/*
- * 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.gui;
import java.beans.*;
import java.io.*;
+import java.util.Hashtable;
import java.util.Vector;
import java.awt.*;
AlignmentI al = av.getAlignment();
int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth
- / 3));
+ int maxwidth = Math.max(20,
+ Math.min(afwidth - 200, (int) 2 * afwidth / 3));
int i = 0;
int idWidth = 0;
String id;
}
int start = r[0];
int end = r[1];
+ // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
+ // DEBUG
if (start < 0)
{
return false;
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), height));
annotationScroller.validate();// repaint();
+ addNotify();
repaint();
}
{
int x = hscroll.getValue();
av.setStartRes(x);
- av
- .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av
- .getCharWidth())) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av
- .getCharHeight());
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ av.getCharHeight());
pg.setColor(currentTextColor);
- 4;
}
- pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ pg.drawString(
+ seq.getDisplayId(av.getShowJVSuffix()),
+ xPos,
(((i - startSeq) * av.charHeight) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
*/
public void updateAnnotation()
{
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
boolean updateCalcs = false;
boolean conv = av.isShowGroupConservation();
boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
boolean sortg = true;
// remove old automatic annotation
// intersect alignment annotation with alignment groups
AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
- for (int an = 0; an < aan.length; an++)
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
{
- if (aan[an].autoCalculated && aan[an].groupRef != null)
+ for (int an = 0; an < aan.length; an++)
{
- av.alignment.deleteAnnotation(aan[an]);
- aan[an] = null;
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
}
}
SequenceGroup sg;
- for (int g = 0; g < gr.size(); g++)
+ if (gr != null)
{
- updateCalcs = false;
- sg = (SequenceGroup) gr.elementAt(g);
-
- if (conv)
- {
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConservationRow(),0);
- }
- if (cons)
+ for (int g = 0; g < gr.size(); g++)
{
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConsensus(),0);
- }
- // refresh the annotation rows
- if (updateCalcs)
- {
- sg.recalcConservation();
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
}
}
+ oldrfs.clear();
adjustAnnotationHeight();
}
}
git://source.jalview.org / jalview.git / blobdiff