X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=3eced2fc89b44548f20593715a652ba96eaf4511;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=3d52ee18e0782d021d6115a0ecf83633ef48fc05;hpb=70f9c4700f20a8fa57ed7eb974277d8bad0723c2;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 3d52ee1..3eced2f 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -20,6 +20,30 @@ */ 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.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.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; + import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.DataFlavor; @@ -28,25 +52,14 @@ 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; -import jalview.api.ComplexAlignFile; -import jalview.datamodel.Alignment; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.SequenceI; -import jalview.io.FileParse; -import jalview.io.FormatAdapter; -import jalview.io.IdentifyFile; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GCutAndPasteTransfer; -import jalview.schemes.ColourSchemeI; -import jalview.util.MessageManager; - /** * Cut'n'paste files into the desktop See JAL-1105 * @@ -56,13 +69,17 @@ import jalview.util.MessageManager; 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(); @@ -74,9 +91,13 @@ 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")); @@ -111,6 +132,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -118,7 +140,8 @@ 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); @@ -127,8 +150,8 @@ 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(); @@ -146,6 +169,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -159,6 +183,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -184,39 +209,74 @@ 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) + "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); + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } + ((AlignViewport) viewport).addAlignment(al, title); } else { @@ -224,40 +284,41 @@ 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(); - af = new AlignFrame(al, hiddenSeqs, colSel, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - + 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.changeColour(cs); - // ((HtmlFile) source).applySettingsToAlignmentView(af); + af.getViewport().setFeaturesDisplayed(fd); + af.setMenusForViewport(); + ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( + colourSchemeName, al); + if (cs != null) + { + af.changeColour(cs); + } } - // else if (source instanceof JSONFile) - // { - // ColumnSelection colSel = ((JSONFile) source).getColumnSelection(); - // SequenceI[] hiddenSeqs = ((JSONFile) source).getHiddenSequences(); - // boolean showSeqFeatures = ((HtmlFile) source).isShowSeqFeatures(); - // ColourSchemeI cs = ((HtmlFile) source).getColourScheme(); - // af = new AlignFrame(al, hiddenSeqs, colSel, - // AlignFrame.DEFAULT_WIDTH, - // AlignFrame.DEFAULT_HEIGHT); - // af.getViewport().setShowSequenceFeatures(showSeqFeatures); - // af.changeColour(cs); - // // ((JSONFile) source).applySettingsToAlignmentView(af); - // } 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); @@ -273,15 +334,27 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } } } + 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 @@ -292,9 +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")); @@ -302,6 +380,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -311,6 +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);