X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=090779e06d7d06bfa5ca60565593c52e26f3e2a5;hb=c94c1390298db2e80abc04b371d3e7767f5e5968;hp=6486647d0e62df79a6cd3da00c0a5f488e56df7d;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
old mode 100755
new mode 100644
index 6486647..090779e
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,35 +1,58 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * 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.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;
+import jalview.structure.VamsasSource;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
+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.List;
+import java.util.Vector;
public class SeqPanel extends Panel implements MouseMotionListener,
- MouseListener, SequenceListener
+ MouseListener, SequenceListener, SelectionListener
{
public SeqCanvas seqCanvas;
@@ -90,8 +113,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
seqCanvas.addMouseMotionListener(this);
seqCanvas.addMouseListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
seqCanvas.repaint();
}
@@ -142,10 +166,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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();
}
@@ -153,19 +176,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
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)
+ 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;
}
@@ -179,22 +203,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
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);
}
@@ -208,7 +232,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
ap.scrollUp(false);
}
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
@@ -217,7 +241,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
@@ -226,7 +250,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
@@ -234,17 +258,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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;
+ SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ 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;
@@ -286,10 +309,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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);
}
}
}
@@ -302,8 +325,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
sg.addSequence(sequence, false);
av.setSelectionGroup(sg);
}
-
ap.paintAlignment(false);
+ av.sendSelection();
}
void insertGapAtCursor(boolean group)
@@ -343,63 +366,139 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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)
- {
- text.append(" Residue: ");
- }
- }
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ResidueProperties.aa2Triplet.get(displayChar);
+ if (residue != null)
+ {
+ text.append(" Residue: ").append(residue);
+ }
+ }
+
+ int pos = -1;
+ if (residue != null)
+ {
+ pos = sequence.findPosition(res);
+ text.append(" (").append(Integer.toString(pos)).append(")");
+ }
+ // Object obj = null;
+ // if (av.getAlignment().isNucleotide())
+ // {
+ // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ // + "");
+ // if (obj != null)
+ // {
+ // text.append(" Nucleotide: ");
+ // }
+ // }
+ // else
+ // {
+ // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ // if (obj != null)
+ // {
+ // text.append(" Residue: ");
+ // }
+ // }
+ //
+ // if (obj != null)
+ // {
+ //
+ // if (obj != "")
+ // {
+ // text.append(obj + " (" + sequence.findPosition(res) + ")");
+ // }
+ // }
- if (obj != null)
- {
+ ap.alignFrame.statusBar.setText(text.toString());
- if (obj != "")
- {
- text.append(obj + " (" + sequence.findPosition(res) + ")");
- }
- }
+ }
- ap.alignFrame.statusBar.setText(text.toString());
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResults results)
+ {
+ List matches = results.getResults();
+ if (!matches.isEmpty())
+ {
+ Match m = matches.get(0);
+ SequenceI seq = m.getSequence();
+ int sequenceIndex = this.av.getAlignment().findIndex(seq);
+ /*
+ * Convert position in sequence (base 1) to sequence character array index
+ * (base 0)
+ */
+ int start = m.getStart() - 1;
+ setStatusMessage(seq, start, sequenceIndex);
+ }
}
public void mousePressed(MouseEvent evt)
@@ -454,24 +553,25 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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
+ 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)
@@ -509,16 +609,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
int y = evt.getY();
@@ -542,7 +643,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -567,20 +668,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap
+ seqCanvas.getAnnotationHeight();
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
.getHeight() - 1);
if (seq < 0)
{
@@ -589,8 +691,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
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;
@@ -631,18 +733,31 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
String tmp = sequence.hashCode() + index + "";
if (lastMessage == null || !lastMessage.equals(tmp))
- ssm.mouseOverSequence(sequence, index, pos);
+ {
+ ssm.mouseOverSequence(sequence, index, pos, av);
+ }
lastMessage = tmp;
}
public void highlightSequence(SearchResults results)
{
- seqCanvas.highlightSearchResults(results);
if (av.followHighlight)
{
- ap.scrollToPosition(results);
+ 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;
}
public void updateColours(SequenceI seq, int index)
@@ -677,42 +792,43 @@ public class SeqPanel extends Panel implements MouseMotionListener,
int respos = sequence.findPosition(res);
if (ssm != null)
+ {
mouseOverSequence(sequence, res, respos);
+ }
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
- + sequence.getName());
+ StringBuilder text = new StringBuilder();
+ text.append("Sequence ").append(Integer.toString(seq + 1))
+ .append(" ID: ").append(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++)
@@ -722,7 +838,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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)
{
@@ -734,8 +850,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
// 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)
@@ -780,19 +896,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
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))
@@ -814,7 +928,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
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()
@@ -822,7 +936,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
int fontSize = av.font.getSize();
- if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
{
fontSize--;
}
@@ -836,32 +950,30 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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));
+ 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();
@@ -913,14 +1025,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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;
}
}
@@ -928,15 +1039,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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)
{
@@ -944,7 +1058,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage(
+ "label.edit_params", new String[]
+ { label }));
}
}
@@ -962,7 +1078,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences)
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
@@ -971,14 +1087,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// 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();
@@ -1005,7 +1120,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
@@ -1035,13 +1150,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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)
@@ -1049,9 +1159,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// 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)
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
@@ -1063,12 +1173,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
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;
@@ -1083,19 +1193,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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;
@@ -1120,16 +1231,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// / 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();
@@ -1151,8 +1262,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
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
@@ -1167,8 +1278,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
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);
}
}
@@ -1189,8 +1300,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
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
@@ -1224,8 +1335,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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);
}
}
}
@@ -1260,10 +1371,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
- 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,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
true);
}
@@ -1271,11 +1382,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+ 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);
}
// ////////////////////////////////////////
@@ -1299,7 +1410,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if (sequence == null || res > sequence.getLength())
{
@@ -1310,7 +1421,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if (stretchGroup != null && res > stretchGroup.getStartRes()
&& res < stretchGroup.getEndRes())
{
@@ -1328,7 +1439,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
@@ -1348,8 +1459,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// DETECT RIGHT MOUSE BUTTON IN AWT
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;
if (allFeatures != null)
@@ -1416,33 +1527,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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.recalcConservation();
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
else
{
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup
- .getName());
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
}
}
changeEndRes = false;
@@ -1450,6 +1550,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
stretchGroup = null;
PaintRefresher.Refresh(ap, av.getSequenceSetId());
ap.paintAlignment(true);
+ av.sendSelection();
}
public void doMouseDraggedDefineMode(MouseEvent evt)
@@ -1469,14 +1570,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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)
@@ -1521,7 +1622,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
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.
@@ -1658,7 +1760,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
if (mouseDragging && evt.getY() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
running = ap.scrollUp(false);
}
@@ -1684,4 +1786,189 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
+ /**
+ * modify current selection according to a received message.
+ */
+ 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 && ((AlignViewport) 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)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ 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)
+ && (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);
+ }
+ 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.size() == 0)
+ {
+ if (av.getColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
+ }
+ }
+ 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);
+ av.isColSelChanged(true);
+
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
+
+ return true;
+ }
+
}