/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, 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 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.
- *
+ *
* 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
*/
-
package jalview.io;
import jalview.bin.Cache;
}
}
}
-
- if (sq.getDBRef() != null)
+ if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
{
+ // only sync database references for dataset sequences
DBRefEntry[] entries = sq.getDBRef();
jalview.datamodel.DBRefEntry dbentry;
for (int db = 0; db < entries.length; db++)
// ////////////////////////////////////////////
if (!av.getAlignment().isAligned())
return; // TODO: trees could be written - but for the moment we just
- // skip
+ // skip
// ////////////////////////////////////////////
// Save the Alignments
Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId()); // bind
- // to
- // the
- // value
- // used
- // to
- // associate
- // different
- // views
- // to
- // same
- // alignment
+ // to
+ // the
+ // value
+ // used
+ // to
+ // associate
+ // different
+ // views
+ // to
+ // same
+ // alignment
if (alignment == null)
{
{
// info in the undo
addProvenance(alignment.getProvenance(), "Edited"); // TODO:
- // insert
- // something
- // sensible
- // here again
+ // insert
+ // something
+ // sensible
+ // here again
}
else
{
// info in the undo
addProvenance(alignment.getProvenance(), "Attributes Edited"); // TODO:
- // insert
- // something
- // sensible
- // here
- // again
+ // insert
+ // something
+ // sensible
+ // here
+ // again
}
}
if (alismod)
// of
// utf8
// translation
- ae.addValue(aa[i].annotations[a].value);
+ if (an.isGraph())
+ {
+ ae.addValue(aa[i].annotations[a].value);
+ }
ae.setPosition(a + 1);
if (aa[i].annotations[a].secondaryStructure != ' ')
{
if (type == 0)
{
type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
- // type of
- // value
- // annotation
+ // type of
+ // value
+ // annotation
if (has[HASHPHOB])
{
// no hints - so we ensure HPHOB display is like this.
}
if (annotation.getModifiable() == null
|| annotation.getModifiable().length() == 0) // TODO: USE VAMSAS
- // LIBRARY OBJECT
+ // LIBRARY OBJECT
// LOCK METHODS)
{
jan.editable = true;
&& annotation.getGroup().length() > 0)
{
jan.graphGroup = Integer.parseInt(annotation.getGroup()); // TODO:
- // group
- // similarly
- // named
- // annotation
- // together
- // ?
+ // group
+ // similarly
+ // named
+ // annotation
+ // together
+ // ?
}
} catch (Exception e)
{