// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
+ String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
"No sort");
if (sortby.equals("Id"))
});
buildColourMenu();
- if (Desktop.getDesktopPane() != null)
+ if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
if (!Platform.isJS())
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
- Desktop.getInstance().addJalviewPropertyChangeListener("services",
+ Desktop.instance.addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
@Override
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
- Desktop.getInstance().removeJalviewPropertyChangeListener("services",
+ Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
}
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
- Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
}
@Override
// file is reloaded.
if (FileFormat.Jalview.equals(currentFileFormat))
{
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
if (frames[i] instanceof AlignFrame && frames[i] != this
try
{
frames[i].setSelected(true);
- Desktop.getInstance().closeAssociatedWindows();
+ Desktop.instance.closeAssociatedWindows();
} catch (java.beans.PropertyVetoException ex)
{
}
}
}
- Desktop.getInstance().closeAssociatedWindows();
+ Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
DataSourceType protocol = fileName.startsWith("http:")
? DataSourceType.URL
: DataSourceType.FILE;
- loader.loadFile(viewport, fileName, protocol, currentFileFormat);
+ loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
else
{
DataSourceType protocol = (fileName.startsWith("http:")
? DataSourceType.URL
: DataSourceType.FILE);
- newframe = loader.loadFileWaitTillLoaded(fileName, protocol,
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
else
{
- newframe = loader.loadFileWaitTillLoaded(fileObject,
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
DataSourceType.FILE, currentFileFormat);
}
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.getInstance()
+ Desktop.instance
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
- Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
}
@Override
// todo is this (2005) test now obsolete - value is never null?
while (currentFileFormat == null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager.getString("label.file_format_not_specified"),
String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
PrintWriter out = new PrintWriter(
new FileWriter(tempFilePath));
-
out.print(output);
out.close();
AlignFrame.this.setTitle(file);
StringSelection ss = new StringSelection(output);
- Desktop d = Desktop.getInstance();
try
{
- d.internalCopy = true;
+ 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(ss,
- Desktop.getInstance());
+ Desktop.instance);
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
hiddenCutoff, hiddenOffset);
}
- d.jalviewClipboard = new Object[] { seqs,
+ Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
boolean annotationAdded = false;
AlignmentI alignment = null;
- Desktop d = Desktop.getInstance();
-
- if (d.jalviewClipboard != null)
+ if (Desktop.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
+ SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
if (newAlignment)
{
- if (d.jalviewClipboard != null)
+ if (Desktop.jalviewClipboard != null)
{
// dataset is inherited
- alignment.setDataset((Alignment) d.jalviewClipboard[1]);
+ alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
}
else
{
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
- boolean importDs = d.jalviewClipboard != null
- && d.jalviewClipboard[1] != alignment.getDataset();
+ boolean importDs = Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
- Desktop d = Desktop.getInstance();
-
- if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
+ if (Desktop.jalviewClipboard != null
+ && Desktop.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
if (wholeHeight && wholeWidth)
{
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.getInstance().gatherViews(this);
+ Desktop.instance.gatherViews(this);
}
/**
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
{
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
JvOptionPane.WARNING_MESSAGE);
}
if (fin != null && fin.hasWarningMessage())
{
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
fin.getWarningMessage(),
MessageManager.getString(
"label.possible_problem_with_tree_file"),
final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
- Hashtable<String, Vector<ServiceHandle>> services = Discoverer
- .getInstance().getServices();
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- services != null && (services.size() > 0))
+ // &&
+ Discoverer.services != null && (Discoverer.services.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector<ServiceHandle> secstrpr = services.get("SecStrPred");
+ Vector<ServiceHandle> secstrpr = Discoverer.services
+ .get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- // boolean new_sspred = false;
+ boolean new_sspred = false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
+ Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
if (jws2servs.hasServices())
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JvOptionPane.ERROR_MESSAGE);
return;
}
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JvOptionPane.WARNING_MESSAGE);
}
else
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
+ viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = AssociatePdbFileWithSeq
+ PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq(fm[0].toString(),
- (DataSourceType) fm[1], toassoc, false);
+ (DataSourceType) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showMessageDialog(Desktop.desktop,
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
}
else
{
- new FileLoader().loadFile(viewport, file, sourceType, format);
+ new FileLoader().LoadFile(viewport, file, sourceType, format);
}
}
}
if (isAnnotation)
{
- updateForAnnotations();
+
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
}
} catch (Exception ex)
{
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
- oom, Desktop.getDesktopPane());
+ oom, Desktop.desktop);
}
}
/**
- * Do all updates necessary after an annotation file such as jnet. Also called
- * from Jalview.loadAppletParams for "annotations", "jnetFile"
- */
- public void updateForAnnotations()
- {
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
- }
-
- /**
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
}
/**
- * Change the display state for the given feature groups -- Added by BH from
- * JalviewLite
- *
- * @param groups
- * list of group strings
- * @param state
- * visible or invisible
- */
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- jalview.api.FeatureRenderer fr = null;
- viewport.setShowSequenceFeatures(true);
- if (alignPanel != null
- && (fr = alignPanel.getFeatureRenderer()) != null)
- {
-
- fr.setGroupVisibility(Arrays.asList(groups), state);
- alignPanel.getSeqPanel().seqCanvas.repaint();
- if (alignPanel.overviewPanel != null)
- {
- alignPanel.overviewPanel.updateOverviewImage();
- }
- }
- }
-
- /**
* Open the dialog for regex description parsing.
*/
@Override
@Override
public void run()
{
+ final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = jalview.ws.SequenceFetcher.getInstance()
- .getNonAlignmentSources();
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
int dbi = 0;
for (String dbclass : dbclasses)
{
- otherdb = jalview.ws.SequenceFetcher.getInstance()
- .getSourceProxy(dbclass);
+ otherdb = sf.getSourceProxy(dbclass);
// add a single entry for this class, or submenu allowing 'fetch
// all' or pick one
if (otherdb == null || otherdb.size() < 1)
}
if (otherdb.size() == 1)
{
+ final DbSourceProxy[] dassource = otherdb
+ .toArray(new DbSourceProxy[0]);
DbSourceProxy src = otherdb.get(0);
- DbSourceProxy[] dassource = new DbSourceProxy[] {
- src };
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
}
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff