/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
+import java.awt.Color;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
* view
*/
protected Hashtable[] hStrucConsensus = null;
-
+
+ protected Conservation hconservation = null;
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
/**
* percentage gaps allowed in a column before all amino acid properties should
* be considered unconserved
*
* @return null or the currently selected sequence region
*/
+ @Override
public SequenceGroup getSelectionGroup()
{
return selectionGroup;
* - group holding references to sequences in this alignment view
*
*/
+ @Override
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
protected boolean showConsensus = true;
+ Hashtable sequenceColours;
+
/**
* Property change listener for changes in alignment
*
*
* @return array of references to sequence objects
*/
+ @Override
public SequenceI[] getSequenceSelection()
{
SequenceI[] sequences = null;
*
* @return String[]
*/
+ @Override
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
* boolean true to just return the selected view
* @return AlignmentView
*/
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
* is true)
* @return AlignmentView
*/
+ @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
*
* @return String[]
*/
+ @Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
String[] selection = null;
int charHeight = getCharHeight();
if (aa != null)
{
- boolean graphgrp[] = null;
+ BitSet graphgrp = new BitSet();
for (int i = 0; i < aa.length; i++)
{
if (aa[i] == null)
}
if (aa[i].graphGroup > -1)
{
- if (graphgrp == null)
- {
- graphgrp = new boolean[aa.length];
- }
- if (graphgrp[aa[i].graphGroup])
+ if (graphgrp.get(aa[i].graphGroup))
{
continue;
}
else
{
- graphgrp[aa[i].graphGroup] = true;
+ graphgrp.set(aa[i].graphGroup);
}
}
aa[i].height = 0;
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.add(aan[an].groupRef);
- alignment.deleteAnnotation(aan[an]);
- aan[an] = null;
+ alignment.deleteAnnotation(aan[an],false);
}
}
}
oldrfs.clear();
}
+ @Override
+ public Color getSequenceColour(SequenceI seq)
+ {
+ Color sqc=Color.white;
+ if (sequenceColours != null)
+ {
+ sqc = (Color) sequenceColours.get(seq);
+ if (sqc == null) {
+ sqc = Color.white;
+ }
+ }
+ return sqc;
+ }
+
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ @Override
+ 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);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours = null;
+ };
}