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JAL-3132 set status message when over sequence id or annotation label
[jalview.git]
/
src
/
jalview
/
gui
/
CutAndPasteTransfer.java
diff --git
a/src/jalview/gui/CutAndPasteTransfer.java
b/src/jalview/gui/CutAndPasteTransfer.java
index
ca79a83
..
b3bff0d
100644
(file)
--- 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.api.FeaturesSourceI;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
@@
-52,9
+52,11
@@
import java.awt.datatransfer.Transferable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
import java.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.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
@@
-71,7
+73,7
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
AlignViewportI viewport;
AlignViewportI viewport;
- AlignmentFileI source = null;
+ AlignmentFileReaderI source = null;
public CutAndPasteTransfer()
{
public CutAndPasteTransfer()
{
@@
-138,8
+140,8
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
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);
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@
-148,8
+150,8
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
{
try
{
{
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();
out.print(getText());
out.close();
@@
-194,8
+196,8
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
try
{
try
{
- textarea.append((String) contents
- .getTransferData(DataFlavor.stringFlavor));
+ textarea.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
} catch (Exception ex)
{
}
} catch (Exception ex)
{
}
@@
-226,14
+228,14
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
}
if (format == null)
{
}
if (format == null)
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
if (!Jalview.isHeadlessMode())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- AppletFormatAdapter.SUPPORTED_FORMATS,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
}
return;
}
@@
-247,20
+249,20
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
al = fa.readFile(getText(), DataSourceType.PASTE, format);
source = fa.getAlignFile();
al = fa.readFile(getText(), DataSourceType.PASTE, format);
source = fa.getAlignFile();
- } catch (java.io.IOException ex)
+ } catch (IOException ex)
{
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.couldnt_read_pasted_text", new String[]
.formatMessage("label.couldnt_read_pasted_text", new String[]
- { ex.toString() }), MessageManager
- .getString("label.error_parsing_text"),
- JOptionPane.WARNING_MESSAGE);
+ { ex.toString() }),
+ MessageManager.getString("label.error_parsing_text"),
+ JvOptionPane.WARNING_MESSAGE);
}
if (al != null && al.hasValidSequence())
{
}
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();
FeatureSettingsModelI proxyColourScheme = source
.getFeatureColourScheme();
@@
-282,8
+284,8
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
AlignFrame af;
if (source instanceof ComplexAlignFile)
{
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)
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
@@
-292,10
+294,11
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
.getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
.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);
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)
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
if (cs != null)
@@
-319,13
+322,13
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
af.currentFileFormat = format;
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
af.currentFileFormat = format;
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText(MessageManager
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
{
.getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
} catch (Exception ex)
{
}
@@
-333,14
+336,14
@@
public class CutAndPasteTransfer extends GCutAndPasteTransfer
}
else
{
}
else
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- AppletFormatAdapter.SUPPORTED_FORMATS,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
}
}
}