+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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 java.util.Vector;
-
import jalview.util.MapList;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.Vector;
+
public class Mapping
{
/**
+ * An iterator that serves the aligned codon positions (with their protein
+ * products).
+ *
+ * @author gmcarstairs
+ *
+ */
+ 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;
+
+ /*
+ * 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 cs
+ * the aligned sequence characters
+ * @param gapChar
+ */
+ public AlignedCodonIterator(char[] cs, char gapChar)
+ {
+ this.alignedSeq = cs;
+ 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])
+ {
+ char pep = Mapping.this.to.getSequence()[toPosition - 1];
+ 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)
+ {
+ while (alignedBases < sequencePos
+ && 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
+ * 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;
* @param other
* @return
*/
- public boolean equals(Mapping other)
+ @Override
+ public boolean equals(Object o)
{
- if (other == null)
+ // TODO should override Object.hashCode() to ensure that equal objects have
+ // equal hashcodes
+ if (o == null || !(o instanceof Mapping))
+ {
return false;
+ }
+ Mapping other = (Mapping) o;
if (other == this)
+ {
return true;
+ }
if (other.to != to)
+ {
return false;
+ }
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;
}
int[] mp = map.shiftFrom(pos);
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;
if (map != null)
{
int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
- if (frange==null)
+ if (frange == null)
{
// JBPNote - this isprobably not the right thing to doJBPHack
return null;
vf[v].setBegin(frange[i]);
vf[v].setEnd(frange[i + 1]);
if (frange.length > 2)
- vf[v].setDescription(f.getDescription() + "\nPart " + (v+1));
+ {
+ vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
+ }
}
return vf;
}
}
}
// give up and just return the feature.
- return new SequenceFeature[]
- { f };
+ return new SequenceFeature[] { f };
}
/**
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 new int[] { 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 new int[] { from, to };
}
/**
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);
+ 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] });
+ 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] });
+ fromRange.addElement(new int[] { xpos[x], xpos[x + 1] });
}
}
}
}
- int[] from = new int[fromRange.size()*2];
- int[] to = new int[toRange.size()*2];
+ 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++)
+ 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];
+ from[f * 2] = r[0];
+ from[f * 2 + 1] = r[1];
}
- for (int f=0,fSize=toRange.size(); f<fSize; f++)
+ 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];
+ to[f * 2] = r[0];
+ to[f * 2 + 1] = r[1];
}
- copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+ copy.setMap(new MapList(from, to, map.getFromRatio(), map
+ .getToRatio()));
}
return copy;
}
- public static void main(String[] args)
- {
- /**
- * trite test of the intersectVisContigs method
- * for a simple DNA -> Protein exon map and a range of visContigs
- */
- MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
- Mapping m = new Mapping(fk);
- Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
- Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
- System.out.println(""+m_1.map.getFromRanges());
-
-
- }
+
/**
* 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)
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable
to = null;
super.finalize();
}
-
+
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ {
+ return new AlignedCodonIterator(seq.getSequence(), gapChar);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff