/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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.
*
- * 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
+ * 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;
public static final int PROTEIN = 0;
public static final int NUCLEOTIDE = 1;
+
+ public boolean hasRNAStructure = false;
/** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
{
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.
+ return sequences;
+ }
public SequenceI[] getSequencesArray()
{
*/
public SequenceI getSequenceAt(int i)
{
- if (i < sequences.size())
+ if (i>-1 && i < sequences.size())
{
return (SequenceI) sequences.elementAt(i);
}
/**
* remove any annotation that references gp
- * @param gp (if null, removes all group associated annotation)
+ *
+ * @param gp
+ * (if null, removes all group associated annotation)
*/
private void removeAnnotationForGroup(SequenceGroup gp)
{
- if (annotations==null || annotations.length==0)
+ if (annotations == null || annotations.length == 0)
{
return;
}
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
- '-', gc).replace(' ', gc));
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
}
}
return gapCharacter;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#isAligned()
*/
public boolean isAligned()
{
return isAligned(false);
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#isAligned(boolean)
*/
- public boolean isAligned(boolean includeHidden) {
+ public boolean isAligned(boolean includeHidden)
+ {
int width = getWidth();
- if (hiddenSequences==null || hiddenSequences.getSize()==0) {
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
includeHidden = true; // no hidden sequences to check against.
}
for (int i = 0; i < sequences.size(); i++)
*/
public boolean deleteAnnotation(AlignmentAnnotation aa)
{
+ return deleteAnnotation(aa, true);
+ }
+
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
int aSize = 1;
if (annotations != null)
if (swap)
{
annotations = temp;
- unhookAnnotation(aa);
+ if (unhook) {
+ unhookAnnotation(aa);
+ }
}
return swap;
}
*/
public void addAnnotation(AlignmentAnnotation aa, int pos)
{
+ if(aa.getRNAStruc()!= null){
+ hasRNAStructure=true;
+ }
+
int aSize = 1;
if (annotations != null)
{
annotations = temp;
}
+ @Override
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * returns all annotation on the alignment
*/
public AlignmentAnnotation[] getAlignmentAnnotation()
{
return false;
}
}
+
+ public boolean hasRNAStructure(){
+ //TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
public void setDataset(Alignment data)
{
{
this.addCodonFrame(acod[a]);
}
- Vector sg = toappend.getGroups();
+ List<SequenceGroup> 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)
}
}
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
+ SequenceI seqRef, SequenceGroup groupRef)
+ {
+ for (AlignmentAnnotation annot :
+ getAlignmentAnnotation())
+ {
+ if (annot.autoCalculated == autoCalc
+ && annot.getCalcId().equals(name)
+ && 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.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation a:getAlignmentAnnotation())
+ {
+ if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
+ }
+ return aa;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff