import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
if (viewport.cursorMode
&& ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
if (viewport.cursorMode
&& ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
+ alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
+ alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
- alignPanel.setScrollValues(viewport.getStartRes(),
- 2 * viewport.getStartSeq() - viewport.getEndSeq());
+ alignPanel.setScrollValues(ranges.getStartRes(),
+ 2 * ranges.getStartSeq() - ranges.getEndSeq());
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
viewport.getAlignment().getWidth();
viewport.firePropertyChange("alignment", null, viewport.getAlignment()
.getSequences());
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
}
else
{
trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
}
else
{
trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
{
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ viewport.firePropertyChange("alignment", null, al.getSequences());
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 1;
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.getStartRes());
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- viewport.setStartRes(seq.findIndex(startRes) - 1);
- viewport.firePropertyChange("alignment", null, viewport.getAlignment()
- .getSequences());
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.firePropertyChange("alignment", null, al.getSequences());
- int start = 0, end = viewport.getAlignment().getWidth() - 1;
+ AlignmentI al = viewport.getAlignment();
+ ViewportRanges ranges = viewport.getRanges();
+ int start = 0;
+ int end = ranges.getAbsoluteAlignmentWidth() - 1;
- SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(viewport.getStartRes());
+ SequenceI seq = al.getSequenceAt(0);
+ int startRes = seq.findPosition(ranges.getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
- // conservationMenuItem.setState(false);
- // viewport.setConservationSelected(false);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);