X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=5c45232b6deac2361b75512773ec8dd24eacab21;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=39aa257ff521255a30e21f81fb3c90f411524d28;hpb=1a3aea90a65991ab5e47c1d3c7e663ede50bca6b;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 39aa257..5c45232 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -1106,8 +1106,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), MessageManager + new Object[] { url }), MessageManager .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); @@ -1495,9 +1494,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void saveState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp" }, new String[] - { "Jalview Project" }, "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "jvp" }, new String[] { "Jalview Project" }, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); @@ -1516,8 +1515,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( - "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + "label.saving_jalview_project", + new Object[] { choice.getName() }), choice.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); // TODO catch and handle errors for savestate @@ -1536,8 +1535,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements ex); JOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", - new Object[] - { choice.getName() }), MessageManager + new Object[] { choice.getName() }), MessageManager .getString("label.couldnt_save_project"), JOptionPane.WARNING_MESSAGE); } @@ -1567,10 +1565,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void loadState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { + "jvp", "jar" }, new String[] { "Jalview Project", + "Jalview Project (old)" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); @@ -1587,9 +1584,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements { public void run() { - setProgressBar(MessageManager.formatMessage( - "label.loading_jalview_project", new Object[] - { choice }), choice.hashCode()); + setProgressBar( + MessageManager.formatMessage( + "label.loading_jalview_project", + new Object[] { choice }), choice.hashCode()); try { new Jalview2XML().loadJalviewAlign(choice); @@ -1603,8 +1601,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.error_whilst_loading_project_from", - new Object[] - { choice }), MessageManager + new Object[] { choice }), MessageManager .getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE); } @@ -1629,8 +1626,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (fileLoadingCount == 0) { fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( - "label.loading_file", new Object[] - { fileName }))); + "label.loading_file", new Object[] { fileName }))); } fileLoadingCount++; } @@ -1724,7 +1720,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { for (AlignmentPanel ap : af.alignPanels) { - if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) + if (alignmentId == null + || alignmentId.equals(ap.av.getSequenceSetId())) { aps.add(ap); } @@ -1755,7 +1752,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (AlignFrame afr : frames) { - if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (sequenceSetId == null + || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) { if (afr.alignPanels != null) { @@ -1894,8 +1893,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.desktop, MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", - new Object[] - { fle }), + new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), JOptionPane.ERROR_MESSAGE); @@ -1972,16 +1970,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements } setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); jalview.bin.Cache.log.error( "New vamsas session from existing session file failed:", ex); return false; @@ -1989,8 +1987,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -2097,8 +2095,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new Object[] - { sess[i] })); + "label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() @@ -2151,8 +2148,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - new String[] - { "Vamsas Document" }, "Vamsas Document"); + new String[] { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2164,8 +2160,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { java.io.File choice = chooser.getSelectedFile(); JPanel progpanel = addProgressPanel(MessageManager.formatMessage( - "label.saving_vamsas_doc", new Object[] - { choice.getName() })); + "label.saving_vamsas_doc", + new Object[] { choice.getName() })); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; @@ -2331,9 +2327,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { g.drawString(MessageManager.formatMessage( "label.memory_stats", - new Object[] - { df.format(totalFreeMemory), df.format(maxMemory), - df.format(percentUsage) }), 10, + new Object[] { df.format(totalFreeMemory), + df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); } } @@ -2463,12 +2458,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements "groovy.ui.Console"); Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", - new Class[] - { String.class, Object.class }); + new Class[] { String.class, Object.class }); java.lang.reflect.Method run = gcClass.getMethod("run"); Object gc = gccons.newInstance(); - setvar.invoke(gc, new Object[] - { "Jalview", this }); + setvar.invoke(gc, new Object[] { "Jalview", this }); run.invoke(gc); } catch (Exception ex) { @@ -2546,9 +2539,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { handler.cancelActivity(id); us.setProgressBar(MessageManager.formatMessage( - "label.cancelled_params", new Object[] - { ((JLabel) progressPanel.getComponent(0)).getText() }), - id); + "label.cancelled_params", + new Object[] { ((JLabel) progressPanel.getComponent(0)) + .getText() }), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2570,8 +2563,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * This will return the first AlignFrame holding the given viewport instance. It - * will break if there are more than one AlignFrames viewing a particular av. + * This will return the first AlignFrame holding the given viewport instance. + * It will break if there are more than one AlignFrames viewing a particular + * av. * * @param viewport * @return alignFrame for viewport @@ -2580,8 +2574,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(viewport - .getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == viewport) @@ -2790,8 +2783,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progress != null) { progress.setProgressBar(MessageManager.formatMessage( - "status.opening_params", new Object[] - { url }), this.hashCode()); + "status.opening_params", new Object[] { url }), this + .hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) @@ -3020,7 +3013,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - + JInternalFrame[] frames = desktop.getAllFrames(); for (JInternalFrame frame : frames) { @@ -3048,7 +3041,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements myBottomFrame.addAlignmentPanel(bottomPanel, false); } } - + if (gatherThis) { topFrame.getAlignPanels().clear(); @@ -3065,15 +3058,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - // public static AlignFrame getCurrentAlignFrame() - // { - // return currentAlignFrame; - // } - // - // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) - // { - // Desktop.currentAlignFrame = currentAlignFrame; - // } + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } }