/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 <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.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
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);
}
public SequenceI[] getSequencesArray()
{
if (sequences == null)
+ {
return null;
+ }
synchronized (sequences)
{
return sequences.toArray(new SequenceI[sequences.size()]);
}
}
if (hiddenSequences != null)
+ {
hiddenSequences.adjustHeightSequenceAdded();
+ }
}
/**
public void finalize()
{
if (getDataset() != null)
+ {
getDataset().removeAlignmentRef();
+ }
dataset = null;
sequences = null;
return;
}
}
-
+ sg.setContext(this);
groups.add(sg);
}
}
{
removeAnnotationForGroup(null);
}
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null);
+ }
groups.clear();
}
}
{
removeAnnotationForGroup(g);
groups.remove(g);
+ g.setContext(null);
}
}
}
continue;
}
if (tIndex < temp.length)
+ {
temp[tIndex++] = annotations[i];
+ }
}
if (swap)
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();
}
public void setProperty(Object key, Object value)
{
if (alignmentProperties == null)
+ {
alignmentProperties = new Hashtable();
+ }
alignmentProperties.put(key, value);
}
public Object getProperty(Object key)
{
if (alignmentProperties != null)
+ {
return alignmentProperties.get(key);
+ }
else
+ {
return null;
+ }
}
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
if (codons == null)
+ {
return;
+ }
if (codonFrameList == null)
{
codonFrameList = new AlignedCodonFrame[]
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
if (seq == null || codonFrameList == null)
+ {
return null;
+ }
Vector cframes = new Vector();
for (int f = 0; f < codonFrameList.length; f++)
{
if (codonFrameList[f].involvesSequence(seq))
+ {
cframes.addElement(codonFrameList[f]);
+ }
}
if (cframes.size() == 0)
+ {
return null;
+ }
AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
cframes.copyInto(cfr);
return cfr;
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
if (codons == null || codonFrameList == null)
+ {
return false;
+ }
boolean removed = false;
int i = 0, iSize = codonFrameList.length;
while (i < iSize)
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)
+
+ @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()
{
- alignmentAnnotation.validateRangeAndDisplay();
- if (isNucleotide() && alignmentAnnotation.isValidStruc())
- {
- hasRNAStructure = true;
- }
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff