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JAL-535 todo: refactor logic to desktop controller class
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
68d7397
..
8e4030d
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-795,7
+795,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- System.out.println("deregistering discoverer listener");
+ // System.out.println("deregistering discoverer listener");
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
@@
-1251,7
+1251,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
- public static AlignmentExportData getAlignmentForExport(String exportFomat,
+ public static AlignmentExportData getAlignmentForExport(String exportFormat,
AlignViewportI viewport)
{
AlignmentI alignmentToExport = null;
AlignViewportI viewport)
{
AlignmentI alignmentToExport = null;
@@
-1268,7
+1268,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), exportFomat);
+ viewport.hasHiddenColumns(), exportFormat);
settings.isExportAnnotations();
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
settings.isExportAnnotations();
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
@@
-1291,7
+1291,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
return ed;
}
return ed;
}
- private static int[] getStartEnd(int[] aligmentStartEnd,
+ public static int[] getStartEnd(int[] aligmentStartEnd,
List<int[]> hiddenCols)
{
int startPos = aligmentStartEnd[0];
List<int[]> hiddenCols)
{
int startPos = aligmentStartEnd[0];
@@
-1303,7
+1303,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
for (int[] hiddenCol : hiddenCols)
{
// System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
for (int[] hiddenCol : hiddenCols)
{
// System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
-
lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
}
lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
}
@@
-1498,6
+1497,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (closeAllTabs)
{
if (closeAllTabs)
{
+ /*
+ * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+ * be called recursively, with the frame now in 'closed' state
+ */
this.setClosed(true);
}
} catch (Exception ex)
this.setClosed(true);
}
} catch (Exception ex)
@@
-2750,12
+2753,17
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
/*
}
/*
- * Views share the same edits, undo and redo stacks, mappings.
+ * Views share the same edits undo and redo stacks
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
- newap.av.getAlignment().setCodonFrames(
- viewport.getAlignment().getCodonFrames());
+
+ /*
+ * Views share the same mappings; need to deregister any new mappings
+ * created by copyAlignPanel, and register the new reference to the shared
+ * mappings
+ */
+ newap.av.replaceMappings(viewport.getAlignment());
newap.av.viewName = getNewViewName(viewTitle);
newap.av.viewName = getNewViewName(viewTitle);
@@
-4526,8
+4534,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
try
{
final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
try
{
- System.err.println("Building ws menu again "
- + Thread.currentThread());
+ // System.err.println("Building ws menu again "
+ // + Thread.currentThread());
// TODO: add support for context dependent disabling of services based
// on
// alignment and current selection
// TODO: add support for context dependent disabling of services based
// on
// alignment and current selection
@@
-4879,7
+4887,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
al.getCodonFrames().addAll(cf);
final StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
al.getCodonFrames().addAll(cf);
final StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(cf);
+ ssm.registerMappings(cf);
}
else
{
}
else
{
@@
-4969,10
+4977,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
"Exception during translation. Please report this !", ex);
final String msg = MessageManager
.getString("label.error_when_translating_sequences_submit_bug_report");
"Exception during translation. Please report this !", ex);
final String msg = MessageManager
.getString("label.error_when_translating_sequences_submit_bug_report");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("translation_failed");
.getString("label.implementation_error")
+ MessageManager.getString("translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
}
JOptionPane.ERROR_MESSAGE);
return;
}
@@
-4980,9
+4988,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
final String msg = MessageManager
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
{
final String msg = MessageManager
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.translation_failed");
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.WARNING_MESSAGE);
}
else
JOptionPane.WARNING_MESSAGE);
}
else
@@
-4996,8
+5004,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs),
- al.getCodonFrames());
+ viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
}
else
{
@@
-6089,7
+6096,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
sf.setComplementVisible(this, show);
}
}
sf.setComplementVisible(this, show);
}
}
-
}
class PrintThread extends Thread
}
class PrintThread extends Thread