/*
- * 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.
- *
+ * 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.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
Stack redoList = new Stack();
- Hashtable sequenceColours;
-
int thresholdTextColour = 0;
Color textColour = Color.black;
showHiddenMarkers = show;
}
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
/**
* returns the visible column regions of the alignment
*
centreColumnLabels = centrecolumnlabels;
}
- public void updateSequenceIdColours()
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (SequenceGroup sg : alignment.getGroups())
- {
- if (sg.idColour != null)
- {
- for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
- {
- sequenceColours.put(s, sg.idColour);
- }
- }
- }
- }
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip