X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=7a0b0affd06e8104422d3ba715fe05d7a7481dff;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=e9478d9fc1ac30ee7108ce5f96d9999b87d098d4;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index e9478d9..7a0b0af 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -23,13 +23,18 @@ 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.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; @@ -47,9 +52,11 @@ 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; @@ -66,12 +73,13 @@ 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(); @@ -124,6 +132,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -141,8 +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(); @@ -160,6 +169,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -173,6 +183,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -198,6 +209,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { String text = getText(); @@ -206,17 +218,24 @@ 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 + { + 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; } @@ -224,31 +243,39 @@ 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) + "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) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } ((AlignViewport) viewport).addAlignment(al, title); } else @@ -282,8 +309,15 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { 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); @@ -305,10 +339,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer .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); } } } @@ -319,6 +353,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void cancel_actionPerformed(ActionEvent e) { try @@ -329,9 +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")); @@ -339,6 +379,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -348,6 +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);