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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
143e672
..
1c19eb1
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-26,6
+26,7
@@
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
@@
-34,7
+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;
@@
-60,6
+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;
@@
-163,8
+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<>();
@@
-336,7
+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)
@@
-654,9
+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();
@@
-689,10
+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;
}
}
@@
-2147,7
+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.
@@
-2548,7
+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
{
@@
-2613,13
+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());
@@
-2652,12
+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());
@@
-2713,8
+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)
{
/*
@@
-3557,15
+3558,15
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/**
* Constructs a tree panel and adds it to the desktop
*
/**
* Constructs a tree panel and adds it to the desktop
*
- * @param type
- * tree type (NJ or AV)
- * @param modelName
- * name of score model used to compute the tree
- * @param options
- * parameters for the distance or similarity calculation
+ * @param params
+ * @param treeAlgo
+ *
+ * @param tree
+ *
+ *
*/
*/
- void newTreePanel(String type, String modelName,
- SimilarityParamsI options)
+ void newTreePanel(TreeModel tree, String treeAlgo,
+ String substitutionMatrix)
{
String frameTitle = "";
TreePanel tp;
{
String frameTitle = "";
TreePanel tp;
@@
-3577,7
+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())
{
@@
-3601,7
+3602,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
- tp = new TreePanel(alignPanel, type, modelName, options);
+ tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
@@
-3884,9
+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);
@@
-3894,9
+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)
@@
-3917,6
+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);
@@
-4032,6
+4056,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
final JMenu analymenu = new JMenu("Analysis");
final JMenu dismenu = new JMenu("Protein Disorder");
+ final JMenu phylogenmenu = new JMenu("Phylogenetic inference");
+
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
// JAL-940 - only show secondary structure prediction services from
// the legacy server
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@
-4072,6
+4098,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
wsmenu.add(secstrmenu);
wsmenu.add(dismenu);
wsmenu.add(analymenu);
+ wsmenu.add(phylogenmenu);
// No search services yet
// wsmenu.add(seqsrchmenu);
// No search services yet
// wsmenu.add(seqsrchmenu);
@@
-4152,7
+4179,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildingMenu = false;
}
}
buildingMenu = false;
}
- }).start();
+ }, "BuildWebServiceThread").start();
}
}
@@
-4260,7
+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();
}
@@
-4539,7
+4567,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFileThread").start();
}
}
}
}
@@
-4910,7
+4938,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
dbRefFetcher.fetchDBRefs(false);
}
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenuThread").start();
}
}