/*
- * 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 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.structure;
for (int i = 0; i < pdb.chains.size(); i++)
{
+
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
- .elementAt(i)).sequence, AlignSeq.PEP);
+ .elementAt(i)).sequence, ((PDBChain) pdb.chains
+ .elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
return pdb;
}
- public void removeStructureViewerListener(Object svl, String pdbfile)
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
-
+ if (pdbfiles==null)
+ {
+ return;
+ }
boolean removeMapping = true;
-
+ String[] handlepdbs;
+ Vector pdbs = new Vector();
+ for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+ ;
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (sl.getPdbFile().equals(pdbfile))
+ handlepdbs = sl.getPdbFile();
+ for (int j = 0; j < handlepdbs.length; j++)
{
- removeMapping = false;
- break;
+ if (pdbs.contains(handlepdbs[j]))
+ {
+ pdbs.removeElement(handlepdbs[j]);
+ }
}
+
}
}
-
- if (removeMapping && mappings != null)
+
+ if (pdbs.size()>0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
- if (!mappings[i].pdbfile.equals(pdbfile))
+ if (!pdbs.contains(mappings[i].pdbfile))
{
tmp.addElement(mappings[i]);
}
* highlight regions associated with a position (indexpos) in seq
*
* @param seq
- * the sequeence that the mouse over occured on
+ * the sequeence that the mouse over occured on
* @param indexpos
- * the absolute position being mouseovered in seq (0 to
- * seq.length())
+ * the absolute position being mouseovered in seq (0 to seq.length())
* @param index
- * the sequence position (if -1, seq.findPosition is called to
- * resolve the residue number)
+ * the sequence position (if -1, seq.findPosition is called to
+ * resolve the residue number)
*/
public void mouseOverSequence(SequenceI seq, int indexpos, int index)
{
*
* @param sequenceI
* @param position
- * in an alignment sequence
+ * in an alignment sequence
*/
public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
{
*
* for (int j = 0; j < mappings.length; j++) {
*
- * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) &&
- * mappings[j].pdbfile.equals(sl.getPdbFile())) { System.out.println(pdbid+"
- * "+mappings[j].getPdbId() +" "+mappings[j].pdbfile);
+ * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+ * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+ * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+ * "+mappings[j].pdbfile);
*
* java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
* if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
}
Vector sel_listeners = new Vector();
+
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
sel_listeners.addElement(selecter);
}
}
+
public void removeSelectionListener(SelectionListener toremove)
{
if (sel_listeners.contains(toremove))
sel_listeners.removeElement(toremove);
}
}
- public synchronized void sendSelection(jalview.datamodel.SequenceGroup selection, jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- if (sel_listeners!=null && sel_listeners.size()>0)
+ if (sel_listeners != null && sel_listeners.size() > 0)
{
Enumeration listeners = sel_listeners.elements();
while (listeners.hasMoreElements())
{
- SelectionListener slis = ((SelectionListener) listeners.nextElement());
- if (slis!=source) {
- slis.selection(selection, colsel, source);
- };
+ SelectionListener slis = ((SelectionListener) listeners
+ .nextElement());
+ if (slis != source)
+ {
+ slis.selection(selection, colsel, source);
+ }
+ ;
}
}
}
git://source.jalview.org / jalview.git / blobdiff