/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.datamodel;
import java.util.*;
-import jalview.analysis.*;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
+/**
+ * @author JimP
+ *
+ */
public class Alignment implements AlignmentI
{
protected Alignment dataset;
- protected Vector sequences;
+ protected List<SequenceI> sequences;
- protected Vector groups = new Vector();
+ protected List<SequenceGroup> groups = java.util.Collections
+ .synchronizedList(new ArrayList<SequenceGroup>());
protected char gapCharacter = '-';
public static final int NUCLEOTIDE = 1;
+ public boolean hasRNAStructure = false;
+
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
type = PROTEIN;
}
- sequences = new Vector();
+ sequences = java.util.Collections
+ .synchronizedList(new ArrayList<SequenceI>());
for (i = 0; i < seqs.length; i++)
{
- sequences.addElement(seqs[i]);
+ sequences.add(seqs[i]);
}
}
* Make a new alignment from an array of SeqCigars
*
* @param seqs
- * SeqCigar[]
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
* appropriately.
*
* @param compactAlignment
- * CigarArray
+ * CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
*
* @return DOCUMENT ME!
*/
- public Vector getSequences()
+ @Override
+ public List<SequenceI> getSequences()
{
return sequences;
}
+ @Override
+ public List<SequenceI> getSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+ // work on this.
+ return sequences;
+ }
+
+ @Override
public SequenceI[] getSequencesArray()
{
if (sequences == null)
return null;
- SequenceI[] reply = new SequenceI[sequences.size()];
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- reply[i] = (SequenceI) sequences.elementAt(i);
+ return sequences.toArray(new SequenceI[sequences.size()]);
}
- return reply;
}
/**
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ @Override
public SequenceI getSequenceAt(int i)
{
- if (i < sequences.size())
+ synchronized (sequences)
{
- return (SequenceI) sequences.elementAt(i);
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
}
-
return null;
}
*
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
}
else
{
- sequences.addElement(snew);
+ synchronized (sequences)
+ {
+ sequences.add(snew);
+ }
}
if (hiddenSequences != null)
hiddenSequences.adjustHeightSequenceAdded();
*
* @param snew
*/
+ @Override
public void setSequenceAt(int i, SequenceI snew)
{
SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
-
- sequences.setElementAt(snew, i);
+ deleteSequence(i);
+ synchronized (sequences)
+ {
+ sequences.set(i, snew);
+ }
}
/**
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List<SequenceGroup> getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void deleteSequence(SequenceI s)
{
deleteSequence(findIndex(s));
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void deleteSequence(int i)
{
if (i > -1 && i < getHeight())
{
- sequences.removeElementAt(i);
+ synchronized (sequences)
+ {
+ sequences.remove(i);
+ }
hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
- /** */
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ */
+ @Override
public SequenceGroup findGroup(SequenceI s)
{
- for (int i = 0; i < this.groups.size(); i++)
+ synchronized (groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (sg.getSequences(null).contains(s))
+ for (int i = 0; i < this.groups.size(); i++)
{
- return sg;
+ SequenceGroup sg = groups.get(i);
+
+ if (sg.getSequences(null).contains(s))
+ {
+ return sg;
+ }
}
}
-
return null;
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
+ /*
+ * (non-Javadoc)
*
- * @return DOCUMENT ME!
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
+ @Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- Vector temp = new Vector();
+ ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
- int gSize = groups.size();
- for (int i = 0; i < gSize; i++)
+ synchronized (groups)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg == null || sg.getSequences(null) == null)
+ int gSize = groups.size();
+ for (int i = 0; i < gSize; i++)
{
- this.deleteGroup(sg);
- gSize--;
- continue;
- }
+ SequenceGroup sg = groups.get(i);
+ if (sg == null || sg.getSequences(null) == null)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- if (sg.getSequences(null).contains(s))
- {
- temp.addElement(sg);
+ if (sg.getSequences(null).contains(s))
+ {
+ temp.add(sg);
+ }
}
}
-
SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
- for (int i = 0; i < temp.size(); i++)
- {
- ret[i] = (SequenceGroup) temp.elementAt(i);
- }
-
- return ret;
+ return temp.toArray(ret);
}
/** */
+ @Override
public void addGroup(SequenceGroup sg)
{
- if (!groups.contains(sg))
+ synchronized (groups)
{
- if (hiddenSequences.getSize() > 0)
+ if (!groups.contains(sg))
{
- int i, iSize = sg.getSize();
- for (i = 0; i < iSize; i++)
+ if (hiddenSequences.getSize() > 0)
{
- if (!sequences.contains(sg.getSequenceAt(i)))
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
{
- sg.deleteSequence(sg.getSequenceAt(i), false);
- iSize--;
- i--;
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
}
- }
- if (sg.getSize() < 1)
- {
- return;
+ if (sg.getSize() < 1)
+ {
+ return;
+ }
}
- }
- groups.addElement(sg);
+ groups.add(sg);
+ }
}
}
/**
- * DOCUMENT ME!
+ * remove any annotation that references gp
+ *
+ * @param gp
+ * (if null, removes all group associated annotation)
*/
+ private void removeAnnotationForGroup(SequenceGroup gp)
+ {
+ if (annotations == null || annotations.length == 0)
+ {
+ return;
+ }
+ // remove annotation very quickly
+ AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ int i, p, k;
+ if (gp == null)
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef != null)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ else
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef == gp)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ if (p > 0)
+ {
+ // clear out the group associated annotation.
+ for (i = 0; i < p; i++)
+ {
+ unhookAnnotation(todelete[i]);
+ todelete[i] = null;
+ }
+ t = new AlignmentAnnotation[k];
+ for (i = 0; i < k; i++)
+ {
+ t[i] = tokeep[i];
+ }
+ annotations = t;
+ }
+ }
+
+ @Override
public void deleteAllGroups()
{
- groups.removeAllElements();
+ synchronized (groups)
+ {
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ groups.clear();
+ }
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
- if (groups.contains(g))
+ synchronized (groups)
{
- groups.removeElement(g);
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ }
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
*
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
+ @Override
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
* (non-Javadoc)
*
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
- * boolean)
+ * boolean)
*/
+ @Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
*
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
*
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
* DOCUMENT ME!
*
* @param gc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void setGapCharacter(char gc)
{
gapCharacter = gc;
-
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
- '-', gc).replace(' ', gc));
+ for (SequenceI seq : sequences)
+ {
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
}
}
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
}
- /**
- * DOCUMENT ME!
+ /*
+ * (non-Javadoc)
*
- * @return DOCUMENT ME!
+ * @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
- int width = getWidth();
+ return isAligned(false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ @Override
+ public boolean isAligned(boolean includeHidden)
+ {
+ int width = getWidth();
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
+ includeHidden = true; // no hidden sequences to check against.
+ }
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() != width)
+ if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
{
- return false;
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
+ }
}
}
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
*/
+ @Override
public boolean deleteAnnotation(AlignmentAnnotation aa)
{
+ return deleteAnnotation(aa, true);
+ }
+
+ @Override
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
int aSize = 1;
if (annotations != null)
if (swap)
{
annotations = temp;
- if (aa.sequenceRef != null)
- aa.sequenceRef.removeAlignmentAnnotation(aa);
+ if (unhook)
+ {
+ unhookAnnotation(aa);
+ }
}
return swap;
}
/**
- * DOCUMENT ME!
+ * remove any object references associated with this annotation
*
* @param aa
- * DOCUMENT ME!
*/
+ private void unhookAnnotation(AlignmentAnnotation aa)
+ {
+ if (aa.sequenceRef != null)
+ {
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
+ }
+ if (aa.groupRef != null)
+ {
+ // probably need to do more here in the future (post 2.5.0)
+ aa.groupRef = null;
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
+ addAnnotation(aa, -1);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation, int)
+ */
+ @Override
+ public void addAnnotation(AlignmentAnnotation aa, int pos)
+ {
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
+ }
+
int aSize = 1;
if (annotations != null)
{
}
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
- temp[aSize - 1] = aa;
-
int i = 0;
-
+ if (pos == -1 || pos >= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
if (aSize > 1)
{
- for (i = 0; i < (aSize - 1); i++)
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
{
- temp[i] = annotations[i];
+ if (p == pos)
+ {
+ p++;
+ }
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
}
}
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
annotations = temp;
}
+ @Override
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * returns all annotation on the alignment
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
return annotations;
}
+ @Override
public void setNucleotide(boolean b)
{
if (b)
}
}
+ @Override
public boolean isNucleotide()
{
if (type == NUCLEOTIDE)
}
}
+ @Override
+ public boolean hasRNAStructure()
+ {
+ // TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
+
+ @Override
public void setDataset(Alignment data)
{
if (dataset == null && data == null)
currentSeq = getSequenceAt(i);
if (currentSeq.getDatasetSequence() != null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ seqs[i] = currentSeq.getDatasetSequence();
}
else
{
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
}
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
+ * 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
*/
+ @Override
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];
+ 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++)
+ 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)
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
{
- maxLength = j-ends[i*2];
+ maxLength = j - ends[i * 2];
}
}
}
maxLength++;
// now edit the flanking gaps to justify to either left or right
- int cLength,extent,diff;
+ 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
+
+ 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])
+ if (extent > ends[i * 2 + 1])
{
- current.deleteChars(ends[i*2+1]+1, extent);
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
modified = true;
}
- if (ends[i*2]>diff)
+ if (ends[i * 2] > diff)
{
- current.deleteChars(0, ends[i*2]-diff);
+ current.deleteChars(0, ends[i * 2] - diff);
modified = true;
- } else {
- if (ends[i*2]<diff)
+ }
+ else
+ {
+ if (ends[i * 2] < diff)
{
- current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+ current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
modified = true;
}
}
- } else {
+ }
+ else
+ {
// left justify
- if (ends[i*2]>0)
+ if (ends[i * 2] > 0)
{
- current.deleteChars(0, ends[i*2]);
+ current.deleteChars(0, ends[i * 2]);
modified = true;
- ends[i*2+1]-=ends[i*2];
- extent-=ends[i*2];
+ ends[i * 2 + 1] -= ends[i * 2];
+ extent -= ends[i * 2];
}
- if (extent>maxLength)
+ if (extent > maxLength)
{
- current.deleteChars(maxLength+1, extent);
+ current.deleteChars(maxLength + 1, extent);
modified = true;
- } else {
- if (extent<maxLength)
+ }
+ else
+ {
+ if (extent < maxLength)
{
- current.insertCharAt(extent, maxLength-extent,gapCharacter);
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
modified = true;
}
}
return modified;
}
+ @Override
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
}
+ @Override
public CigarArray getCompactAlignment()
{
- SeqCigar alseqs[] = new SeqCigar[sequences.size()];
- for (int i = 0; i < sequences.size(); i++)
+ synchronized (sequences)
{
- alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ int i = 0;
+ for (SequenceI seq : sequences)
+ {
+ alseqs[i++] = new SeqCigar(seq);
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
}
- CigarArray cal = new CigarArray(alseqs);
- cal.addOperation(CigarArray.M, getWidth());
- return cal;
}
+ @Override
public void setProperty(Object key, Object value)
{
if (alignmentProperties == null)
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
return null;
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
*
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
+ @Override
public AlignedCodonFrame getCodonFrame(int index)
{
return codonFrameList[index];
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
+ @Override
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
+ @Override
public AlignedCodonFrame[] getCodonFrames()
{
return codonFrameList;
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * AlignedCodonFrame)
*/
+ @Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
return removed;
}
+ @Override
public void append(AlignmentI toappend)
{
+ if (toappend == this)
+ {
+ System.err.println("Self append may cause a deadlock.");
+ }
// TODO test this method for a future 2.5 release
// currently tested for use in jalview.gui.SequenceFetcher
- boolean samegap = toappend.getGapCharacter()==getGapCharacter();
+ boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
- boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+ 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();
+ List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
+ .getFullAlignment().getSequences() : toappend.getSequences();
if (sqs != null)
{
- Enumeration sq = sqs.elements();
- while (sq.hasMoreElements())
+ synchronized (sqs)
{
- SequenceI addedsq=(SequenceI) sq.nextElement();
- if (!samegap)
+ for (SequenceI addedsq : sqs)
{
- char[] oldseq = addedsq.getSequence();
- for (int c=0;c<oldseq.length;c++)
+ if (!samegap)
{
- if (oldseq[c]==oldc)
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
{
- oldseq[c] = gapCharacter;
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
}
}
+ addSequence(addedsq);
}
- addSequence(addedsq);
}
}
AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
{
this.addCodonFrame(acod[a]);
}
- Vector sg = toappend.getGroups();
+ List<SequenceGroup> sg = toappend.getGroups();
if (sg != null)
{
- Enumeration el = sg.elements();
- while (el.hasMoreElements())
+ for (SequenceGroup _sg : sg)
{
- addGroup((SequenceGroup) el.nextElement());
+ addGroup(_sg);
}
}
- if (toappend.getHiddenSequences()!=null)
+ if (toappend.getHiddenSequences() != null)
{
HiddenSequences hs = toappend.getHiddenSequences();
- if (hiddenSequences==null)
+ if (hiddenSequences == null)
{
hiddenSequences = new HiddenSequences(this);
}
- if (hs.hiddenSequences!=null)
+ if (hs.hiddenSequences != null)
{
- for (int s=0;s<hs.hiddenSequences.length; s++)
+ for (int s = 0; s < hs.hiddenSequences.length; s++)
{
// hide the newly appended sequence in the alignment
- if (hs.hiddenSequences[s]!=null)
+ if (hs.hiddenSequences[s] != null)
{
hiddenSequences.hideSequence(hs.hiddenSequences[s]);
}
}
}
}
- if (toappend.getProperties()!=null)
+ if (toappend.getProperties() != null)
{
- // we really can't do very much here - just try to concatenate strings where property collisions occur.
+ // 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 != null)
{
- if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+ if (ourval.getClass().equals(toapprop.getClass())
+ && !ourval.equals(toapprop))
{
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
- } else {
+ 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);
+ ((Vector) ourval).addElement(theirv);
}
}
}
}
- } else {
+ }
+ else
+ {
// just add new property directly
setProperty(k, toapprop);
}
-
+
+ }
+ }
+ }
+
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ assert (name != null);
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ {
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+ new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+ annot.hasText = false;
+ annot.setCalcId(new String(calcId));
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
+ {
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up)
+ {
+ synchronized (sequences)
+ {
+ if (up)
+ {
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
+ }
+ }
+ else
+ {
+ for (int i = sequences.size() - 2; i > -1; i--)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i + 1);
+ if (sg.getSequences(map).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i + 1, seq);
+ }
}
+
}
}