/*
- * 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 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
-import jalview.analysis.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
/**
* Data structure to hold and manipulate a multiple sequence alignment
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
-
+
public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
public Hashtable alignmentProperties;
+ private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+
private void initAlignment(SequenceI[] seqs)
{
int i = 0;
}
/**
+ * Make a 'copy' alignment - sequences have new copies of features and
+ * annotations, but share the original dataset sequences.
+ */
+ public Alignment(AlignmentI al)
+ {
+ SequenceI[] seqs = al.getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = new Sequence(seqs[i]);
+ }
+
+ /*
+ * Share the same dataset sequence mappings (if any). TODO: find a better
+ * place for these to live (alignment dataset?).
+ */
+ this.codonFrameList = ((Alignment) al).codonFrameList;
+
+ initAlignment(seqs);
+ }
+
+ /**
* Make an alignment from an array of Sequences.
*
* @param sequences
*/
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!
- */
@Override
public List<SequenceI> getSequences()
{
return sequences;
}
+
@Override
public List<SequenceI> getSequences(
Map<SequenceI, SequenceCollectionI> hiddenReps)
{
- // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to work on this.
+ // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+ // work on this.
return sequences;
}
+ @Override
public SequenceI[] getSequencesArray()
{
if (sequences == null)
+ {
return null;
+ }
synchronized (sequences)
{
return sequences.toArray(new SequenceI[sequences.size()]);
}
/**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map<String, List<SequenceI>> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
+
+ /**
* DOCUMENT ME!
*
* @param i
*
* @return DOCUMENT ME!
*/
+ @Override
public SequenceI getSequenceAt(int i)
{
synchronized (sequences)
*
* @param snew
*/
+ @Override
public void addSequence(SequenceI snew)
{
if (dataset != null)
}
if (sequences == null)
{
- initAlignment(new SequenceI[]
- { snew });
+ initAlignment(new SequenceI[] { snew });
}
else
{
}
}
if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
+ }
}
/**
*
* @param snew
*/
+ @Override
public void setSequenceAt(int i, SequenceI snew)
{
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(i);
synchronized (sequences)
{
+ deleteSequence(i);
sequences.set(i, snew);
}
}
*
* @return DOCUMENT ME!
*/
- public Vector getGroups()
+ @Override
+ public List<SequenceGroup> getGroups()
{
return groups;
}
+ @Override
public void finalize()
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
dataset = null;
sequences = null;
* @param s
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(SequenceI s)
{
deleteSequence(findIndex(s));
* @param i
* DOCUMENT ME!
*/
+ @Override
public void deleteSequence(int i)
{
if (i > -1 && i < getHeight())
synchronized (sequences)
{
sequences.remove(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
}
- hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
/*
* (non-Javadoc)
- *
+ *
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
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)
{
ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
- if (sg == null || sg.getSequences(null) == null)
+ if (sg == null || sg.getSequences() == null)
{
this.deleteGroup(sg);
gSize--;
continue;
}
- if (sg.getSequences(null).contains(s))
+ if (sg.getSequences().contains(s))
{
temp.add(sg);
}
}
/** */
+ @Override
public void addGroup(SequenceGroup sg)
{
synchronized (groups)
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
}
}
+ @Override
public void deleteAllGroups()
{
synchronized (groups)
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
groups.clear();
}
}
/** */
+ @Override
public void deleteGroup(SequenceGroup g)
{
synchronized (groups)
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
/** */
+ @Override
public SequenceI findName(String name)
{
return findName(name, false);
*
* @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
*/
+ @Override
public SequenceI findName(String token, boolean b)
{
return findName(null, token, b);
* @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();
*
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
+ @Override
public int findIndex(SequenceI s)
{
int i = 0;
* @see
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
+ @Override
public int findIndex(SearchResults results)
{
int i = 0;
*
* @return DOCUMENT ME!
*/
+ @Override
public int getHeight()
{
return sequences.size();
*
* @return DOCUMENT ME!
*/
+ @Override
public int getWidth()
{
int maxLength = -1;
* @param gc
* DOCUMENT ME!
*/
+ @Override
public void setGapCharacter(char gc)
{
gapCharacter = gc;
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return gapCharacter;
*
* @see jalview.datamodel.AlignmentI#isAligned()
*/
+ @Override
public boolean isAligned()
{
return isAligned(false);
*
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
+ @Override
public boolean isAligned(boolean includeHidden)
{
int width = getWidth();
return true;
}
+ /**
+ * 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;
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
{
annotations = temp;
- if (unhook) {
+ if (unhook)
+ {
unhookAnnotation(aa);
}
}
* @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
* AlignmentAnnotation)
*/
+ @Override
public void addAnnotation(AlignmentAnnotation aa)
{
addAnnotation(aa, -1);
* @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
{
else if (dataset == null && data != null)
{
dataset = data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
}
dataset.addAlignmentRef();
}
alignmentRefs++;
}
+ @Override
public Alignment getDataset()
{
return dataset;
}
+ @Override
public boolean padGaps()
{
boolean modified = false;
* 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)
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)
*
* jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
* )
*/
+ @Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons == null)
- return;
- if (codonFrameList == null)
+ if (codons != null)
{
- codonFrameList = new AlignedCodonFrame[]
- { codons };
- return;
+ codonFrameList.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)
- */
- public AlignedCodonFrame getCodonFrame(int index)
- {
- return codonFrameList[index];
}
/*
* @see
* jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
- public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ @Override
+ public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
{
- if (seq == null || codonFrameList == null)
+ if (seq == null)
+ {
return null;
- Vector cframes = new Vector();
- for (int f = 0; f < codonFrameList.length; f++)
+ }
+ List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+ for (AlignedCodonFrame acf : codonFrameList)
{
- if (codonFrameList[f].involvesSequence(seq))
- cframes.addElement(codonFrameList[f]);
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
}
- if (cframes.size() == 0)
- return null;
- AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
- cframes.copyInto(cfr);
- return cfr;
+ return cframes;
}
- /*
- * (non-Javadoc)
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings).
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ {
+ this.codonFrameList = acfs;
+ }
+
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment.
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
- public AlignedCodonFrame[] getCodonFrames()
+ @Override
+ public Set<AlignedCodonFrame> getCodonFrames()
{
return codonFrameList;
}
* @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
* AlignedCodonFrame)
*/
+ @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)
{
- 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 codonFrameList.remove(codons);
}
+ @Override
public void append(AlignmentI toappend)
{
if (toappend == this)
{
addAnnotation(alan[a]);
}
- AlignedCodonFrame[] acod = toappend.getCodonFrames();
- for (int a = 0; acod != null && a < acod.length; a++)
- {
- this.addCodonFrame(acod[a]);
- }
+
+ this.codonFrameList.addAll(toappend.getCodonFrames());
+
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,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
{
- for (AlignmentAnnotation annot :
- getAlignmentAnnotation())
+ assert (name != null);
+ if (annotations != null)
{
- if (annot.autoCalculated == autoCalc
- && annot.getCalcId().equals(name)
- && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
{
- return annot;
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef
+ && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
}
}
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
annot.hasText = false;
- annot.setCalcId(new String(name));
+ annot.setCalcId(new String(calcId));
annot.autoCalculated = autoCalc;
if (seqRef != null)
{
@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);
}
return aa;
}
+ /**
+ * Returns an iterable collection of any annotations that match on given
+ * sequence ref, calcId and label (ignoring null values).
+ */
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation ann : getAlignmentAnnotation())
+ {
+ if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
+ && ann.sequenceRef != null && ann.sequenceRef == seq
+ && ann.label != null && ann.label.equals(label))
+ {
+ aa.add(ann);
+ }
+ }
+ return aa;
+ }
+
@Override
public void moveSelectedSequencesByOne(SequenceGroup sg,
Map<SequenceI, SequenceCollectionI> map, boolean up)
}
}
+ @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
+ */
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
+
+ /**
+ * Align this alignment like the given (mapped) one.
+ */
+ @Override
+ public int alignAs(AlignmentI al)
+ {
+ /*
+ * Currently retains unmapped gaps (in introns), regaps mapped regions
+ * (exons)
+ */
+ return alignAs(al, false, true);
+ }
+
+ /**
+ * Align this alignment 'the same as' the given one. Mapped sequences only are
+ * realigned. If both of the same type (nucleotide/protein) then align both
+ * identically. If this is nucleotide and the other is protein, make 3 gaps
+ * for each gap in the protein sequences. If this is protein and the other is
+ * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+ * nucleotide bases. If this is protein and the other is nucleotide, gaps
+ * protein to match the relative ordering of codons in the nucleotide.
+ *
+ * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+ * regions are preserved. Gaps that connect introns to exons are treated
+ * conservatively, i.e. only preserved if both intron and exon gaps are
+ * preserved.
+ *
+ * @param al
+ * @param preserveMappedGaps
+ * if true, gaps within and between mapped codons are preserved
+ * @param preserveUnmappedGaps
+ * if true, gaps within and between unmapped codons are preserved
+ */
+ // @Override
+ public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO should this method signature be the one in the interface?
+ int count = 0;
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+
+ char thisGapChar = this.getGapCharacter();
+ String gap = thisIsNucleotide && thatIsProtein ? String
+ .valueOf(new char[] { thisGapChar, thisGapChar, thisGapChar })
+ : String.valueOf(thisGapChar);
+
+ // TODO handle intron regions? Needs a 'holistic' alignment of dna,
+ // not just sequence by sequence. But how to 'gap' intron regions?
+
+ /*
+ * Get mappings from 'that' alignment's sequences to this.
+ */
+ for (SequenceI alignTo : getSequences())
+ {
+ count += AlignmentUtils.alignSequenceAs(alignTo, al, gap,
+ preserveMappedGaps, preserveUnmappedGaps) ? 1 : 0;
+ }
+ return count;
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray());
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set<String> getSequenceNames()
+ {
+ Set<String> names = new HashSet<String>();
+ for (SequenceI seq : getSequences())
+ {
+ names.add(seq.getName());
+ }
+ return names;
+ }
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
}
git://source.jalview.org / jalview.git / blobdiff