/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
import jalview.analysis.*;
-/** Data structure to hold and manipulate a multiple sequence alignment
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
*/
-public class Alignment
- implements AlignmentI
+public class Alignment implements AlignmentI
{
protected Alignment dataset;
+
protected Vector sequences;
+
protected Vector groups = new Vector();
+
protected char gapCharacter = '-';
+
protected int type = NUCLEOTIDE;
+
public static final int PROTEIN = 0;
+
public static final int NUCLEOTIDE = 1;
/** DOCUMENT ME!! */
HiddenSequences hiddenSequences = new HiddenSequences(this);
+ public Hashtable alignmentProperties;
+
private void initAlignment(SequenceI[] seqs)
{
int i = 0;
}
- /** Make an alignment from an array of Sequences.
- *
+ /**
+ * Make an alignment from an array of Sequences.
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
/**
* Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
+ *
+ * @param seqs
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
- SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter,
- new ColumnSelection(), null);
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+ gapCharacter, new ColumnSelection(), null);
initAlignment(seqs);
}
/**
- * Make a new alignment from an CigarArray
- * JBPNote - can only do this when compactAlignment does not contain hidden regions.
- * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
- * @param compactAlignment CigarArray
+ * Make a new alignment from an CigarArray JBPNote - can only do this when
+ * compactAlignment does not contain hidden regions. JBPNote - must also check
+ * that compactAlignment resolves to a set of SeqCigars - or construct them
+ * appropriately.
+ *
+ * @param compactAlignment
+ * CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getSequences()
public SequenceI[] getSequencesArray()
{
+ if (sequences == null)
+ return null;
SequenceI[] reply = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceI getSequenceAt(int i)
return null;
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void addSequence(SequenceI snew)
{
if (dataset != null)
{
+ // maintain dataset integrity
if (snew.getDatasetSequence() != null)
{
getDataset().addSequence(snew.getDatasetSequence());
}
else
{
- Sequence ds = new Sequence(snew.getName(),
- AlignSeq.extractGaps("-. ",
- snew.getSequenceAsString()),
- snew.getStart(),
- snew.getEnd());
-
- snew.setDatasetSequence(ds);
- getDataset().addSequence(ds);
+ // derive new sequence
+ SequenceI adding = snew.deriveSequence();
+ getDataset().addSequence(adding.getDatasetSequence());
+ snew = adding;
}
}
- sequences.addElement(snew);
-
- hiddenSequences.adjustHeightSequenceAdded();
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[]
+ { snew });
+ }
+ else
+ {
+ sequences.addElement(snew);
+ }
+ if (hiddenSequences != null)
+ hiddenSequences.adjustHeightSequenceAdded();
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
* @param snew
*/
public void setSequenceAt(int i, SequenceI snew)
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public Vector getGroups()
return groups;
}
- public void destroyAlignment()
+ public void finalize()
{
- if(getDataset()!=null)
- getDataset().destroyAlignment();
+ if (getDataset() != null)
+ getDataset().removeAlignmentRef();
dataset = null;
sequences = null;
hiddenSequences = null;
}
+ /**
+ * decrement the alignmentRefs counter by one and call finalize if it goes to
+ * zero.
+ */
+ private void removeAlignmentRef()
+ {
+ if (--alignmentRefs == 0)
+ {
+ finalize();
+ }
+ }
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
public void deleteSequence(SequenceI s)
{
/**
* DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
*/
public void deleteSequence(int i)
{
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public SequenceGroup[] findAllGroups(SequenceI s)
/** */
public SequenceI findName(String name)
{
- int i = 0;
+ return findName(name, false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ */
+ public SequenceI findName(String token, boolean b)
+ {
+ return findName(null, token, b);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
+ */
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
+
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
+ {
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i++) == startAfter)
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
+ }
while (i < sequences.size())
{
- if (getSequenceAt(i).getName().equals(name))
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
}
- /** */
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
public int findIndex(SequenceI s)
{
int i = 0;
return -1;
}
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ public int findIndex(SearchResults results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
+
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getHeight()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public int getWidth()
/**
* DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gc)
{
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString()
- .replace('.', gc)
- .replace('-', gc)
- .replace(' ', gc)
- );
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
+ '-', gc).replace(' ', gc));
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public char getGapCharacter()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean isAligned()
return true;
}
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
*/
- public void deleteAnnotation(AlignmentAnnotation aa)
+ public boolean deleteAnnotation(AlignmentAnnotation aa)
{
int aSize = 1;
if (aSize < 1)
{
- return;
+ return false;
}
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+ boolean swap = false;
int tIndex = 0;
for (int i = 0; i < aSize; i++)
{
if (annotations[i] == aa)
{
+ swap = true;
continue;
}
-
- temp[tIndex] = annotations[i];
- tIndex++;
+ if (tIndex < temp.length)
+ temp[tIndex++] = annotations[i];
}
- annotations = temp;
+ if (swap)
+ {
+ annotations = temp;
+ if (aa.sequenceRef != null)
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+ }
+ return swap;
}
/**
* DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
+ *
+ * @param aa
+ * DOCUMENT ME!
*/
public void addAnnotation(AlignmentAnnotation aa)
{
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
// Create a new dataset for this alignment.
// Can only be done once, if dataset is not null
// This will not be performed
- Sequence[] seqs = new Sequence[getHeight()];
+ SequenceI[] seqs = new SequenceI[getHeight()];
SequenceI currentSeq;
for (int i = 0; i < getHeight(); i++)
{
}
else
{
- seqs[i] = new Sequence(currentSeq.getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- currentSeq.getSequenceAsString()
- ),
- currentSeq.getStart(),
- currentSeq.getEnd());
- seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
- seqs[i].setDescription(currentSeq.getDescription());
- getSequenceAt(i).setSequenceFeatures(null);
- getSequenceAt(i).setDatasetSequence(seqs[i]);
+ seqs[i] = currentSeq.createDatasetSequence();
}
}
{
dataset = data;
}
+ dataset.addAlignmentRef();
+ }
+
+ /**
+ * reference count for number of alignments referencing this one.
+ */
+ int alignmentRefs = 0;
+
+ /**
+ * increase reference count to this alignment.
+ */
+ private void addAlignmentRef()
+ {
+ alignmentRefs++;
}
public Alignment getDataset()
{
boolean modified = false;
- //Remove excess gaps from the end of alignment
+ // Remove excess gaps from the end of alignment
int maxLength = -1;
SequenceI current;
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
{
- if (j > maxLength && !jalview.util.Comparison.isGap(
- current.getCharAt(j)))
+ if (j > maxLength
+ && !jalview.util.Comparison.isGap(current.getCharAt(j)))
{
maxLength = j;
break;
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size();
- i++)
+ for (int i = 0; i < sequences.size(); i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
if (cLength < maxLength)
{
- current.insertCharAt(cLength,
- maxLength - cLength, gapCharacter);
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
modified = true;
}
else if (current.getLength() > maxLength)
}
return modified;
}
+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
+ * @param right true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed
+ */
+ public boolean justify(boolean right)
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+ int ends[] = new int[sequences.size()*2];
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ // This should really be a sequence method
+ ends[i*2] = current.findIndex(current.getStart());
+ ends[i*2+1] = current.findIndex(current.getStart()+current.getLength());
+ boolean hitres=false;
+ for (int j = 0,rs=0,ssiz=current.getLength(); j<ssiz; j++)
+ {
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ if (!hitres)
+ {
+ ends[i*2] = j;
+ hitres=true;
+ } else {
+ ends[i*2+1] = j;
+ if (j-ends[i*2]>maxLength)
+ {
+ maxLength = j-ends[i*2];
+ }
+ }
+ }
+ }
+ }
+
+ maxLength++;
+ // now edit the flanking gaps to justify to either left or right
+ int cLength,extent,diff;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+
+ cLength = 1+ends[i*2+1]-ends[i*2];
+ diff = maxLength-cLength; // number of gaps to indent
+ extent = current.getLength();
+ if (right)
+ {
+ // right justify
+ if (extent>ends[i*2+1])
+ {
+ current.deleteChars(ends[i*2+1]+1, extent);
+ modified = true;
+ }
+ if (ends[i*2]>diff)
+ {
+ current.deleteChars(0, ends[i*2]-diff);
+ modified = true;
+ } else {
+ if (ends[i*2]<diff)
+ {
+ current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+ modified = true;
+ }
+ }
+ } else {
+ // left justify
+ if (ends[i*2]>0)
+ {
+ current.deleteChars(0, ends[i*2]);
+ modified = true;
+ ends[i*2+1]-=ends[i*2];
+ extent-=ends[i*2];
+ }
+ if (extent>maxLength)
+ {
+ current.deleteChars(maxLength+1, extent);
+ modified = true;
+ } else {
+ if (extent<maxLength)
+ {
+ current.insertCharAt(extent, maxLength-extent,gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ }
+ return modified;
+ }
public HiddenSequences getHiddenSequences()
{
SeqCigar alseqs[] = new SeqCigar[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
- alseqs[i] = new SeqCigar( (SequenceI) sequences.elementAt(i));
+ alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
}
CigarArray cal = new CigarArray(alseqs);
cal.addOperation(CigarArray.M, getWidth());
return cal;
}
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
+ alignmentProperties = new Hashtable();
+
+ alignmentProperties.put(key, value);
+ }
+
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
+ return alignmentProperties.get(key);
+ else
+ return null;
+ }
+
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
+
+ AlignedCodonFrame[] codonFrameList = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ */
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null)
+ return;
+ if (codonFrameList == null)
+ {
+ codonFrameList = new AlignedCodonFrame[]
+ { codons };
+ return;
+ }
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
+ System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+ t[codonFrameList.length] = codons;
+ codonFrameList = t;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+ */
+ public AlignedCodonFrame getCodonFrame(int index)
+ {
+ return codonFrameList[index];
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ {
+ if (seq == null || codonFrameList == null)
+ return null;
+ Vector cframes = new Vector();
+ for (int f = 0; f < codonFrameList.length; f++)
+ {
+ if (codonFrameList[f].involvesSequence(seq))
+ cframes.addElement(codonFrameList[f]);
+ }
+ if (cframes.size() == 0)
+ return null;
+ AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+ cframes.copyInto(cfr);
+ return cfr;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ public AlignedCodonFrame[] getCodonFrames()
+ {
+ return codonFrameList;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null || codonFrameList == null)
+ return false;
+ boolean removed = false;
+ int i = 0, iSize = codonFrameList.length;
+ while (i < iSize)
+ {
+ if (codonFrameList[i] == codons)
+ {
+ removed = true;
+ if (i + 1 < iSize)
+ {
+ System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+ - i - 1);
+ }
+ iSize--;
+ }
+ else
+ {
+ i++;
+ }
+ }
+ return removed;
+ }
+
+ public void append(AlignmentI toappend)
+ {
+ // TODO test this method for a future 2.5 release
+ // currently tested for use in jalview.gui.SequenceFetcher
+ boolean samegap = toappend.getGapCharacter()==getGapCharacter();
+ char oldc = toappend.getGapCharacter();
+ boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+ // get all sequences including any hidden ones
+ Vector sqs = (hashidden) ? toappend.getHiddenSequences().getFullAlignment().getSequences() : toappend.getSequences();
+ if (sqs != null)
+ {
+ Enumeration sq = sqs.elements();
+ while (sq.hasMoreElements())
+ {
+ SequenceI addedsq=(SequenceI) sq.nextElement();
+ if (!samegap)
+ {
+ char[] oldseq = addedsq.getSequence();
+ for (int c=0;c<oldseq.length;c++)
+ {
+ if (oldseq[c]==oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
+ }
+ }
+ addSequence(addedsq);
+ }
+ }
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
+ {
+ addAnnotation(alan[a]);
+ }
+ AlignedCodonFrame[] acod = toappend.getCodonFrames();
+ for (int a = 0; acod != null && a < acod.length; a++)
+ {
+ this.addCodonFrame(acod[a]);
+ }
+ Vector sg = toappend.getGroups();
+ if (sg != null)
+ {
+ Enumeration el = sg.elements();
+ while (el.hasMoreElements())
+ {
+ addGroup((SequenceGroup) el.nextElement());
+ }
+ }
+ if (toappend.getHiddenSequences()!=null)
+ {
+ HiddenSequences hs = toappend.getHiddenSequences();
+ if (hiddenSequences==null)
+ {
+ hiddenSequences = new HiddenSequences(this);
+ }
+ if (hs.hiddenSequences!=null)
+ {
+ for (int s=0;s<hs.hiddenSequences.length; s++)
+ {
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s]!=null)
+ {
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+ }
+ }
+ }
+ }
+ if (toappend.getProperties()!=null)
+ {
+ // we really can't do very much here - just try to concatenate strings where property collisions occur.
+ Enumeration key = toappend.getProperties().keys();
+ while (key.hasMoreElements())
+ {
+ Object k = key.nextElement();
+ Object ourval = this.getProperty(k);
+ Object toapprop = toappend.getProperty(k);
+ if (ourval!=null)
+ {
+ if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+ {
+ if (ourval instanceof String)
+ {
+ // append strings
+ this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
+ } else {
+ if (ourval instanceof Vector)
+ {
+ // append vectors
+ Enumeration theirv = ((Vector) toapprop).elements();
+ while (theirv.hasMoreElements())
+ {
+ ((Vector)ourval).addElement(theirv);
+ }
+ }
+ }
+ }
+ } else {
+ // just add new property directly
+ setProperty(k, toapprop);
+ }
+
+ }
+ }
+ }
+
}