/*
- * 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 2.6)
+ * 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.datamodel;
*/
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++)