X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c49626be8d9af88118ca9a795ba8c8ec75b47c31;hb=5640ec0623c6d1205e62f9fe15292f32bfdab7d9;hp=9e4b18081139d5c27d4dd15775dabe8892fd1e90;hpb=c764fbfdffe3a52349038c957d7a73b8e22e9985;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9e4b180..c49626b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; import java.io.IOException; +import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -94,6 +95,7 @@ import jalview.api.analysis.SimilarityParamsI; import jalview.bin.Cache; import jalview.bin.Console; import jalview.bin.Jalview; +import jalview.bin.groovy.JalviewObjectI; import jalview.commands.CommandI; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -502,7 +504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void focusGained(FocusEvent e) { - Jalview.setCurrentAlignFrame(AlignFrame.this); + Jalview.getInstance().setCurrentAlignFrame(AlignFrame.this); } }); @@ -623,12 +625,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if (viewport.cursorMode) // { // alignPanel.seqPanel.insertNucAtCursor(false,"A"); - // //System.out.println("A"); + // //jalview.bin.Console.outPrintln("A"); // } // break; /* * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) { - * System.out.println("closing bracket"); } break; + * jalview.bin.Console.outPrintln("closing bracket"); } break; */ case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: @@ -829,7 +831,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void propertyChange(PropertyChangeEvent evt) { - // // System.out.println("Discoverer property change."); + // // jalview.bin.Console.outPrintln("Discoverer property + // change."); // if (evt.getPropertyName().equals("services")) { SwingUtilities.invokeLater(new Runnable() @@ -838,7 +841,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - System.err.println( + jalview.bin.Console.errPrintln( "Rebuild WS Menu for service change"); BuildWebServiceMenu(); } @@ -853,7 +856,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { - // System.out.println("deregistering discoverer listener"); + // jalview.bin.Console.outPrintln("deregistering discoverer listener"); Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); @@ -1250,8 +1253,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void saveAlignment(String file, FileFormatI format) { + saveAlignment(file, format, false, false); + } + + public void saveAlignment(String file, FileFormatI format, boolean stdout, + boolean forceBackup) + { lastSaveSuccessful = true; - lastFilenameSaved = file; + if (!stdout) + { + lastFilenameSaved = file; + } lastFormatSaved = format; if (FileFormat.Jalview.equals(format)) @@ -1262,6 +1274,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, shortName = shortName .substring(shortName.lastIndexOf(File.separatorChar) + 1); } + // TODO deal with stdout=true lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); @@ -1297,7 +1310,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // create backupfiles object and get new temp filename destination - boolean doBackup = BackupFiles.getEnabled(); + boolean doBackup = forceBackup + || (BackupFiles.getEnabled() && !stdout); BackupFiles backupfiles = null; if (doBackup) { @@ -1309,7 +1323,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; Console.trace("ALIGNFRAME setting PrintWriter"); - PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + PrintWriter out = stdout + ? new PrintWriter(new OutputStreamWriter(System.out)) + : new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { @@ -1318,13 +1334,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } out.print(output); - Console.trace("ALIGNFRAME about to close file"); - out.close(); - Console.trace("ALIGNFRAME closed file"); - AlignFrame.this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); + out.flush(); + if (!stdout) + { + Console.trace("ALIGNFRAME about to close file"); + out.close(); + Console.trace("ALIGNFRAME closed file"); + } + AlignFrame.this.setTitle(stdout ? "STDOUT" : file); + if (stdout) + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_printed_to_stdout_in_format", + new Object[] + { format.getName() })); + } + else + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); + } lastSaveSuccessful = true; } catch (IOException e) { @@ -1534,7 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void createPNG(File f) throws ImageOutputException { - createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing()); + createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing()); } public void createPNG(File f, String renderer, BitmapImageSizing userBis) @@ -1766,7 +1797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @return alignment objects for all views */ - AlignmentI[] getViewAlignments() + public AlignmentI[] getViewAlignments() { if (alignPanels != null) { @@ -2474,7 +2505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); - System.out.println("Exception whilst pasting: " + ex); + jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } @@ -2522,7 +2553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { ex.printStackTrace(); - System.out.println("Exception whilst pasting: " + ex); + jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex); // could be anything being pasted in here } catch (OutOfMemoryError oom) { @@ -3158,11 +3189,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { - scaleAbove.setVisible(wrapMenuItem.isSelected()); - scaleLeft.setVisible(wrapMenuItem.isSelected()); - scaleRight.setVisible(wrapMenuItem.isSelected()); - viewport.setWrapAlignment(wrapMenuItem.isSelected()); + setWrapFormat(wrapMenuItem.isSelected(), false); + } + + public void setWrapFormat(boolean b, boolean setMenuItem) + { + scaleAbove.setVisible(b); + scaleLeft.setVisible(b); + scaleRight.setVisible(b); + viewport.setWrapAlignment(b); alignPanel.updateLayout(); + if (setMenuItem) + { + wrapMenuItem.setSelected(b); + } } @Override @@ -3500,7 +3540,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - + frame.setFrameIcon(null); frame.getContentPane().add(new JScrollPane(pane)); Desktop.addInternalFrame(frame, MessageManager @@ -3528,12 +3568,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return alignPanel.overviewPanel; } JInternalFrame frame = new JInternalFrame(); + frame.setFrameIcon(null); final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, "", true, frame.getWidth(), - frame.getHeight(), true, true); - frame.setFrameIcon(null); + + alignPanel.setOverviewPanel(overview); + alignPanel.setOverviewTitle(this); + + Desktop.addInternalFrame(frame, overview.getTitle(), true, + frame.getWidth(), frame.getHeight(), true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); final AlignmentPanel thePanel = this.alignPanel; @@ -3553,9 +3597,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frame.addKeyListener(getKeyListeners()[0]); } - alignPanel.setOverviewPanel(overview); - alignPanel.setOverviewTitle(this); - return overview; } @@ -3807,6 +3848,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { JInternalFrame frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.setContentPane(new PairwiseAlignPanel(viewport)); Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, @@ -4268,10 +4310,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { NewickFile fin = new NewickFile( new FileParse(cm.getNewick(), DataSourceType.PASTE)); - String title = cm.getAnnotLabel() + " " + cm.getTreeMethod() + " tree" - + aa.sequenceRef != null + String title = aa.label + " " + cm.getTreeMethod() + " tree" + + (aa.sequenceRef != null ? (" for " + aa.sequenceRef.getDisplayId(false)) - : ""; + : ""); showColumnWiseTree(fin, aa, title, w, h, x, y); } catch (Throwable xx) @@ -4291,7 +4333,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return null; } - TreePanel tp = new TreePanel(alignPanel, nf, aa, title); + TreePanel tp = new TreePanel(alignPanel, nf, aa, treeTitle); tp.setSize(w, h); @@ -4300,7 +4342,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, title, w, h); + Desktop.addInternalFrame(tp, treeTitle, w, h); return tp; } catch (Throwable xx) { @@ -4322,7 +4364,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - System.err.println("Waiting for building menu to finish."); + jalview.bin.Console + .errPrintln("Waiting for building menu to finish."); Thread.sleep(10); } catch (Exception e) { @@ -4338,7 +4381,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final List legacyItems = new ArrayList<>(); try { - // System.err.println("Building ws menu again " + // jalview.bin.Console.errPrintln("Building ws menu again " // + Thread.currentThread()); // TODO: add support for context dependent disabling of services based // on @@ -4776,7 +4819,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Object[] { String,SequenceI} */ ArrayList filesmatched = new ArrayList<>(); - ArrayList filesnotmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); for (int i = 0; i < files.size(); i++) { // BH 2018 @@ -4822,9 +4865,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } mtch = idm.findAllIdMatches(pdbfn); } + FileFormatI type = null; if (mtch != null) { - FileFormatI type; try { type = new IdentifyFile().identify(file, protocol); @@ -4840,7 +4883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } // File wasn't named like one of the sequences or wasn't a PDB // file. - filesnotmatched.add(file); + filesnotmatched.add(new Object[] { file, protocol, type }); } } int assocfiles = 0; @@ -4876,7 +4919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance); if (pe != null) { - System.err.println("Associated file : " + jalview.bin.Console.errPrintln("Associated file : " + (fm[0].toString()) + " with " + toassoc.getDisplayId(true)); assocfiles++; @@ -4894,7 +4937,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ for (Object[] o : filesmatched) { - filesnotmatched.add(o[0]); + filesnotmatched.add(new Object[] { o[0], o[1] }); } } } @@ -4916,9 +4959,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - for (Object fn : filesnotmatched) + for (Object[] fn : filesnotmatched) { - loadJalviewDataFile(fn, null, null, null); + loadJalviewDataFile(fn[0], (DataSourceType) fn[1], + (FileFormatI) fn[2], null); } } @@ -5014,7 +5058,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { format = new IdentifyFile().identify(file, sourceType); } - if (FileFormat.ScoreMatrix == format) + if (FileFormat.FeatureSettings == format) + { + if (featureSettings != null) + { + featureSettings.load(file, sourceType); + } + else + { + FeatureSettings.loadFeatureSettingsFile(getFeatureRenderer(), + fileObject, sourceType); + } + } + else if (FileFormat.ScoreMatrix == format) { ScoreMatrixFile sm = new ScoreMatrixFile( new FileParse(file, sourceType)); @@ -5800,6 +5856,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } alignPanel.validateAnnotationDimensions(true); + // TODO this triggers relayout of annotation panel - otherwise annotation + // label height is different to panel height + alignPanel.fontChanged(); alignPanel.alignmentChanged(); } @@ -5909,7 +5968,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment())); } catch (Exception ex) { - System.err.println(ex.getMessage()); + jalview.bin.Console.errPrintln(ex.getMessage()); return; } } @@ -5922,16 +5981,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void runGroovy_actionPerformed() { - Jalview.setCurrentAlignFrame(this); - groovy.ui.Console console = Desktop.getGroovyConsole(); + Jalview.getInstance().setCurrentAlignFrame(this); + groovy.console.ui.Console console = Desktop.getGroovyConsole(); if (console != null) { try { + console.setVariable(JalviewObjectI.currentAlFrameName, this); console.runScript(); } catch (Exception ex) { - System.err.println((ex.toString())); + jalview.bin.Console.errPrintln((ex.toString())); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_run_groovy_script"), MessageManager.getString("label.groovy_support_failed"), @@ -5940,7 +6000,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - System.err.println("Can't run Groovy script as console not found"); + jalview.bin.Console + .errPrintln("Can't run Groovy script as console not found"); } }