/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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
+ * 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.
- *
- * 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
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.*;
import jalview.structure.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision: 1.130 $
*/
StringBuffer keyboardNo2;
java.net.URL linkImageURL;
+
private final SequenceAnnotationReport seqARep;
+
StringBuffer tooltipText = new StringBuffer("<html>");
String tmpString;
/**
* Creates a new SeqPanel object.
- *
+ *
* @param avp
* DOCUMENT ME!
* @param p
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
- seqARep=new SequenceAnnotationReport(linkImageURL.toString());
+ seqARep = new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
}
else
{
- if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
{
- // make sure we calculate relative to visible alignment, rather than right-hand gutter
- x = seqCanvas.getX()+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();
}
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ .getAlignment().getHeight() - 1);
}
return seq;
void setCursorPosition()
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns()
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
endEditing();
}
- void insertNucAtCursor(boolean group,String nuc){
- groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
- editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
- 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)
int getKeyboardNo1()
{
- if (keyboardNo1 == null)
- return 1;
- else
+ try {
+ if (keyboardNo1 != null)
{
int value = Integer.parseInt(keyboardNo1.toString());
keyboardNo1 = null;
return value;
}
+ } catch (Exception x)
+ {}
+ keyboardNo1 = null;
+ return 1;
}
int getKeyboardNo2()
{
- if (keyboardNo2 == null)
- return 1;
- else
- {
+ try {
+ if (keyboardNo2!=null){
int value = Integer.parseInt(keyboardNo2.toString());
keyboardNo2 = null;
return value;
}
+ } catch (Exception x)
+ {}
+ keyboardNo2 = null;
+ return 1;
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
{
if (ap.scrollToPosition(results, false))
{
- seqCanvas.revalidate();
+ seqCanvas.revalidate();
}
}
seqCanvas.highlightSearchResults(results);
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
SequenceFeature[] features = findFeaturesAtRes(
sequence.getDatasetSequence(),
rpos = sequence.findPosition(res));
- seqARep.appendFeatures(tooltipText, rpos, features,
+ seqARep.appendFeatures(tooltipText, rpos, features,
this.ap.seqPanel.seqCanvas.fr.minmax);
}
if (tooltipText.length() == 6) // <html></html>
return lastp = p;
}
-
String lastTooltip;
/**
* Set status message in alignment panel
- *
+ *
* @param sequence
* aligned sequence object
* @param res
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
- editSequence(false, false,res);
+ editSequence(false, false, res);
}
else
{
- editSequence(true, false,res);
+ editSequence(true, false, res);
}
mouseDragging = true;
}
}
- //TODO: Make it more clever than many booleans
- synchronized void editSequence(boolean insertGap, boolean editSeq, 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;
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
- .getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av
+ .getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
int alWidth = av.getAlignment().getWidth();
if (av.hasHiddenRows())
{
- int hwidth = av.getAlignment().getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
- }
+ }
}
else
{
- if(!editSeq){
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
+ if (!editSeq)
{
- for (int j = lastres; j > startres; j--)
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ for (int j = lastres; j > startres; j--)
{
- endEditing();
- break;
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ new SequenceI[]
+ { seq }, startres, max, av.getAlignment(), true);
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
}
}
else
- {
- // could be a keyboard edit trying to delete none gaps
- int max = 0;
- for (int m = startres; m < lastres; m++)
+ {// insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ for (int j = lastres; j < startres; j++)
{
- break;
+ insertChar(j, new SequenceI[]
+ { seq }, fixedRight);
}
- max++;
}
-
- if (max > 0)
+ else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.getAlignment(), true);
+ editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.getAlignment(), 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.getAlignment(), true);
- }
- }
}
}
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
- true);
+ 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.getAlignment(),
- true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ av.getAlignment(), true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
/**
* DOCUMENT ME!
- *
+ *
* @param e
* DOCUMENT ME!
*/
if (e.isShiftDown())
{
ap.scrollRight(true);
-
- } else {
+
+ }
+ else
+ {
ap.scrollUp(false);
}
}
if (e.isShiftDown())
{
ap.scrollRight(false);
- } else {
+ }
+ else
+ {
ap.scrollUp(true);
}
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
if (av.wrapAlignment && seq > av.getAlignment().getHeight())
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE);
return;
}
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
// state
if (stretchGroup.cs != null)
{
- stretchGroup.cs.alignmentChanged(
- stretchGroup,av.getHiddenRepSequences());
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
/**
* DOCUMENT ME!
- *
+ *
* @param evt
* DOCUMENT ME!
*/
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().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.
// shared between viewports.
if (av == source
|| !av.followSelection
- || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ || (av.isSelectionGroupChanged(false) || av
+ .isColSelChanged(false))
|| (source instanceof AlignViewport && ((AlignViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())))
{
// if (!av.isSelectionGroupChanged(false))
{
SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize()>0)
+ if (seqsel != null && seqsel.getSize() > 0)
{
if (av.getAlignment() == null)
{
if (av.getColumnSelection() != null)
{
av.getColumnSelection().clear();
- repaint=true;
+ repaint = true;
}
}
else
av.isColSelChanged(true);
repaint = true;
}
- if (copycolsel && av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .getHiddenColumns() == null))
{
System.err.println("Bad things");
}
git://source.jalview.org / jalview.git / blobdiff