X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=112d502d9abb2335cbece27b241f1229f947cf74;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=19814882b784438b1905acbb0931adcd6d722254;hpb=7ce1382b998c007a78c9b33a3dc331e966eebc4b;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 1981488..112d502 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -20,15 +20,29 @@ */ package jalview.gui; -import jalview.datamodel.Alignment; -import jalview.io.FileParse; +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.HiddenColumns; +import jalview.datamodel.SequenceI; +import jalview.io.AlignmentFileReaderI; +import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; -import jalview.io.HtmlFile; import jalview.io.IdentifyFile; -import jalview.io.JSONFile; 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; import java.awt.Toolkit; @@ -39,9 +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; @@ -54,13 +70,17 @@ import javax.swing.SwingUtilities; public class CutAndPasteTransfer extends GCutAndPasteTransfer { - AlignViewport viewport; + AlignmentViewPanel alignpanel; + + AlignViewportI viewport; + + AlignmentFileReaderI source = null; - FileParse source = null; public CutAndPasteTransfer() { SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { textarea.requestFocus(); @@ -72,9 +92,13 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer /** * DOCUMENT ME! */ - public void setForInput(AlignViewport viewport) + public void setForInput(AlignmentViewPanel viewpanel) { - this.viewport = viewport; + this.alignpanel = viewpanel; + if (alignpanel != null) + { + this.viewport = alignpanel.getAlignViewport(); + } if (viewport != null) { ok.setText(MessageManager.getString("action.add")); @@ -109,14 +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); @@ -125,8 +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(); @@ -144,6 +172,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -157,6 +186,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -169,8 +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) { } @@ -182,78 +212,148 @@ 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. - Alignment al = null; - - if (FormatAdapter.isValidFormat(format)) + String text = getText(); + if (text.trim().length() < 1) { - try - { - FormatAdapter fa = new FormatAdapter(viewport); - 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"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), + MessageManager.getString("label.couldnt_read_data"), + JvOptionPane.WARNING_MESSAGE); } + return; + } + + // 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 (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) + 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) { - viewport.addAlignment(al, title); + ((AlignViewport) viewport).addAlignment(al, title); + viewport.applyFeaturesStyle(proxyColourScheme); } else { - AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - af.currentFileFormat = format; - Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - af.statusBar.setText(MessageManager - .getString("label.successfully_pasted_alignment_file")); - if (source instanceof HtmlFile) + AlignFrame af; + if (source instanceof ComplexAlignFile) { - ((HtmlFile) source).applySettingsToAlignFrame(af); + HiddenColumns hidden = ((ComplexAlignFile) source) + .getHiddenColumns(); + SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) + .getHiddenSequences(); + boolean showSeqFeatures = ((ComplexAlignFile) source) + .isShowSeqFeatures(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); + FeaturesDisplayedI fd = ((ComplexAlignFile) source) + .getDisplayedFeatures(); + af = new AlignFrame(al, hiddenSeqs, hidden, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + af.getViewport().setShowSequenceFeatures(showSeqFeatures); + af.getViewport().setFeaturesDisplayed(fd); + af.setMenusForViewport(); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(colourSchemeName, al); + if (cs != null) + { + af.changeColour(cs); + } } - else if (source instanceof JSONFile) + else { - ((JSONFile) source).applySettingsToAlignFrame(af); + 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.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) { } } } + else + { + System.err + .println(MessageManager.getString("label.couldnt_read_data")); + if (!Jalview.isHeadlessMode()) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + AppletFormatAdapter.getSupportedFormats(), + MessageManager.getString("label.couldnt_read_data"), + JvOptionPane.WARNING_MESSAGE); + } + } } - /** * DOCUMENT ME! * * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -264,9 +364,14 @@ 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")); @@ -274,6 +379,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -283,6 +389,7 @@ 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);