/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* 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.
- *
- * 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
+ * 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.
+ *
+ * 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/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
SequenceNode highlightNode;
AlignmentPanel ap;
+
public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
{
this.ap = ap;
// Colour selected leaves differently
SequenceGroup selected = av.getSelectionGroup();
if (selected != null
- && selected.getSequences(null).contains(
- node.element()))
+ && selected.getSequences(null).contains(node.element()))
{
g.setColor(Color.gray);
// for
// scrollbar
- float wscale = (width - labelLength - offx * 2)
- / tree.getMaxHeight();
+ float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
g.setColor(Color.gray);
}
- int x = (int) (threshold
- * (getSize().width - labelLength - 2 * offx) + offx);
+ int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
g.drawLine(x, 0, x, getSize().height);
}
av.setSelectionGroup(null);
av.getAlignment().deleteAllGroups();
- av.sequenceColours = null;
+ av.clearSequenceColours();
colourGroups();
}
else
{
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
- if (cs!=null)
+ if (cs != null)
{
cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
av.getIgnoreGapsConsensus());
}
}
- // TODO: cs used to be initialized with a sequence collection and recalcConservation called automatically
+ // TODO: cs used to be initialized with a sequence collection and
+ // recalcConservation called automatically
// instead we set it manually - recalc called after updateAnnotation
- sg.cs=cs;
+ sg.cs = cs;
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);