/*
- * 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.appletgui;
import jalview.datamodel.*;
import jalview.schemes.*;
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
{
AlignViewport av;
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void prepare(Graphics g, boolean renderGaps)
{
}
}
-
+
public Color findSequenceColour(SequenceI seq, int i)
{
allGroups = av.alignment.findAllGroups(seq);
getBoxColour(currentSequenceGroup.cs, seq, i);
graphics.setColor(resBoxColour.darker());
}
- if (currentSequenceGroup.getShowunconserved())
+ if (currentSequenceGroup.getShowNonconserved())
{
- // cheat - use this if we have a consensus for each group: s = getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+ // cheat - use this if we have a consensus for each group: s =
+ // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
s = getDisplayChar(av.consensus, i, s, '.');
}
}
}
if (av.getShowunconserved())
{
- s = getDisplayChar(av.consensus, i, s, '.');
-
+ s = getDisplayChar(av.consensus, i, s, '.');
+
}
}
}
}
-
+
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + av.charWidth
* (i - start), y1);
}
-
- private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
+ private char getDisplayChar(AlignmentAnnotation consensus, int position,
+ char s, char c)
{
- char conschar = consensus.annotations[position].displayCharacter.charAt(0);
- if (conschar!='-' && s==conschar)
+ char conschar = consensus.annotations[position].displayCharacter
+ .charAt(0);
+ if (conschar != '-' && s == conschar)
{
- s= c;
+ s = c;
}
return s;
}