- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.bin.JalviewLite;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
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.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.ZappoColourScheme;
import jalview.structure.StructureSelectionManager;
.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()))
- String annotation = new AnnotationFile().printAnnotations(
- viewport.showAnnotation ? viewport.getAlignment()
- .getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), ((Alignment) viewport
- .getAlignment()).alignmentProperties);
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(viewport);
+ appendProtocol(viewport.applet.getParameter("file")));
if (viewport.applet.getParameter("features") != null)
+ appendProtocol(viewport.applet.getParameter("file")));
if (viewport.applet.getParameter("features") != null)
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)))
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++)
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
copiedHiddenColumns.addElement(new int[]
{ region[0] - hiddenOffset, region[1] - hiddenOffset });
copiedHiddenColumns.addElement(new int[]
{ region[0] - hiddenOffset, region[1] - hiddenOffset });
- 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")))
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
- addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"), Action.PASTE,
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
seqs, 0, viewport.getAlignment().getWidth(),
viewport.getAlignment()));
- addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
- sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
MessageManager.getString("label.load_features_annotations"));
MenuItem outputFeatures = new MenuItem(
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
removeRedundancyMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(MessageManager
.getString("action.pairwise_alignment"));
removeRedundancyMenuItem.addActionListener(this);
pairwiseAlignmentMenuItem.setLabel(MessageManager
.getString("action.pairwise_alignment"));
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
annotationColour.addActionListener(this);
annotationColour.setLabel(MessageManager
.getString("action.by_annotation"));
annotationColour.addActionListener(this);
invertSequenceMenuItem.setLabel(MessageManager
.getString("action.invert_sequence_selection"));
invertColSel.setLabel(MessageManager
invertSequenceMenuItem.setLabel(MessageManager
.getString("action.invert_sequence_selection"));
invertColSel.setLabel(MessageManager
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);
}
pdbentry.getProperty().put("protocol", protocol);
toaddpdb.addPDBId(pdbentry);