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Undo changes to JabaWsServerQuery.java
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
cc1703c
..
34ec2cf
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-21,7
+21,6
@@
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
@@
-56,7
+55,6
@@
import jalview.schemes.PIDColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.RNAInteractionColourScheme;
import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.RNAHelicesColourChooser;
import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
@@
-324,7
+322,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
+ {
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
switch (evt.getKeyCode())
{
@@
-385,16
+385,24
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
else
+ {
alignPanel.seqPanel.moveCursor(1, 0);
alignPanel.seqPanel.moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
break;
case KeyEvent.VK_SPACE:
@@
-1257,7
+1265,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
else
{
if (features == null)
else
{
if (features == null)
+ {
features = "";
features = "";
+ }
}
return features;
}
return features;
@@
-1573,7
+1583,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
@@
-1581,30
+1593,44
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
.size()]);
for (int i = 0; i < invertGroup.size(); i++)
SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
.size()]);
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = invertGroup.elementAt(i);
seqs2[i] = invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(size, 0);
alignPanel.seqPanel.moveCursor(size, 0);
+ }
else
else
+ {
groupAdjustment = size;
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(-size, 0);
alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
else
+ {
groupAdjustment = -size;
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
}
if (groupAdjustment != 0)
@@
-1625,7
+1651,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
if (!appendHistoryItem)
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
addHistoryItem(ssc);
+ }
repaint();
}
repaint();
}
@@
-1763,14
+1791,14
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (newAlignment)
{
if (newAlignment)
{
- String newtitle = new String("Copied sequences");
- if (getTitle().startsWith("Copied sequences"))
+ String newtitle = MessageManager.getString("label.copied_sequences");
+ if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
{
newtitle = getTitle();
}
else
{
{
newtitle = getTitle();
}
else
{
- newtitle = newtitle.concat("- from " + getTitle());
+ newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
@@
-1805,7
+1833,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
// !newAlignment
}
// !newAlignment
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
@@
-1855,7
+1883,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
/*
* //ADD HISTORY ITEM
*/
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
+ addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
viewport.getAlignment()));
@@
-2780,10
+2808,10
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
- MessageManager.getString("label.export_features"));
+ MessageManager.getString("label.export_features").concat("..."));
MenuItem outputAnnotations = new MenuItem(
MenuItem outputAnnotations = new MenuItem(
- MessageManager.getString("label.export_annotations"));
+ MessageManager.getString("label.export_annotations").concat("..."));
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
MenuItem closeMenuItem = new MenuItem(
MessageManager.getString("action.close"));
@@
-3043,7
+3071,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel(MessageManager
sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
sortGroupMenuItem.addActionListener(this);
removeRedundancyMenuItem.setLabel(MessageManager
- .getString("action.remove_redundancy"));
+ .getString("action.remove_redundancy").concat("..."));
removeRedundancyMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(MessageManager
.getString("action.pairwise_alignment"));
removeRedundancyMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(MessageManager
.getString("action.pairwise_alignment"));
@@
-3656,6
+3684,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
+ alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
return true;
}
}
return true;