X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=54e41254221070ff0e2d9dbb70147898ed4bb849;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=7268ae5f79b47d2978700b4bd6cb8f5809b25b4b;hpb=bccb3f12a82f40bea6836bd7dcb4b45abd45b0be;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 7268ae5..54e4125 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -23,15 +23,21 @@ 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.AppletFormatAdapter; 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.json.binding.biojson.v1.ColourSchemeMapper; import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; @@ -63,10 +69,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignViewportI viewport; FileParse source = null; + public CutAndPasteTransfer() { SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { textarea.requestFocus(); @@ -119,6 +127,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer textarea.append(text); } + @Override public void save_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -126,7 +135,8 @@ 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); @@ -154,6 +164,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void copyItem_actionPerformed(ActionEvent e) { textarea.getSelectedText(); @@ -167,6 +178,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void pasteMenu_actionPerformed(ActionEvent e) { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); @@ -192,9 +204,30 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer * @param e * DOCUMENT ME! */ + @Override public void ok_actionPerformed(ActionEvent e) { - String format = new IdentifyFile().Identify(getText(), "Paste"); + String text = getText(); + if (text.trim().length() < 1) + { + return; + } + + String format = new IdentifyFile().identify(text, "Paste"); + if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE")) + { + 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); + } + return; + } + // TODO: identify feature, annotation or tree file and parse appropriately. AlignmentI al = null; @@ -210,20 +243,30 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage( - "label.couldnt_read_pasted_text", new String[] - { ex.toString() }), MessageManager + "label.couldnt_read_pasted_text", + new String[] { ex.toString() }), MessageManager .getString("label.error_parsing_text"), JOptionPane.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 }); + 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 @@ -238,20 +281,34 @@ 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.changeColour(cs); + af.getViewport().setFeaturesDisplayed(fd); + 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); @@ -267,15 +324,27 @@ 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 @@ -286,9 +355,14 @@ 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")); @@ -296,6 +370,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copyItem_actionPerformed(e); @@ -305,6 +380,7 @@ 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);