/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
*/
package jalview.viewmodel;
// calculation till later or to do all calculations in thread.
// via changecolour
globalColourScheme = cs;
- boolean recalc=false;
- if (cs!=null)
+ boolean recalc = false;
+ if (cs != null)
{
cs.setConservationApplied(recalc = getConservationSelected());
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
{
recalc = true;
cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
- } else {
+ }
+ else
+ {
cs.setThreshold(0, ignoreGapsInConsensusCalculation);
}
if (recalc)
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- recalc=true;
+ recalc = true;
}
else
{
if (getConservationSelected())
{
sg.cs.setConservationApplied(true);
- recalc=true;
+ recalc = true;
}
else
{
sg.cs.setConservation(null);
// sg.cs.setThreshold(0, getIgnoreGapsConsensus());
}
- if (recalc) {
+ if (recalc)
+ {
sg.recalcConservation();
- } else {
+ }
+ else
+ {
sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
}
* 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
}
+ @Override
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ {
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] aa;
+ if ((aa=alignment.getAlignmentAnnotation())!=null)
+ {
+ for (AlignmentAnnotation annot:aa)
+ {
+ AlignmentAnnotation clone = new AlignmentAnnotation(annot);
+ if (selectedOnly && selectionGroup!=null)
+ {
+ colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
+ } else {
+ colSel.makeVisibleAnnotation(clone);
+ }
+ ala.add(clone);
+ }
+ }
+ return ala;
+ }
+
/**
* @return the padGaps
*/
{
conservation = new AlignmentAnnotation("Conservation",
"Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ + getConsPercGaps() + "% gaps", new Annotation[1],
+ 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
alignment.addAnnotation(conservation);
}
}
}
+
private void initQuality()
{
if (showQuality)
{
quality = new AlignmentAnnotation("Quality",
"Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
}
}
+
private void initRNAStructure()
{
- if (alignment.hasRNAStructure() && strucConsensus==null)
+ if (alignment.hasRNAStructure() && strucConsensus == null)
{
strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
}
}
}
+
/*
* (non-Javadoc)
*
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.add(aan[an].groupRef);
- alignment.deleteAnnotation(aan[an],false);
+ alignment.deleteAnnotation(aan[an], false);
}
}
}
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc=Color.white;
+ Color sqc = Color.white;
if (sequenceColours != null)
{
sqc = (Color) sequenceColours.get(seq);
- if (sqc == null) {
+ if (sqc == null)
+ {
sqc = Color.white;
}
}