X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=f2881889cf600ac72b569a81473d2197d30db63d;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=858c055dc3deba637837bfe48dbcca9b99a916e8;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 858c055..f288188 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,32 +1,55 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.util.ParseHtmlBodyAndLinks;
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Vector;
+
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
{
@@ -93,10 +116,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
@@ -217,7 +243,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
return true;
}
else
+ {
return false;
+ }
}
@@ -407,7 +435,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations"));
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
MenuItem item = new MenuItem(ADDNEW);
item.addActionListener(this);
@@ -450,7 +479,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
{
popup.addSeparator();
final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus",
+ MessageManager.getString("label.ignore_gaps_consensus"),
(aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
.getIgnoreGapsConsensus() : ap.av
.getIgnoreGapsConsensus());
@@ -475,7 +504,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
if (aaa.groupRef != null)
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- "Show Group Histogram",
+ MessageManager.getString("label.show_group_histogram"),
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
@@ -494,7 +523,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
});
popup.add(chist);
final CheckboxMenuItem cprofl = new CheckboxMenuItem(
- "Show Group Logo",
+ MessageManager.getString("label.show_group_logo"),
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addItemListener(new ItemListener()
{
@@ -514,7 +543,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
popup.add(cprofl);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- "Normalise Group Logo",
+ MessageManager.getString("label.normalise_group_logo"),
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
@@ -537,7 +566,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
else
{
final CheckboxMenuItem chist = new CheckboxMenuItem(
- "Show Histogram", av.isShowConsensusHistogram());
+ MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
@@ -559,7 +588,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
});
popup.add(chist);
final CheckboxMenuItem cprof = new CheckboxMenuItem(
- "Show Logo", av.isShowSequenceLogo());
+ MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
@@ -582,7 +611,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
});
popup.add(cprof);
final CheckboxMenuItem cprofn = new CheckboxMenuItem(
- "Normalise Logo", av.isNormaliseSequenceLogo());
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
@@ -643,17 +672,40 @@ public class AnnotationLabels extends Panel implements ActionListener,
}
else if (aa[selectedRow].sequenceRef != null)
{
- Vector sr = new Vector();
- sr.addElement(aa[selectedRow].sequenceRef);
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+ ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+ .asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ // we make a copy rather than edit the current selection if no modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(evt.isControlDown() || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ } else {
+ if (evt.isControlDown())
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ } else {
+ // notionally, we should also add intermediate sequences from last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ } else {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
ap.av.setSelectionGroup(sg);
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
@@ -685,11 +737,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
if (av.hasHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(i);
-
jalview.appletgui.AlignFrame.copiedHiddenColumns
.addElement(new int[]
{ region[0], region[1] });
@@ -768,7 +817,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
{
g.setColor(Color.black);
g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
}
}