X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3ba35b6bf749e8b202797a4bbfab30b6d4c74cf1;hb=aad3640b07f836362df7ea025fa09127a0a06145;hp=708e566ad6fe87389af2ed9a370514df934fe852;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 708e566..3ba35b6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,25 +1,44 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
-
-import jalview.analysis.*;
+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.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+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
@@ -30,49 +49,67 @@ import jalview.analysis.*;
*/
public class Alignment implements AlignmentI
{
- protected Alignment dataset;
+ private Alignment dataset;
- protected Vector sequences;
+ private List sequences;
- protected Vector groups = new Vector();
+ protected List groups;
protected char gapCharacter = '-';
- protected int type = NUCLEOTIDE;
+ private boolean nucleotide = true;
- public static final int PROTEIN = 0;
-
- public static final int NUCLEOTIDE = 1;
-
public boolean hasRNAStructure = false;
- /** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ HiddenSequences hiddenSequences;
+
+ HiddenColumns hiddenCols;
public Hashtable alignmentProperties;
+ private List codonFrameList;
+
private void initAlignment(SequenceI[] seqs)
{
- int i = 0;
+ groups = Collections.synchronizedList(new ArrayList());
+ hiddenSequences = new HiddenSequences(this);
+ hiddenCols = new HiddenColumns();
+ codonFrameList = new ArrayList<>();
+
+ nucleotide = Comparison.isNucleotide(seqs);
- if (jalview.util.Comparison.isNucleotide(seqs))
+ sequences = Collections.synchronizedList(new ArrayList());
+
+ for (int i = 0; i < seqs.length; i++)
{
- type = NUCLEOTIDE;
+ sequences.add(seqs[i]);
}
- else
+
+ }
+
+ /**
+ * 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++)
{
- type = PROTEIN;
+ seqs[i] = new Sequence(seqs[i]);
}
- sequences = new Vector();
+ initAlignment(seqs);
- for (i = 0; i < seqs.length; i++)
+ /*
+ * Share the same dataset sequence mappings (if any).
+ */
+ if (dataset == null && al.getDataset() == null)
{
- sequences.addElement(seqs[i]);
+ this.setCodonFrames(al.getCodonFrames());
}
-
}
/**
@@ -94,7 +131,7 @@ public class Alignment implements AlignmentI
public Alignment(SeqCigar[] alseqs)
{
SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
- gapCharacter, new ColumnSelection(), null);
+ gapCharacter, new HiddenColumns(), null);
initAlignment(seqs);
}
@@ -109,96 +146,148 @@ public class Alignment implements AlignmentI
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error("Alignment(CigarArray) not yet implemented");
+ throw new Error(MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getSequences()
+ @Override
+ public List 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;
- 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!
+ * Returns a map of lists of sequences keyed by sequence name.
*
- * @return DOCUMENT ME!
+ * @return
*/
+ @Override
+ public Map> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
+
+ @Override
public SequenceI getSequenceAt(int i)
{
- if (i>-1 && i < sequences.size())
+ synchronized (sequences)
{
- return (SequenceI) sequences.elementAt(i);
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
}
return null;
}
+ @Override
+ public SequenceI getSequenceAtAbsoluteIndex(int i)
+ {
+ SequenceI seq = null;
+ if (getHiddenSequences().getSize() > 0)
+ {
+ seq = getHiddenSequences().getHiddenSequence(i);
+ if (seq == null)
+ {
+ // didn't find the sequence in the hidden sequences, get it from the
+ // alignment
+ int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+ seq = getSequenceAt(index);
+ }
+ }
+ else
+ {
+ seq = getSequenceAt(i);
+ }
+ return seq;
+ }
+
/**
- * Adds a sequence to the alignment. Recalculates maxLength and size.
+ * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+ * this currently does not recalculate whether or not the alignment is
+ * nucleotide, so mixed alignments may have undefined behaviour.
*
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
{
+
// maintain dataset integrity
- if (snew.getDatasetSequence() != null)
- {
- getDataset().addSequence(snew.getDatasetSequence());
- }
- else
+ SequenceI dsseq = snew.getDatasetSequence();
+ if (dsseq == null)
{
// derive new sequence
SequenceI adding = snew.deriveSequence();
- getDataset().addSequence(adding.getDatasetSequence());
snew = adding;
+ dsseq = snew.getDatasetSequence();
}
+ if (getDataset().findIndex(dsseq) == -1)
+ {
+ getDataset().addSequence(dsseq);
+ }
+
}
if (sequences == null)
{
- initAlignment(new SequenceI[]
- { snew });
+ initAlignment(new SequenceI[] { snew });
}
else
{
- sequences.addElement(snew);
+ synchronized (sequences)
+ {
+ sequences.add(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)
+ @Override
+ public SequenceI replaceSequenceAt(int i, SequenceI snew)
{
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
+ synchronized (sequences)
+ {
+ if (sequences.size() > i)
+ {
+ return sequences.set(i, snew);
- sequences.setElementAt(snew, i);
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return null;
+ }
}
/**
@@ -206,16 +295,30 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List getGroups()
{
return groups;
}
- public void finalize()
+ @Override
+ public void finalize() throws Throwable
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
+ nullReferences();
+ super.finalize();
+ }
+
+ /**
+ * Defensively nulls out references in case this object is not garbage
+ * collected
+ */
+ void nullReferences()
+ {
dataset = null;
sequences = null;
groups = null;
@@ -224,123 +327,140 @@ public class Alignment implements AlignmentI
}
/**
- * decrement the alignmentRefs counter by one and call finalize if it goes to
- * zero.
+ * decrement the alignmentRefs counter by one and null references if it goes
+ * to zero.
+ *
+ * @throws Throwable
*/
- private void removeAlignmentRef()
+ private void removeAlignmentRef() throws Throwable
{
if (--alignmentRefs == 0)
{
- finalize();
+ nullReferences();
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- */
+ @Override
public void deleteSequence(SequenceI s)
{
- deleteSequence(findIndex(s));
+ synchronized (sequences)
+ {
+ deleteSequence(findIndex(s));
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- */
+ @Override
public void deleteSequence(int i)
{
- if (i > -1 && i < getHeight())
+ synchronized (sequences)
{
- sequences.removeElementAt(i);
- hiddenSequences.adjustHeightSequenceDeleted(i);
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
+ }
}
}
- /** */
- public SequenceGroup findGroup(SequenceI s)
+ @Override
+ public void deleteHiddenSequence(int i)
{
- for (int i = 0; i < this.groups.size(); i++)
+ synchronized (sequences)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
- if (sg.getSequences(null).contains(s))
+ if (i > -1 && i < getHeight())
{
- return sg;
+ sequences.remove(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 (position >= sg.getStartRes() && position <= sg.getEndRes())
+ {
+ 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 temp = new ArrayList<>();
- 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)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- if (sg.getSequences(null).contains(s))
- {
- temp.addElement(sg);
+ if (sg.getSequences().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;
+ }
}
+ sg.setContext(this, true);
+ groups.add(sg);
}
-
- groups.addElement(sg);
}
}
@@ -357,7 +477,9 @@ public class Alignment implements AlignmentI
return;
}
// remove annotation very quickly
- AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ AlignmentAnnotation[] t,
+ todelete = new AlignmentAnnotation[annotations.length],
+ tokeep = new AlignmentAnnotation[annotations.length];
int i, p, k;
if (gp == null)
{
@@ -404,26 +526,40 @@ public class Alignment implements AlignmentI
}
}
+ @Override
public void deleteAllGroups()
{
- if (annotations != null)
+ synchronized (groups)
{
- removeAnnotationForGroup(null);
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null, false);
+ }
+ groups.clear();
}
- groups.removeAllElements();
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
- if (groups.contains(g))
+ synchronized (groups)
{
- removeAnnotationForGroup(g);
- groups.removeElement(g);
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ g.setContext(null, false);
+ }
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
@@ -434,6 +570,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
+ @Override
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
@@ -445,6 +582,7 @@ public class Alignment implements AlignmentI
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
* boolean)
*/
+ @Override
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
@@ -474,7 +612,7 @@ public class Alignment implements AlignmentI
sqname = sq.getName();
if (sqname.equals(token) // exact match
|| (b && // allow imperfect matches - case varies
- (sqname.equalsIgnoreCase(token))))
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
@@ -485,6 +623,7 @@ public class Alignment implements AlignmentI
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
@@ -514,6 +653,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
@@ -537,7 +677,8 @@ public class Alignment implements AlignmentI
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
- public int findIndex(SearchResults results)
+ @Override
+ public int findIndex(SearchResultsI results)
{
int i = 0;
@@ -552,25 +693,23 @@ public class Alignment implements AlignmentI
return -1;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
+ @Override
public int getHeight()
{
return sequences.size();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
+ @Override
+ public int getAbsoluteHeight()
+ {
+ return sequences.size() + getHiddenSequences().getSize();
+ }
+
+ @Override
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
if (getSequenceAt(i).getLength() > maxLength)
@@ -578,9 +717,34 @@ public class Alignment implements AlignmentI
maxLength = getSequenceAt(i).getLength();
}
}
-
+
return maxLength;
}
+ /*
+ @Override
+ public int getWidth()
+ {
+ final Wrapper temp = new Wrapper();
+
+ forEachSequence(new Consumer()
+ {
+ @Override
+ public void accept(SequenceI s)
+ {
+ if (s.getLength() > temp.inner)
+ {
+ temp.inner = s.getLength();
+ }
+ }
+ }, 0, sequences.size() - 1);
+
+ return temp.inner;
+ }
+
+ public static class Wrapper
+ {
+ public int inner;
+ }*/
/**
* DOCUMENT ME!
@@ -588,15 +752,17 @@ public class Alignment implements AlignmentI
* @param gc
* 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));
+ }
}
}
@@ -605,6 +771,7 @@ public class Alignment implements AlignmentI
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
@@ -615,6 +782,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
return isAligned(false);
@@ -625,6 +793,7 @@ public class Alignment implements AlignmentI
*
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
+ @Override
public boolean isAligned(boolean includeHidden)
{
int width = getWidth();
@@ -646,17 +815,47 @@ public class Alignment implements AlignmentI
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;
@@ -684,13 +883,16 @@ public class Alignment implements AlignmentI
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
{
annotations = temp;
- if (unhook) {
+ if (unhook)
+ {
unhookAnnotation(aa);
}
}
@@ -721,6 +923,7 @@ public class Alignment implements AlignmentI
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
addAnnotation(aa, -1);
@@ -732,12 +935,14 @@ public class Alignment implements AlignmentI
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation, int)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
- if(aa.getRNAStruc()!= null){
- hasRNAStructure=true;
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
}
-
+
int aSize = 1;
if (annotations != null)
{
@@ -773,6 +978,7 @@ public class Alignment implements AlignmentI
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
@@ -814,64 +1020,162 @@ public class Alignment implements AlignmentI
return annotations;
}
- public void setNucleotide(boolean b)
+ @Override
+ public boolean isNucleotide()
{
- if (b)
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
+ return nucleotide;
}
- public boolean isNucleotide()
+ @Override
+ public boolean hasRNAStructure()
{
- if (type == NUCLEOTIDE)
- {
- return true;
- }
- else
- {
- return false;
- }
- }
-
- public boolean hasRNAStructure(){
- //TODO can it happen that structure is removed from alignment?
+ // TODO can it happen that structure is removed from alignment?
return hasRNAStructure;
}
- public void setDataset(Alignment data)
+ @Override
+ public void setDataset(AlignmentI 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;
+ 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++)
{
- currentSeq = getSequenceAt(i);
- if (currentSeq.getDatasetSequence() != null)
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
}
else
{
- seqs[i] = currentSeq.createDatasetSequence();
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
}
}
+ }
+ dataset.addAlignmentRef();
+ }
- dataset = new Alignment(seqs);
+ /**
+ * 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)
+ {
+ currentSeq = currentSeq.getDatasetSequence();
}
- else if (dataset == null && data != null)
+ else
+ {
+ if (createDatasetSequence)
+ {
+ currentSeq = currentSeq.createDatasetSequence();
+ }
+ }
+
+ List toProcess = new ArrayList<>();
+ toProcess.add(currentSeq);
+ while (toProcess.size() > 0)
{
- dataset = data;
+ // use a queue ?
+ SequenceI curDs = toProcess.remove(0);
+
+ 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 (dbr.getMap() != null && dbr.getMap().getTo() != null)
+ {
+ if (dbr.getMap().getTo() == alignedSeq)
+ {
+ /*
+ * update mapping to be to the newly created dataset sequence
+ */
+ dbr.getMap().setTo(currentSeq);
+ }
+ 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());
+ }
+ }
+ }
}
- dataset.addAlignmentRef();
+ }
+
+ /**
+ * 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;
}
/**
@@ -887,11 +1191,13 @@ public class Alignment implements AlignmentI
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
@@ -943,6 +1249,7 @@ public class Alignment implements AlignmentI
* 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;
@@ -956,8 +1263,8 @@ public class Alignment implements AlignmentI
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());
+ 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++)
{
@@ -1040,172 +1347,185 @@ public class Alignment implements AlignmentI
return modified;
}
+ @Override
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
}
+ @Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenCols;
+ }
+
+ @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 = new Hashtable();
+ }
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
+ {
return alignmentProperties.get(key);
+ }
else
+ {
return null;
+ }
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
}
- AlignedCodonFrame[] codonFrameList = null;
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
- * )
+ /**
+ * Adds the given mapping to the stored set. Note this may be held on the
+ * dataset alignment.
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons == null)
- return;
- if (codonFrameList == null)
+ List acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
{
- codonFrameList = new AlignedCodonFrame[]
- { codons };
- return;
+ acfs.add(codons);
}
- AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
- System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
- t[codonFrameList.length] = codons;
- codonFrameList = t;
}
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
- public AlignedCodonFrame getCodonFrame(int index)
+ @Override
+ public List getCodonFrame(SequenceI seq)
{
- return codonFrameList[index];
+ if (seq == null)
+ {
+ return null;
+ }
+ List cframes = new ArrayList<>();
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
+ }
+ return cframes;
}
- /*
- * (non-Javadoc)
+ /**
+ * 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#getCodonFrame(jalview.datamodel.SequenceI)
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
*/
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ @Override
+ public void setCodonFrames(List acfs)
{
- if (seq == null || codonFrameList == null)
- return null;
- Vector cframes = new Vector();
- for (int f = 0; f < codonFrameList.length; f++)
+ if (dataset != null)
{
- if (codonFrameList[f].involvesSequence(seq))
- cframes.addElement(codonFrameList[f]);
+ dataset.setCodonFrames(acfs);
+ }
+ else
+ {
+ this.codonFrameList = acfs;
}
- if (cframes.size() == 0)
- return null;
- AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
- cframes.copyInto(cfr);
- return cfr;
}
- /*
- * (non-Javadoc)
+ /**
+ * 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()
*/
- public AlignedCodonFrame[] getCodonFrames()
+ @Override
+ public List getCodonFrames()
{
- return codonFrameList;
+ // 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;
}
- /*
- * (non-Javadoc)
- *
- * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
- * AlignedCodonFrame)
+ /**
+ * 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)
{
- if (codons == null || codonFrameList == null)
- return false;
- boolean removed = false;
- int i = 0, iSize = codonFrameList.length;
- while (i < iSize)
+ List acfs = getCodonFrames();
+ if (codons == null || acfs == null)
{
- if (codonFrameList[i] == codons)
- {
- removed = true;
- if (i + 1 < iSize)
- {
- System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
- - i - 1);
- }
- iSize--;
- }
- else
- {
- i++;
- }
+ return false;
}
- return removed;
+ return acfs.remove(codons);
}
+ @Override
public void append(AlignmentI toappend)
{
- // TODO test this method for a future 2.5 release
+ // TODO JAL-1270 needs test coverage
// currently tested for use in jalview.gui.SequenceFetcher
- boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
+ boolean samegap = oldc == getGapCharacter();
boolean hashidden = toappend.getHiddenSequences() != null
&& toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- Vector sqs = (hashidden) ? toappend.getHiddenSequences()
- .getFullAlignment().getSequences() : toappend.getSequences();
+ List sqs = (hashidden)
+ ? toappend.getHiddenSequences().getFullAlignment()
+ .getSequences()
+ : toappend.getSequences();
if (sqs != null)
{
- Enumeration sq = sqs.elements();
- while (sq.hasMoreElements())
+ // avoid self append deadlock by
+ List toappendsq = new ArrayList<>();
+ 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)
- {
- oldseq[c] = gapCharacter;
- }
+ addedsq.replace(oldc, gapCharacter);
}
+ toappendsq.add(addedsq);
}
+ }
+ for (SequenceI addedsq : toappendsq)
+ {
addSequence(addedsq);
}
}
@@ -1214,18 +1534,16 @@ public class Alignment implements AlignmentI
{
addAnnotation(alan[a]);
}
- AlignedCodonFrame[] acod = toappend.getCodonFrames();
- for (int a = 0; acod != null && a < acod.length; a++)
- {
- this.addCodonFrame(acod[a]);
- }
- Vector sg = toappend.getGroups();
+
+ // use add method
+ getCodonFrames().addAll(toappend.getCodonFrames());
+
+ List 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)
@@ -1265,8 +1583,8 @@ public class Alignment implements AlignmentI
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval) + "; "
- + ((String) toapprop));
+ this.setProperty(k,
+ ((String) ourval) + "; " + ((String) toapprop));
}
else
{
@@ -1292,4 +1610,433 @@ public class Alignment implements AlignmentI
}
}
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ 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;
+ if (calcId != null)
+ {
+ annot.setCalcId(new String(calcId));
+ }
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable findAnnotation(String calcId)
+ {
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
+ {
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
+ }
+ return Arrays.asList(new AlignmentAnnotation[] {});
+ }
+
+ @Override
+ public Iterable findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+ }
+
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map 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);
+ }
+ }
+
+ }
+ }
+
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+ private SequenceI seqrep = null;
+
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ @Override
+ 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)
+ */
+ @Override
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ @Override
+ 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. 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 AlignmentUtils.alignCdsAsProtein(this, al);
+ }
+ 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())
+ {
+ 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;
+ }
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ @Override
+ public int realiseMappings(List seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * 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)
+ {
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+ {
+ return acf;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void setHiddenColumns(HiddenColumns cols)
+ {
+ hiddenCols = cols;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
+
}