X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=5e3650079533ddf0cb6bd73ea78930d0ec0de767;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=cd5c79277e59d9d14f87ec18d8623c34922319d7;hpb=3f25214f0a8d25899d472a024e3b49d84fefc3a4;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index cd5c792..5e36500 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -20,21 +20,28 @@ */ package jalview.gui; +import jalview.bin.Cache; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ComplexAlignFile; +import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; +import jalview.api.FeaturesSourceI; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; +import jalview.io.AlignmentFileReaderI; import jalview.io.AppletFormatAdapter; -import jalview.io.FileParse; +import jalview.io.DataSourceType; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GCutAndPasteTransfer; +import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; @@ -46,9 +53,11 @@ import java.awt.datatransfer.Transferable; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; @@ -65,11 +74,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignViewportI viewport; - FileParse source = null; + AlignmentFileReaderI source = null; + public CutAndPasteTransfer() { SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { textarea.requestFocus(); @@ -122,14 +133,18 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 JalviewFileChooser - Save option + JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setAcceptAllFileFilterUsed(false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file")); + chooser.setDialogTitle( + MessageManager.getString("label.save_text_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -138,8 +153,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { try { - java.io.PrintWriter out = new java.io.PrintWriter( - new java.io.FileWriter(chooser.getSelectedFile())); + PrintWriter out = new PrintWriter( + new FileWriter(chooser.getSelectedFile())); out.print(getText()); out.close(); @@ -157,6 +172,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -170,6 +186,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -182,8 +199,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer try { - textarea.append((String) contents - .getTransferData(DataFlavor.stringFlavor)); + textarea.append( + (String) contents.getTransferData(DataFlavor.stringFlavor)); } catch (Exception ex) { } @@ -195,6 +212,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { String text = getText(); @@ -203,17 +221,24 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer return; } - String format = new IdentifyFile().Identify(text, "Paste"); - if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE")) + FileFormatI format = null; + try { - System.err.println(MessageManager - .getString("label.couldnt_read_data")); + format = new IdentifyFile().identify(text, DataSourceType.PASTE); + } catch (FileFormatException e1) + { + // leave as null + } + if (format == null) + { + System.err + .println(MessageManager.getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return; } @@ -221,33 +246,37 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer // TODO: identify feature, annotation or tree file and parse appropriately. AlignmentI al = null; - if (FormatAdapter.isValidFormat(format)) + try { - try - { - FormatAdapter fa = new FormatAdapter(alignpanel); - al = fa.readFile(getText(), "Paste", format); - source = fa.getAlignFile(); + FormatAdapter fa = new FormatAdapter(alignpanel); + al = fa.readFile(getText(), DataSourceType.PASTE, format); + source = fa.getAlignFile(); - } catch (java.io.IOException ex) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.couldnt_read_pasted_text", new String[] - { ex.toString() }), MessageManager - .getString("label.error_parsing_text"), - JOptionPane.WARNING_MESSAGE); - } + } catch (IOException ex) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .formatMessage("label.couldnt_read_pasted_text", new String[] + { ex.toString() }), + MessageManager.getString("label.error_parsing_text"), + JvOptionPane.WARNING_MESSAGE); } if (al != null && al.hasValidSequence()) { - String title = MessageManager.formatMessage( - "label.input_cut_paste_params", new String[] - { format }); - if (viewport != null) + String title = MessageManager + .formatMessage("label.input_cut_paste_params", new String[] + { format.getName() }); + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); + + /* + * if the view panel was closed its alignment is nulled + * and this is an orphaned cut and paste window + */ + if (viewport != null && viewport.getAlignment() != null) { ((AlignViewport) viewport).addAlignment(al, title); + viewport.applyFeaturesStyle(proxyColourScheme); } else { @@ -255,38 +284,51 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignFrame af; if (source instanceof ComplexAlignFile) { - ColumnSelection colSel = ((ComplexAlignFile) source) - .getColumnSelection(); + HiddenColumns hidden = ((ComplexAlignFile) source) + .getHiddenColumns(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); boolean showSeqFeatures = ((ComplexAlignFile) source) .isShowSeqFeatures(); - ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); FeaturesDisplayedI fd = ((ComplexAlignFile) source) .getDisplayedFeatures(); - af = new AlignFrame(al, hiddenSeqs, colSel, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + af = new AlignFrame(al, hiddenSeqs, hidden, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); af.getViewport().setShowSequenceFeatures(showSeqFeatures); af.getViewport().setFeaturesDisplayed(fd); - af.changeColour(cs); + af.setMenusForViewport(); + ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( + colourSchemeName, al); + if (cs != null) + { + af.changeColour(cs); + } } else { af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + if (source instanceof FeaturesSourceI) + { + af.getViewport().setShowSequenceFeatures(true); + } + } + if (proxyColourScheme != null) + { + af.getViewport().applyFeaturesStyle(proxyColourScheme); } - af.currentFileFormat = format; Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - af.statusBar.setText(MessageManager + af.setStatus(MessageManager .getString("label.successfully_pasted_alignment_file")); try { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", - false)); + af.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { } @@ -294,25 +336,25 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } else { - System.err.println(MessageManager - .getString("label.couldnt_read_data")); + System.err + .println(MessageManager.getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } } - /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -323,9 +365,14 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } } + @Override public void textarea_mousePressed(MouseEvent e) { - if (SwingUtilities.isRightMouseButton(e)) + /* + * isPopupTrigger is checked in mousePressed on Mac, + * in mouseReleased on Windows + */ + if (e.isPopupTrigger()) { JPopupMenu popup = new JPopupMenu( MessageManager.getString("action.edit")); @@ -333,6 +380,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -342,6 +390,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer item = new JMenuItem(MessageManager.getString("action.paste")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteMenu_actionPerformed(e);