X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=e9478d9fc1ac30ee7108ce5f96d9999b87d098d4;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=77d8fc727f18e152d725d63fa059612ec458c56b;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 77d8fc7..e9478d9 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 2.8.2) - * Copyright (C) 2014 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. * @@ -20,16 +20,39 @@ */ package jalview.gui; -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.io.*; -import jalview.jbgui.*; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.ComplexAlignFile; +import jalview.api.FeaturesDisplayedI; +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; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; + +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; + /** * Cut'n'paste files into the desktop See JAL-1105 * @@ -39,7 +62,11 @@ import jalview.util.MessageManager; public class CutAndPasteTransfer extends GCutAndPasteTransfer { - AlignViewport viewport; + AlignmentViewPanel alignpanel; + + AlignViewportI viewport; + + FileParse source = null; public CutAndPasteTransfer() { @@ -56,9 +83,13 @@ 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")); @@ -100,7 +131,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer chooser.setAcceptAllFileFilterUsed(false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Text to File"); + chooser.setDialogTitle(MessageManager + .getString("label.save_text_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -168,43 +200,95 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer */ 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. - Alignment al = null; + AlignmentI al = null; if (FormatAdapter.isValidFormat(format)) { try { - al = new FormatAdapter().readFile(getText(), "Paste", format); + FormatAdapter fa = new FormatAdapter(alignpanel); + al = fa.readFile(getText(), "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); + MessageManager.formatMessage( + "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) { - for (int i = 0; i < al.getHeight(); i++) - { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); - } - - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + ((AlignViewport) viewport).addAlignment(al, title); } else { - AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + + AlignFrame af; + if (source instanceof ComplexAlignFile) + { + ColumnSelection colSel = ((ComplexAlignFile) source) + .getColumnSelection(); + 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, colSel, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + af.getViewport().setShowSequenceFeatures(showSeqFeatures); + 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); + } + af.currentFileFormat = format; - Desktop.addInternalFrame(af, MessageManager.formatMessage("label.input_cut_paste_params", new String[]{format}), - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file")); + Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + af.statusBar.setText(MessageManager + .getString("label.successfully_pasted_alignment_file")); try { @@ -215,6 +299,18 @@ 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); + } + } } /** @@ -237,8 +333,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { if (SwingUtilities.isRightMouseButton(e)) { - JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit")); - JMenuItem item = new JMenuItem(MessageManager.getString("action.copy")); + JPopupMenu popup = new JPopupMenu( + MessageManager.getString("action.edit")); + JMenuItem item = new JMenuItem( + MessageManager.getString("action.copy")); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e)