/*
* 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.
*
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
+ int maxWidth = av.getAlignment().getWidth();
- while (!av.colSel.isVisible(seqCanvas.cursorX)
+ while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
{
seqCanvas.cursorX = 0;
}
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
{
- seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
{
- seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
}
endEditing();
{
ap.scrollUp(false);
}
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
if (av.getSelectionGroup() != null)
{
- SequenceGroup sg = av.selectionGroup;
+ SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ int min = av.getAlignment().getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
- int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
if (index > max)
{
max = index;
else
{
// Now add any sequences between min and max
- sg.getSequences(null).removeAllElements();
+ sg.clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
y -= hgap;
seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ av.getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
else
{
seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ av.getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
ap.alignFrame.statusBar.setText(text.toString());
StringBuffer tooltipText = new StringBuffer();
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
- if (!groupEditing && av.hasHiddenRows)
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = (SequenceGroup) av.getRepresentedSequences(seq);
groupEditing = true;
}
}
// Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences)
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
// but the sequence represents a group
if (sg == null)
{
- if (av.hiddenRepSequences == null
- || !av.hiddenRepSequences.containsKey(seq))
+ if (!av.isHiddenRepSequence(seq))
{
endEditing();
return;
}
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
}
fixedLeft = sg.getStartRes();
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
- int g, groupSize = vseqs.size();
- SequenceI[] groupSeqs = new SequenceI[groupSize];
- for (g = 0; g < groupSeqs.length; g++)
- {
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
- }
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()).toArray(new SequenceI[0]);
// drag to right
if (insertGap)
// If the user has selected the whole sequence, and is dragging to
// the right, we can still extend the alignment and selectionGroup
if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
- && sg.getEndRes() == av.alignment.getWidth() - 1)
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
{
blank = true;
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs:groupSeqs)
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
+ if (!jalview.util.Comparison.isGap(gs
.getCharAt(fixedRight - j)))
{
blank = false;
if (!blank)
{
- if (sg.getSize() == av.alignment.getHeight())
+ if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+ if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
.getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
- int alWidth = av.alignment.getWidth();
- if (av.hasHiddenRows)
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
{
- int hwidth = av.alignment.getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences().getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
// / Are we able to delete?
// ie are all columns blank?
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs:groupSeqs)
{
for (int j = startres; j < lastres; j++)
{
- if (groupSeqs[g].getLength() <= j)
+ if (gs.getLength() <= j)
{
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.alignment, true);
+ startres, startres - lastres, av.getAlignment(), true);
}
}
else
else
{
editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.alignment, true);
+ startres, lastres - startres, av.getAlignment(), true);
}
}
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
else
if (max > 0)
{
editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.alignment, true);
+ { seq }, startres, max, av.getAlignment(), true);
}
}
}
}
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
}
// ////////////////////////////////////////
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if (stretchGroup != null && res > stretchGroup.getStartRes()
&& res < stretchGroup.getEndRes())
{
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
return;
}
+ stretchGroup.recalcConservation(); // always do this - annotation has own
+ // state
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.hiddenRepSequences),
- stretchGroup.getWidth());
- }
-
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
- }
-
+ stretchGroup.cs.alignmentChanged(stretchGroup,av.getHiddenRepSequences());
+
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
- stretchGroup.recalcConservation();
}
else
{
mouseDragging = true;
- if (y > av.alignment.getHeight())
+ if (y > av.getAlignment().getHeight())
{
- y = av.alignment.getHeight() - 1;
+ y = av.getAlignment().getHeight() - 1;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
}
if (mouseDragging && evt.getY() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
running = ap.scrollUp(false);
}
// rules are: colsel is copied if there is a real intersection between
// sequence selection
boolean repaint = false, copycolsel = true;
- if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
{
SequenceGroup sgroup = null;
if (seqsel != null && seqsel.getSize()>0)
{
- if (av.alignment == null)
+ if (av.getAlignment() == null)
{
System.out
.println("Selection message: alignviewport av SeqSetId="
+ " 's alignment is NULL! returning immediatly.");
return;
}
- sgroup = seqsel.intersect(av.alignment,
- (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
if ((sgroup == null || sgroup.getSize() == 0)
&& (colsel == null || colsel.size() == 0))
{
{
av.setSelectionGroup(null);
}
- repaint = av.isSelectionGroupChanged();
+ repaint = av.isSelectionGroupChanged(true);
}
- if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+ if (copycolsel && (av.getColumnSelection() == null || !av.isColSelChanged(true)))
{
// the current selection is unset or from a previous message
// so import the new colsel.
if (colsel == null || colsel.size() == 0)
{
- if (av.colSel != null)
+ if (av.getColumnSelection() != null)
{
- av.colSel.clear();
+ av.getColumnSelection().clear();
}
}
else
{
// TODO: shift colSel according to the intersecting sequences
- if (av.colSel == null)
+ if (av.getColumnSelection() == null)
{
- av.colSel = new ColumnSelection(colsel);
+ av.setColumnSelection(new ColumnSelection(colsel));
}
else
{
- av.colSel.setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel);
}
}
- repaint |= av.isColSelChanged();
+ repaint |= av.isColSelChanged(true);
}
- if (copycolsel && av.hasHiddenColumns
- && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ if (copycolsel && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
{
System.err.println("Bad things");
}
row = row<0 ? ap.av.startSeq : row;
column = column<0 ? ap.av.startRes : column;
- ap.scrollTo(row, row, column, true, true);
+ ap.scrollTo(column, column, row, true, true);
}
/**
* scroll to the given row - or nearest visible location
{
row = row<0 ? ap.av.startSeq : row;
- ap.scrollTo(row, row, ap.av.startRes, true, true);
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
}
/**
* scroll to the given column - or nearest visible location
{
column = column<0 ? ap.av.startRes : column;
- ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+ ap.scrollTo( column, column, ap.av.startSeq, true, true);
}
}