import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.analysis.ScoreModelI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.commands.OrderCommand;
import jalview.commands.RemoveGapColCommand;
import jalview.commands.RemoveGapsCommand;
import java.io.File;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
.getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
.getKeyCode() <= KeyEvent.VK_NUMPAD9))
&& Character.isDigit(evt.getKeyChar()))
+ {
alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+ }
switch (evt.getKeyCode())
{
case KeyEvent.VK_DOWN:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(false);
+ }
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(0, 1);
+ }
break;
case KeyEvent.VK_UP:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
moveSelectedSequences(true);
+ }
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(0, -1);
+ }
break;
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(-1, 0);
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+ }
else
+ {
alignPanel.seqPanel.moveCursor(1, 0);
+ }
break;
case KeyEvent.VK_SPACE:
{
case KeyEvent.VK_LEFT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
case KeyEvent.VK_RIGHT:
if (evt.isAltDown() || !viewport.cursorMode)
+ {
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
+ }
break;
}
}
scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
/*
- * Show/hide all annotations only enabled if annotation panel is shown
+ * Show/hide annotations only enabled if annotation panel is shown
*/
- showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
if (viewport.historyList.size() > 0)
{
undoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.historyList.peek();
+ CommandI command = viewport.historyList.peek();
undoMenuItem.setText(MessageManager.formatMessage(
"label.undo_command", new String[]
{ command.getDescription() }));
{
redoMenuItem.setEnabled(true);
- CommandI command = (CommandI) viewport.redoList.peek();
+ CommandI command = viewport.redoList.peek();
redoMenuItem.setText(MessageManager.formatMessage(
"label.redo_command", new String[]
{ command.getDescription() }));
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
if (viewport.historyList.empty())
+ {
return;
- CommandI command = (CommandI) viewport.historyList.pop();
+ }
+ CommandI command = viewport.historyList.pop();
viewport.redoList.push(command);
command.undoCommand(getViewAlignments());
return;
}
- CommandI command = (CommandI) viewport.redoList.pop();
+ CommandI command = viewport.redoList.pop();
viewport.historyList.push(command);
command.doCommand(getViewAlignments());
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
{
if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+ {
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+ }
}
SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
+ {
seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+ }
SlideSequencesCommand ssc;
if (right)
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
size, viewport.getGapCharacter());
+ }
else
+ {
ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
size, viewport.getGapCharacter());
+ }
int groupAdjustment = 0;
if (ssc.getGapsInsertedBegin() && right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(size, 0);
+ }
else
+ {
groupAdjustment = size;
+ }
}
else if (!ssc.getGapsInsertedBegin() && !right)
{
if (viewport.cursorMode)
+ {
alignPanel.seqPanel.moveCursor(-size, 0);
+ }
else
+ {
groupAdjustment = -size;
+ }
}
if (groupAdjustment != 0)
}
if (!appendHistoryItem)
+ {
addHistoryItem(ssc);
+ }
repaint();
}
// /////
// ADD HISTORY ITEM
//
- addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE,
sequences, 0, alignment.getWidth(), alignment));
}
// Add any annotations attached to sequences
{
AlignmentAnnotation sann[] = sequences[i].getAnnotation();
if (sann == null)
+ {
continue;
+ }
for (int avnum = 0; avnum < alview.length; avnum++)
{
if (alview[avnum] != alignment)
/*
* //ADD HISTORY ITEM
*/
- addHistoryItem(new EditCommand(MessageManager.getString("label.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,
viewport.getAlignment()));
viewport.setSelectionGroup(null);
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
alignPanel.setAnnotationVisible(setVisible);
- this.showAllAnnotations.setEnabled(setVisible);
- this.hideAllAnnotations.setEnabled(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
}
@Override
*/
msa = viewport.getAlignmentView(true);
}
+ else if (viewport.getSelectionGroup() != null
+ && viewport.getSelectionGroup().getSize() == 1)
+ {
+ int option = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.oneseq_msainput_selection"),
+ MessageManager.getString("label.invalid_selection"),
+ JOptionPane.OK_CANCEL_OPTION);
+ if (option == JOptionPane.OK_OPTION)
+ {
+ msa = viewport.getAlignmentView(false);
+ }
+
+ }
else
{
/*
if (ds.getSequences() == null
|| !ds.getSequences().contains(
sprods[s].getDatasetSequence()))
+ {
ds.addSequence(sprods[s].getDatasetSequence());
+ }
sprods[s].updatePDBIds();
}
Alignment al = new Alignment(sprods);
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
}
/**
- * Action on selection of menu option to Show or Hide all annotations.
+ * Action on selection of menu options to Show or Hide annotations.
*
- * @param visibile
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
@Override
- protected void setAllAnnotationsVisibility(boolean visible)
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
.getAlignmentAnnotation())
{
- aa.visible = visible;
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
+ {
+ aa.visible = visible;
+ }
}
- this.alignPanel.paintAlignment(true);
+ alignPanel.validateAnnotationDimensions(false);
+ alignPanel.alignmentChanged();
+ }
+
+ /**
+ * Store selected annotation sort order for the view and repaint.
+ */
+ @Override
+ protected void sortAnnotations_actionPerformed()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ *
+ * @return alignment panels in this alignemnt frame
+ */
+ public List<AlignmentViewPanel> getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
}
}
git://source.jalview.org / jalview.git / blobdiff