X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=d59998343dd2c9866c605b1a764efa9f0c5f848e;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=158f0abdbc98dc13589b0ae04a36c1625560440a;hpb=41e1e412121ed83380bd33fcb9e3969dc055aa4c;p=jalview.git
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
old mode 100755
new mode 100644
index 158f0ab..d599983
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,73 +1,107 @@
/*
- * 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.api.AlignViewportI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+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.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
-
-public class SeqPanel
- extends Panel implements MouseMotionListener, MouseListener, SequenceListener
+import jalview.structure.VamsasSource;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
+
+public class SeqPanel extends Panel implements MouseMotionListener,
+ MouseListener, SequenceListener, SelectionListener
{
public SeqCanvas seqCanvas;
+
public AlignmentPanel ap;
protected int lastres;
+
protected int startseq;
protected AlignViewport av;
- // if character is inserted or deleted, we will need to recalculate the conservation
+ // if character is inserted or deleted, we will need to recalculate the
+ // conservation
boolean seqEditOccurred = false;
ScrollThread scrollThread = null;
+
boolean mouseDragging = false;
+
boolean editingSeqs = false;
+
boolean groupEditing = false;
int oldSeq = -1;
+
boolean changeEndSeq = false;
+
boolean changeStartSeq = false;
+
boolean changeEndRes = false;
+
boolean changeStartRes = false;
+
SequenceGroup stretchGroup = null;
StringBuffer keyboardNo1;
+
StringBuffer keyboardNo2;
boolean mouseWheelPressed = false;
+
Point lastMousePress;
EditCommand editCommand;
StructureSelectionManager ssm;
-
public SeqPanel(AlignViewport avp, AlignmentPanel p)
{
this.av = avp;
@@ -80,8 +114,9 @@ public class SeqPanel
seqCanvas.addMouseMotionListener(this);
seqCanvas.addMouseListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
seqCanvas.repaint();
}
@@ -91,8 +126,8 @@ public class SeqPanel
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null,
- av.getAlignment().getSequences());
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
}
startseq = -1;
@@ -132,12 +167,9 @@ 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();
}
@@ -145,20 +177,20 @@ 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;
}
@@ -172,22 +204,22 @@ 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);
}
@@ -201,7 +233,8 @@ public class SeqPanel
{
ap.scrollUp(false);
}
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+ while (seqCanvas.cursorX < av.getColumnSelection()
+ .adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
@@ -209,7 +242,8 @@ public class SeqPanel
break;
}
}
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+ while (seqCanvas.cursorX > av.getColumnSelection()
+ .adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
{
@@ -217,25 +251,24 @@ 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;
@@ -277,10 +310,10 @@ public class SeqPanel
else
{
// Now add any sequences between min and max
- sg.getSequences(null).removeAllElements();
+ sg.clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
@@ -293,8 +326,8 @@ public class SeqPanel
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
}
-
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
@@ -334,83 +367,143 @@ 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;
}
-
+ /**
+ * 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
+ */
void setStatusMessage(SequenceI sequence, int res, int seq)
{
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
+ // TODO remove duplication of identical gui method
+ StringBuilder text = new StringBuilder(32);
+ 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)
{
-
- if (obj != "")
- {
- text.append(obj + " (" + sequence.findPosition(res) +
- ")");
- }
+ pos = sequence.findPosition(res);
+ text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
+ }
+
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ * @return true if results were matched, false if not
+ */
+ private boolean setStatusMessage(SearchResults results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return false;
+ }
+ 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 true;
+ }
+ }
+ return false;
}
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
- //For now, ignore the mouseWheel font resizing on Macs
- //As the Button2_mask always seems to be true
- if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
- InputEvent.BUTTON2_MASK && !av.MAC)
+ // For now, ignore the mouseWheel font resizing on Macs
+ // As the Button2_mask always seems to be true
+ if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+ && !av.MAC)
{
mouseWheelPressed = true;
return;
}
- if (evt.isShiftDown()
- || evt.isControlDown()
- || evt.isAltDown())
+ if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
{
if (evt.isControlDown() || evt.isAltDown())
{
@@ -432,8 +525,8 @@ 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;
@@ -447,42 +540,41 @@ public class SeqPanel
return;
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup().getSize() == 1
- && av.getSelectionGroup().getEndRes()
- - av.getSelectionGroup().getStartRes() < 2)
+ if (av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() == 1
+ && av.getSelectionGroup().getEndRes()
+ - av.getSelectionGroup().getStartRes() < 2)
{
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(
- sequence,
- sequence.findPosition(findRes(evt))
- );
+ SequenceFeature[] features = findFeaturesAtRes(sequence,
+ sequence.findPosition(findRes(evt)));
if (features != null && features.length > 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence,
- features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features[0].getBegin(),
+ features[0].getEnd());
seqCanvas.highlightSearchResults(highlight);
}
if (features != null && features.length > 0)
{
seqCanvas.getFeatureRenderer().amendFeatures(
- new SequenceI[]
- {sequence}, features, false, ap);
+ new SequenceI[] { sequence }, features, false, ap);
seqCanvas.highlightSearchResults(null);
}
}
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
@@ -500,23 +592,25 @@ public class SeqPanel
}
int startWrapBlock = -1;
+
int wrappedBlock = -1;
+
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;
@@ -539,7 +633,7 @@ public class SeqPanel
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -551,8 +645,9 @@ public class SeqPanel
int findSeq(MouseEvent evt)
{
final int sqnum = findAlRow(evt);
- return (sqnum<0) ? 0 : sqnum;
+ return (sqnum < 0) ? 0 : sqnum;
}
+
/**
*
* @param evt
@@ -563,21 +658,21 @@ 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);
if (seq < 0)
{
seq = -1;
@@ -585,8 +680,8 @@ public class SeqPanel
}
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);
if (seq < 0)
{
seq = -1;
@@ -596,18 +691,16 @@ public class SeqPanel
return seq;
}
-
-
public void doMousePressed(MouseEvent evt)
{
int seq = findSeq(evt);
int res = findRes(evt);
- if (seq < av.getAlignment().getHeight() &&
- res < av.getAlignment().getSequenceAt(seq).getLength())
+ if (seq < av.getAlignment().getHeight()
+ && res < av.getAlignment().getSequenceAt(seq).getLength())
{
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
+ // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
// Find the residue's position in the sequence (res is the position
// in the alignment
@@ -623,29 +716,49 @@ public class SeqPanel
return;
}
-
String lastMessage;
+
+ @Override
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
- String tmp = sequence.hashCode()+index+"";
+ String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
- ssm.mouseOverSequence(sequence, index, pos);
+ {
+ ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
-
+ @Override
public void highlightSequence(SearchResults results)
{
+ if (av.isFollowHighlight())
+ {
+ if (ap.scrollToPosition(results, true))
+ {
+ ap.alignFrame.repaint();
+ }
+ }
+ 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();
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
int res = findRes(evt);
@@ -672,53 +785,53 @@ public class SeqPanel
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(Integer.toString(seq + 1))
+ .append(" ID: ").append(sequence.getName());
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
-
- Object obj = null;
- if (av.alignment.isNucleotide())
+ String obj = null;
+ final String ch = String.valueOf(sequence.getCharAt(res));
+ if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
- "");
+ obj = ResidueProperties.nucleotideName.get(ch);
if (obj != null)
{
- text.append(" Nucleotide: ");
+ text.append(" Nucleotide: ").append(obj);
}
}
else
{
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
+ .get(ch);
if (obj != null)
{
- text.append(" Residue: ");
+ text.append(" Residue: ").append(obj);
}
}
if (obj != null)
{
- if (obj != "")
- {
- text.append(obj + " (" + respos + ")");
- }
+ text.append(" (").append(Integer.toString(respos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
- StringBuffer tooltipText = new StringBuffer();
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ StringBuilder tooltipText = new StringBuilder();
+ 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].getName().startsWith("JTreeGroup") &&
- !groups[g].getName().startsWith("JGroup"))
+ if (!groups[g].getName().startsWith("JTreeGroup")
+ && !groups[g].getName().startsWith("JGroup"))
{
- tooltipText.append(groups[g].getName() + " ");
+ tooltipText.append(groups[g].getName()).append(" ");
}
if (groups[g].getDescription() != null)
{
@@ -730,33 +843,33 @@ public class SeqPanel
}
// use aa to see if the mouse pointer is on a
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
- int index = 0;
- while (index < allFeatures.length)
- {
- SequenceFeature sf = allFeatures[index];
+ int index = 0;
+ while (index < allFeatures.length)
+ {
+ SequenceFeature sf = allFeatures[index];
- tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
- if (sf.getDescription() != null)
- {
- tooltipText.append(" " + sf.getDescription());
- }
+ if (sf.getDescription() != null)
+ {
+ tooltipText.append(" " + sf.getDescription());
+ }
- if (sf.getValue("status") != null)
+ if (sf.getValue("status") != null)
+ {
+ String status = sf.getValue("status").toString();
+ if (status.length() > 0)
{
- String status = sf.getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText.append(" (" + sf.getValue("status") + ")");
- }
+ tooltipText.append(" (" + sf.getValue("status") + ")");
}
- tooltipText.append("\n");
-
- index++;
}
+ tooltipText.append("\n");
+
+ index++;
+ }
if (tooltip == null)
{
@@ -776,23 +889,22 @@ public class SeqPanel
{
for (int i = 0; i < features.length; i++)
{
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
+ if (av.getFeaturesDisplayed() == null
+ || !av.getFeaturesDisplayed().isVisible(
+ 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())
+ && !seqCanvas.fr.checkGroupVisibility(
+ features[i].featureGroup, false))
+ {
continue;
+ }
-
- if ( (features[i].getBegin() <= res) &&
- (features[i].getEnd() >= res))
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
{
tmp.addElement(features[i]);
}
@@ -805,22 +917,30 @@ public class SeqPanel
return features;
}
-
Tooltip tooltip;
+ /**
+ * set when the current UI interaction has resulted in a change that requires
+ * overview shading to be recalculated. this could be changed to something
+ * more expressive that indicates what actually has changed, so selective
+ * redraws can be applied
+ */
+ private boolean needOverviewUpdate; // TODO: refactor to avcontroller
+
+ @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.y)
- > Math.abs(evt.getX() - lastMousePress.x))
+ // Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
+ - lastMousePress.x))
{
int fontSize = av.font.getSize();
- if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
{
fontSize--;
}
@@ -835,29 +955,29 @@ public class SeqPanel
}
av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
- av.charWidth = oldWidth;
+ av.setCharWidth(oldWidth);
}
else
{
- if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
{
- av.charWidth--;
+ av.setCharWidth(av.getCharWidth() - 1);
}
else if (evt.getX() > lastMousePress.x)
{
- av.charWidth++;
+ av.setCharWidth(av.getCharWidth() + 1);
}
- if (av.charWidth < 1)
+ if (av.getCharWidth() < 1)
{
- av.charWidth = 1;
+ av.setCharWidth(1);
}
}
ap.fontChanged();
FontMetrics fm = getFontMetrics(av.getFont());
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
lastMousePress = evt.getPoint();
@@ -879,12 +999,12 @@ 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);
@@ -909,14 +1029,13 @@ public class SeqPanel
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
- if (!groupEditing && av.hasHiddenRows)
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
@@ -924,15 +1043,18 @@ public class SeqPanel
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append("Edit group:");
+ message.append(MessageManager.getString("action.edit_group")).append(
+ ":");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(
+ MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append("Edit sequence: " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence"))
+ .append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
@@ -940,7 +1062,8 @@ public class SeqPanel
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[] { label }));
}
}
@@ -956,33 +1079,33 @@ 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;
@@ -1000,21 +1123,21 @@ 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)
@@ -1030,25 +1153,18 @@ public class SeqPanel
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
- int g, groupSize = vseqs.size();
- SequenceI[] groupSeqs = new SequenceI[groupSize];
- for (g = 0; g < groupSeqs.length; g++)
- {
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
- }
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
+ .toArray(new SequenceI[0]);
// drag to right
if (insertGap)
{
- //If the user has selected the whole sequence, and is dragging to
+ // 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();
}
@@ -1056,18 +1172,16 @@ 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;
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+ - j)))
{
blank = false;
break;
@@ -1082,27 +1196,27 @@ 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;
}
@@ -1117,20 +1231,19 @@ 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++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = startres; j < lastres; j++)
{
- if (groupSeqs[g].getLength() <= j)
+ if (gs.getLength() <= j)
{
continue;
}
- if (!jalview.util.Comparison.isGap(
- groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
@@ -1152,11 +1265,8 @@ public class SeqPanel
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- groupSeqs,
- startres, startres - lastres,
- av.alignment,
- true);
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres, av.getAlignment(), true);
}
}
else
@@ -1171,16 +1281,14 @@ public class SeqPanel
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- groupSeqs,
- startres, lastres - startres,
- av.alignment,
- true);
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres, av.getAlignment(), true);
}
}
}
- else /////Editing a single sequence///////////
+ else
+ // ///Editing a single sequence///////////
{
if (insertGap)
{
@@ -1189,18 +1297,14 @@ 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);
+ editCommand.appendEdit(Action.INSERT_GAP,
+ new SequenceI[] { seq }, lastres, startres - lastres,
+ av.getAlignment(), true);
}
}
else
@@ -1215,13 +1319,12 @@ public class SeqPanel
endEditing();
break;
}
- deleteChar(startres, new SequenceI[]
- {seq}, fixedRight);
+ deleteChar(startres, new SequenceI[] { seq }, fixedRight);
}
}
else
{
- //could be a keyboard edit trying to delete none gaps
+ // could be a keyboard edit trying to delete none gaps
int max = 0;
for (int m = startres; m < lastres; m++)
{
@@ -1234,12 +1337,9 @@ public class SeqPanel
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- new SequenceI[]
- {seq},
- startres, max,
- av.alignment,
- true);
+ editCommand.appendEdit(Action.DELETE_GAP,
+ new SequenceI[] { seq }, startres, max,
+ av.getAlignment(), true);
}
}
}
@@ -1254,14 +1354,14 @@ 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;
}
}
@@ -1274,32 +1374,27 @@ public class SeqPanel
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- blankColumn, 1, av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- j, 1, av.alignment,
- true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
+ true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
- seq,
- j, 1, av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
+ true);
- editCommand.appendEdit(EditCommand.INSERT_GAP,
- seq,
- fixedColumn, 1, av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
+ av.getAlignment(), true);
}
-//////////////////////////////////////////
-/////Everything below this is for defining the boundary of the rubberband
-//////////////////////////////////////////
+ // ////////////////////////////////////////
+ // ///Everything below this is for defining the boundary of the rubberband
+ // ////////////////////////////////////////
public void doMousePressedDefineMode(MouseEvent evt)
{
if (scrollThread != null)
@@ -1318,7 +1413,7 @@ public class SeqPanel
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{
@@ -1329,9 +1424,9 @@ public class SeqPanel
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
- if (stretchGroup != null && res > stretchGroup.getStartRes() &&
- res < stretchGroup.getEndRes())
+ stretchGroup = av.getAlignment().findGroup(sequence);
+ if (stretchGroup != null && res > stretchGroup.getStartRes()
+ && res < stretchGroup.getEndRes())
{
av.setSelectionGroup(stretchGroup);
}
@@ -1342,19 +1437,19 @@ public class SeqPanel
}
else if (!stretchGroup.getSequences(null).contains(sequence)
- || stretchGroup.getStartRes() > res
- || stretchGroup.getEndRes() < res)
+ || 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;
@@ -1365,20 +1460,22 @@ public class SeqPanel
}
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
- InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
- sequence.findPosition(res));
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
- Vector links = null;
+ Vector links = null;
if (allFeatures != null)
{
for (int i = 0; i < allFeatures.length; i++)
{
if (allFeatures[i].links != null)
{
- links = new Vector();
+ if (links == null)
+ {
+ links = new Vector();
+ }
for (int j = 0; j < allFeatures[i].links.size(); j++)
{
links.addElement(allFeatures[i].links.elementAt(j));
@@ -1400,7 +1497,7 @@ public class SeqPanel
return;
}
- //Only if left mouse button do we want to change group sizes
+ // Only if left mouse button do we want to change group sizes
if (stretchGroup == null)
{
@@ -1415,12 +1512,12 @@ public class SeqPanel
if (av.getConservationSelected())
{
SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
- "Background");
+ "Background");
}
if (av.getAbovePIDThreshold())
{
SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ "Background");
}
}
@@ -1432,41 +1529,34 @@ public class SeqPanel
{
return;
}
-
+ // always do this - annotation has own state
+ // but defer colourscheme update until hidden sequences are passed in
+ boolean vischange = stretchGroup.recalcConservation(true);
+ // here we rely on stretchGroup == av.getSelection()
+ needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.hiddenRepSequences),
- stretchGroup.getWidth());
- }
-
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
- }
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
- stretchGroup.recalcConservation();
+ stretchGroup.getName());
}
else
{
SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
+ stretchGroup.getName());
}
}
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ ap.paintAlignment(needOverviewUpdate);
+ needOverviewUpdate = false;
changeEndRes = false;
changeStartRes = false;
stretchGroup = null;
- PaintRefresher.Refresh(ap, av.getSequenceSetId());
- ap.paintAlignment(true);
+ av.sendSelection();
}
public void doMouseDraggedDefineMode(MouseEvent evt)
@@ -1486,14 +1576,14 @@ public class SeqPanel
mouseDragging = true;
- if (y > av.alignment.getHeight())
+ if (y > av.getAlignment().getHeight())
{
- y = av.alignment.getHeight() - 1;
+ y = av.getAlignment().getHeight() - 1;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
@@ -1517,6 +1607,7 @@ public class SeqPanel
if (res > (stretchGroup.getStartRes() - 1))
{
stretchGroup.setEndRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
else if (changeStartRes)
@@ -1524,6 +1615,7 @@ public class SeqPanel
if (res < (stretchGroup.getEndRes() + 1))
{
stretchGroup.setStartRes(res);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
@@ -1538,7 +1630,8 @@ 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.
@@ -1556,6 +1649,7 @@ public class SeqPanel
if (stretchGroup.getSequences(null).contains(nextSeq))
{
stretchGroup.deleteSequence(seq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
else
{
@@ -1565,6 +1659,7 @@ public class SeqPanel
}
stretchGroup.addSequence(nextSeq, false);
+ needOverviewUpdate |= av.isSelectionDefinedGroup();
}
}
@@ -1573,8 +1668,8 @@ public class SeqPanel
oldSeq = -1;
}
- if (res > av.endRes || res < av.startRes
- || y < av.startSeq || y > av.endSeq)
+ if (res > av.endRes || res < av.startRes || y < av.startSeq
+ || y > av.endSeq)
{
mouseExited(evt);
}
@@ -1587,6 +1682,7 @@ public class SeqPanel
seqCanvas.repaint();
}
+ @Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
@@ -1601,6 +1697,7 @@ public class SeqPanel
}
}
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -1639,11 +1736,12 @@ 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()
{
start();
@@ -1659,6 +1757,7 @@ public class SeqPanel
running = false;
}
+ @Override
public void run()
{
running = true;
@@ -1673,8 +1772,8 @@ public class SeqPanel
running = ap.scrollUp(true);
}
- if (mouseDragging && evt.getY() >= getSize().height &&
- av.alignment.getHeight() > av.getEndSeq())
+ if (mouseDragging && evt.getY() >= getSize().height
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
running = ap.scrollUp(false);
}
@@ -1693,11 +1792,199 @@ public class SeqPanel
try
{
Thread.sleep(75);
+ } 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.
+ if (av != null
+ && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId()))))
+ {
+ 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)
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
+ boolean repaint = false;
+ boolean copycolsel = false;
+ if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
+ {
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ if (av.getAlignment() == null)
+ {
+ System.out
+ .println("Selection message: alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId="
+ + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
+ 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);
+ }
+ repaint = av.isSelectionGroupChanged(true);
+ }
+ if (copycolsel
+ && (av.getColumnSelection() == null || !av
+ .isColSelChanged(true)))
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.isEmpty())
+ {
+ if (av.getColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
}
- catch (Exception ex)
- {}
}
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.getColumnSelection() == null)
+ {
+ av.setColumnSelection(new ColumnSelection(colsel));
+ }
+ else
+ {
+ av.getColumnSelection().setElementsFrom(colsel);
+ }
+ }
+ repaint |= av.isColSelChanged(true);
+ }
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint)
+ {
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
+ }
+ }
+
+ /**
+ * scroll to the given row/column - or nearest visible location
+ *
+ * @param row
+ * @param column
+ */
+ public void scrollTo(int row, int column)
+ {
+
+ row = row < 0 ? ap.av.startSeq : row;
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, row, true, true);
+ }
+
+ /**
+ * scroll to the given row - or nearest visible location
+ *
+ * @param row
+ */
+ public void scrollToRow(int row)
+ {
+
+ row = row < 0 ? ap.av.startSeq : row;
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+ }
+
+ /**
+ * scroll to the given column - or nearest visible location
+ *
+ * @param column
+ */
+ public void scrollToColumn(int column)
+ {
+
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, ap.av.startSeq, true, true);
+ }
+
+ /**
+ * 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);
+
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
+
+ return true;
}
}