/*
- * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
import jalview.jbgui.*;
import jalview.schemes.*;
import jalview.ws.*;
+import jalview.ws.jws2.Jws2Discoverer;
/**
* DOCUMENT ME!
{
boolean toggleSeqs = !evt.isControlDown();
boolean toggleCols = !evt.isShiftDown();
- toggleHiddenRegions(toggleSeqs,toggleCols);
- break;
+ toggleHiddenRegions(toggleSeqs, toggleCols);
+ break;
}
case KeyEvent.VK_PAGE_UP:
if (viewport.wrapAlignment)
}
JPanel progressPanel;
- Long lId=new Long(id);
+ Long lId = new Long(id);
GridLayout layout = (GridLayout) statusPanel.getLayout();
if (progressBars.get(lId) != null)
{
{
if (fileName != null)
{
- // TODO: work out how to recover feature settings for correct view(s) when file is reloaded.
+ // 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();
protocol, currentFileFormat);
newframe.setBounds(bounds);
- if (featureSettings!=null && featureSettings.isShowing()) {
+ 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
+ // 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() {
+ SwingUtilities.invokeLater(new Runnable()
+ {
public void run()
{
nfs.frame.setBounds(fspos);
}
});
this.featureSettings.close();
- this.featureSettings=null;
+ this.featureSettings = null;
}
this.closeMenuItem_actionPerformed(true);
}
viewport.historyList.push(command);
viewport.redoList.clear();
updateEditMenuBar();
- viewport.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
+ viewport.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
}
}
if (originalSource != null)
{
- originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
if (originalSource != null)
{
- originalSource.hasHiddenColumns = (viewport.colSel!=null && viewport.colSel.getHiddenColumns() != null && viewport.colSel.getHiddenColumns().size()>0);
+ originalSource.hasHiddenColumns = (viewport.colSel != null
+ && viewport.colSel.getHiddenColumns() != null && viewport.colSel
+ .getHiddenColumns().size() > 0);
originalSource.firePropertyChange("alignment", null,
originalSource.alignment.getSequences());
}
viewport.hideAllSelectedSeqs();
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)
+ 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
+ // 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()))
+ 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;
+ // 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())
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())
{
hideSelSequences_actionPerformed(null);
hide = true;
{
showAllColumns_actionPerformed(null);
}
- }
+ }
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (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)
+ /*
+ * (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.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
+ * ActionEvent)
*/
public void showAllhidden_actionPerformed(ActionEvent e)
{
}
else
{
- // are the sequences aligned?
- if (!viewport.alignment.isAligned())
+ // are the visible sequences aligned?
+ if (!viewport.alignment.isAligned(false))
{
JOptionPane
.showMessageDialog(
// 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!
+ // TODO: if seqs.getSequences().length>1 then should really have warned
+ // user!
}
return seqs;
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
.get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
.getServiceClient(sh);
impl.attachWSMenuEntry(msawsmenu, this);
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
.get(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
.getServiceClient(sh);
impl.attachWSMenuEntry(secstrmenu, this);
}
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
.elementAt(i);
- jalview.ws.WSClient impl = jalview.ws.Discoverer
+ jalview.ws.WSMenuEntryProviderI impl = jalview.ws.Discoverer
.getServiceClient(sh);
impl.attachWSMenuEntry(seqsrchmenu, this);
}
wsmenu.add(seqsrchmenu);
}
+ // TODO: move into separate menu builder class.
+ {
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ if (jws2servs!=null && jws2servs.hasServices())
+ {
+ JMenu jws2men = new JMenu("Jalview 2 Services");
+ jws2servs.attachWSMenuEntry(jws2men, this);
+ wsmenu.add(jws2men);
+ }
+ }
// finally, add the whole shebang onto the webservices menu
resetWebServiceMenu();
for (int i = 0, j = wsmenu.size(); i < j; i++)
/**
* construct any groupURL type service menu entries.
+ *
* @param webService
*/
private void build_urlServiceMenu(JMenu webService)
{
- jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(webService, this);
+ jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+ webService, this);
}
/*
// update the min/max ranges where necessary
alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
}
- if (featureSettings!=null)
+ if (featureSettings != null)
{
featureSettings.setTableData();
}
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
+ * .event.ActionEvent)
*/
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
- /* (non-Javadoc)
- * @see jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt.event.ActionEvent)
+ /*
+ * (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());
for (int g = 0; g < gps.length; g++)
{
gps[g].setShowunconserved(viewport.getShowUnconserved());
- gps[g].setIncludeAllConsSymbols(viewport.isIncludeAllConsensusSymbols());
+ gps[g].setIncludeAllConsSymbols(viewport
+ .isIncludeAllConsensusSymbols());
viewport.alignment.addGroup(gps[g]);
Color col = new Color((int) (Math.random() * 255), (int) (Math
.random() * 255), (int) (Math.random() * 255));
git://source.jalview.org / jalview.git / blobdiff