/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.datamodel;
-import jalview.util.MapList;
-
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Vector;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
public class Mapping
{
/**
/*
* The characters of the aligned sequence e.g. "-cGT-ACgTG-"
*/
- private final char[] alignedSeq;
+ private final SequenceI alignedSeq;
/*
* the sequence start residue
*/
public AlignedCodonIterator(SequenceI seq, char gapChar)
{
- this.alignedSeq = seq.getSequence();
+ this.alignedSeq = seq;
this.start = seq.getStart();
this.gap = gapChar;
fromRanges = map.getFromRanges().iterator();
int[] alignedCodon = getAlignedCodon(codon);
String peptide = getPeptide();
+ int peptideCol = toPosition - 1 - Mapping.this.to.getStart();
return new AlignedCodon(alignedCodon[0], alignedCodon[1],
- alignedCodon[2], peptide);
+ alignedCodon[2], peptide, peptideCol);
}
/**
* sequence.
*
* @return
+ * @throws NoSuchElementException
+ * if the 'toRange' is exhausted (nothing to map to)
*/
private String getPeptide()
{
if (toPosition <= currentToRange[1])
{
SequenceI seq = Mapping.this.to;
- char pep = seq.getSequence()[toPosition - seq.getStart()];
+ char pep = seq.getCharAt(toPosition - seq.getStart());
toPosition++;
return String.valueOf(pep);
}
if (!toRanges.hasNext())
{
- throw new NoSuchElementException("Ran out of peptide at position "
- + toPosition);
+ throw new NoSuchElementException(
+ "Ran out of peptide at position " + toPosition);
}
currentToRange = toRanges.next();
toPosition = currentToRange[0];
* 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)
+ int length = alignedSeq.getLength();
+ while (alignedBases < truePos && alignedColumn < length)
{
- if (alignedSeq[alignedColumn++] != gap)
+ char c = alignedSeq.getCharAt(alignedColumn++);
+ if (c != gap && !Comparison.isGap(c))
{
alignedBases++;
}
}
- /**
+ /*
* 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 sequence that map maps the associated sequence to (if any).
*/
SequenceI to = null;
+ /*
+ * optional sequence id for the 'from' ranges
+ */
+ private String mappedFromId;
+
public Mapping(MapList map)
{
super();
map = new MapList(map2.map);
}
to = map2.to;
+ mappedFromId = map2.mappedFromId;
}
}
/**
* Equals that compares both the to references and MapList mappings.
*
- * @param other
+ * @param o
* @return
+ * @see MapList#equals
*/
@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;
}
/**
+ * Returns a hashCode made from the sequence and maplist
+ */
+ @Override
+ public int hashCode()
+ {
+ int hashCode = (this.to == null ? 1 : this.to.hashCode());
+ if (this.map != null)
+ {
+ hashCode = hashCode * 31 + this.map.hashCode();
+ }
+
+ return hashCode;
+ }
+
+ /**
* get the 'initial' position in the associated sequence for a position in the
* mapped reference frame
*
}
/**
- * 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
*
*/
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]);
+ vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
+ f.getFeatureGroup(), f.getScore());
if (frange.length > 2)
{
vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
return vf;
}
}
- if (false) // else
- {
- int[] word = getWord(f.getBegin());
- if (word[0] < word[1])
- {
- f.setBegin(word[0]);
- }
- else
- {
- f.setBegin(word[1]);
- }
- word = getWord(f.getEnd());
- if (word[0] > word[1])
- {
- f.setEnd(word[0]);
- }
- else
- {
- f.setEnd(word[1]);
- }
- }
+
// give up and just return the feature.
return new SequenceFeature[] { f };
}
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;
}
to = tto;
}
- /*
- * (non-Javadoc)
+ /**
+ * Returns an iterator which can serve up the aligned codon column positions
+ * and their corresponding peptide products
+ *
+ * @param seq
+ * an aligned (i.e. possibly gapped) sequence
+ * @param gapChar
+ * @return
+ */
+ public Iterator<AlignedCodon> getCodonIterator(SequenceI seq,
+ char gapChar)
+ {
+ return new AlignedCodonIterator(seq, gapChar);
+ }
+
+ /**
+ * Readable representation for debugging only, not guaranteed not to change
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("%s %s", this.map.toString(),
+ this.to == null ? "" : this.to.getName());
+ }
+
+ /**
+ * Returns the identifier for the 'from' range sequence, or null if not set
*
- * @see java.lang.Object#finalize()
+ * @return
*/
- protected void finalize() throws Throwable
+ public String getMappedFromId()
{
- map = null;
- to = null;
- super.finalize();
+ return mappedFromId;
}
- public Iterator<AlignedCodon> getCodonIterator(SequenceI seq, char gapChar)
+ /**
+ * Sets the identifier for the 'from' range sequence
+ */
+ public void setMappedFromId(String mappedFromId)
{
- return new AlignedCodonIterator(seq, gapChar);
+ this.mappedFromId = mappedFromId;
}
}
git://source.jalview.org / jalview.git / blobdiff