X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ca4b88073df161ebf2b91432c43de04fd2f90fdc;hb=1d534b200f4a912f02f869c9d860f462511ea46f;hp=131e79e1529ac8827b0dcee0a51dd7b63eabf258;hpb=25e662ba13098a2a0085b44c44bd1193d683e3d7;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 131e79e..ca4b880 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.gui;
@@ -31,12 +30,15 @@ import javax.swing.*;
import javax.swing.event.MenuEvent;
import jalview.analysis.*;
+import jalview.bin.Cache;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
/**
* DOCUMENT ME!
@@ -406,39 +408,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
-
- boolean hide = false;
-
- SequenceGroup sg = viewport.getSelectionGroup();
- if (toggleSeqs)
- {
- if (sg != null
- && sg.getSize() != viewport.alignment.getHeight())
- {
- hideSelSequences_actionPerformed(null);
- hide = true;
- }
- else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
- {
- showAllSeqs_actionPerformed(null);
- }
- }
-
- if (toggleCols)
- {
- if (viewport.colSel.getSelected().size() > 0)
- {
- hideSelColumns_actionPerformed(null);
- if (!toggleSeqs)
- {
- viewport.selectionGroup = sg;
- }
- }
- else if (!hide)
- {
- showAllColumns_actionPerformed(null);
- }
- }
+ toggleHiddenRegions(toggleSeqs, toggleCols);
break;
}
case KeyEvent.VK_PAGE_UP:
@@ -546,32 +516,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
- // Do this once to get current state
- BuildWebServiceMenu();
- Desktop.discoverer
- .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+ Desktop.instance.addJalviewPropertyChangeListener("services",
+ thisListener = new java.beans.PropertyChangeListener()
{
public void propertyChange(PropertyChangeEvent evt)
{
- // System.out.println("Discoverer property change.");
- if (evt.getPropertyName().equals("services"))
+ // // System.out.println("Discoverer property change.");
+ // if (evt.getPropertyName().equals("services"))
{
- // System.out.println("Rebuilding web service menu");
- BuildWebServiceMenu();
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ public void run()
+ {
+ System.err
+ .println("Rebuild WS Menu for service change");
+ BuildWebServiceMenu();
+ }
+
+ });
}
}
});
-
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
- Desktop.discoverer.removePropertyChangeListener(thisListener);
+ System.out.println("deregistering discoverer listener");
+ Desktop.instance.removeJalviewPropertyChangeListener("services",
+ thisListener);
closeMenuItem_actionPerformed(true);
};
});
+ // Finally, build the menu once to get current service state
+ new Thread(new Runnable()
+ {
+ public void run()
+ {
+ BuildWebServiceMenu();
+ }
+ }).start();
}
public void setGUINucleotide(boolean nucleotide)
@@ -579,7 +564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
showTranslation.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
-
+ showGroupConservation.setEnabled(!nucleotide);
// Remember AlignFrame always starts as protein
if (!nucleotide)
{
@@ -621,9 +606,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
annotationPanelMenuItem.setState(av.showAnnotation);
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
- showUnconservedMenuItem.setSelected(av.showUnconserved);
+ showNonconservedMenuItem.setSelected(av.showUnconserved);
showGroupConsensus.setSelected(av.showGroupConsensus);
showGroupConservation.setSelected(av.showGroupConservation);
+ showConsensusHistogram.setSelected(av.showConsensusHistogram);
+ showSequenceLogo.setSelected(av.showSequenceLogo);
setColourSelected(ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
@@ -654,20 +641,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
JPanel progressPanel;
+ Long lId = new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
- if (progressBars.get(new Long(id)) != null)
+ if (progressBars.get(lId) != null)
{
progressPanel = (JPanel) progressBars.get(new Long(id));
statusPanel.remove(progressPanel);
- progressBars.remove(progressPanel);
+ progressBars.remove(lId);
progressPanel = null;
if (message != null)
{
statusBar.setText(message);
}
- if (progressBarHandlers.contains(new Long(id)))
+ if (progressBarHandlers.contains(lId))
{
- progressBarHandlers.remove(new Long(id));
+ progressBarHandlers.remove(lId);
}
layout.setRows(layout.getRows() - 1);
}
@@ -684,7 +672,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
layout.setRows(layout.getRows() + 1);
statusPanel.add(progressPanel);
- progressBars.put(new Long(id), progressPanel);
+ progressBars.put(lId, progressPanel);
}
// update GUI
setMenusForViewport();
@@ -711,8 +699,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void actionPerformed(ActionEvent e)
{
handler.cancelActivity(id);
- us.setProgressBar("Cancelled "
- + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+ us.setProgressBar(
+ "Cancelled "
+ + ((JLabel) progressPanel.getComponent(0))
+ .getText(), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
@@ -759,6 +749,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (fileName != null)
{
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
if (currentFileFormat.equals("Jalview"))
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -793,7 +785,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
protocol, currentFileFormat);
newframe.setBounds(bounds);
-
+ if (featureSettings != null && featureSettings.isShowing())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
+ }
this.closeMenuItem_actionPerformed(true);
}
}
@@ -832,8 +840,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
public void saveAs_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"),
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
currentFileFormat, false);
@@ -895,9 +903,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
{
- warningMessage("Cannot save file "
- + fileName + " using format " + format,
- "Alignment output format not supported");
+ warningMessage("Cannot save file " + fileName + " using format "
+ + format, "Alignment output format not supported");
saveAs_actionPerformed(null);
// JBPNote need to have a raise_gui flag here
return false;
@@ -964,10 +971,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
if (new jalview.util.Platform().isHeadless())
{
- System.err.println("Warning: "+title+"\nWarning: "+warning);
-
- } else {
- JOptionPane.showInternalMessageDialog(this,warning,title,JOptionPane.WARNING_MESSAGE);
+ System.err.println("Warning: " + title + "\nWarning: " + warning);
+
+ }
+ else
+ {
+ JOptionPane.showInternalMessageDialog(this, warning, title,
+ JOptionPane.WARNING_MESSAGE);
}
return;
}
@@ -1001,11 +1011,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + e.getActionCommand(), 600, 500);
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- viewport.alignment, omitHidden, viewport.colSel));
+ try
+ {
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+ viewport.alignment, omitHidden, viewport.colSel));
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+ cap.dispose();
+ }
+
}
/**
@@ -1016,9 +1034,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
- .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer());
+ new HTMLOutput(alignPanel,
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
}
public void createImageMap(File file, String image)
@@ -1074,7 +1092,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void exportAnnotations_actionPerformed(ActionEvent e)
{
- new AnnotationExporter().exportAnnotations(alignPanel,
+ new AnnotationExporter().exportAnnotations(
+ alignPanel,
viewport.showAnnotation ? viewport.alignment
.getAlignmentAnnotation() : null, viewport.alignment
.getGroups(),
@@ -1084,8 +1103,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void associatedData_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Load Jalview Annotations or Features File");
chooser.setToolTipText("Load Jalview Annotations / Features file");
@@ -1216,7 +1235,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ viewport.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
}
}
@@ -1263,7 +1284,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
@@ -1291,7 +1314,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (originalSource != null)
{
- originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
@@ -1519,11 +1544,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.gui.Desktop.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
- new StringSelection(""), null);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(""), null);
- Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(ss, Desktop.instance);
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
@@ -1534,15 +1559,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.hasHiddenColumns)
{
hiddenColumns = new Vector();
- int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+ .getSelectionGroup().getEndRes();
for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
.size(); i++)
{
int[] region = (int[]) viewport.getColumnSelection()
.getHiddenColumns().elementAt(i);
-
- hiddenColumns.addElement(new int[]
- { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+ {
+ hiddenColumns.addElement(new int[]
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });
+ }
}
}
@@ -1783,8 +1811,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildSortByAnnotationScoresMenu();
}
- viewport.firePropertyChange("alignment", null, alignment
- .getSequences());
+ viewport.firePropertyChange("alignment", null,
+ alignment.getSequences());
}
else
@@ -2368,6 +2396,116 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.paintAlignment(true);
}
+ /**
+ * called by key handler and the hide all/show all menu items
+ *
+ * @param toggleSeqs
+ * @param toggleCols
+ */
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ {
+
+ boolean hide = false;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (!toggleSeqs && !toggleCols)
+ {
+ // Hide everything by the current selection - this is a hack - we do the
+ // invert and then hide
+ // first check that there will be visible columns after the invert.
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+ .getSelected().size() > 0)
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
+ .getEndRes()))
+ {
+ // now invert the sequence set, if required - empty selection implies
+ // that no hiding is required.
+ if (sg != null)
+ {
+ invertSequenceMenuItem_actionPerformed(null);
+ sg = viewport.getSelectionGroup();
+ toggleSeqs = true;
+
+ }
+ viewport.expandColSelection(sg, true);
+ // finally invert the column selection and get the new sequence
+ // selection.
+ invertColSel_actionPerformed(null);
+ toggleCols = true;
+ }
+ }
+
+ if (toggleSeqs)
+ {
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+ {
+ hideSelSequences_actionPerformed(null);
+ hide = true;
+ }
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+ {
+ showAllSeqs_actionPerformed(null);
+ }
+ }
+
+ if (toggleCols)
+ {
+ if (viewport.colSel.getSelected().size() > 0)
+ {
+ hideSelColumns_actionPerformed(null);
+ if (!toggleSeqs)
+ {
+ viewport.selectionGroup = sg;
+ }
+ }
+ else if (!hide)
+ {
+ showAllColumns_actionPerformed(null);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
+ * event.ActionEvent)
+ */
+ public void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ toggleHiddenRegions(false, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ public void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = viewport.getSelectionGroup();
+ viewport.expandColSelection(sg, false);
+ viewport.hideAllSelectedSeqs();
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
+ */
+ public void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ viewport.showAllHiddenColumns();
+ viewport.showAllHiddenSeqs();
+ alignPanel.paintAlignment(true);
+ }
+
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
@@ -2461,6 +2599,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
featureSettings.close();
featureSettings = null;
}
+ if (!showSeqFeatures.isSelected())
+ {
+ // make sure features are actually displayed
+ showSeqFeatures.setSelected(true);
+ showSeqFeatures_actionPerformed(null);
+ }
featureSettings = new FeatureSettings(this);
}
@@ -2565,8 +2709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
pos = npos + 1;
} while (npos != -1);
- contents
- .append("| " + key + " | " + val + " |
");
+ contents.append("| " + key + " | " + val + " |
");
}
contents.append("");
}
@@ -2594,19 +2737,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
JInternalFrame frame = new JInternalFrame();
OverviewPanel overview = new OverviewPanel(alignPanel);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
- .getWidth(), frame.getHeight());
+ Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+ frame.getWidth(), frame.getHeight());
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- frame
- .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- alignPanel.setOverviewPanel(null);
- };
- });
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ alignPanel.setOverviewPanel(null);
+ };
+ });
alignPanel.setOverviewPanel(overview);
}
@@ -2636,8 +2778,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void clustalColour_actionPerformed(ActionEvent e)
{
changeColour(new ClustalxColourScheme(
- viewport.alignment.getSequences(), viewport.alignment
- .getWidth()));
+ viewport.alignment.getSequences(),
+ viewport.alignment.getWidth()));
}
/**
@@ -2775,8 +2917,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Alignment al = (Alignment) viewport.alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
@@ -2812,8 +2954,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(viewport.hiddenRepSequences), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getWidth());
}
else if (cs instanceof UserColourScheme)
{
@@ -2835,9 +2978,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
else
{
@@ -2847,9 +2990,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getConservationSelected())
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(viewport.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3,
+ sg.getSequences(viewport.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, viewport.ConsPercGaps);
sg.cs.setConservation(c);
@@ -2880,8 +3023,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.getAbovePIDThreshold()
&& viewport.globalColourScheme != null)
{
- SliderPanel.setPIDSliderSource(alignPanel, viewport
- .getGlobalColourScheme(), "Background");
+ SliderPanel.setPIDSliderSource(alignPanel,
+ viewport.getGlobalColourScheme(), "Background");
SliderPanel.showPIDSlider();
}
}
@@ -2991,8 +3134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (evt.isControlDown()
|| SwingUtilities.isRightMouseButton(evt))
{
- radioItem
- .removeActionListener(radioItem.getActionListeners()[0]);
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
int option = JOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop,
@@ -3281,8 +3423,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
- // are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the visible sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
JOptionPane
.showMessageDialog(
@@ -3366,8 +3508,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
- AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
- .getAlignment());// ,viewport.getSelectionGroup());
+ AlignmentSorter.sortByAnnotationScore(scoreLabel,
+ viewport.getAlignment());// ,viewport.getSelectionGroup());
addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
viewport.alignment));
alignPanel.paintAlignment(true);
@@ -3415,8 +3557,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
Enumeration labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
- .nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore,
+ (String) labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
@@ -3551,10 +3693,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// jobs
// TODO: viewport.alignment.isAligned is a global state - the local
// selection may well be aligned - we preserve 2.0.8 behaviour for moment.
- if (!viewport.alignment.isAligned())
+ if (!viewport.alignment.isAligned(false))
{
seqs.setSequences(new SeqCigar[]
{ seqs.getSequences()[0] });
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
+
}
return seqs;
}
@@ -3568,8 +3713,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
// Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Select a newick-like tree file");
chooser.setToolTipText("Load a tree file");
@@ -3593,8 +3738,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop, fin
- .getWarningMessage(), "Possible problem with tree file",
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(), "Possible problem with tree file",
JOptionPane.WARNING_MESSAGE);
}
}
@@ -3667,87 +3812,150 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return tp;
}
+ private boolean buildingMenu = false;
+
/**
* Generates menu items and listener event actions for web service clients
*
*/
public void BuildWebServiceMenu()
{
- // TODO: add support for context dependent disabling of services based on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or introduce
- // object broker mechanism.
- if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to be
- // stored or retrieved from elsewhere
- Vector msaws = (Vector) Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
- Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
- // TODO: move GUI generation code onto service implementation - so a
- // client instance attaches itself to the GUI with method call like
- // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
- // alignframe)
- Vector wsmenu = new Vector();
- final IProgressIndicator af = this;
- if (msaws != null)
+ while (buildingMenu)
+ {
+ try
{
- // Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
- for (int i = 0, j = msaws.size(); i < j; i++)
+ System.err.println("Waiting for building menu to finish.");
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ final AlignFrame me = this;
+ buildingMenu = true;
+ new Thread(new Runnable() {
+ public void run() {
+ try
+ {
+ System.err
+ .println("Building ws menu again " + Thread.currentThread());
+ // TODO: add support for context dependent disabling of services based on
+ // alignment and current selection
+ // TODO: add additional serviceHandle parameter to specify abstract
+ // handler
+ // class independently of AbstractName
+ // TODO: add in rediscovery GUI function to restart discoverer
+ // TODO: group services by location as well as function and/or introduce
+ // object broker mechanism.
+ final Vector wsmenu = new Vector();
+ final IProgressIndicator af = me;
+ if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
+ && Discoverer.services != null
+ && (Discoverer.services.size() > 0))
+ {
+ // TODO: refactor to allow list of AbstractName/Handler bindings to be
+ // stored or retrieved from elsewhere
+ Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+ Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
+ Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
+ // TODO: move GUI generation code onto service implementation - so a
+ // client instance attaches itself to the GUI with method call like
+ // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+ // alignframe)
+ if (msaws != null)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
- .get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(msawsmenu, this);
+ // Add any Multiple Sequence Alignment Services
+ final JMenu msawsmenu = new JMenu("Alignment");
+ for (int i = 0, j = msaws.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(msawsmenu, me);
+ }
+ wsmenu.add(msawsmenu);
+ }
+ if (secstrpr != null)
+ {
+ // Add any secondary structure prediction services
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ for (int i = 0, j = secstrpr.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ .get(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(secstrmenu, me);
+ }
+ wsmenu.add(secstrmenu);
+ }
+ if (seqsrch != null)
+ {
+ // Add any sequence search services
+ final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+ for (int i = 0, j = seqsrch.size(); i < j; i++)
+ {
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+ .elementAt(i);
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+ .getServiceClient(sh);
+ impl.attachWSMenuEntry(seqsrchmenu, me);
+ }
+ wsmenu.add(seqsrchmenu);
}
- wsmenu.add(msawsmenu);
}
- if (secstrpr != null)
+
+ // TODO: move into separate menu builder class.
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- // Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
- for (int i = 0, j = secstrpr.size(); i < j; i++)
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs != null)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(secstrmenu, this);
+ if (jws2servs.hasServices())
+ {
+ JMenu jws2men = new JMenu("Jalview 2 Services");
+ jws2servs.attachWSMenuEntry(jws2men, me);
+ for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+ {
+ wsmenu.add(jws2men.getMenuComponent(i));
+ }
+ }
}
- wsmenu.add(secstrmenu);
}
- if (seqsrch != null)
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() {
+ try {
+
+ resetWebServiceMenu();
+ // finally, add the whole shebang onto the webservices menu
+ if (wsmenu.size() > 0)
{
- // Add any sequence search services
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- for (int i = 0, j = seqsrch.size(); i < j; i++)
+ for (int i = 0, j = wsmenu.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
- .elementAt(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
- .getServiceClient(sh);
- impl.attachWSMenuEntry(seqsrchmenu, this);
+ webService.add((JMenu) wsmenu.get(i));
}
- // finally, add the whole shebang onto the webservices menu
- wsmenu.add(seqsrchmenu);
}
- resetWebServiceMenu();
- for (int i = 0, j = wsmenu.size(); i < j; i++)
+ else
{
- webService.add((JMenu) wsmenu.get(i));
+ me.webService.add(me.webServiceNoServices);
}
- }
- else
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ });
+ } catch (Exception e)
{
- resetWebServiceMenu();
- this.webService.add(this.webServiceNoServices);
}
+ ;
+
+ buildingMenu = false;
+ }}).start();
+
}
/**
@@ -3759,6 +3967,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
webService.removeAll();
build_fetchdbmenu(webService);
+ build_urlServiceMenu(webService);
+ }
+
+ /**
+ * construct any groupURL type service menu entries.
+ *
+ * @param webService
+ */
+ private void build_urlServiceMenu(JMenu webService)
+ {
+ if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+ {
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+ webService, this);
+ }
}
/*
@@ -3843,8 +4066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn(
- "canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
e);
return false;
}
@@ -3934,13 +4156,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// old way
try
{
- return (jalview.analysis.Dna.canTranslate(selection, viewport
- .getViewAsVisibleContigs(true)));
+ return (jalview.analysis.Dna.canTranslate(selection,
+ viewport.getViewAsVisibleContigs(true)));
} catch (Exception e)
{
jalview.bin.Cache.log
- .warn(
- "canTranslate threw an exception - please report to help@jalview.org",
+ .warn("canTranslate threw an exception - please report to help@jalview.org",
e);
return false;
}
@@ -4029,9 +4250,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean featuresFile = false;
try
{
- featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
- .getDataset(), alignPanel.seqPanel.seqCanvas
- .getFeatureRenderer().featureColours, false);
+ featuresFile = new FeaturesFile(file, type)
+ .parse(viewport.alignment.getDataset(),
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
+ false);
} catch (Exception ex)
{
ex.printStackTrace();
@@ -4046,6 +4268,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// update the min/max ranges where necessary
alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
}
+ if (featureSettings != null)
+ {
+ featureSettings.setTableData();
+ }
alignPanel.paintAlignment(true);
}
@@ -4135,9 +4361,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/**
- * Attempt to load a "dropped" file or URL string: First by testing whether it's and
- * Annotation file, then a JNet file, and finally a features file. If all are
- * false then the user may have dropped an alignment file onto this
+ * Attempt to load a "dropped" file or URL string: First by testing whether
+ * it's and Annotation file, then a JNet file, and finally a features file. If
+ * all are false then the user may have dropped an alignment file onto this
* AlignFrame.
*
* @param file
@@ -4148,8 +4374,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
try
{
String protocol = jalview.io.FormatAdapter.FILE;
- String f=file.toLowerCase();
- if (f.indexOf("http:") == 0 || f.indexOf("https:")==0 || f.indexOf("file:") == 0)
+ String f = file.toLowerCase();
+ if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
+ || f.indexOf("file:") == 0)
{
protocol = jalview.io.FormatAdapter.URL;
}
@@ -4166,8 +4393,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
protocol);
- new JnetAnnotationMaker().add_annotation(predictions, viewport
- .getAlignment(), 0, false);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
isAnnotation = true;
}
else
@@ -4308,13 +4535,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// preferences and have checkboxes.. rather than individual sources selected
// here
JMenu rfetch = new JMenu("Fetch DB References");
- rfetch
- .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+ rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
webService.add(rfetch);
JMenuItem fetchr = new JMenuItem("Standard Databases");
- fetchr
- .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+ fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
fetchr.addActionListener(new ActionListener()
{
@@ -4423,27 +4648,105 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
- viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+ viewport.setShowUnconserved(showNonconservedMenuItem.getState());
alignPanel.paintAlignment(true);
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
+ * .ActionEvent)
*/
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConsensus(showGroupConsensus.getState());
- alignPanel.updateAnnotation();
-
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
+ * .event.ActionEvent)
*/
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
viewport.setShowGroupConservation(showGroupConservation.getState());
- alignPanel.updateAnnotation();
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
+ * .event.ActionEvent)
+ */
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ if (viewport.getSelectionGroup() != null)
+ {
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true).getSequenceStrings(
+ viewport.getGapCharacter()),
+ viewport.alignment.getGroups());
+ viewport.alignment.deleteAllGroups();
+ viewport.sequenceColours = null;
+ viewport.setSelectionGroup(null);
+ // set view properties for each group
+ for (int g = 0; g < gps.length; g++)
+ {
+ gps[g].setShowNonconserved(viewport.getShowUnconserved());
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+ viewport.alignment.addGroup(gps[g]);
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ col = col.brighter();
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq
+ .hasMoreElements(); viewport.setSequenceColour(
+ (SequenceI) sq.nextElement(), col))
+ ;
+ }
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+ alignPanel.updateAnnotation();
+ alignPanel.paintAlignment(true);
+ }
}
}