/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * 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.
- *
- * 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 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
+ * 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.analysis.*;
-
-import jalview.util.*;
-
-import java.util.*;
-
-/** Data structure to hold and manipulate a multiple sequence alignment
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
+ */
+/**
+ * @author JimP
+ *
*/
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;
+ protected Alignment dataset;
- /** DOCUMENT ME!! */
- public AlignmentAnnotation[] annotations;
+ protected List<SequenceI> sequences;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ protected List<SequenceGroup> groups = java.util.Collections
+ .synchronizedList(new ArrayList<SequenceGroup>());
- private void initAlignment(SequenceI[] seqs) {
- int i=0;
+ protected char gapCharacter = '-';
- if( jalview.util.Comparison.isNucleotide(seqs))
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ protected int type = NUCLEOTIDE;
- sequences = new Vector();
+ public static final int PROTEIN = 0;
- for (i = 0; i < seqs.length; i++)
- {
- sequences.addElement(seqs[i]);
- }
+ public static final int NUCLEOTIDE = 1;
+
+ public boolean hasRNAStructure = false;
+ /** DOCUMENT ME!! */
+ public AlignmentAnnotation[] annotations;
+
+ HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+ public Hashtable alignmentProperties;
+
+ private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+
+ private void initAlignment(SequenceI[] seqs)
+ {
+ int i = 0;
+
+ if (jalview.util.Comparison.isNucleotide(seqs))
+ {
+ type = NUCLEOTIDE;
}
- /** Make an alignment from an array of Sequences.
- *
- * @param sequences
- */
- public Alignment(SequenceI[] seqs)
+ else
{
- initAlignment(seqs);
+ type = PROTEIN;
}
- /**
- * Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
- */
- public Alignment(SeqCigar[] alseqs) {
- 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
- */
- public static AlignmentI createAlignment(CigarArray compactAlignment) {
- throw new Error("Alignment(CigarArray) not yet implemented");
- // this(compactAlignment.refCigars);
+
+ sequences = java.util.Collections
+ .synchronizedList(new ArrayList<SequenceI>());
+
+ for (i = 0; i < seqs.length; i++)
+ {
+ sequences.add(seqs[i]);
+ }
+
+ }
+
+ /**
+ * Make a 'copy' alignment - sequences have new copies of features and
+ * annotations, but share the original dataset sequences.
+ */
+ public Alignment(AlignmentI al)
+ {
+ SequenceI[] seqs = al.getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = new Sequence(seqs[i]);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * Share the same dataset sequence mappings (if any). TODO: find a better
+ * place for these to live (alignment dataset?).
*/
- public Vector getSequences()
+ this.codonFrameList = ((Alignment) al).codonFrameList;
+
+ initAlignment(seqs);
+ }
+
+ /**
+ * Make an alignment from an array of Sequences.
+ *
+ * @param sequences
+ */
+ public Alignment(SequenceI[] seqs)
+ {
+ initAlignment(seqs);
+ }
+
+ /**
+ * Make a new alignment from an array of SeqCigars
+ *
+ * @param seqs
+ * SeqCigar[]
+ */
+ public Alignment(SeqCigar[] alseqs)
+ {
+ 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
+ */
+ public static AlignmentI createAlignment(CigarArray compactAlignment)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
+ // this(compactAlignment.refCigars);
+ }
+
+ @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;
+ }
+ synchronized (sequences)
{
- return sequences;
+ return sequences.toArray(new SequenceI[sequences.size()]);
}
+ }
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map<String, List<SequenceI>> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
- public SequenceI [] getSequencesArray()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public SequenceI getSequenceAt(int i)
+ {
+ synchronized (sequences)
{
- SequenceI [] reply = new SequenceI[sequences.size()];
- for(int i=0; i<sequences.size(); i++)
+ if (i > -1 && i < sequences.size())
{
- reply[i] = (SequenceI)sequences.elementAt(i);
+ return sequences.get(i);
}
- return reply;
}
+ return null;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI getSequenceAt(int i)
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ @Override
+ public void addSequence(SequenceI snew)
+ {
+ if (dataset != null)
{
- if (i < sequences.size())
- {
- return (SequenceI) sequences.elementAt(i);
- }
-
- return null;
+ // maintain dataset integrity
+ if (snew.getDatasetSequence() != null)
+ {
+ getDataset().addSequence(snew.getDatasetSequence());
+ }
+ else
+ {
+ // derive new sequence
+ SequenceI adding = snew.deriveSequence();
+ getDataset().addSequence(adding.getDatasetSequence());
+ snew = adding;
+ }
}
-
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
- public void addSequence(SequenceI snew)
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[] { snew });
+ }
+ else
{
- if(dataset!=null)
+ synchronized (sequences)
{
- if(snew.getDatasetSequence()!=null)
- {
- getDataset().addSequence(snew.getDatasetSequence());
- }
- else
- {
- Sequence ds = new Sequence(snew.getName(),
- AlignSeq.extractGaps("-. ",
- snew.getSequence()),
- snew.getStart(),
- snew.getEnd());
-
- snew.setDatasetSequence(ds);
- getDataset().addSequence(ds);
- }
+ sequences.add(snew);
}
- sequences.addElement(snew);
-
+ }
+ if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
}
+ }
-
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
- public void setSequenceAt(int i, SequenceI snew)
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ @Override
+ public void setSequenceAt(int i, SequenceI snew)
+ {
+ synchronized (sequences)
{
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
-
- sequences.setElementAt(snew, i);
+ deleteSequence(i);
+ sequences.set(i, snew);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getGroups()
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public List<SequenceGroup> getGroups()
+ {
+ return groups;
+ }
+
+ @Override
+ public void finalize()
+ {
+ if (getDataset() != null)
{
- return groups;
+ getDataset().removeAlignmentRef();
}
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- */
- public void deleteSequence(SequenceI s)
+ dataset = null;
+ sequences = null;
+ groups = null;
+ annotations = null;
+ hiddenSequences = null;
+ }
+
+ /**
+ * decrement the alignmentRefs counter by one and call finalize if it goes to
+ * zero.
+ */
+ private void removeAlignmentRef()
+ {
+ if (--alignmentRefs == 0)
{
- deleteSequence(findIndex(s));
+ finalize();
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteSequence(int i)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ */
+ @Override
+ public void deleteSequence(SequenceI s)
+ {
+ deleteSequence(findIndex(s));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ */
+ @Override
+ public void deleteSequence(int i)
+ {
+ if (i > -1 && i < getHeight())
{
- if(i>-1 && i<getHeight())
+ synchronized (sequences)
{
- sequences.removeElementAt(i);
+ sequences.remove(i);
hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
+ }
-
- /** */
- public SequenceGroup findGroup(SequenceI s)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup findGroup(SequenceI s)
+ {
+ synchronized (groups)
{
- for (int i = 0; i < this.groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ for (int i = 0; i < this.groups.size(); i++)
+ {
+ SequenceGroup sg = groups.get(i);
- if (sg.getSequences(false).contains(s))
- {
- return sg;
- }
+ if (sg.getSequences(null).contains(s))
+ {
+ return sg;
}
-
- return null;
+ }
}
+ return null;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup[] findAllGroups(SequenceI s)
- {
- Vector temp = new Vector();
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup[] findAllGroups(SequenceI s)
+ {
+ ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
- int gSize = groups.size();
- for (int i = 0; i < gSize; i++)
+ synchronized (groups)
+ {
+ int gSize = groups.size();
+ for (int i = 0; i < gSize; i++)
+ {
+ SequenceGroup sg = groups.get(i);
+ if (sg == null || sg.getSequences() == null)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if(sg==null || sg.getSequences(false)==null)
- {
- this.deleteGroup(sg);
- gSize--;
- continue;
- }
-
- if (sg.getSequences(false).contains(s))
- {
- temp.addElement(sg);
- }
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
}
- SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
- for (int i = 0; i < temp.size(); i++)
+ if (sg.getSequences().contains(s))
{
- ret[i] = (SequenceGroup) temp.elementAt(i);
+ temp.add(sg);
}
-
- return ret;
+ }
}
+ SequenceGroup[] ret = new SequenceGroup[temp.size()];
+ return temp.toArray(ret);
+ }
-
-
- /** */
- public void addGroup(SequenceGroup sg)
+ /** */
+ @Override
+ public void addGroup(SequenceGroup sg)
+ {
+ synchronized (groups)
{
- if (!groups.contains(sg))
+ if (!groups.contains(sg))
+ {
+ if (hiddenSequences.getSize() > 0)
{
- if(hiddenSequences.getSize()>0)
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
{
- //We're not going to make groups of
- //Hidden sequences
- int i, iSize = sg.getSize(false);
- for (i = 0; i < iSize; i++)
+ if (!sequences.contains(sg.getSequenceAt(i)))
{
- if (!sequences.contains(sg.getSequenceAt(i)))
- {
- sg.deleteSequence(sg.getSequenceAt(i), false);
- iSize--;
- i--;
- }
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
}
-
- if (sg.getSize(true) < 1)
- return;
}
- groups.addElement(sg);
+ if (sg.getSize() < 1)
+ {
+ return;
+ }
}
+ sg.setContext(this);
+ groups.add(sg);
+ }
}
+ }
- /**
- * DOCUMENT ME!
- */
- public void deleteAllGroups()
+ /**
+ * 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)
{
- groups.removeAllElements();
+ return;
}
-
- /** */
- public void deleteGroup(SequenceGroup g)
+ // remove annotation very quickly
+ AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ int i, p, k;
+ if (gp == null)
{
- if (groups.contains(g))
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef != null)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
{
- groups.removeElement(g);
+ tokeep[k++] = annotations[i];
}
+ }
}
-
- /** */
- public SequenceI findName(String name)
+ else
{
- int i = 0;
-
- while (i < sequences.size())
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef == gp)
{
- if (getSequenceAt(i).getName().equals(name))
- {
- return getSequenceAt(i);
- }
-
- i++;
+ todelete[p++] = annotations[i];
}
-
- return null;
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
}
-
- public SequenceI [] findSequenceMatch(String name)
+ if (p > 0)
{
- Vector matches = new Vector();
- int i = 0;
-
- while (i < sequences.size())
+ // clear out the group associated annotation.
+ for (i = 0; i < p; i++)
{
- if (getSequenceAt(i).getName().equals(name))
- {
- matches.addElement(getSequenceAt(i));
- }
- i++;
+ unhookAnnotation(todelete[i]);
+ todelete[i] = null;
}
-
- SequenceI [] result = new SequenceI[matches.size()];
- for(i=0; i<result.length; i++)
- result[i] = (SequenceI)matches.elementAt(i);
-
- return result;
-
+ t = new AlignmentAnnotation[k];
+ for (i = 0; i < k; i++)
+ {
+ t[i] = tokeep[i];
+ }
+ annotations = t;
}
+ }
-
- /** */
- public int findIndex(SequenceI s)
+ @Override
+ public void deleteAllGroups()
+ {
+ synchronized (groups)
{
- int i = 0;
-
- while (i < sequences.size())
- {
- if (s == getSequenceAt(i))
- {
- return i;
- }
-
- i++;
- }
-
- return -1;
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
+ groups.clear();
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getHeight()
+ /** */
+ @Override
+ public void deleteGroup(SequenceGroup g)
+ {
+ synchronized (groups)
{
- return sequences.size();
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ g.setContext(null);
+ }
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWidth()
- {
- int maxLength = -1;
-
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
- }
+ /** */
+ @Override
+ public SequenceI findName(String name)
+ {
+ return findName(name, false);
+ }
- return maxLength;
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @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)
+ */
+ @Override
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
- /**
- * DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
- */
- public void setGapCharacter(char gc)
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
{
- gapCharacter = gc;
-
- for (int i = 0; i < sequences.size(); i++)
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i++) == startAfter)
{
- Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence( seq.getSequence().replace('.', gc) );
- seq.setSequence( seq.getSequence().replace('-', gc) );
- seq.setSequence( seq.getSequence().replace(' ', gc) );
+ matched = true;
+ break;
}
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
+ while (i < sequences.size())
{
- return gapCharacter;
- }
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
+ {
+ return getSequenceAt(i);
+ }
+ i++;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean isAligned()
- {
- int width = getWidth();
+ return null;
+ }
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() != width)
- {
- return false;
- }
- }
+ @Override
+ public SequenceI[] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
- return true;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
}
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void deleteAnnotation(AlignmentAnnotation aa)
+ SequenceI[] result = new SequenceI[matches.size()];
+ for (i = 0; i < result.length; i++)
{
- int aSize = 1;
-
- if (annotations != null)
- {
- aSize = annotations.length;
- }
-
- if(aSize<1)
- return;
+ result[i] = (SequenceI) matches.elementAt(i);
+ }
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+ return result;
- int tIndex = 0;
+ }
- for (int i = 0; i < aSize; i++)
- {
- if (annotations[i] == aa)
- {
- continue;
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
- temp[tIndex] = annotations[i];
- tIndex++;
- }
+ while (i < sequences.size())
+ {
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
- annotations = temp;
+ i++;
}
+ return -1;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ @Override
+ public int findIndex(SearchResults results)
+ {
+ int i = 0;
- public void adjustSequenceAnnotations()
+ while (i < sequences.size())
{
- if(annotations!=null)
+ if (results.involvesSequence(getSequenceAt(i)))
{
- for (int a = 0; a < annotations.length; a++)
- {
- if (annotations[a].sequenceRef != null)
- {
- annotations[a].adjustForAlignment();
- }
- }
+ return i;
}
+ i++;
}
+ return -1;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void addAnnotation(AlignmentAnnotation aa)
- {
- int aSize = 1;
- if (annotations != null)
- {
- aSize = annotations.length + 1;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getHeight()
+ {
+ return sequences.size();
+ }
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public int getWidth()
+ {
+ int maxLength = -1;
- temp[aSize-1] = aa;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (getSequenceAt(i).getLength() > maxLength)
+ {
+ maxLength = getSequenceAt(i).getLength();
+ }
+ }
- int i = 0;
+ return maxLength;
+ }
- if (aSize > 1)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setGapCharacter(char gc)
+ {
+ gapCharacter = gc;
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
+ */
+ @Override
+ public boolean isAligned()
+ {
+ 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 (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
+ {
+ if (getSequenceAt(i).getLength() != width)
{
- for (i = 0; i < (aSize-1); i++)
- {
- temp[i] = annotations[i];
- }
+ return false;
}
+ }
+ }
+
+ return true;
+ }
- annotations = temp;
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ @Override
+ public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+ {
+ boolean result = false;
+ for (AlignmentAnnotation alan : getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated || includingAutoCalculated)
+ {
+ deleteAnnotation(alan);
+ result = true;
+ }
}
+ return result;
+ }
- public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ /*
+ * (non-Javadoc)
+ *
+ * @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(aa==null || annotations==null || annotations.length-1<index)
- return;
+ aSize = annotations.length;
+ }
- int aSize = annotations.length;
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+ if (aSize < 1)
+ {
+ return false;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
- temp[index] = aa;
+ boolean swap = false;
+ int tIndex = 0;
- for (int i = 0; i < aSize; i++)
+ for (int i = 0; i < aSize; i++)
+ {
+ if (annotations[i] == aa)
{
- if(i==index)
- continue;
+ swap = true;
+ continue;
+ }
+ if (tIndex < temp.length)
+ {
+ temp[tIndex++] = annotations[i];
+ }
+ }
- if(i<index)
- temp[i] = annotations[i];
- else
- temp[i] = annotations[i-1];
+ if (swap)
+ {
+ annotations = temp;
+ if (unhook)
+ {
+ unhookAnnotation(aa);
}
+ }
+ return swap;
+ }
- annotations = temp;
+ /**
+ * remove any object references associated with this annotation
+ *
+ * @param aa
+ */
+ 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;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentAnnotation[] getAlignmentAnnotation()
+ /*
+ * (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)
{
- return annotations;
+ hasRNAStructure = true;
}
- public void setNucleotide(boolean b)
+ int aSize = 1;
+ if (annotations != null)
{
- if(b)
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ aSize = annotations.length + 1;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+ int i = 0;
+ if (pos == -1 || pos >= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
+ if (aSize > 1)
+ {
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
+ {
+ 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)
+ {
+ return;
}
- public boolean isNucleotide()
+ int aSize = annotations.length;
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+ temp[index] = aa;
+
+ for (int i = 0; i < aSize; i++)
{
- if(type==NUCLEOTIDE)
- return true;
+ if (i == index)
+ {
+ continue;
+ }
+
+ if (i < index)
+ {
+ temp[i] = annotations[i];
+ }
else
- return false;
+ {
+ temp[i] = annotations[i - 1];
+ }
+ }
+
+ annotations = temp;
+ }
+
+ @Override
+ /**
+ * returns all annotation on the alignment
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ return annotations;
+ }
+
+ @Override
+ public void setNucleotide(boolean b)
+ {
+ if (b)
+ {
+ type = NUCLEOTIDE;
+ }
+ else
+ {
+ type = PROTEIN;
+ }
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ if (type == NUCLEOTIDE)
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ @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)
+ {
+ // Create a new dataset for this alignment.
+ // Can only be done once, if dataset is not null
+ // This will not be performed
+ SequenceI[] seqs = new SequenceI[getHeight()];
+ SequenceI currentSeq;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ currentSeq = getSequenceAt(i);
+ if (currentSeq.getDatasetSequence() != null)
+ {
+ seqs[i] = currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ seqs[i] = currentSeq.createDatasetSequence();
+ }
+ }
+
+ dataset = new Alignment(seqs);
+ }
+ else if (dataset == null && data != null)
+ {
+ dataset = data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
+ }
+ dataset.addAlignmentRef();
+ }
+
+ /**
+ * reference count for number of alignments referencing this one.
+ */
+ int alignmentRefs = 0;
+
+ /**
+ * increase reference count to this alignment.
+ */
+ private void addAlignmentRef()
+ {
+ alignmentRefs++;
+ }
+
+ @Override
+ public Alignment getDataset()
+ {
+ return dataset;
+ }
+
+ @Override
+ public boolean padGaps()
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ for (int j = current.getLength(); j > maxLength; 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++)
+ {
+ current = getSequenceAt(i);
+ cLength = current.getLength();
+
+ if (cLength < maxLength)
+ {
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
+ modified = true;
+ }
+ else if (current.getLength() > maxLength)
+ {
+ current.deleteChars(maxLength, current.getLength());
+ }
}
+ 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
+ */
+ @Override
+ public boolean justify(boolean right)
+ {
+ boolean modified = false;
- public void setDataset(Alignment data)
+ // 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++)
{
- if(dataset==null && data==null)
+ 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++)
{
- // 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 currentSeq;
- for (int i = 0; i < getHeight(); i++)
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
{
- currentSeq = getSequenceAt(i);
- if(currentSeq.getDatasetSequence()!=null)
+ if (!hitres)
{
- seqs[i] = (Sequence)currentSeq.getDatasetSequence();
+ ends[i * 2] = j;
+ hitres = true;
}
else
{
- seqs[i] = new Sequence(currentSeq.getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- currentSeq.getSequence()
- ),
- currentSeq.getStart(),
- currentSeq.getEnd());
- seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
- seqs[i].setDescription(currentSeq.getDescription());
- getSequenceAt(i).setSequenceFeatures(null);
- getSequenceAt(i).setDatasetSequence(seqs[i]);
+ 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);
- dataset = new Alignment(seqs);
+ 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 if(dataset==null && data!=null)
+ else
{
- dataset = data;
+ // 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;
+ }
+
+ @Override
+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ @Override
+ public CigarArray getCompactAlignment()
+ {
+ synchronized (sequences)
+ {
+ 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;
+ }
+ }
+
+ @Override
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
+ {
+ alignmentProperties = new Hashtable();
+ }
+
+ alignmentProperties.put(key, value);
+ }
- public Alignment getDataset()
+ @Override
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
+ {
+ return alignmentProperties.get(key);
+ }
+ else
{
- return dataset;
+ return null;
}
+ }
+
+ @Override
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
- public boolean padGaps()
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
+ */
+ @Override
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons != null)
{
- boolean modified=false;
+ codonFrameList.add(codons);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
+ {
+ if (seq == null)
+ {
+ return null;
+ }
+ List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+ for (AlignedCodonFrame acf : codonFrameList)
+ {
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
+ }
+ return cframes;
+ }
+
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings).
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ {
+ this.codonFrameList = acfs;
+ }
+
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment.
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ @Override
+ public Set<AlignedCodonFrame> getCodonFrames()
+ {
+ return codonFrameList;
+ }
- //Remove excess gaps from the end of alignment
- int maxLength = -1;
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * AlignedCodonFrame)
+ */
+ @Override
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null || codonFrameList == null)
+ {
+ return false;
+ }
+ return codonFrameList.remove(codons);
+ }
- SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ @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();
+ char oldc = toappend.getGapCharacter();
+ boolean hashidden = toappend.getHiddenSequences() != null
+ && toappend.getHiddenSequences().hiddenSequences != null;
+ // get all sequences including any hidden ones
+ List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
+ .getFullAlignment().getSequences() : toappend.getSequences();
+ if (sqs != null)
+ {
+ synchronized (sqs)
{
- current = getSequenceAt(i);
- for (int j = current.getLength(); j > maxLength; j--)
+ for (SequenceI addedsq : sqs)
{
- if (j > maxLength && !jalview.util.Comparison.isGap(
- current.getCharAt(j)))
+ if (!samegap)
{
- maxLength = j;
- break;
+ 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]);
+ }
- maxLength++;
+ this.codonFrameList.addAll(toappend.getCodonFrames());
- int cLength;
- for (int i = 0; i < sequences.size();
- i++)
+ List<SequenceGroup> sg = toappend.getGroups();
+ if (sg != null)
+ {
+ for (SequenceGroup _sg : sg)
{
- current = getSequenceAt(i);
- cLength = current.getLength();
-
- if (cLength < maxLength)
+ addGroup(_sg);
+ }
+ }
+ 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++)
{
- current.insertCharAt(cLength,
- maxLength-cLength, gapCharacter);
- modified=true;
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s] != null)
+ {
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+ }
}
- else if(current.getLength() > maxLength)
+ }
+ }
+ 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)
{
- current.deleteChars(maxLength, current.getLength());
+ 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);
+ }
+
}
- return modified;
}
+ }
- public HiddenSequences getHiddenSequences()
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ assert (name != null);
+ if (annotations != 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)
{
- return hiddenSequences;
+ annot.setSequenceRef(seqRef);
}
- SequenceI [] getVisibleAndRepresentedSeqs()
+ 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(hiddenSequences==null || hiddenSequences.getSize()<1)
- return getSequencesArray();
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ */
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
- Vector seqs = new Vector();
- SequenceI seq;
- SequenceGroup hidden;
- for (int i = 0; i < sequences.size(); i++)
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up)
+ {
+ synchronized (sequences)
+ {
+ if (up)
{
- seq = (SequenceI) sequences.elementAt(i);
- seqs.addElement(seq);
- hidden = seq.getHiddenSequences();
- if(hidden!=null)
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
{
- for(int j=0; j<hidden.getSize(false); j++)
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
{
- seqs.addElement(hidden.getSequenceAt(j));
+ continue;
}
+
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
}
}
- SequenceI [] result = new SequenceI[seqs.size()];
- for(int i=0; i<seqs.size(); i++)
- result[i] = (SequenceI)seqs.elementAt(i);
+ else
+ {
+ for (int i = sequences.size() - 2; i > -1; i--)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
- return result;
+ SequenceI temp = sequences.get(i + 1);
+ if (sg.getSequences(map).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i + 1, seq);
+ }
+ }
}
+ }
- public CigarArray getCompactAlignment()
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- SeqCigar alseqs[] = new SeqCigar[sequences.size()];
- for (int i=0; i<sequences.size(); i++) {
- alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
}
- CigarArray cal = new CigarArray(alseqs);
- cal.addOperation(CigarArray.M, getWidth());
- return cal;
}
+ private SequenceI seqrep = null;
+
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
+
+ /**
+ * Align this alignment like the given (mapped) one.
+ */
+ @Override
+ public int alignAs(AlignmentI al)
+ {
+ /*
+ * Currently retains unmapped gaps (in introns), regaps mapped regions
+ * (exons)
+ */
+ return alignAs(al, false, true);
+ }
+
+ /**
+ * Align this alignment 'the same as' the given one. Mapped sequences only are
+ * realigned. If both of the same type (nucleotide/protein) then align both
+ * identically. If this is nucleotide and the other is protein, make 3 gaps
+ * for each gap in the protein sequences. If this is protein and the other is
+ * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+ * nucleotide bases. If this is protein and the other is nucleotide, gaps
+ * protein to match the relative ordering of codons in the nucleotide.
+ *
+ * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+ * regions are preserved. Gaps that connect introns to exons are treated
+ * conservatively, i.e. only preserved if both intron and exon gaps are
+ * preserved.
+ *
+ * @param al
+ * @param preserveMappedGaps
+ * if true, gaps within and between mapped codons are preserved
+ * @param preserveUnmappedGaps
+ * if true, gaps within and between unmapped codons are preserved
+ */
+ // @Override
+ public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO should this method signature be the one in the interface?
+ int count = 0;
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+
+ char thisGapChar = this.getGapCharacter();
+ String gap = thisIsNucleotide && thatIsProtein ? String
+ .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+ : String.valueOf(thisGapChar);
+
+ // TODO handle intron regions? Needs a 'holistic' alignment of dna,
+ // not just sequence by sequence. But how to 'gap' intron regions?
+
+ /*
+ * Get mappings from 'that' alignment's sequences to this.
+ */
+ for (SequenceI alignTo : getSequences())
+ {
+ count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+ preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+ }
+ return count;
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray());
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set<String> getSequenceNames()
+ {
+ Set<String> names = new HashSet<String>();
+ for (SequenceI seq : getSequences())
+ {
+ names.add(seq.getName());
+ }
+ return names;
+ }
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
}
git://source.jalview.org / jalview.git / blobdiff