X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=02b207823b9a6f704348f4d78a831ad63d3fea85;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;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..02b2078
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,43 +1,75 @@
/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+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.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.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+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 +77,72 @@ public class SeqPanel
/** DOCUMENT ME!! */
public AlignmentPanel ap;
+
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;
+
+ StringBuffer tooltipText = new StringBuffer();
+
String tmpString;
EditCommand editCommand;
StructureSelectionManager ssm;
+ SearchResults 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);
@@ -106,29 +160,39 @@ public class SeqPanel
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
}
}
int startWrapBlock = -1;
+
int wrappedBlock = -1;
+
+ /**
+ * Returns the aligned sequence position (base 0) at the mouse position, or
+ * the closest visible one
+ *
+ * @param evt
+ * @return
+ */
int findRes(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
- 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();
int y = evt.getY();
y -= hgap;
@@ -148,10 +212,21 @@ public class SeqPanel
}
else
{
+ 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()) + av.getStartRes();
+ if (res > av.getEndRes())
+ {
+ // moused off right
+ res = av.getEndRes();
+ }
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -165,83 +240,58 @@ 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.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 +322,9 @@ 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 +332,20 @@ public class SeqPanel
{
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)
- && seqCanvas.cursorX < maxWidth
- && seqCanvas.cursorX > 0)
+ 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;
}
@@ -313,22 +360,22 @@ 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);
}
@@ -342,16 +389,18 @@ public class SeqPanel
{
ap.scrollUp(false);
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+ while (seqCanvas.cursorX < av.getColumnSelection()
+ .adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
{
break;
}
}
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+ while (seqCanvas.cursorX > av.getColumnSelection()
+ .adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
{
@@ -360,25 +409,24 @@ public class SeqPanel
}
}
}
- 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 +471,7 @@ 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);
}
}
}
@@ -438,6 +486,7 @@ public class SeqPanel
}
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
@@ -445,7 +494,7 @@ 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 +503,16 @@ 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)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
endEditing();
}
@@ -477,33 +535,45 @@ 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)
{
mouseDragging = false;
@@ -520,9 +590,11 @@ public class SeqPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
@@ -533,8 +605,7 @@ public class SeqPanel
return;
}
- if (evt.isShiftDown() || evt.isAltDown() ||
- evt.isControlDown())
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
{
if (evt.isAltDown() || evt.isControlDown())
{
@@ -556,8 +627,8 @@ public class SeqPanel
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 +643,73 @@ 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(SearchResults results)
{
- seqCanvas.highlightSearchResults(results);
+ if (results == null || results.equals(lastSearchResults))
+ {
+ return;
+ }
+ lastSearchResults = results;
+
+ if (av.isFollowHighlight())
+ {
+ /*
+ * if scrollToPosition requires a scroll adjustment, this flag prevents
+ * another scroll event being propagated back to the originator
+ *
+ * @see AlignmentPanel#adjustmentValueChanged
+ */
+ ap.setDontScrollComplement(true);
+ if (ap.scrollToPosition(results, false))
+ {
+ seqCanvas.revalidate();
+ }
+ }
+ setStatusMessage(results);
+ seqCanvas.highlightSearchResults(results);
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ 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!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
@@ -626,26 +735,22 @@ public class SeqPanel
}
pos = setStatusMessage(sequence, res, seq);
- if (ssm != null && pos>-1)
+ if (ssm != null && pos > -1)
+ {
mouseOverSequence(sequence, res, 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 (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());
}
@@ -659,184 +764,169 @@ public class SeqPanel
}
// use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
+ 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(" ");
- }
-
- }
- }
- }
+ int rpos;
+ List features = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ rpos = sequence.findPosition(res));
+ seqARep.appendFeatures(tooltipText, rpos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
-
if (tooltipText.length() == 6) //
{
setToolTipText(null);
+ lastTooltip = null;
}
else
{
- tooltipText.append("");
- if (lastTooltip == null || !lastTooltip.equals(tooltipText.toString()))
- setToolTipText(tooltipText.toString());
+ if (lastTooltip == null
+ || !lastTooltip.equals(tooltipText.toString()))
+ {
+ String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltipText.toString());
+ // String formatedTooltipText = tooltipText.toString();
+ setToolTipText(formatedTooltipText);
+ lastTooltip = tooltipText.toString();
+ }
- lastTooltip = tooltipText.toString();
}
}
+
+ private Point lastp = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ 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
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param res
+ * alignment column
+ * @param seq
+ * index of sequence in alignment
* @return position of res in sequence
*/
int setStatusMessage(SequenceI sequence, int res, int seq)
{
- int pos=-1;
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
+ StringBuilder text = new StringBuilder(32);
+
+ /*
+ * Sequence number (if known), and sequence name.
+ */
+ String seqno = seq == -1 ? "" : " " + (seq + 1);
+ text.append("Sequence" + seqno + " ID: " + sequence.getName());
- Object obj = null;
- if (av.alignment.isNucleotide())
+ String residue = null;
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ final String displayChar = String.valueOf(sequence.getCharAt(res));
+ if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
- "");
- if (obj != null)
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ if (residue != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(residue);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if (obj != null)
+ residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
+ .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
+ .get(displayChar));
+ if (residue != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(residue);
}
}
- if (obj != null)
+ int pos = -1;
+ if (residue != null)
{
- pos=sequence.findPosition(res);
- if (obj != "")
- {
- text.append(obj + " (" + pos +
- ")");
- }
+ pos = sequence.findPosition(res);
+ text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
return pos;
}
/**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResults results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return;
+ }
+ SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ for (Match m : results.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ if (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ if (seq == ds)
+ {
+ /*
+ * Convert position in sequence (base 1) to sequence character array
+ * index (base 0)
+ */
+ int start = m.getStart() - m.getSequence().getStart();
+ setStatusMessage(seq, start, sequenceIndex);
+ return;
+ }
+ }
+ }
+
+ /**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
{
- int oldWidth = av.charWidth;
+ 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()))
+ // Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
+ .getX() - lastMousePress.getX()))
{
int fontSize = av.font.getSize();
@@ -854,26 +944,28 @@ public class SeqPanel
fontSize = 1;
}
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setFont(
+ new Font(av.font.getName(), av.font.getStyle(), fontSize),
+ true);
+ av.setCharWidth(oldWidth);
ap.fontChanged();
}
else
{
- if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.getX())
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
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();
@@ -893,19 +985,19 @@ public class SeqPanel
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;
@@ -915,35 +1007,35 @@ public class SeqPanel
}
}
-
-
- 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 +1048,8 @@ public class SeqPanel
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[] { label }));
}
}
@@ -972,32 +1065,32 @@ public class SeqPanel
message.append(Math.abs(startres - lastres) + " gaps.");
ap.alignFrame.statusBar.setText(message.toString());
- //Are we editing within a selection group?
+ // Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+ || (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 +1108,21 @@ public class SeqPanel
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
int y2 = av.getColumnSelection().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 +1138,23 @@ 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 +1162,7 @@ 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 = fixedRight; fixedRight > lastres; fixedRight--)
{
blank = true;
@@ -1081,8 +1170,8 @@ public class SeqPanel
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!jalview.util.Comparison.isGap(groupSeqs[g]
+ .getCharAt(fixedRight - j)))
{
blank = false;
break;
@@ -1097,27 +1186,27 @@ 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
+ .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;
}
}
- //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 +1221,7 @@ 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 +1233,7 @@ public class SeqPanel
continue;
}
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
@@ -1167,11 +1255,8 @@ 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 +1271,14 @@ 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 +1287,65 @@ 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 +1360,14 @@ 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)))
{
- //Theres a space, so break and insert the gap
+ // Theres a space, so break and insert the gap
break;
}
}
@@ -1289,34 +1380,45 @@ public class SeqPanel
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- blankColumn, 1, av.alignment, true);
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- j, 1, av.alignment,
- true);
+ 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)
+ {
+
+ 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)
@@ -1333,9 +1435,11 @@ public class SeqPanel
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -1349,59 +1453,78 @@ public class SeqPanel
}
}
+ @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))
- );
+ List features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt)));
- if (features != null && features.length > 0)
+ if (features != null && features.size() > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence,
- features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
}
- if (features != null && features.length > 0)
+ if (features != null && features.size() > 0)
{
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[]
- {sequence}, features, false, ap);
+ new SequenceI[] { sequence },
+ features.toArray(new SequenceFeature[features.size()]),
+ false, ap);
seqCanvas.highlightSearchResults(null);
}
}
}
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
- if (e.getWheelRotation() > 0)
+ if (e.getWheelRotation() > 0)
+ {
+ if (e.isShiftDown())
+ {
+ ap.scrollRight(true);
+
+ }
+ else
{
ap.scrollUp(false);
}
+ }
+ else
+ {
+ if (e.isShiftDown())
+ {
+ ap.scrollRight(false);
+ }
else
{
ap.scrollUp(true);
}
+ }
+ // TODO Update tooltip for new position.
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
@@ -1411,12 +1534,12 @@ public class SeqPanel
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);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -1425,9 +1548,9 @@ 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;
}
@@ -1436,10 +1559,10 @@ public class SeqPanel
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
- if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
- (res < stretchGroup.getEndRes()))
+ if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
+ && (res < stretchGroup.getEndRes()))
{
av.setSelectionGroup(stretchGroup);
}
@@ -1448,20 +1571,20 @@ public class SeqPanel
stretchGroup = null;
}
}
- else if (!stretchGroup.getSequences(null).contains(sequence) ||
- (stretchGroup.getStartRes() > res) ||
- (stretchGroup.getEndRes() < res))
+ else if (!stretchGroup.getSequences(null).contains(sequence)
+ || (stretchGroup.getStartRes() > res)
+ || (stretchGroup.getEndRes() < res))
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
for (int i = 0; i < allGroups.length; i++)
{
- if ( (allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
+ if ((allGroups[i].getStartRes() <= res)
+ && (allGroups[i].getEndRes() >= res))
{
stretchGroup = allGroups[i];
break;
@@ -1475,16 +1598,17 @@ public class SeqPanel
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(res));
+ List allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(res));
Vector links = new Vector();
- for (int i = 0; i < allFeatures.length; i++)
+ for (SequenceFeature sf : allFeatures)
{
- if (allFeatures[i].links != null)
+ if (sf.links != null)
{
- for (int j = 0; j < allFeatures[i].links.size(); j++)
+ for (int j = 0; j < sf.links.size(); j++)
{
- links.addElement(allFeatures[i].links.elementAt(j));
+ links.addElement(sf.links.elementAt(j));
}
}
}
@@ -1504,7 +1628,7 @@ public class SeqPanel
if (stretchGroup == null)
{
- //Only if left mouse button do we want to change group sizes
+ // Only if left mouse button do we want to change group sizes
// define a new group here
SequenceGroup sg = new SequenceGroup();
@@ -1512,27 +1636,27 @@ public class SeqPanel
sg.setEndRes(res);
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
+
stretchGroup = sg;
if (av.getConservationSelected())
{
- SliderPanel.setConservationSlider(ap,
- av.getGlobalColourScheme(),
- "Background");
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+ "Background");
}
if (av.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ "Background");
}
- if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
{
// Edit end res position of selected group
changeEndRes = true;
}
- else if ( (stretchGroup != null) &&
- (stretchGroup.getStartRes() == res))
+ else if ((stretchGroup != null)
+ && (stretchGroup.getStartRes() == res))
{
// Edit end res position of selected group
changeStartRes = true;
@@ -1545,8 +1669,9 @@ public class SeqPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMouseReleasedDefineMode(MouseEvent evt)
{
@@ -1555,47 +1680,38 @@ public class SeqPanel
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.getName());
}
else
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ stretchGroup.getName());
}
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- ap.paintAlignment(true);
}
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ ap.paintAlignment(true);
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
-
+ av.sendSelection();
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
@@ -1612,9 +1728,9 @@ 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)
@@ -1659,7 +1775,8 @@ 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.
@@ -1729,10 +1846,10 @@ 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;
public ScrollThread()
@@ -1750,6 +1867,7 @@ public class SeqPanel
running = false;
}
+ @Override
public void run()
{
running = true;
@@ -1758,14 +1876,13 @@ public class SeqPanel
{
if (evt != null)
{
- if (mouseDragging && (evt.getY() < 0) &&
- (av.getStartSeq() > 0))
+ if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
{
running = ap.scrollUp(true);
}
- if (mouseDragging && (evt.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
+ if (mouseDragging && (evt.getY() >= getHeight())
+ && (av.getAlignment().getHeight() > av.getEndSeq()))
{
running = ap.scrollUp(false);
}
@@ -1783,11 +1900,168 @@ public class SeqPanel
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,
+ 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 || !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, source))
+ {
+ return;
+ }
+
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false;
+ boolean copycolsel = true;
+
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ if (av.getAlignment() == null)
+ {
+ jalview.bin.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)
+ || (colsel == null || colsel.size() == 0))
+ {
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
+ }
+ }
+ 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.size() == 0)
+ {
+ 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.isColSelChanged(true);
+ repaint = true;
}
+
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .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);
+ }
+ }
+
+ /**
+ * 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, 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);
+ av.setColumnSelection(cs);
+ av.isColSelChanged(true);
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
}
}