X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1b09868fe23694a9ab375096d4173a000dc4dc5d;hb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;hp=594319f1996950b204098e046aa5cbecfde436d5;hpb=87256ba36fb105a1115067ffe2563412e9281d2d;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 594319f..1b09868 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -392,7 +392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); buildColourMenu(); - if (Desktop.getDesktopPane() != null) + if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); if (!Platform.isJS()) @@ -815,7 +815,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, private void addServiceListeners() { final java.beans.PropertyChangeListener thisListener; - Desktop.getInstance().addJalviewPropertyChangeListener("services", + Desktop.instance.addJalviewPropertyChangeListener("services", thisListener = new java.beans.PropertyChangeListener() { @Override @@ -846,7 +846,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.event.InternalFrameEvent evt) { // System.out.println("deregistering discoverer listener"); - Desktop.getInstance().removeJalviewPropertyChangeListener("services", + Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); } @@ -1027,7 +1027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromFile_actionPerformed(ActionEvent e) { - Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport); + Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } @Override @@ -1041,7 +1041,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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 @@ -1051,14 +1051,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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:") @@ -1116,14 +1116,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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 @@ -1167,7 +1167,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // 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"), @@ -1289,7 +1289,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; PrintWriter out = new PrintWriter( new FileWriter(tempFilePath)); - out.print(output); out.close(); AlignFrame.this.setTitle(file); @@ -1939,7 +1938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .setContents(new StringSelection(""), null); Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, - Desktop.getInstance()); + Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); @@ -2158,7 +2157,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2205,7 +2204,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2439,7 +2438,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + 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") }; @@ -2913,7 +2912,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void gatherViews_actionPerformed(ActionEvent e) { - Desktop.getInstance().gatherViews(this); + Desktop.instance.gatherViews(this); } /** @@ -3690,7 +3689,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { 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( @@ -4012,7 +4011,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -4020,7 +4019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (fin != null && fin.hasWarningMessage()) { - JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), + JvOptionPane.showMessageDialog(Desktop.desktop, fin.getWarningMessage(), MessageManager.getString( "label.possible_problem_with_tree_file"), @@ -4400,7 +4399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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; } @@ -4410,7 +4409,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "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 @@ -4626,7 +4625,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq(fm[0].toString(), (DataSourceType) fm[1], toassoc, false, - Desktop.getInstance()); + Desktop.instance); if (pe != null) { System.err.println("Associated file : " @@ -4737,7 +4736,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // 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") @@ -4830,7 +4829,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + (format != null ? "(parsing as '" + format + "' file)" : ""), - oom, Desktop.getDesktopPane()); + oom, Desktop.desktop); } } @@ -5639,7 +5638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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);