X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=098222f0ca5a6f4468126e3cad20f09a09680935;hb=92e39eb6a3ab1a0e3ab45cef49a64a1c7a7007b6;hp=588134ae7ca7cdd3e2f0d4c66f66e024d7e337de;hpb=8963cf56e542ec741295e8c4dfcee06ba3e140fb;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 588134a..098222f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,819 +1,1923 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * 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.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+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;
+ private Alignment dataset;
- /** DOCUMENT ME!! */
- public AlignmentAnnotation[] annotations;
+ protected List sequences;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ protected List groups;
- private void initAlignment(SequenceI[] seqs) {
- int i=0;
+ protected char gapCharacter = '-';
- if( jalview.util.Comparison.isNucleotide(seqs))
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ private boolean nucleotide = true;
- sequences = new Vector();
+ public boolean hasRNAStructure = false;
- for (i = 0; i < seqs.length; i++)
- {
- sequences.addElement(seqs[i]);
- }
+ public AlignmentAnnotation[] annotations;
+
+ HiddenSequences hiddenSequences;
+
+ HiddenColumns hiddenCols;
+
+ public Hashtable alignmentProperties;
+
+ private List codonFrameList;
+
+ private void initAlignment(SequenceI[] seqs)
+ {
+ groups = Collections.synchronizedList(new ArrayList());
+ hiddenSequences = new HiddenSequences(this);
+ hiddenCols = new HiddenColumns();
+ codonFrameList = new ArrayList<>();
+
+ nucleotide = Comparison.isNucleotide(seqs);
+ sequences = Collections.synchronizedList(new ArrayList());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ sequences.add(seqs[i]);
}
- /** Make an alignment from an array of Sequences.
- *
- * @param sequences
- */
- public Alignment(SequenceI[] seqs)
+
+ }
+
+ /**
+ * 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++)
{
- initAlignment(seqs);
+ seqs[i] = new Sequence(seqs[i]);
}
- /**
- * Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
+
+ initAlignment(seqs);
+
+ /*
+ * Share the same dataset sequence mappings (if any).
*/
- public Alignment(SeqCigar[] alseqs) {
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
+ }
- SequenceI[] seqs = new SequenceI[alseqs.length];
- for (int i=0; i getSequences()
+ {
+ return sequences;
+ }
+
+ @Override
+ public List getSequences(
+ Map 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;
}
- /**
- * 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 Alignment(CigarArray compactAlignment) {
- throw new Error("Alignment(CigarArray) not yet implemented");
- // this(compactAlignment.refCigars);
+ synchronized (sequences)
+ {
+ return sequences.toArray(new SequenceI[sequences.size()]);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getSequences()
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
+
+
+ @Override
+ public SequenceI getSequenceAt(int i)
+ {
+ synchronized (sequences)
{
- return sequences;
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
}
+ return null;
+ }
- public SequenceI [] getSequencesArray()
+ @Override
+ public SequenceI getSequenceAtAbsoluteIndex(int i)
+ {
+ SequenceI seq = null;
+ if (getHiddenSequences().getSize() > 0)
{
- SequenceI [] reply = new SequenceI[sequences.size()];
- for(int i=0; i i)
{
- if(snew.getDatasetSequence()!=null)
- {
- System.out.println(snew.getName());
- getDataset().addSequence(snew.getDatasetSequence());
- }
- else
- {
- Sequence ds = new Sequence(snew.getName(),
- AlignSeq.extractGaps("-. ",
- snew.getSequence()),
- snew.getStart(),
- snew.getEnd());
+ return sequences.set(i, snew);
- snew.setDatasetSequence(ds);
- getDataset().addSequence(ds);
- }
}
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return null;
+ }
+ }
- sequences.addElement(snew);
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public List getGroups()
+ {
+ return groups;
+ }
+
+ @Override
+ public void finalize() throws Throwable
+ {
+ if (getDataset() != null)
+ {
+ getDataset().removeAlignmentRef();
}
+ nullReferences();
+ super.finalize();
+ }
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
- public void setSequenceAt(int i, SequenceI snew)
+ /**
+ * Defensively nulls out references in case this object is not garbage
+ * collected
+ */
+ void nullReferences()
+ {
+ dataset = null;
+ sequences = null;
+ groups = null;
+ annotations = null;
+ hiddenSequences = null;
+ }
+
+ /**
+ * decrement the alignmentRefs counter by one and null references if it goes
+ * to zero.
+ *
+ * @throws Throwable
+ */
+ private void removeAlignmentRef() throws Throwable
+ {
+ if (--alignmentRefs == 0)
{
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
+ nullReferences();
+ }
+ }
- sequences.setElementAt(snew, i);
+ @Override
+ public void deleteSequence(SequenceI s)
+ {
+ synchronized (sequences)
+ {
+ deleteSequence(findIndex(s));
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getGroups()
+ @Override
+ public void deleteSequence(int i)
+ {
+ synchronized (sequences)
{
- return groups;
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
+ }
}
+ }
- /** Takes out columns consisting entirely of gaps (-,.," ")
- */
- public void removeGaps()
+ @Override
+ public void deleteHiddenSequence(int i)
+ {
+ synchronized (sequences)
{
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();
- int j, jSize = seqs.length;
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ }
+ }
+ }
- int width = 0;
- for (int i = 0; i < jSize; i++)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup findGroup(SequenceI seq, int position)
+ {
+ synchronized (groups)
+ {
+ for (SequenceGroup sg : groups)
+ {
+ if (sg.getSequences(null).contains(seq))
{
- if (seqs[i].getLength() > width)
+ if (position >= sg.getStartRes() && position <= sg.getEndRes())
{
- width = seqs[i].getLength();
+ return sg;
}
}
+ }
+ }
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup[] findAllGroups(SequenceI s)
+ {
+ ArrayList temp = new ArrayList<>();
- int startCol = -1, endCol = -1;
- boolean delete = true;
- for (int i = 0; i < width; 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)
{
- delete = true;
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- for (j = 0; j < jSize; j++)
- {
- if (seqs[j].getLength() > i)
- {
- if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
- {
- if(delete)
- endCol = i;
-
- delete = false;
- break;
- }
- }
- }
+ if (sg.getSequences().contains(s))
+ {
+ temp.add(sg);
+ }
+ }
+ }
+ SequenceGroup[] ret = new SequenceGroup[temp.size()];
+ return temp.toArray(ret);
+ }
- if(delete && startCol==-1)
+ /** */
+ @Override
+ public void addGroup(SequenceGroup sg)
+ {
+ synchronized (groups)
+ {
+ if (!groups.contains(sg))
+ {
+ if (hiddenSequences.getSize() > 0)
+ {
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
+ {
+ if (!sequences.contains(sg.getSequenceAt(i)))
{
- startCol = i;
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
}
+ }
-
- if (!delete && startCol > -1)
- {
- deleteColumns(seqs, startCol, endCol);
- width -= (endCol - startCol);
- i -= (endCol - startCol);
- startCol = -1;
- endCol = -1;
- }
+ if (sg.getSize() < 1)
+ {
+ return;
+ }
}
+ sg.setContext(this, true);
+ groups.add(sg);
+ }
+ }
+ }
- if (delete && startCol > -1)
+ /**
+ * 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
{
- deleteColumns(seqs, startCol, endCol);
+ 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;
}
+ }
- /** Removes a range of columns (start to end inclusive).
- *
- * @param seqs Sequences to remove columns from
- * @param start Start column in the alignment
- * @param end End column in the alignment
- */
- public void deleteColumns(SequenceI [] seqs, int start, int end)
+ @Override
+ public void deleteAllGroups()
+ {
+ synchronized (groups)
{
- for(int i=0; iseqs[j].getLength())
- {
- sequences.removeElement(seqs[j]);
- j--;
- jSize--;
- }
- else
- {
- seqs[j].setStart(newstart);
- seqs[j].setSequence(seqs[j].getSequence().substring(i));
- }
+ matched = true;
+ break;
}
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void trimRight(int i)
+ while (i < sequences.size())
{
- SequenceI[] seqs = getVisibleAndRepresentedSeqs();
- int j, jSize = seqs.length;
- for (j = 0; j < jSize; j++)
- {
- int newend = seqs[j].findPosition(i);
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
+ {
+ return getSequenceAt(i);
+ }
- seqs[j].setEnd(newend);
- if(seqs[j].getLength()>i)
- seqs[j].setSequence(seqs[j].getSequence().substring(0, i + 1));
- }
+ i++;
}
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- */
- public void deleteSequence(SequenceI s)
+ return null;
+ }
+
+ @Override
+ public SequenceI[] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
{
- for (int i = 0; i < getHeight(); i++)
- {
- if (getSequenceAt(i) == s)
- {
- deleteSequence(i);
- }
- }
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteSequence(int i)
+ SequenceI[] result = new SequenceI[matches.size()];
+ for (i = 0; i < result.length; i++)
{
- sequences.removeElementAt(i);
+ result[i] = (SequenceI) matches.elementAt(i);
}
+ return result;
- /** */
- public SequenceGroup findGroup(SequenceI s)
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
{
- for (int i = 0; i < this.groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
- if (sg.getSequences(false).contains(s))
- {
- return sg;
- }
- }
+ i++;
+ }
+
+ return -1;
+ }
- return null;
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ @Override
+ public int findIndex(SearchResultsI results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
}
+ return -1;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup[] findAllGroups(SequenceI s)
+
+ @Override
+ public int getHeight()
+ {
+ return sequences.size();
+ }
+
+ @Override
+ public int getAbsoluteHeight()
+ {
+ return sequences.size() + getHiddenSequences().getSize();
+ }
+
+ @Override
+ public int getWidth()
+ {
+ int maxLength = -1;
+
+ for (int i = 0; i < sequences.size(); i++)
{
- Vector temp = new Vector();
+ if (getSequenceAt(i).getLength() > maxLength)
+ {
+ maxLength = getSequenceAt(i).getLength();
+ }
+ }
- int gSize = groups.size();
- for (int i = 0; i < gSize; i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if(sg==null || sg.getSequences(false)==null)
- {
- this.deleteGroup(sg);
- gSize--;
- continue;
- }
+ return maxLength;
+ }
- if (sg.getSequences(false).contains(s))
- {
- temp.addElement(sg);
- }
- }
+ /**
+ * 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));
+ }
+ }
+ }
- SequenceGroup[] ret = new SequenceGroup[temp.size()];
+ /**
+ * 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);
+ }
- for (int i = 0; i < temp.size(); i++)
+ /*
+ * (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)
{
- ret[i] = (SequenceGroup) temp.elementAt(i);
+ return false;
}
+ }
+ }
+
+ return true;
+ }
+
+ @Override
+ public boolean isHidden(int alignmentIndex)
+ {
+ return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+ }
+
+ /**
+ * 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;
+ }
+
+ /*
+ * (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)
+ {
+ aSize = annotations.length;
+ }
- return ret;
+ if (aSize < 1)
+ {
+ return false;
}
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+ boolean swap = false;
+ int tIndex = 0;
- /** */
- public void addGroup(SequenceGroup sg)
+ for (int i = 0; i < aSize; i++)
{
- if (!groups.contains(sg))
- {
- groups.addElement(sg);
- }
+ if (annotations[i] == aa)
+ {
+ swap = true;
+ continue;
+ }
+ if (tIndex < temp.length)
+ {
+ temp[tIndex++] = annotations[i];
+ }
}
- /**
- * DOCUMENT ME!
- */
- public void deleteAllGroups()
+ if (swap)
{
- groups.removeAllElements();
+ annotations = temp;
+ if (unhook)
+ {
+ unhookAnnotation(aa);
+ }
+ }
+ return swap;
+ }
- int i = 0;
+ /**
+ * 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;
+ }
+ }
- while (i < sequences.size())
+ /*
+ * (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)
+ {
+ 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)
{
- SequenceI s = getSequenceAt(i);
- s.setColor(java.awt.Color.white);
- i++;
+ 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;
+ }
+
+ int aSize = annotations.length;
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+ temp[index] = aa;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if (i == index)
+ {
+ continue;
+ }
+
+ if (i < index)
+ {
+ temp[i] = annotations[i];
+ }
+ else
+ {
+ temp[i] = annotations[i - 1];
+ }
}
- /** */
- public void deleteGroup(SequenceGroup g)
+ annotations = temp;
+ }
+
+ @Override
+ /**
+ * returns all annotation on the alignment
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ return annotations;
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ return nucleotide;
+ }
+
+ @Override
+ public boolean hasRNAStructure()
+ {
+ // TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
+
+ @Override
+ public void setDataset(AlignmentI data)
+ {
+ if (dataset == null && data == null)
{
- if (groups.contains(g))
+ createDatasetAlignment();
+ }
+ else if (dataset == null && data != null)
+ {
+ if (data == this)
+ {
+ throw new IllegalArgumentException("Circular dataset reference");
+ }
+ if (!(data instanceof Alignment))
+ {
+ throw new Error(
+ "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+ }
+ dataset = (Alignment) 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
{
- groups.removeElement(g);
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
}
+ }
}
+ dataset.addAlignmentRef();
+ }
- /** */
- public SequenceI findName(String name)
+ /**
+ * add dataset sequences to seq for currentSeq and any sequences it references
+ */
+ private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+ Set seqs, boolean createDatasetSequence)
+ {
+ SequenceI alignedSeq = currentSeq;
+ if (currentSeq.getDatasetSequence() != null)
{
- int i = 0;
+ currentSeq = currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ if (createDatasetSequence)
+ {
+ currentSeq = currentSeq.createDatasetSequence();
+ }
+ }
+
+ List toProcess = new ArrayList<>();
+ toProcess.add(currentSeq);
+ while (toProcess.size() > 0)
+ {
+ // use a queue ?
+ SequenceI curDs = toProcess.remove(0);
- while (i < sequences.size())
+ if (!seqs.add(curDs))
+ {
+ continue;
+ }
+ // iterate over database references, making sure we add forward referenced
+ // sequences
+ if (curDs.getDBRefs() != null)
+ {
+ for (DBRefEntry dbr : curDs.getDBRefs())
{
- if (getSequenceAt(i).getName().equals(name))
+ if (dbr.getMap() != null && dbr.getMap().getTo() != null)
+ {
+ if (dbr.getMap().getTo() == alignedSeq)
{
- return getSequenceAt(i);
+ /*
+ * update mapping to be to the newly created dataset sequence
+ */
+ dbr.getMap().setTo(currentSeq);
}
-
- i++;
+ if (dbr.getMap().getTo().getDatasetSequence() != null)
+ {
+ throw new Error(
+ "Implementation error: Map.getTo() for dbref " + dbr
+ + " from " + curDs.getName()
+ + " is not a dataset sequence.");
+ }
+ // we recurse to add all forward references to dataset sequences via
+ // DBRefs/etc
+ toProcess.add(dbr.getMap().getTo());
+ }
}
+ }
+ }
+ }
- return null;
+ /**
+ * Creates a new dataset for this alignment. Can only be done once - if
+ * dataset is not null this will not be performed.
+ */
+ public void createDatasetAlignment()
+ {
+ if (dataset != null)
+ {
+ return;
+ }
+ // try to avoid using SequenceI.equals at this stage, it will be expensive
+ Set seqs = new LinkedIdentityHashSet<>();
+
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ resolveAndAddDatasetSeq(currentSeq, seqs, true);
+ }
+
+ // verify all mappings are in dataset
+ for (AlignedCodonFrame cf : codonFrameList)
+ {
+ for (SequenceToSequenceMapping ssm : cf.getMappings())
+ {
+ if (!seqs.contains(ssm.getFromSeq()))
+ {
+ resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+ }
+ if (!seqs.contains(ssm.getMapping().getTo()))
+ {
+ resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+ }
+ }
}
+ // finally construct dataset
+ dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ // move mappings to the dataset alignment
+ dataset.codonFrameList = this.codonFrameList;
+ this.codonFrameList = null;
+ }
+
+ /**
+ * 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;
- /** */
- public int findIndex(SequenceI s)
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
{
- int i = 0;
-
- while (i < sequences.size())
+ current = getSequenceAt(i);
+ for (int j = current.getLength(); j > maxLength; j--)
+ {
+ if (j > maxLength
+ && !jalview.util.Comparison.isGap(current.getCharAt(j)))
{
- if (s == getSequenceAt(i))
- {
- return i;
- }
-
- i++;
+ maxLength = j;
+ break;
}
-
- return -1;
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getHeight()
- {
- return sequences.size();
- }
+ maxLength++;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWidth()
+ int cLength;
+ for (int i = 0; i < sequences.size(); i++)
{
- int maxLength = -1;
-
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
- }
+ current = getSequenceAt(i);
+ cLength = current.getLength();
- return maxLength;
+ if (cLength < maxLength)
+ {
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
+ modified = true;
+ }
+ else if (current.getLength() > maxLength)
+ {
+ current.deleteChars(maxLength, current.getLength());
+ }
}
+ return modified;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getMaxIdLength()
- {
- int max = 0;
- int i = 0;
+ /**
+ * 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;
- while (i < sequences.size())
+ // 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)))
{
- SequenceI seq = getSequenceAt(i);
- String tmp = seq.getName() + "/" + seq.getStart() + "-" +
- seq.getEnd();
-
- if (tmp.length() > max)
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
{
- max = tmp.length();
+ maxLength = j - ends[i * 2];
}
-
- i++;
+ }
}
-
- return max;
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
- */
- public void setGapCharacter(char gc)
+ 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++)
{
- gapCharacter = gc;
+ current = getSequenceAt(i);
- for (int i = 0; i < sequences.size(); 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
{
- Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence( seq.getSequence().replace('.', gc) );
- seq.setSequence( seq.getSequence().replace('-', gc) );
- seq.setSequence( seq.getSequence().replace(' ', gc) );
+ if (extent < maxLength)
+ {
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
+ modified = true;
+ }
}
+ }
}
+ return modified;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
+ @Override
+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ @Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenCols;
+ }
+
+ @Override
+ public CigarArray getCompactAlignment()
+ {
+ synchronized (sequences)
{
- return gapCharacter;
+ 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;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getAAFrequency()
+ @Override
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
{
- return AAFrequency.calculate(sequences, 0, getWidth());
+ alignmentProperties = new Hashtable();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean isAligned()
+ alignmentProperties.put(key, value);
+ }
+
+ @Override
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
{
- int width = getWidth();
+ return alignmentProperties.get(key);
+ }
+ else
+ {
+ return null;
+ }
+ }
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() != width)
- {
- return false;
- }
- }
+ @Override
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
- return true;
+ /**
+ * Adds the given mapping to the stored set. Note this may be held on the
+ * dataset alignment.
+ */
+ @Override
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ List acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
+ {
+ acfs.add(codons);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void deleteAnnotation(AlignmentAnnotation aa)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public List getCodonFrame(SequenceI seq)
+ {
+ if (seq == null)
+ {
+ return null;
+ }
+ List cframes = new ArrayList<>();
+ for (AlignedCodonFrame acf : getCodonFrames())
{
- int aSize = 1;
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
+ }
+ return cframes;
+ }
- if (annotations != null)
- {
- aSize = annotations.length;
- }
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings). Note the
+ * mappings are set on the dataset alignment instead if there is one.
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(List acfs)
+ {
+ if (dataset != null)
+ {
+ dataset.setCodonFrames(acfs);
+ }
+ else
+ {
+ this.codonFrameList = acfs;
+ }
+ }
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment. The mappings are held on (and read from) the
+ * dataset alignment if there is one.
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ @Override
+ public List getCodonFrames()
+ {
+ // TODO: Fix this method to fix failing AlignedCodonFrame tests
+ // this behaviour is currently incorrect. method should return codon frames
+ // for just the alignment,
+ // selected from dataset
+ return dataset != null ? dataset.getCodonFrames() : codonFrameList;
+ }
- int tIndex = 0;
+ /**
+ * Removes the given mapping from the stored set. Note that the mappings are
+ * held on the dataset alignment if there is one.
+ */
+ @Override
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ List acfs = getCodonFrames();
+ if (codons == null || acfs == null)
+ {
+ return false;
+ }
+ return acfs.remove(codons);
+ }
- for (int i = 0; i < aSize; i++)
+ @Override
+ public void append(AlignmentI toappend)
+ {
+ // TODO JAL-1270 needs test coverage
+ // 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 sqs = (hashidden) ? toappend.getHiddenSequences()
+ .getFullAlignment().getSequences() : toappend.getSequences();
+ if (sqs != null)
+ {
+ // avoid self append deadlock by
+ List toappendsq = new ArrayList<>();
+ synchronized (sqs)
+ {
+ for (SequenceI addedsq : sqs)
{
- if (annotations[i] == aa)
+ if (!samegap)
+ {
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
{
- continue;
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
}
-
- temp[tIndex] = annotations[i];
- tIndex++;
+ }
+ toappendsq.add(addedsq);
}
-
- annotations = temp;
+ }
+ for (SequenceI addedsq : toappendsq)
+ {
+ addSequence(addedsq);
+ }
+ }
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
+ {
+ addAnnotation(alan[a]);
}
+ // use add method
+ getCodonFrames().addAll(toappend.getCodonFrames());
- public void adjustSequenceAnnotations()
+ List sg = toappend.getGroups();
+ if (sg != null)
+ {
+ for (SequenceGroup _sg : sg)
+ {
+ addGroup(_sg);
+ }
+ }
+ if (toappend.getHiddenSequences() != null)
{
- if(annotations!=null)
+ HiddenSequences hs = toappend.getHiddenSequences();
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new HiddenSequences(this);
+ }
+ if (hs.hiddenSequences != null)
{
- for (int a = 0; a < annotations.length; a++)
+ for (int s = 0; s < hs.hiddenSequences.length; s++)
{
- if (annotations[a].sequenceRef != null)
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s] != null)
{
- annotations[a].adjustForAlignment();
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
}
}
}
}
-
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void addAnnotation(AlignmentAnnotation aa)
+ if (toappend.getProperties() != null)
{
- int aSize = 1;
- if (annotations != null)
- {
- aSize = annotations.length + 1;
- }
-
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
- temp[aSize-1] = aa;
-
- int i = 0;
-
- if (aSize > 1)
+ // 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)
{
- for (i = 0; i < (aSize-1); i++)
+ if (ourval.getClass().equals(toapprop.getClass())
+ && !ourval.equals(toapprop))
+ {
+ if (ourval instanceof String)
+ {
+ // append strings
+ this.setProperty(k, ((String) ourval) + "; "
+ + ((String) toapprop));
+ }
+ else
{
- temp[i] = annotations[i];
+ 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);
}
- annotations = temp;
+ }
}
+ }
- public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ if (annotations != null)
{
- if(aa==null || annotations==null || annotations.length-1 findAnnotation(String calcId)
+ {
+ List aa = new ArrayList<>();
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
{
- if(b)
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ for (AlignmentAnnotation a : alignmentAnnotation)
+ {
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a
+ .getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
}
+ return aa;
+ }
- public boolean isNucleotide()
+ @Override
+ public Iterable findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList aa = new ArrayList<>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
{
- if(type==NUCLEOTIDE)
- return true;
- else
- return false;
+ if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
+ .equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq))
+ && (label == null || (ann.label != null && ann.label
+ .equals(label))))
+ {
+ aa.add(ann);
+ }
}
+ return aa;
+ }
- public void setDataset(Alignment data)
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map map, boolean up)
+ {
+ synchronized (sequences)
{
- if(dataset==null && data==null)
+ if (up)
{
- // 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()];
- for (int i = 0; i < getHeight(); i++)
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
{
- if(getSequenceAt(i).getDatasetSequence()!=null)
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
{
- seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+ continue;
}
- else
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
{
- seqs[i] = new Sequence(getSequenceAt(i).getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- getSequenceAt(i).getSequence()
- ),
- getSequenceAt(i).getStart(),
- getSequenceAt(i).getEnd());
-
- getSequenceAt(i).setDatasetSequence(seqs[i]);
+ continue;
}
- }
- dataset = new Alignment(seqs);
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
+ }
}
- else if(dataset==null && data!=null)
+ else
{
- dataset = data;
+ 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);
+ }
}
+
}
+ }
- public Alignment getDataset()
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
{
- return dataset;
+ hasRNAStructure = true;
}
+ }
- public boolean padGaps() {
- boolean modified=false;
+ private SequenceI seqrep = null;
- //Remove excess gaps from the end of alignment
- int maxLength = -1;
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ @Override
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
- 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;
- }
- }
- }
+ /**
+ * 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)
+ */
+ @Override
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
- maxLength++;
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ @Override
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
- for (int i = 0; i < sequences.size();
- i++)
- {
- current = getSequenceAt(i);
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
- if (current.getLength() < maxLength)
- {
- current.insertCharAt(maxLength - 1, gapCharacter);
- modified=true;
- }
- else if(current.getLength() > maxLength)
- {
- current.deleteChars(maxLength, current.getLength());
- }
- }
- return modified;
- }
+ @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);
+ }
- public HiddenSequences getHiddenSequences()
+ /**
+ * 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. TODO: check caveats below where the implementation fails
+ *
+ * @param al
+ * - must have same dataset, and sequences in al must have equivalent
+ * dataset sequence and start/end bounds under given mapping
+ * @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?
+ // JBPComment - yes - neither flag is used, so should be deleted.
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+ else if (thatIsProtein && thisIsNucleotide)
{
- return hiddenSequences;
+ return AlignmentUtils.alignCdsAsProtein(this, al);
}
- SequenceI [] getVisibleAndRepresentedSeqs()
+ return AlignmentUtils.alignAs(this, al);
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray(), true);
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set getSequenceNames()
+ {
+ Set names = new HashSet<>();
+ for (SequenceI seq : getSequences())
{
- if(hiddenSequences==null || hiddenSequences.getSize()<1)
- return getSequencesArray();
+ names.add(seq.getName());
+ }
+ return names;
+ }
- Vector seqs = new Vector();
- SequenceI seq;
- SequenceGroup hidden;
- for (int i = 0; i < sequences.size(); i++)
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
{
- seq = (SequenceI) sequences.elementAt(i);
- seqs.addElement(seq);
- hidden = seq.getHiddenSequences();
- if(hidden!=null)
- {
- for(int j=0; j seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
}
+ return count;
+ }
- public CigarArray getCompactAlignment()
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ @Override
+ public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
{
- SeqCigar alseqs[] = new SeqCigar[sequences.size()];
- for (int i=0; i