/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
*/
public class SeqPanel extends JPanel implements MouseListener,
MouseMotionListener, MouseWheelListener, SequenceListener,
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
else
{
+ if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ {
+ // make sure we calculate relative to visible alignment, rather than right-hand gutter
+ x = seqCanvas.getX()+seqCanvas.getWidth();
+ }
res = (x / av.getCharWidth()) + av.getStartRes();
}
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
- editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+ editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX + getKeyboardNo1();
- editSequence(false, seqCanvas.cursorX);
+ editSequence(false, false, seqCanvas.cursorX);
endEditing();
}
+
+ void insertNucAtCursor(boolean group,String nuc){
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
void numberPressed(char value)
{
if (lastMessage == null || !lastMessage.equals(tmp))
{
// System.err.println("mouseOver Sequence: "+tmp);
- ssm.mouseOverSequence(sequence, index, pos);
+ ssm.mouseOverSequence(sequence, index, pos, av);
}
lastMessage = tmp;
}
{
if (av.followHighlight)
{
- ap.scrollToPosition(results, false);
+ if (ap.scrollToPosition(results, false))
+ {
seqCanvas.revalidate();
+ }
}
seqCanvas.highlightSearchResults(results);
}
.getType()))
{
tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("<HTML>");
+ String tmp2up=tmpString.toUpperCase();
+ int startTag = tmp2up.indexOf("<HTML>");
if (startTag > -1)
{
tmpString = tmpString.substring(startTag + 6);
+ tmp2up = tmp2up.substring(startTag+6);
}
- int endTag = tmpString.toUpperCase().indexOf("</BODY>");
+ int endTag = tmp2up.indexOf("</BODY>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
+ tmp2up = tmp2up.substring(0, endTag);
}
- endTag = tmpString.toUpperCase().indexOf("</HTML>");
+ endTag = tmp2up.indexOf("</HTML>");
if (endTag > -1)
{
tmpString = tmpString.substring(0, endTag);
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
- editSequence(false, res);
+ editSequence(false, false,res);
}
else
{
- editSequence(true, res);
+ editSequence(true, false,res);
}
mouseDragging = true;
}
}
- synchronized void editSequence(boolean insertGap, int startres)
+ //TODO: Make it more clever than many booleans
+ synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.alignment, true);
- }
+ }
}
else
{
+ if(!editSeq){
// dragging to the left
if (fixedColumns && fixedRight != -1)
{
{ seq }, startres, max, av.alignment, true);
}
}
+ }else{//insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.alignment, true);
+ }
+ }
}
}
// shared between viewports.
if (av == source
|| !av.followSelection
+ || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
|| (source instanceof AlignViewport && ((AlignViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())))
{
// 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.isSelectionGroupChanged(false))
{
SequenceGroup sgroup = null;
- if (seqsel != null)
+ if (seqsel != null && seqsel.getSize()>0)
{
if (av.alignment == null)
{
sgroup = seqsel.intersect(av.alignment,
(av.hasHiddenRows) ? av.hiddenRepSequences : null);
if ((sgroup == null || sgroup.getSize() == 0)
- && (colsel == null || colsel.size() == 0))
+ || (colsel == null || colsel.size() == 0))
{
// don't copy columns if the region didn't intersect.
copycolsel = false;
{
av.setSelectionGroup(null);
}
- repaint = av.isSelectionGroupChanged();
+ av.isSelectionGroupChanged(true);
+ repaint = true;
}
- if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+ if (copycolsel)
{
// the current selection is unset or from a previous message
// so import the new colsel.
if (av.colSel != null)
{
av.colSel.clear();
+ repaint=true;
}
}
else
av.colSel.setElementsFrom(colsel);
}
}
- repaint |= av.isColSelChanged();
+ av.isColSelChanged(true);
+ repaint = true;
}
if (copycolsel && av.hasHiddenColumns
&& (av.colSel == null || av.colSel.getHiddenColumns() == null))