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JAL-2089 cleared out old ‘What’s new’
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
401ccb7
..
bfbc969
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-473,7
+473,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void focusGained(FocusEvent e)
{
@Override
public void focusGained(FocusEvent e)
{
- Desktop.setCurrentAlignFrame(AlignFrame.this);
+ Jalview.setCurrentAlignFrame(AlignFrame.this);
}
});
}
});
@@
-1313,7
+1313,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{
- omitHidden = viewport.getViewAsString(false);
+ omitHidden = viewport.getViewAsString(false,
+ settings.isExportHiddenSequences());
}
int[] alignmentStartEnd = new int[2];
}
int[] alignmentStartEnd = new int[2];
@@
-1324,17
+1325,15
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
else
{
alignmentToExport = viewport.getAlignment();
else
{
alignmentToExport = viewport.getAlignment();
- alignmentStartEnd = viewport.getAlignment()
- .getVisibleStartAndEndIndex(
- viewport
- .getColumnSelection().getHiddenColumns());
}
}
+ alignmentStartEnd = alignmentToExport
+ .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+ .getHiddenColumns());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
}
-
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-4681,6
+4680,17
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
return showp;
}
return showp;
}
+ /**
+ * Finds and displays cross-references for the selected sequences (protein
+ * products for nucleotide sequences, dna coding sequences for peptides).
+ *
+ * @param sel
+ * the sequences to show cross-references for
+ * @param dna
+ * true if from a nucleotide alignment (so showing proteins)
+ * @param source
+ * the database to show cross-references for
+ */
protected void showProductsFor(final SequenceI[] sel, final boolean dna,
final String source)
{
protected void showProductsFor(final SequenceI[] sel, final boolean dna,
final String source)
{
@@
-4751,7
+4761,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
System.err.println("Failed to make CDS alignment");
}
al.getCodonFrames().clear();
System.err.println("Failed to make CDS alignment");
}
al.getCodonFrames().clear();
- al.getCodonFrames().addAll(copyAlignment.getCodonFrames());
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
/*
* pending getting Embl transcripts to 'align',
/*
* pending getting Embl transcripts to 'align',
@@
-4769,7
+4780,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
copyAlignment = AlignmentUtils.makeCopyAlignment(
sequenceSelection, xrefs.getSequencesArray());
{
copyAlignment = AlignmentUtils.makeCopyAlignment(
sequenceSelection, xrefs.getSequencesArray());
- copyAlignment.getCodonFrames().addAll(cf);
+ copyAlignment.addCodonFrames(cf);
+ al.addCodonFrames(copyAlignment.getCodonFrames());
+ al.addCodonFrames(cf);
}
copyAlignment.setGapCharacter(AlignFrame.this.viewport
.getGapCharacter());
}
copyAlignment.setGapCharacter(AlignFrame.this.viewport
.getGapCharacter());
@@
-4844,15
+4857,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- Cache.log.error(
- "Exception when finding crossreferences", e);
+ Cache.log.error("Exception when finding crossreferences", e);
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
} catch (OutOfMemoryError e)
{
new OOMWarning("whilst fetching crossreferences", e);
} catch (Throwable e)
{
- Cache.log.error("Error when finding crossreferences",
- e);
+ Cache.log.error("Error when finding crossreferences", e);
} finally
{
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
} finally
{
AlignFrame.this.setProgressBar(MessageManager.formatMessage(
@@
-4930,7
+4941,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getString("label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
.getString("label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
.getString("label.implementation_error")
- + MessageManager.getString("translation_failed");
+ + MessageManager.getString("label.translation_failed");
JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
@@
-5508,8
+5519,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
AlignFrame.this.setMenusForViewport();
}
});
AlignFrame.this.setMenusForViewport();
}
});
- dbRefFetcher
- .fetchDBRefs(false);
+ dbRefFetcher.fetchDBRefs(false);
}
}).start();
}
}).start();
@@
-6067,9
+6077,12
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
-
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
al = dna.reverseCdna(complement);
viewport.addAlignment(al, "");
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.add_sequences"),
+ Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+ viewport.getAlignment()));
} catch (Exception ex)
{
System.err.println(ex.getMessage());
} catch (Exception ex)
{
System.err.println(ex.getMessage());
@@
-6085,7
+6098,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
protected void runGroovy_actionPerformed()
{
@Override
protected void runGroovy_actionPerformed()
{
- Desktop.setCurrentAlignFrame(this);
+ Jalview.setCurrentAlignFrame(this);
groovy.ui.Console console = Desktop.getGroovyConsole();
if (console != null)
{
groovy.ui.Console console = Desktop.getGroovyConsole();
if (console != null)
{