon
+ * int[] {start,end,start,end} series on associated sequence
+ * @param is
+ * int[] {start,end,...} ranges on the reference frame being mapped
+ * to
+ * @param i
+ * step size on associated sequence
+ * @param j
+ * step size on mapped frame
*/
public Mapping(SequenceI to, int[] exon, int[] is, int i, int j)
{
this(to, new MapList(exon, is, i, j));
}
+
/**
- * create a duplicate (and independent) mapping object with
- * the same reference to any SequenceI being mapped to.
+ * create a duplicate (and independent) mapping object with the same reference
+ * to any SequenceI being mapped to.
+ *
* @param map2
*/
public Mapping(Mapping map2)
{
- if (map2!=this && map2!=null) {
- if (map2.map!=null)
+ if (map2 != this && map2 != null)
+ {
+ if (map2.map != null)
{
- map=new MapList(map2.map);
+ map = new MapList(map2.map);
}
to = map2.to;
}
}
+
/**
* @return the map
*/
- public MapList getMap() {
+ public MapList getMap()
+ {
return map;
}
/**
- * @param map the map to set
+ * @param map
+ * the map to set
*/
- public void setMap(MapList map) {
+ public void setMap(MapList map)
+ {
this.map = map;
}
+
/**
* Equals that compares both the to references and MapList mappings.
+ *
* @param other
- * @return
+ * @return
*/
- public boolean equals(Mapping other) {
- if (other==null)
+ @Override
+ public boolean equals(Object o)
+ {
+ // TODO should override Object.hashCode() to ensure that equal objects have
+ // equal hashcodes
+ if (o == null || !(o instanceof Mapping))
+ {
return false;
- if (other==this)
+ }
+ Mapping other = (Mapping) o;
+ if (other == this)
+ {
return true;
- if (other.to!=to)
+ }
+ if (other.to != to)
+ {
return false;
- if ((map!=null && other.map==null) || (map==null && other.map!=null))
+ }
+ if ((map != null && other.map == null)
+ || (map == null && other.map != null))
+ {
return false;
- if (map.equals(other.map))
+ }
+ if ((map == null && other.map == null) || map.equals(other.map))
+ {
return true;
+ }
return false;
}
+
/**
- * get the 'initial' position in the associated
- * sequence for a position in the mapped reference frame
+ * get the 'initial' position in the associated sequence for a position in the
+ * mapped reference frame
+ *
* @param mpos
* @return
*/
- public int getPosition(int mpos)
+ public int getPosition(int mpos)
{
- if (map!=null) {
+ if (map != null)
+ {
int[] mp = map.shiftTo(mpos);
- if (mp!=null)
+ if (mp != null)
{
return mp[0];
}
}
return mpos;
}
- public int[] getWord(int mpos) {
- if (map!=null) {
- int[] mp=map.shiftTo(mpos);
- if (mp!=null) {
- return new int[] {mp[0], mp[0]+mp[2]*(map.getFromRatio()-1)};
- }
+
+ /**
+ * gets boundary in direction of mapping
+ *
+ * @param position
+ * in mapped reference frame
+ * @return int{start, end} positions in associated sequence (in direction of
+ * mapped word)
+ */
+ public int[] getWord(int mpos)
+ {
+ if (map != null)
+ {
+ return map.getToWord(mpos);
}
return null;
}
+
/**
- * width of mapped unit in associated sequence
+ * width of mapped unit in associated sequence
*
*/
- public int getWidth() {
- if (map!=null) {
+ public int getWidth()
+ {
+ if (map != null)
+ {
return map.getFromRatio();
}
return 1;
/**
* width of unit in mapped reference frame
+ *
* @return
*/
- public int getMappedWidth() {
- if (map!=null) {
+ public int getMappedWidth()
+ {
+ if (map != null)
+ {
return map.getToRatio();
}
return 1;
}
+
/**
- * get mapped position in the associated
- * reference frame for position pos in the
- * associated sequence.
+ * get mapped position in the associated reference frame for position pos in
+ * the associated sequence.
+ *
* @param pos
* @return
*/
- public int getMappedPosition(int pos) {
- if (map!=null) {
+ public int getMappedPosition(int pos)
+ {
+ if (map != null)
+ {
int[] mp = map.shiftFrom(pos);
- if (mp!=null)
+ if (mp != null)
{
return mp[0];
}
}
return pos;
}
- public int[] getMappedWord(int pos) {
- if (map!=null) {
+
+ public int[] getMappedWord(int pos)
+ {
+ if (map != null)
+ {
int[] mp = map.shiftFrom(pos);
- if (mp!=null)
+ if (mp != null)
{
- return new int[] { mp[0], mp[0]+mp[2]*(map.getToRatio()-1)};
+ return new int[] { mp[0], mp[0] + mp[2] * (map.getToRatio() - 1) };
}
}
return null;
}
+
/**
- * locates the region of feature f in the associated sequence's reference frame
+ * locates the region of feature f in the associated sequence's reference
+ * frame
+ *
* @param f
* @return one or more features corresponding to f
*/
public SequenceFeature[] locateFeature(SequenceFeature f)
{
- // this is a stopgap - features broken over exon boundaries will not be
- // broken into a collection of feature fragments.
- // TODO: implement creation of several features from a single feature on a discontinuously mapped seuqence
- // need a function like int [] fromrange = map.getRange(from,to)
- // need to make subgrouped sequence features.
- if (true) {
- if (map!=null) {
+ if (true)
+ { // f.getBegin()!=f.getEnd()) {
+ if (map != null)
+ {
int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
- SequenceFeature[] vf = new SequenceFeature[frange.length/2];
- for (int i=0,v=0;i<frange.length;i+=2) {
+ if (frange == null)
+ {
+ // JBPNote - this isprobably not the right thing to doJBPHack
+ return null;
+ }
+ SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
+ for (int i = 0, v = 0; i < frange.length; i += 2, v++)
+ {
vf[v] = new SequenceFeature(f);
vf[v].setBegin(frange[i]);
- vf[v].setEnd(frange[i+1]);
- if (frange.length>2)
- vf[v].setDescription(f.getDescription() +"\nPart "+v);
+ vf[v].setEnd(frange[i + 1]);
+ if (frange.length > 2)
+ {
+ vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
+ }
}
return vf;
}
}
- if (false){
+ if (false) // else
+ {
int[] word = getWord(f.getBegin());
- if (word[0]<word[1])
+ if (word[0] < word[1])
{
f.setBegin(word[0]);
- } else {
+ }
+ else
+ {
f.setBegin(word[1]);
}
word = getWord(f.getEnd());
- if (word[0]>word[1])
+ if (word[0] > word[1])
{
f.setEnd(word[0]);
- } else {
+ }
+ else
+ {
f.setEnd(word[1]);
}
}
// give up and just return the feature.
return new SequenceFeature[] { f };
}
-
- /**
- * return a series of contigs on the associated sequence corresponding to
- * the from,to interval on the mapped reference frame
+
+ /**
+ * return a series of contigs on the associated sequence corresponding to the
+ * from,to interval on the mapped reference frame
+ *
* @param from
* @param to
- * @return
+ * @return int[] { from_i, to_i for i=1 to n contiguous regions in the
+ * associated sequence}
*/
- public int[] locateRange(int from, int to) {
- //TODO
- return null;
+ public int[] locateRange(int from, int to)
+ {
+ if (map != null)
+ {
+ if (from <= to)
+ {
+ from = (map.getToLowest() < from) ? from : map.getToLowest();
+ to = (map.getToHighest() > to) ? to : map.getToHighest();
+ if (from > to)
+ {
+ return null;
+ }
+ }
+ else
+ {
+ from = (map.getToHighest() > from) ? from : map.getToHighest();
+ to = (map.getToLowest() < to) ? to : map.getToLowest();
+ if (from < to)
+ {
+ return null;
+ }
+ }
+ return map.locateInFrom(from, to);
+ }
+ return new int[] { from, to };
}
+
/**
- * return a series of contigs on the mapped reference frame corresponding to
- * the from,to interval on the associated sequence
+ * return a series of mapped contigs mapped from a range on the associated
+ * sequence
+ *
* @param from
* @param to
* @return
*/
- public int[] locateMappedRange(int from, int to) {
- //TODO
- return null;
+ public int[] locateMappedRange(int from, int to)
+ {
+ if (map != null)
+ {
+
+ if (from <= to)
+ {
+ from = (map.getFromLowest() < from) ? from : map.getFromLowest();
+ to = (map.getFromHighest() > to) ? to : map.getFromHighest();
+ if (from > to)
+ {
+ return null;
+ }
+ }
+ else
+ {
+ from = (map.getFromHighest() > from) ? from : map.getFromHighest();
+ to = (map.getFromLowest() < to) ? to : map.getFromLowest();
+ if (from < to)
+ {
+ return null;
+ }
+ }
+ return map.locateInTo(from, to);
+ }
+ return new int[] { from, to };
+ }
+
+ /**
+ * return a new mapping object with a maplist modifed to only map the visible
+ * regions defined by viscontigs.
+ *
+ * @param viscontigs
+ * @return
+ */
+ public Mapping intersectVisContigs(int[] viscontigs)
+ {
+ Mapping copy = new Mapping(this);
+ if (map != null)
+ {
+ int vpos = 0;
+ int apos = 0;
+ Vector toRange = new Vector();
+ Vector fromRange = new Vector();
+ for (int vc = 0; vc < viscontigs.length; vc += 2)
+ {
+ // find a mapped range in this visible region
+ int[] mpr = locateMappedRange(1 + viscontigs[vc],
+ viscontigs[vc + 1] - 1);
+ if (mpr != null)
+ {
+ for (int m = 0; m < mpr.length; m += 2)
+ {
+ toRange.addElement(new int[] { mpr[m], mpr[m + 1] });
+ int[] xpos = locateRange(mpr[m], mpr[m + 1]);
+ for (int x = 0; x < xpos.length; x += 2)
+ {
+ fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
+ }
+ }
+ }
+ }
+ int[] from = new int[fromRange.size() * 2];
+ int[] to = new int[toRange.size() * 2];
+ int[] r;
+ for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
+ {
+ r = (int[]) fromRange.elementAt(f);
+ from[f * 2] = r[0];
+ from[f * 2 + 1] = r[1];
+ }
+ for (int f = 0, fSize = toRange.size(); f < fSize; f++)
+ {
+ r = (int[]) toRange.elementAt(f);
+ to[f * 2] = r[0];
+ to[f * 2 + 1] = r[1];
+ }
+ copy.setMap(new MapList(from, to, map.getFromRatio(), map
+ .getToRatio()));
+ }
+ return copy;
+ }
+
+ /**
+ * get the sequence being mapped to - if any
+ *
+ * @return null or a dataset sequence
+ */
+ public SequenceI getTo()
+ {
+ return to;
+ }
+
+ /**
+ * set the dataset sequence being mapped to if any
+ *
+ * @param tto
+ */
+ public void setTo(SequenceI tto)
+ {
+ to = tto;
}
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ map = null;
+ to = null;
+ super.finalize();
+ }
+
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ {
+ return new AlignedCodonIterator(seq, gapChar);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff