X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;fp=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=2a96daf35b271498f4f9beff9e6657922c102a61;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=df0142cd524919c33d86ce11932b2cdf0a87339e;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index df0142c..2a96daf 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -28,9 +28,9 @@ import jalview.api.FeaturesDisplayedI; import jalview.api.FeaturesSourceI; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; -import jalview.io.AlignmentFileI; +import jalview.io.AlignmentFileReaderI; import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormatException; @@ -73,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer AlignViewportI viewport; - AlignmentFileI source = null; + AlignmentFileReaderI source = null; public CutAndPasteTransfer() { @@ -140,8 +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); @@ -150,8 +150,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { try { - PrintWriter out = new PrintWriter(new FileWriter( - chooser.getSelectedFile())); + PrintWriter out = new PrintWriter( + new FileWriter(chooser.getSelectedFile())); out.print(getText()); out.close(); @@ -196,8 +196,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer try { - textarea.append((String) contents - .getTransferData(DataFlavor.stringFlavor)); + textarea.append( + (String) contents.getTransferData(DataFlavor.stringFlavor)); } catch (Exception ex) { } @@ -228,12 +228,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } if (format == null) { - System.err.println(MessageManager - .getString("label.couldnt_read_data")); + System.err + .println(MessageManager.getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } @@ -253,16 +253,16 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.couldnt_read_pasted_text", new String[] - { ex.toString() }), MessageManager - .getString("label.error_parsing_text"), + { 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.toString() }); + String title = MessageManager + .formatMessage("label.input_cut_paste_params", new String[] + { format.getName() }); FeatureSettingsModelI proxyColourScheme = source .getFeatureColourScheme(); @@ -284,8 +284,8 @@ 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) @@ -294,10 +294,11 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer .getGlobalColourScheme(); FeaturesDisplayedI fd = ((ComplexAlignFile) source) .getDisplayedFeatures(); - af = new AlignFrame(al, hiddenSeqs, colSel, + 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) @@ -326,8 +327,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer try { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", - false)); + af.setMaximum( + jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { } @@ -335,12 +336,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } else { - System.err.println(MessageManager - .getString("label.couldnt_read_data")); + System.err + .println(MessageManager.getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - AppletFormatAdapter.SUPPORTED_FORMATS, + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); }