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JAL-2805 couple of method name changes
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
d740303
..
1c19eb1
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-35,7
+35,6
@@
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
@@
-61,6
+60,9
@@
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.ext.forester.io.ExternalTreeParserI;
+import jalview.ext.forester.io.ForesterTreeParser;
+import jalview.ext.forester.io.SupportedTreeFileFilter;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
@@
-164,8
+166,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignViewport viewport;
AlignViewport viewport;
- ViewportRanges vpRanges;
-
public AlignViewControllerI avc;
List<AlignmentPanel> alignPanels = new ArrayList<>();
public AlignViewControllerI avc;
List<AlignmentPanel> alignPanels = new ArrayList<>();
@@
-337,7
+337,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
- vpRanges = viewport.getRanges();
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
avc = new jalview.controller.AlignViewController(this, viewport,
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
@@
-655,9
+654,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+ ViewportRanges ranges = viewport.getRanges();
+ alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
.getStartRes();
.getStartRes();
- alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+ alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
.getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
.getStartSeq();
}
alignPanel.getSeqPanel().seqCanvas.repaint();
@@
-690,10
+690,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
break;
}
case KeyEvent.VK_PAGE_UP:
break;
}
case KeyEvent.VK_PAGE_UP:
- vpRanges.pageUp();
+ viewport.getRanges().pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
break;
case KeyEvent.VK_PAGE_DOWN:
- vpRanges.pageDown();
+ viewport.getRanges().pageDown();
break;
}
}
break;
}
}
@@
-1712,7
+1712,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
synchronized void slideSequences(boolean right, int size)
}
synchronized void slideSequences(boolean right, int size)
@@
-2148,7
+2148,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
// propagate alignment changed.
{
// propagate alignment changed.
- vpRanges.setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight());
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
@@
-2398,7
+2398,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
}
}
@@
-2424,7
+2424,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
}
@@
-2449,7
+2449,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@@
-2480,7
+2480,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// alignPanel to decide if overview needs
// updating.
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
@@
-2489,7
+2489,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
viewport.sendSelection();
}
viewport.sendSelection();
}
@@
-2549,7
+2549,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
{
trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
column, viewport.getAlignment());
- vpRanges.setStartRes(0);
+ viewport.getRanges().setStartRes(0);
}
else
{
}
else
{
@@
-2614,13
+2614,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(vpRanges.getStartRes());
+ ViewportRanges ranges = viewport.getRanges();
+ int startRes = seq.findPosition(ranges.getStartRes());
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
// ShiftList shifts;
// viewport.getAlignment().removeGaps(shifts=new ShiftList());
// edit.alColumnChanges=shifts.getInverse();
// if (viewport.hasHiddenColumns)
// viewport.getColumnSelection().compensateForEdits(shifts);
- vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+ ranges.setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
@@
-2653,12
+2654,12
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
// This is to maintain viewport position on first residue
// of first sequence
SequenceI seq = viewport.getAlignment().getSequenceAt(0);
- int startRes = seq.findPosition(vpRanges.getStartRes());
+ int startRes = seq.findPosition(viewport.getRanges().getStartRes());
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
viewport.getAlignment()));
- vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+ viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
@@
-2714,8
+2715,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
if (!copyAnnotation)
{
/*
@@
-2869,21
+2869,21
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.getIdPanel().getIdCanvas()
.setPreferredSize(alignPanel.calculateIdWidth());
alignPanel.getIdPanel().getIdCanvas()
.setPreferredSize(alignPanel.calculateIdWidth());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.setRightAlignIds(idRightAlign.isSelected());
}
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
viewport.setRightAlignIds(idRightAlign.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
}
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/*
}
/*
@@
-2916,7
+2916,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setColourText(colourTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
}
/**
@@
-2945,7
+2945,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
viewport.sendSelection();
}
@@
-3049,7
+3049,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
viewport.sendSelection();
}
@@
-3065,7
+3065,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
viewport.sendSelection();
}
@@
-3073,7
+3073,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
viewport.sendSelection();
}
@@
-3094,7
+3094,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- alignPanel.paintAlignment(true);
+ // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3107,7
+3108,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3120,7
+3121,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3133,7
+3134,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
}
/**
@@
-3146,7
+3147,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowText(viewTextMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
}
/**
@@
-3159,7
+3160,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
viewport.setRenderGaps(renderGapsMenuItem.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
public FeatureSettings featureSettings;
}
public FeatureSettings featureSettings;
@@
-3197,7
+3198,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
/**
}
/**
@@
-3354,7
+3355,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setGlobalColourScheme(cs);
viewport.setGlobalColourScheme(cs);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
/**
}
/**
@@
-3439,7
+3440,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
viewport.getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3455,7
+3456,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3471,7
+3472,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3488,7
+3489,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
}
/**
@@
-3554,7
+3555,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.followSelection = listenToViewSelections.isSelected();
}
viewport.followSelection = listenToViewSelections.isSelected();
}
-
/**
* Constructs a tree panel and adds it to the desktop
*
/**
* Constructs a tree panel and adds it to the desktop
*
@@
-3566,7
+3566,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
*/
void newTreePanel(TreeModel tree, String treeAlgo,
*
*/
void newTreePanel(TreeModel tree, String treeAlgo,
- SimilarityParamsI params)
+ String substitutionMatrix)
{
String frameTitle = "";
TreePanel tp;
{
String frameTitle = "";
TreePanel tp;
@@
-3578,7
+3578,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s : sg.getSequences())
+ for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
{
if (_s.getLength() < sg.getEndRes())
{
{
if (_s.getLength() < sg.getEndRes())
{
@@
-3602,7
+3602,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
- tp = new TreePanel(alignPanel, tree, treeAlgo, params);
+ tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
@@
-3646,7
+3646,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(new OrderCommand(order.getName(), oldOrder,
viewport.getAlignment()));
addHistoryItem(new OrderCommand(order.getName(), oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
});
}
}
});
}
@@
-3675,7
+3675,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
viewport.getAlignment()));
viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
});
}
}
});
}
@@
-3790,7
+3790,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
return true;
}
return true;
}
@@
-3885,9
+3885,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
- MessageManager.getString("label.select_newick_like_tree_file"));
+ MessageManager.getString("label.select_newick_like_tree_file")); // modify
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
+ for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter.values())
+ {
+ chooser.setFileFilter(treeFormat.getTreeFilter());
+ }
int value = chooser.showOpenDialog(null);
int value = chooser.showOpenDialog(null);
@@
-3895,9
+3899,16
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
+
NewickFile fin = null;
try
{
NewickFile fin = null;
try
{
+ ExternalTreeParserI<?> treeParser = new ForesterTreeParser(
+ filePath);
+ treeParser.loadTreeFile(viewport);
+
+
+
fin = new NewickFile(filePath, DataSourceType.FILE);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
fin = new NewickFile(filePath, DataSourceType.FILE);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
@@
-3918,6
+3929,18
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
+ @Override
+ protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ @Override
+ protected void loadTreeDbItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
{
return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
{
return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
@@
-4156,7
+4179,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildingMenu = false;
}
}
buildingMenu = false;
}
- }).start();
+ }, "BuildWebServiceThread").start();
}
}
@@
-4264,7
+4287,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
+ "CrossReferencesThread")
.start();
}
.start();
}
@@
-4508,7
+4532,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
assocfiles++;
}
}
assocfiles++;
}
}
- alignPanel.paintAlignment(true);
+ // TODO: do we need to update overview ? only if features are
+ // shown I guess
+ alignPanel.paintAlignment(true, false);
}
}
}
}
}
}
@@
-4541,7
+4567,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFileThread").start();
}
}
}
}
@@
-4655,7
+4681,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (parseFeaturesFile(file, sourceType))
{
{
if (parseFeaturesFile(file, sourceType))
{
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
else
}
}
else
@@
-4670,7
+4696,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
alignPanel.adjustAnnotationHeight();
viewport.updateSequenceIdColours();
buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
@@
-4912,7
+4938,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
dbRefFetcher.fetchDBRefs(false);
}
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenuThread").start();
}
}
@@
-5195,7
+5221,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
viewport.setShowUnconserved(showNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/*
}
/*
@@
-5284,7
+5310,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
}
}
@@
-5296,7
+5322,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
viewport.getAlignment().setSeqrep(null);
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
}
}
@@
-5386,7
+5412,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
/**
}
/**