X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=8b21058f8802b0a891a164ef94198439840c7b9e;hb=4815037f13748676b04b91dc761b73cf6f2d6ecd;hp=e663cf87f6bb1087371853e32d31e46a711be54d;hpb=3f3c6c3a2b99fee2e726d18302af1b3320331212;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index e663cf8..8b21058 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -23,16 +23,24 @@ package jalview.gui; 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.SequenceI; -import jalview.io.FileParse; +import jalview.io.AlignmentFileI; +import jalview.io.AppletFormatAdapter; +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; @@ -63,11 +71,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignViewportI viewport; - FileParse source = null; + AlignmentFileI source = null; + public CutAndPasteTransfer() { SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { textarea.requestFocus(); @@ -120,6 +130,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -127,7 +138,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer 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); @@ -155,6 +167,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -168,6 +181,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -193,38 +207,73 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { - String format = new IdentifyFile().Identify(getText(), "Paste"); - // TODO: identify feature, annotation or tree file and parse appropriately. - AlignmentI al = null; - - if (FormatAdapter.isValidFormat(format)) + String text = getText(); + if (text.trim().length() < 1) { - try - { - FormatAdapter fa = new FormatAdapter(alignpanel); - al = fa.readFile(getText(), "Paste", format); - source = fa.getAlignFile(); + return; + } - } catch (java.io.IOException ex) + FileFormatI format = null; + try + { + 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()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.couldnt_read_pasted_text", new String[] - { ex.toString() }), MessageManager - .getString("label.error_parsing_text"), + AppletFormatAdapter.SUPPORTED_FORMATS, + MessageManager.getString("label.couldnt_read_data"), JOptionPane.WARNING_MESSAGE); } + return; } - if (al != null) + // TODO: identify feature, annotation or tree file and parse appropriately. + AlignmentI al = null; + + try + { + 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); + } + + if (al != null && al.hasValidSequence()) { String title = MessageManager.formatMessage( - "label.input_cut_paste_params", new String[] - { format }); - if (viewport != null) + "label.input_cut_paste_params", + new String[] { format.toString() }); + 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) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } ((AlignViewport) viewport).addAlignment(al, title); } else @@ -239,22 +288,34 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer .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); + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); af.getViewport().setShowSequenceFeatures(showSeqFeatures); af.getViewport().setFeaturesDisplayed(fd); - af.changeColour(cs); + 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); @@ -270,15 +331,27 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } } } + else + { + System.err.println(MessageManager + .getString("label.couldnt_read_data")); + if (!Jalview.isHeadlessMode()) + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.SUPPORTED_FORMATS, + MessageManager.getString("label.couldnt_read_data"), + JOptionPane.WARNING_MESSAGE); + } + } } - /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -289,9 +362,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } } + @Override public void textarea_mousePressed(MouseEvent e) { - if (SwingUtilities.isRightMouseButton(e)) + if (e.isPopupTrigger()) { JPopupMenu popup = new JPopupMenu( MessageManager.getString("action.edit")); @@ -299,6 +373,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -308,6 +383,7 @@ 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);