/*
* 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
- *
+ *
* 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
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
import java.util.*;
-import jalview.analysis.*;
-
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
/**
* @author JimP
- *
+ *
*/
public class Alignment implements AlignmentI
{
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
-
+
public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
/**
* Make an alignment from an array of Sequences.
- *
+ *
* @param sequences
*/
public Alignment(SequenceI[] seqs)
/**
* Make a new alignment from an array of SeqCigars
- *
+ *
* @param seqs
* SeqCigar[]
*/
* 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
*/
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
@Override
{
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.
+ // 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)
/**
* DOCUMENT ME!
- *
+ *
* @param i
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public SequenceI getSequenceAt(int i)
{
synchronized (sequences)
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
/**
* Adds a sequence to the alignment. Recalculates maxLength and size.
- *
+ *
* @param snew
*/
+ @Override
public void setSequenceAt(int i, SequenceI snew)
{
SequenceI oldseq = getSequenceAt(i);
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List<SequenceGroup> getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
/**
* DOCUMENT ME!
- *
+ *
* @param s
* DOCUMENT ME!
*/
+ @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())
return null;
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
*/
+ @Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
}
/** */
+ @Override
public void addGroup(SequenceGroup sg)
{
synchronized (groups)
/**
* remove any annotation that references gp
- *
+ *
* @param gp
* (if null, removes all group associated annotation)
*/
}
}
+ @Override
public void deleteAllGroups()
{
synchronized (groups)
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
synchronized (groups)
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
/*
* (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)
{
return null;
}
+ @Override
public SequenceI[] findSequenceMatch(String name)
{
Vector matches = new Vector();
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
/**
* DOCUMENT ME!
- *
+ *
* @param gc
* DOCUMENT ME!
*/
+ @Override
public void setGapCharacter(char gc)
{
gapCharacter = 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();
/*
* (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 (swap)
{
annotations = temp;
- if (unhook) {
+ if (unhook)
+ {
unhookAnnotation(aa);
}
}
/**
* remove any object references associated with this annotation
- *
+ *
* @param aa
*/
private void unhookAnnotation(AlignmentAnnotation aa)
/*
* (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;
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
}
-
+
int aSize = 1;
if (annotations != null)
{
annotations = temp;
}
+ @Override
public void setAnnotationIndex(AlignmentAnnotation aa, int index)
{
if (aa == null || annotations == null || annotations.length - 1 < index)
return annotations;
}
+ @Override
public void setNucleotide(boolean b)
{
if (b)
}
}
+ @Override
public boolean isNucleotide()
{
if (type == NUCLEOTIDE)
return false;
}
}
-
- public boolean hasRNAStructure(){
- //TODO can it happen that structure is removed from alignment?
+
+ @Override
+ public boolean hasRNAStructure()
+ {
+ // TODO can it happen that structure is removed from alignment?
return hasRNAStructure;
}
+ @Override
public void setDataset(Alignment data)
{
if (dataset == null && data == null)
currentSeq = getSequenceAt(i);
if (currentSeq.getDatasetSequence() != null)
{
- seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ seqs[i] = currentSeq.getDatasetSequence();
}
else
{
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
/**
* 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;
return modified;
}
+ @Override
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
}
+ @Override
public CigarArray getCompactAlignment()
{
synchronized (sequences)
alignmentProperties.put(key, value);
}
+ @Override
public Object getProperty(Object key)
{
if (alignmentProperties != null)
return null;
}
+ @Override
public Hashtable getProperties()
{
return alignmentProperties;
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrame(int)
*/
+ @Override
public AlignedCodonFrame getCodonFrame(int index)
{
return codonFrameList[index];
/*
* (non-Javadoc)
- *
+ *
* @see
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
+ @Override
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
+ @Override
public AlignedCodonFrame[] getCodonFrames()
{
return codonFrameList;
/*
* (non-Javadoc)
- *
+ *
* @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
+ @Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
return removed;
}
+ @Override
public void append(AlignmentI toappend)
{
if (toappend == this)
List<SequenceGroup> sg = toappend.getGroups();
if (sg != null)
{
- for (SequenceGroup _sg:sg)
+ for (SequenceGroup _sg : sg)
{
addGroup(_sg);
}
}
@Override
- public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef)
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
{
- for (AlignmentAnnotation annot :
- getAlignmentAnnotation())
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
{
if (annot.autoCalculated == autoCalc
&& annot.getCalcId().equals(name)
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a:getAlignmentAnnotation())
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId)))
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a.getCalcId()
+ .equals(calcId)))
{
aa.add(a);
}
git://source.jalview.org / jalview.git / blobdiff