X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2223ee5e7e325c47ab06838db0995027f4096a28;hb=062ebc02980364930ceb26dd6c06448af971fe20;hp=7d451dad5b6f2d7695a54e443dc4db473307d110;hpb=40ecea964afaaf404465d75873ec915b901117a3;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
old mode 100755
new mode 100644
index 7d451da..2223ee5
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,43 +1,81 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.structure.*;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.130 $
*/
-public class SeqPanel
- extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener, SequenceListener
+public class SeqPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener,
+ SequenceListener, SelectionListener
{
/** DOCUMENT ME!! */
@@ -45,50 +83,82 @@ public class SeqPanel
/** DOCUMENT ME!! */
public AlignmentPanel ap;
+
+ /*
+ * last column position for mouseMoved event
+ */
+ private int lastMouseColumn;
+
+ /*
+ * last sequence offset for mouseMoved event
+ */
+ private int lastMouseSeq;
+
protected int lastres;
+
protected int startseq;
+
protected AlignViewport av;
ScrollThread scrollThread = null;
+
boolean mouseDragging = false;
+
boolean editingSeqs = false;
+
boolean groupEditing = false;
- //////////////////////////////////////////
- /////Everything below this is for defining the boundary of the rubberband
- //////////////////////////////////////////
+ // ////////////////////////////////////////
+ // ///Everything below this is for defining the boundary of the rubberband
+ // ////////////////////////////////////////
int oldSeq = -1;
+
boolean changeEndSeq = false;
+
boolean changeStartSeq = false;
+
boolean changeEndRes = false;
+
boolean changeStartRes = false;
+
SequenceGroup stretchGroup = null;
+
boolean remove = false;
Point lastMousePress;
+
boolean mouseWheelPressed = false;
+
StringBuffer keyboardNo1;
+
StringBuffer keyboardNo2;
java.net.URL linkImageURL;
- StringBuffer tooltipText = new StringBuffer("");
+ private final SequenceAnnotationReport seqARep;
+
+ StringBuilder tooltipText = new StringBuilder();
+
String tmpString;
EditCommand editCommand;
StructureSelectionManager ssm;
+ SearchResultsI lastSearchResults;
/**
* Creates a new SeqPanel object.
- *
- * @param avp DOCUMENT ME!
- * @param p DOCUMENT ME!
+ *
+ * @param avp
+ * DOCUMENT ME!
+ * @param p
+ * DOCUMENT ME!
*/
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
+ seqARep = new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -106,33 +176,47 @@ public class SeqPanel
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
}
+
+ lastMouseColumn = -1;
+ lastMouseSeq = -1;
}
int startWrapBlock = -1;
+
int wrappedBlock = -1;
- int findRes(MouseEvent evt)
+
+ /**
+ * Returns the aligned sequence position (base 0) at the mouse position, or
+ * the closest visible one
+ *
+ * @param evt
+ * @return
+ */
+ int findColumn(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
- if (av.wrapAlignment)
+ int startRes = av.getRanges().getStartRes();
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
int y = evt.getY();
- y -= hgap;
- x -= seqCanvas.LABEL_WEST;
+ y = Math.max(0, y - hgap);
+ x = Math.max(0, x - seqCanvas.getLabelWidthWest());
int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
if (cwidth < 1)
@@ -141,19 +225,32 @@ public class SeqPanel
}
wrappedBlock = y / cHeight;
- wrappedBlock += av.getStartRes() / cwidth;
-
- res = wrappedBlock * cwidth + x / av.getCharWidth();
-
+ wrappedBlock += startRes / cwidth;
+ // allow for wrapped view scrolled right (possible from Overview)
+ int startOffset = startRes % cwidth;
+ res = wrappedBlock * cwidth + startOffset
+ + +Math.min(cwidth - 1, x / av.getCharWidth());
}
else
{
- res = (x / av.getCharWidth()) + av.getStartRes();
+ if (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()) + startRes;
+ if (res > av.getRanges().getEndRes())
+ {
+ // moused off right
+ res = av.getRanges().getEndRes();
+ }
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- res = av.getColumnSelection().adjustForHiddenColumns(res);
+ res = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(res);
}
return res;
@@ -165,83 +262,59 @@ public class SeqPanel
int seq = 0;
int y = evt.getY();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
y -= hgap;
- seq = Math.min( (y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
}
else
{
- seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ seq = Math.min(
+ (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+ av.getAlignment().getHeight() - 1);
}
return seq;
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ /**
+ * When all of a sequence of edits are complete, put the resulting edit list
+ * on the history stack (undo list), and reset flags for editing in progress.
+ */
+ void endEditing()
{
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
+ try
{
- for (int i = 0; i < features.length; i++)
+ if (editCommand != null && editCommand.getSize() > 0)
{
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && seqCanvas.fr.featureGroups!=null
- && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
- && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
- continue;
-
-
- if ( (features[i].getBegin() <= res) &&
- (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
}
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
- }
-
-
- void endEditing()
- {
- if (editCommand != null && editCommand.getSize() > 0)
+ } finally
{
- ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null,
- av.getAlignment().getSequences());
+ /*
+ * Tidy up come what may...
+ */
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
}
-
- startseq = -1;
- lastres = -1;
- editingSeqs = false;
- groupEditing = false;
- keyboardNo1 = null;
- keyboardNo2 = null;
- editCommand = null;
}
void setCursorRow()
@@ -272,12 +345,9 @@ public class SeqPanel
void setCursorPosition()
{
- SequenceI sequence =
- (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();
}
@@ -285,20 +355,22 @@ public class SeqPanel
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+ if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
+ int maxWidth = av.getAlignment().getWidth();
- while (!av.colSel.isVisible(seqCanvas.cursorX)
- && seqCanvas.cursorX < maxWidth
- && seqCanvas.cursorX > 0)
+ while (!hidden.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !hidden.isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
@@ -313,72 +385,47 @@ public class SeqPanel
{
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();
- if (av.wrapAlignment)
+ if (av.getWrapAlignment())
{
- ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
}
else
{
- while (seqCanvas.cursorY < av.startSeq)
- {
- ap.scrollUp(true);
- }
- while (seqCanvas.cursorY + 1 > av.endSeq)
- {
- ap.scrollUp(false);
- }
- if (!av.wrapAlignment)
- {
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
- {
- if (!ap.scrollRight(false))
- {
- break;
- }
- }
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
- {
- if (!ap.scrollRight(true))
- {
- break;
- }
- }
- }
+ av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
- seqCanvas.cursorX, seqCanvas.cursorY);
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
}
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence =
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
if (av.getSelectionGroup() != null)
{
- SequenceGroup sg = av.selectionGroup;
- //Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ SequenceGroup sg = av.getSelectionGroup();
+ // Find the top and bottom of this group
+ 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;
@@ -423,7 +470,7 @@ public class SeqPanel
sg.getSequences(null).clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
@@ -437,7 +484,8 @@ public class SeqPanel
av.setSelectionGroup(sg);
}
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
@@ -445,7 +493,7 @@ public class SeqPanel
groupEditing = group;
startseq = seqCanvas.cursorY;
lastres = seqCanvas.cursorX;
- editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+ editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
@@ -454,7 +502,17 @@ public class SeqPanel
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)
+ {
+ // TODO not called - delete?
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
@@ -477,41 +535,61 @@ public class SeqPanel
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)
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
}
+ 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)
{
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
}
+ keyboardNo2 = null;
+ return 1;
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
+ boolean didDrag = mouseDragging; // did we come here after a drag
mouseDragging = false;
mouseWheelPressed = false;
+ if (evt.isPopupTrigger()) // Windows: mouseReleased
+ {
+ showPopupMenu(evt);
+ evt.consume();
+ return;
+ }
+
if (!editingSeqs)
{
- doMouseReleasedDefineMode(evt);
+ doMouseReleasedDefineMode(evt, didDrag);
return;
}
@@ -520,27 +598,29 @@ public class SeqPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
- if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+ if (SwingUtilities.isMiddleMouseButton(evt))
{
mouseWheelPressed = true;
return;
}
- if (evt.isShiftDown() || evt.isAltDown() ||
- evt.isControlDown())
+ boolean isControlDown = Platform.isControlDown(evt);
+ if (evt.isShiftDown() || isControlDown)
{
- if (evt.isAltDown() || evt.isControlDown())
+ editingSeqs = true;
+ if (isControlDown)
{
groupEditing = true;
}
- editingSeqs = true;
}
else
{
@@ -549,15 +629,15 @@ public class SeqPanel
}
int seq = findSeq(evt);
- int res = findRes(evt);
+ int res = findColumn(evt);
if (seq < 0 || res < 0)
{
return;
}
- if ( (seq < av.getAlignment().getHeight()) &&
- (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ if ((seq < av.getAlignment().getHeight())
+ && (res < av.getAlignment().getSequenceAt(seq).getLength()))
{
startseq = seq;
lastres = res;
@@ -572,35 +652,81 @@ public class SeqPanel
}
String lastMessage;
+
+ @Override
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
- String tmp = sequence.hashCode()+" "+index+" "+pos;
-
+ String tmp = sequence.hashCode() + " " + index + " " + pos;
+
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;
}
+ /**
+ * Highlight the mapped region described by the search results object (unless
+ * unchanged). This supports highlight of protein while mousing over linked
+ * cDNA and vice versa. The status bar is also updated to show the location of
+ * the start of the highlighted region.
+ */
+ @Override
+ public void highlightSequence(SearchResultsI results)
+ {
+ if (results == null || results.equals(lastSearchResults))
+ {
+ return;
+ }
+ lastSearchResults = results;
+
+ boolean wasScrolled = false;
+
+ if (av.isFollowHighlight())
+ {
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
+ wasScrolled = ap.scrollToPosition(results, false);
+ if (wasScrolled)
+ {
+ seqCanvas.revalidate();
+ }
+ ap.setToScrollComplementPanel(true);
+ }
+
+ boolean noFastPaint = wasScrolled && av.getWrapAlignment();
+ if (seqCanvas.highlightSearchResults(results, noFastPaint))
+ {
+ setStatusMessage(results);
+ }
+ }
- public void highlightSequence(SearchResults results)
+ @Override
+ public VamsasSource getVamsasSource()
{
- seqCanvas.highlightSearchResults(results);
+ return this.ap == null ? null : this.ap.av;
}
+ @Override
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
- //repaint();
+ // repaint();
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * Action on mouse movement is to update the status bar to show the current
+ * sequence position, and (if features are shown) to show any features at the
+ * position in a tooltip. Does nothing if the mouse move does not change
+ * residue position.
+ *
+ * @param evt
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
@@ -610,42 +736,53 @@ public class SeqPanel
mouseDragged(evt);
}
- int res = findRes(evt);
- int seq = findSeq(evt);
- int pos;
- if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ final int column = findColumn(evt);
+ final int seq = findSeq(evt);
+
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
+ lastMouseSeq = -1;
return;
}
+ if (column == lastMouseColumn && seq == lastMouseSeq)
+ {
+ /*
+ * just a pixel move without change of residue
+ */
+ return;
+ }
+ lastMouseColumn = column;
+ lastMouseSeq = seq;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res >= sequence.getLength())
+ if (column >= sequence.getLength())
{
return;
}
- pos = setStatusMessage(sequence, res, seq);
- if (ssm != null && pos>-1)
- mouseOverSequence(sequence, res, pos);
-
+ /*
+ * set status bar message, returning residue position in sequence
+ */
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+ final int pos = setStatusMessage(sequence, column, seq);
+ if (ssm != null && !isGapped)
+ {
+ mouseOverSequence(sequence, column, pos);
+ }
tooltipText.setLength(6); // Cuts the buffer back to
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
{
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
-
- if (!groups[g].getName().startsWith("JTreeGroup") &&
- !groups[g].getName().startsWith("JGroup"))
+ if (!groups[g].getName().startsWith("JTreeGroup")
+ && !groups[g].getName().startsWith("JGroup"))
{
tooltipText.append(groups[g].getName());
}
@@ -658,194 +795,229 @@ public class SeqPanel
}
}
- // use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
+ /*
+ * add any features at the position to the tooltip; if over a gap, only
+ * add features that straddle the gap (pos may be the residue before or
+ * after the gap)
+ */
+ if (av.isShowSequenceFeatures())
{
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(), sequence.findPosition(res));
-
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].getType().equals("disulfide bond"))
- {
- if (features[i].getBegin() == sequence.findPosition(res)
- || features[i].getEnd() == sequence.findPosition(res))
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
- tooltipText.append("disulfide bond " + features[i].getBegin() +
- ":" +
- features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText.append(" ![](\"")
");
- }
- }
- }
- else
- {
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
-
- tooltipText.append(features[i].getType() + " " +
- features[i].begin);
- if (features[i].begin != features[i].end)
- {
- tooltipText.append(" " + features[i].end);
- }
-
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i].getType()))
- {
- tmpString = features[i].getDescription();
- int startTag = tmpString.toUpperCase().indexOf("");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- }
- int endTag = tmpString.toUpperCase().indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
- endTag = tmpString.toUpperCase().indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
-
- if (startTag > -1)
- {
- tooltipText.append("; " + tmpString);
- }
- else
- {
- if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
- {
- //The description does not specify html is to
- //be used, so we must remove < > symbols
- tmpString = tmpString.replaceAll("<", "<");
- tmpString = tmpString.replaceAll(">", ">");
-
- tooltipText.append("; ");
- tooltipText.append(tmpString);
-
- }
- else
- {
- tooltipText.append("; " + tmpString);
- }
- }
- }
- if (features[i].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText.append("; (" + features[i].getValue("status") + ")");
- }
- }
-
- if (features[i].links != null)
- {
- tooltipText.append(" ");
- }
-
- }
- }
- }
+ List features = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ seqARep.appendFeatures(tooltipText, pos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
-
- if (tooltipText.length() == 6) //
+ if (tooltipText.length() == 6) //
{
setToolTipText(null);
+ lastTooltip = null;
}
else
{
- tooltipText.append("");
- if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
- setToolTipText(tooltipText.toString());
-
- lastTooltip = tooltipText.toString();
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
+ {
+ String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+ textString);
+ setToolTipText(formattedTooltipText);
+ lastTooltip = textString;
+ }
}
+ }
+ private Point lastp = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent event)
+ {
+ int x = event.getX(), w = getWidth();
+ int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+ // close to edge
+ Point p = lastp;
+ if (!event.isShiftDown() || p == null)
+ {
+ p = (tooltipText != null && tooltipText.length() > 6)
+ ? new Point(event.getX() + wdth, event.getY() - 20)
+ : null;
+ }
+ /*
+ * TODO: try to modify position region is not obcured by tooltip
+ */
+ return lastp = p;
}
+
String lastTooltip;
/**
- * Set status message in alignment panel
- * @param sequence aligned sequence object
- * @param res alignment column
- * @param seq index of sequence in alignment
- * @return position of res in sequence
+ * set when the current UI interaction has resulted in a change that requires
+ * shading in overviews and structures to be recalculated. this could be
+ * changed to a something more expressive that indicates what actually has
+ * changed, so selective redraws can be applied (ie. only structures, only
+ * overview, etc)
+ */
+ private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+
+ /**
+ * set if av.getSelectionGroup() refers to a group that is defined on the
+ * alignment view, rather than a transient selection
+ */
+ // private boolean editingDefinedGroup = false; // TODO: refactor to
+ // avcontroller or viewModel
+
+ /**
+ * Sets the status message in alignment panel, showing the sequence number
+ * (index) and id, and residue and residue position if not at a gap, for the
+ * given sequence and column position. Returns the residue position returned
+ * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+ * if at a gapped position.
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param column
+ * alignment column
+ * @param seqIndex
+ * index of sequence in alignment
+ * @return sequence position of residue at column, or adjacent residue if at a
+ * gap
*/
- int setStatusMessage(SequenceI sequence, int res, int seq)
+ int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
{
- int pos=-1;
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
+ char sequenceChar = sequence.getCharAt(column);
+ int pos = sequence.findPosition(column);
+ setStatusMessage(sequence, seqIndex, sequenceChar, pos);
- Object obj = null;
- if (av.alignment.isNucleotide())
+ return pos;
+ }
+
+ /**
+ * Builds the status message for the current cursor location and writes it to
+ * the status bar, for example
+ *
+ *
+ * Sequence 3 ID: FER1_SOLLC
+ * Sequence 5 ID: FER1_PEA Residue: THR (4)
+ * Sequence 5 ID: FER1_PEA Residue: B (3)
+ * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+ *
+ *
+ * @param sequence
+ * @param seqIndex
+ * sequence position in the alignment (1..)
+ * @param sequenceChar
+ * the character under the cursor
+ * @param residuePos
+ * the sequence residue position (if not over a gap)
+ */
+ protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ char sequenceChar, int residuePos)
+ {
+ StringBuilder text = new StringBuilder(32);
+
+ /*
+ * Sequence number (if known), and sequence name.
+ */
+ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
+
+ String residue = null;
+
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ boolean isGapped = Comparison.isGap(sequenceChar);
+
+ if (!isGapped)
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
- "");
- if (obj != null)
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ String displayChar = String.valueOf(sequenceChar);
+ if (nucleotide)
{
- text.append(" Nucleotide: ");
+ residue = ResidueProperties.nucleotideName.get(displayChar);
}
- }
- else
- {
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
+ else
{
- text.append(" Residue: ");
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
}
+ text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+ .append(": ").append(residue == null ? displayChar : residue);
+
+ text.append(" (").append(Integer.toString(residuePos)).append(")");
}
+ ap.alignFrame.statusBar.setText(text.toString());
+ }
- if (obj != null)
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResultsI results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return;
+ }
+ SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ for (SearchResultMatchI m : results.getResults())
{
- pos=sequence.findPosition(res);
- if (obj != "")
+ SequenceI seq = m.getSequence();
+ if (seq.getDatasetSequence() != null)
{
- text.append(obj + " (" + pos +
- ")");
+ seq = seq.getDatasetSequence();
+ }
+
+ if (seq == ds)
+ {
+ int start = m.getStart();
+ setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+ start);
+ return;
}
}
- ap.alignFrame.statusBar.setText(text.toString());
- return pos;
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * {@inheritDoc}
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ boolean inSplitFrame = ap.av.getCodingComplement() != null;
+ boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
- //Which is bigger, left-right or up-down?
- if (Math.abs(evt.getY() - lastMousePress.getY())
- > Math.abs(evt.getX() - lastMousePress.getX()))
+ int oldWidth = av.getCharWidth();
+
+ // Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+ .abs(evt.getX() - lastMousePress.getX()))
{
+ /*
+ * on drag up or down, decrement or increment font size
+ */
int fontSize = av.font.getSize();
+ boolean fontChanged = false;
if (evt.getY() < lastMousePress.getY())
{
+ fontChanged = true;
fontSize--;
}
else if (evt.getY() > lastMousePress.getY())
{
+ fontChanged = true;
fontSize++;
}
@@ -854,26 +1026,60 @@ public class SeqPanel
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
- ap.fontChanged();
+ if (fontChanged)
+ {
+ Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+ fontSize);
+ av.setFont(newFont, true);
+ av.setCharWidth(oldWidth);
+ ap.fontChanged();
+ if (copyChanges)
+ {
+ ap.av.getCodingComplement().setFont(newFont, true);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
}
else
{
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.charWidth--;
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.charWidth++;
+ newWidth = av.getCharWidth() + 1;
+ av.setCharWidth(newWidth);
+ }
+ if (newWidth > 0)
+ {
+ ap.paintAlignment(false, false);
+ if (copyChanges)
+ {
+ /*
+ * need to ensure newWidth is set on cdna, regardless of which
+ * panel the mouse drag happened in; protein will compute its
+ * character width as 1:1 or 3:1
+ */
+ av.getCodingComplement().setCharWidth(newWidth);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
}
-
- ap.paintAlignment(false);
}
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
@@ -886,64 +1092,64 @@ public class SeqPanel
return;
}
- int res = findRes(evt);
+ int res = findColumn(evt);
if (res < 0)
{
res = 0;
}
- if ( (lastres == -1) || (lastres == res))
+ if ((lastres == -1) || (lastres == res))
{
return;
}
- if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+ 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;
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
scrollThread.setEvent(evt);
}
}
-
-
- 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;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
- //No group, but the sequence may represent a group
- if (!groupEditing && av.hasHiddenRows)
+ // No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
- StringBuffer message = new StringBuffer();
+ StringBuilder message = new StringBuilder(64);
if (groupEditing)
{
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
@@ -956,7 +1162,9 @@ public class SeqPanel
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { label }));
}
}
@@ -972,32 +1180,31 @@ public class SeqPanel
message.append(Math.abs(startres - lastres) + " gaps.");
ap.alignFrame.statusBar.setText(message.toString());
- //Are we editing within a selection group?
- if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+ // Are we editing within a selection group?
+ if (groupEditing || (sg != null
+ && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
{
fixedColumns = true;
- //sg might be null as the user may only see 1 sequence,
- //but the sequence represents a group
+ // sg might be null as the user may only see 1 sequence,
+ // 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();
fixedRight = sg.getEndRes();
- if ( (startres < fixedLeft && lastres >= fixedLeft)
- || (startres >= fixedLeft && lastres < fixedLeft)
- || (startres > fixedRight && lastres <= fixedRight)
- || (startres <= fixedRight && lastres > fixedRight))
+ if ((startres < fixedLeft && lastres >= fixedLeft)
+ || (startres >= fixedLeft && lastres < fixedLeft)
+ || (startres > fixedRight && lastres <= fixedRight)
+ || (startres <= fixedRight && lastres > fixedRight))
{
endEditing();
return;
@@ -1015,21 +1222,23 @@ public class SeqPanel
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+ int y1 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryLeft(startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryRight(startres);
- if ( (insertGap && startres > y1 && lastres < y1)
- || (!insertGap && startres < y2 && lastres > y2))
+ if ((insertGap && startres > y1 && lastres < y1)
+ || (!insertGap && startres < y2 && lastres > y2))
{
endEditing();
return;
}
- //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
- //Selection spans a hidden region
+ // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ // Selection spans a hidden region
if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
{
if (startres >= y2)
@@ -1045,25 +1254,23 @@ public class SeqPanel
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+ List vseqs = sg.getSequences(av.getHiddenRepSequences());
int g, groupSize = vseqs.size();
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+ groupSeqs[g] = vseqs.get(g);
}
// drag to right
if (insertGap)
{
- //If the user has selected the whole sequence, and is dragging to
+ // 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
- )
+ if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
@@ -1071,9 +1278,7 @@ public class SeqPanel
// Find the next gap before the end
// of the visible region boundary
boolean blank = false;
- for (fixedRight = fixedRight;
- fixedRight > lastres;
- fixedRight--)
+ for (; fixedRight > lastres; fixedRight--)
{
blank = true;
@@ -1081,8 +1286,7 @@ public class SeqPanel
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
{
blank = false;
break;
@@ -1097,27 +1301,27 @@ public class SeqPanel
if (!blank)
{
- if (sg.getSize() == av.alignment.getHeight())
+ if (sg.getSize() == av.getAlignment().getHeight())
{
- if ( (av.hasHiddenColumns
- &&
- startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av.getAlignment()
+ .getHiddenColumns().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;
}
}
- //We can still insert gaps if the selectionGroup
- //contains all the sequences
+ // We can still insert gaps if the selectionGroup
+ // contains all the sequences
sg.setEndRes(sg.getEndRes() + startres - lastres);
fixedRight = alWidth + startres - lastres;
}
@@ -1132,7 +1336,7 @@ public class SeqPanel
// drag to left
else if (!insertGap)
{
- /// Are we able to delete?
+ // / Are we able to delete?
// ie are all columns blank?
for (g = 0; g < groupSize; g++)
@@ -1144,8 +1348,7 @@ public class SeqPanel
continue;
}
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
@@ -1167,11 +1370,8 @@ public class SeqPanel
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- groupSeqs,
- startres, startres - lastres,
- av.alignment,
- true);
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres);
}
}
else
@@ -1186,16 +1386,14 @@ public class SeqPanel
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- groupSeqs,
- startres, lastres - startres,
- av.alignment,
- true);
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres);
}
}
}
- else /////Editing a single sequence///////////
+ else
+ // ///Editing a single sequence///////////
{
if (insertGap)
{
@@ -1204,57 +1402,65 @@ public class SeqPanel
{
for (int j = lastres; j < startres; j++)
{
- insertChar(j, new SequenceI[]
- {seq}, fixedRight);
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- new SequenceI[]
- {seq},
- lastres, startres - lastres,
- av.alignment,
- true);
+ appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
else
{
- // 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 (!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 (!Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
}
- 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.alignment,
- true);
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
}
}
}
@@ -1269,14 +1475,14 @@ public class SeqPanel
int blankColumn = fixedColumn;
for (int s = 0; s < seq.length; s++)
{
- //Find the next gap before the end of the visible region boundary
- //If lastCol > j, theres a boundary after the gap insertion
+ // Find the next gap before the end of the visible region boundary
+ // If lastCol > j, theres a boundary after the gap insertion
for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
{
- if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
{
- //Theres a space, so break and insert the gap
+ // Theres a space, so break and insert the gap
break;
}
}
@@ -1289,34 +1495,45 @@ public class SeqPanel
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- blankColumn, 1, av.alignment, true);
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+
+ appendEdit(Action.INSERT_GAP, seq, j, 1);
+
+ }
+
+ /**
+ * Helper method to add and perform one edit action.
+ *
+ * @param action
+ * @param seq
+ * @param pos
+ * @param count
+ */
+ protected void appendEdit(Action action, SequenceI[] seq, int pos,
+ int count)
+ {
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- j, 1, av.alignment,
- true);
+ final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+ av.getAlignment().getGapCharacter());
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- j, 1, av.alignment, true);
+ appendEdit(Action.DELETE_GAP, seq, j, 1);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- fixedColumn, 1, av.alignment, true);
+ appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
@@ -1324,18 +1541,20 @@ public class SeqPanel
oldSeq = 0;
}
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
scrollThread = null;
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -1343,80 +1562,121 @@ public class SeqPanel
return;
}
- if (mouseDragging)
+ if (mouseDragging && scrollThread == null)
{
scrollThread = new ScrollThread();
}
}
+ /**
+ * Handler for double-click on a position with one or more sequence features.
+ * Opens the Amend Features dialog to allow feature details to be amended, or
+ * the feature deleted.
+ */
+ @Override
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceGroup sg = null;
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
{
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(
- sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt))
- );
+ int column = findColumn(evt);
- if (features != null && features.length > 0)
- {
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequence,
- features[0].getBegin(),
- features[0].getEnd());
- seqCanvas.highlightSearchResults(highlight);
- }
- if (features != null && features.length > 0)
+ /*
+ * find features at the position (if not gapped), or straddling
+ * the position (if at a gap)
+ */
+ List features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+
+ if (!features.isEmpty())
{
- seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[]
- {sequence}, features, false, ap);
+ /*
+ * highlight the first feature at the position on the alignment
+ */
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
+ seqCanvas.highlightSearchResults(highlight, false);
- seqCanvas.highlightSearchResults(null);
+ /*
+ * open the Amend Features dialog; clear highlighting afterwards,
+ * whether changes were made or not
+ */
+ List seqs = Collections.singletonList(sequence);
+ seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+ ap);
+ av.setSearchResults(null); // clear highlighting
+ seqCanvas.repaint(); // draw new/amended features
}
}
}
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ if (e.getWheelRotation() > 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(true);
+
+ }
+ else
+ {
+ av.getRanges().scrollUp(false);
+ }
+ }
+ else
+ {
+ if (e.isShiftDown())
{
- ap.scrollUp(false);
+ av.getRanges().scrollRight(false);
}
else
{
- ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
+ }
+
+ /*
+ * update status bar and tooltip for new position
+ * (need to synthesize a mouse movement to refresh tooltip)
+ */
+ mouseMoved(e);
+ ToolTipManager.sharedInstance().mouseMoved(e);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
- int seq = findSeq(evt);
+ final int res = findColumn(evt);
+ final int seq = findSeq(evt);
oldSeq = seq;
+ updateOverviewAndStructs = false;
startWrapBlock = wrappedBlock;
- if (av.wrapAlignment && seq > av.alignment.getHeight())
+ if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@@ -1425,78 +1685,45 @@ public class SeqPanel
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if ( (sequence == null) || (res > sequence.getLength()))
+ if ((sequence == null) || (res > sequence.getLength()))
{
return;
}
stretchGroup = av.getSelectionGroup();
- if (stretchGroup == null)
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
{
- stretchGroup = av.alignment.findGroup(sequence);
-
- if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
- (res < stretchGroup.getEndRes()))
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ if (stretchGroup != null)
{
+ // only update the current selection if the popup menu has a group to
+ // focus on
av.setSelectionGroup(stretchGroup);
}
- else
- {
- stretchGroup = null;
- }
}
- else if (!stretchGroup.getSequences(null).contains(sequence) ||
- (stretchGroup.getStartRes() > res) ||
- (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
-
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
-
- if (allGroups != null)
- {
- for (int i = 0; i < allGroups.length; i++)
- {
- if ( (allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- break;
- }
- }
- }
-
- av.setSelectionGroup(stretchGroup);
+ if (evt.isPopupTrigger()) // Mac: mousePressed
+ {
+ showPopupMenu(evt);
+ return;
}
- if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
{
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(res));
- Vector links = new Vector();
- for (int i = 0; i < allFeatures.length; i++)
- {
- if (allFeatures[i].links != null)
- {
- for (int j = 0; j < allFeatures[i].links.size(); j++)
- {
- links.addElement(allFeatures[i].links.elementAt(j));
- }
- }
- }
-
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
- pop.show(this, evt.getX(), evt.getY());
return;
}
if (av.cursorMode)
{
- seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorX = findColumn(evt);
seqCanvas.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
@@ -1504,102 +1731,145 @@ public class SeqPanel
if (stretchGroup == null)
{
- //Only if left mouse button do we want to change group sizes
+ createStretchGroup(res, sequence);
+ }
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- stretchGroup = sg;
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
- if (av.getConservationSelected())
- {
- SliderPanel.setConservationSlider(ap,
- av.getGlobalColourScheme(),
- "Background");
- }
+ seqCanvas.repaint();
+ }
- if (av.getAbovePIDThreshold())
- {
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
- }
- if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ( (stretchGroup != null) &&
- (stretchGroup.getStartRes() == res))
+ private void createStretchGroup(int res, SequenceI sequence)
+ {
+ // Only if left mouse button do we want to change group sizes
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
+ // or is there a threading issue here?
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+
+ }
+
+ /**
+ * Build and show a pop-up menu at the right-click mouse position
+ *
+ * @param evt
+ * @param res
+ * @param sequences
+ */
+ void showPopupMenu(MouseEvent evt)
+ {
+ final int column = findColumn(evt);
+ final int seq = findSeq(evt);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ List allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ List links = new ArrayList<>();
+ for (SequenceFeature sf : allFeatures)
+ {
+ if (sf.links != null)
{
- // Edit end res position of selected group
- changeStartRes = true;
+ for (String link : sf.links)
+ {
+ links.add(link);
+ }
}
- stretchGroup.getWidth();
}
- seqCanvas.repaint();
+ PopupMenu pop = new PopupMenu(ap, null, links);
+ pop.show(this, evt.getX(), evt.getY());
}
/**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ * Update the display after mouse up on a selection or group
+ *
+ * @param evt
+ * mouse released event details
+ * @param afterDrag
+ * true if this event is happening after a mouse drag (rather than a
+ * mouse down)
*/
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
{
if (stretchGroup == null)
{
return;
}
+ stretchGroup.removePropertyChangeListener(seqCanvas);
+
+ // always do this - annotation has own state
+ // but defer colourscheme update until hidden sequences are passed in
+ boolean vischange = stretchGroup.recalcConservation(true);
+ updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
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());
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
+ String name = stretchGroup.getName();
if (stretchGroup.cs.conservationApplied())
{
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
}
- else
+ if (stretchGroup.cs.getThreshold() > 0)
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
}
-
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // TODO: structure colours only need updating if stretchGroup used to or now
+ // does contain sequences with structure views
+ ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+ updateOverviewAndStructs = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
-
+ av.sendSelection();
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
+ int res = findColumn(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
@@ -1612,9 +1882,9 @@ public class SeqPanel
return;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
@@ -1628,9 +1898,9 @@ public class SeqPanel
changeStartRes = true;
}
- if (res < av.getStartRes())
+ if (res < av.getRanges().getStartRes())
{
- res = av.getStartRes();
+ res = av.getRanges().getStartRes();
}
if (changeEndRes)
@@ -1638,6 +1908,7 @@ public class SeqPanel
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
}
}
else if (changeStartRes)
@@ -1645,6 +1916,7 @@ public class SeqPanel
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
}
}
@@ -1659,7 +1931,8 @@ public class SeqPanel
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.
@@ -1677,6 +1950,7 @@ public class SeqPanel
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
}
else
{
@@ -1686,6 +1960,7 @@ public class SeqPanel
}
stretchGroup.addSequence(nextSeq, false);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
}
}
@@ -1696,21 +1971,19 @@ public class SeqPanel
mouseDragging = true;
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
scrollThread.setEvent(evt);
}
-
- seqCanvas.repaint();
}
void scrollCanvas(MouseEvent evt)
{
if (evt == null)
{
- if (scrollThread != null)
+ if ((scrollThread != null) && (scrollThread.isRunning()))
{
- scrollThread.running = false;
+ scrollThread.stopScrolling();
scrollThread = null;
}
mouseDragging = false;
@@ -1729,11 +2002,11 @@ public class SeqPanel
}
// this class allows scrolling off the bottom of the visible alignment
- class ScrollThread
- extends Thread
+ class ScrollThread extends Thread
{
MouseEvent evt;
- boolean running = false;
+
+ private volatile boolean threadRunning = true;
public ScrollThread()
{
@@ -1747,47 +2020,239 @@ public class SeqPanel
public void stopScrolling()
{
- running = false;
+ threadRunning = false;
}
- public void run()
+ public boolean isRunning()
{
- running = true;
+ return threadRunning;
+ }
- while (running)
+ @Override
+ public void run()
+ {
+ while (threadRunning)
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) &&
- (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
{
- running = ap.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
- running = ap.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
if (mouseDragging && (evt.getX() < 0))
{
- running = ap.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
else if (mouseDragging && (evt.getX() >= getWidth()))
{
- running = ap.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
}
try
{
Thread.sleep(20);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
+ }
+ }
+ }
+
+ /**
+ * modify current selection according to a received message.
+ */
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source)
+ {
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId())));
+
+ if (iSentTheSelection)
+ {
+ // respond to our own event by updating dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ return;
+ }
+
+ // process further ?
+ if (!av.followSelection)
+ {
+ return;
+ }
+
+ /*
+ * Ignore the selection if there is one of our own pending.
+ */
+ if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ {
+ return;
+ }
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, hidden, source))
+ {
+ return;
+ }
+
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
+ boolean repaint = false;
+ boolean copycolsel = false;
+
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ if (av.getAlignment() == null)
+ {
+ Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediately.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup != null && sgroup.getSize() > 0))
+ {
+ copycolsel = true;
+ }
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+
+ if (copycolsel)
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.isEmpty())
+ {
+ if (av.getColumnSelection() != null)
{
+ av.getColumnSelection().clear();
+ repaint = true;
}
}
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.getColumnSelection() == null)
+ {
+ av.setColumnSelection(new ColumnSelection(colsel));
+ }
+ else
+ {
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
+ }
+ }
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+
+ if (copycolsel && av.hasHiddenColumns()
+ && (av.getAlignment().getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint) // always true!
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
}
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ }
+
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI))
+ {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ // av);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
+ av.setColumnSelection(cs);
+ av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
}
}