/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
- jalview.datamodel.AlignmentI jal = av.alignment;
+ jalview.datamodel.AlignmentI jal = av.getAlignment();
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
jal = jal.getHiddenSequences().getFullAlignment();
}
jseq.setId(id); // jseq id should be a string not a number
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+ jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
- .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
+ jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal);
for (int h = 0; h < reps.length; h++)
{
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jal = av.alignment;
+ jal = av.getAlignment();
}
// SAVE MAPPINGS
if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.alignment == jal)
+ if (tp.treeCanvas.av.getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
an.setLabel(aa[i].label);
- if (aa[i] == av.quality || aa[i] == av.conservation
- || aa[i] == av.consensus || aa[i].autoCalculated)
+ if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation()
+ || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated)
{
// new way of indicating autocalculated annotation -
an.setAutoCalculated(aa[i].autoCalculated);
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
if (av.getColumnSelection() == null
|| av.getColumnSelection().getHiddenColumns() == null)
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
+ af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
new java.awt.Color(JSEQ[i].getColour()));
}
jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
.get(uniqueSeqSetId);
- af.viewport.sequenceSetID = uniqueSeqSetId;
+ af.viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
else if (view.getBgColour().startsWith("Annotation"))
{
// int find annotation
- if (af.viewport.alignment.getAlignmentAnnotation() != null)
+ if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < af.viewport.alignment
+ for (int i = 0; i < af.viewport.getAlignment()
.getAlignmentAnnotation().length; i++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
.equals(view.getAnnotationColours().getAnnotation()))
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i]
+ if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
.getThreshold() == null)
{
- af.viewport.alignment.getAlignmentAnnotation()[i]
+ af.viewport.getAlignment().getAlignmentAnnotation()[i]
.setThreshold(new jalview.datamodel.GraphLine(view
.getAnnotationColours().getThreshold(),
"Threshold", java.awt.Color.black)
.equals("None"))
{
cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
+ af.viewport.getAlignment().getAlignmentAnnotation()[i],
new java.awt.Color(view.getAnnotationColours()
.getMinColour()), new java.awt.Color(view
.getAnnotationColours().getMaxColour()),
.startsWith("ucs"))
{
cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
+ af.viewport.getAlignment().getAlignmentAnnotation()[i],
GetUserColourScheme(jms, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
else
{
cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
+ af.viewport.getAlignment().getAlignmentAnnotation()[i],
ColourSchemeProperty.getColour(al, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
* if
* (view.getAnnotationColours().getColourScheme().equals("None"
* )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.alignment.getAlignmentAnnotation()[i], new
+ * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
* java.awt.Color(view.getAnnotationColours().
* getMinColour()), new
* java.awt.Color(view.getAnnotationColours().
*/
{
sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
+ af.viewport.getAlignment().getAlignmentAnnotation()[i],
sg.cs, view.getAnnotationColours()
.getAboveThreshold());
}
if (cs != null)
{
cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());
}
}
}
if (view.hasIgnoreGapsinConsensus())
{
- af.viewport.ignoreGapsInConsensusCalculation = view
- .getIgnoreGapsinConsensus();
+ af.viewport.setIgnoreGapsConsensus(view
+ .getIgnoreGapsinConsensus(), null);
}
if (view.hasFollowHighlight())
{
}
if (view.hasShowSequenceLogo())
{
- af.viewport.showSequenceLogo = view.getShowSequenceLogo();
+ af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
}
else
{
- af.viewport.showSequenceLogo = false;
+ af.viewport.setShowSequenceLogo(false);
}
if (view.hasShowDbRefTooltip())
{
af.closeMenuItem_actionPerformed(true);
/*
- * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
- * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
- * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
- * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
- * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+ * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
+ * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
+ * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
*/
return af.alignPanel;