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Merge branch 'features/JAL-2447experimentalFlag' into develop
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
b6a2430
..
f914108
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-22,7
+22,9
@@
package jalview.appletgui;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
@@
-44,6
+46,7
@@
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
@@
-170,14
+173,14
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded)
{
String title, boolean embedded)
{
- this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+ this(al, hiddenSeqs, hidden, applet, title, embedded, true);
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
@@
-220,9
+223,9
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
viewport.hideSequence(hiddenSeqs);
}
{
viewport.hideSequence(hiddenSeqs);
}
- if (columnSelection != null)
+ if (hidden != null)
{
{
- viewport.setColumnSelection(columnSelection);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
@@
-1072,6
+1075,14
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
delete_actionPerformed();
}
{
delete_actionPerformed();
}
+ else if (source == createGroup)
+ {
+ createGroup_actionPerformed();
+ }
+ else if (source == unGroup)
+ {
+ unGroup_actionPerformed();
+ }
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
else if (source == grpsFromSelection)
{
makeGrpsFromSelection_actionPerformed();
@@
-1917,7
+1928,8
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
{
copiedHiddenColumns = new Vector();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ for (int[] region : viewport.getAlignment().getHiddenColumns()
+ .getHiddenRegions())
{
copiedHiddenColumns.addElement(new int[] {
region[0] - hiddenOffset, region[1] - hiddenOffset });
{
copiedHiddenColumns.addElement(new int[] {
region[0] - hiddenOffset, region[1] - hiddenOffset });
@@
-2682,9
+2694,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
boolean selected = conservationMenuItem.getState();
modifyConservation.setEnabled(selected);
viewport.setConservationSelected(selected);
-
- // viewport.setAbovePIDThreshold(false);
- // abovePIDThreshold.setState(false);
+ viewport.getResidueShading().setConservationApplied(selected);
changeColour(viewport.getGlobalColourScheme());
changeColour(viewport.getGlobalColourScheme());
@@
-2703,8
+2713,11
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
boolean selected = abovePIDThreshold.getState();
modifyPID.setEnabled(selected);
viewport.setAbovePIDThreshold(selected);
- // conservationMenuItem.setState(false);
- // viewport.setConservationSelected(false);
+ if (!selected)
+ {
+ viewport.getResidueShading().setThreshold(0,
+ viewport.isIgnoreGapsConsensus());
+ }
changeColour(viewport.getGlobalColourScheme());
changeColour(viewport.getGlobalColourScheme());
@@
-2722,7
+2735,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
- .getAlignment().getSequenceAt(0), null);
+ .getAlignment().getSequenceAt(0));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
@@
-2814,29
+2827,31
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void averageDistanceTreeMenuItem_actionPerformed()
{
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
"Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
"Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
"Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
"Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+ .getBlosum62().getName(),
"Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
"Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+ .getBlosum62().getName(),
"Average distance tree using BLOSUM62");
}
"Average distance tree using BLOSUM62");
}
- void NewTreePanel(String type, String pwType, String title)
+ void newTreePanel(String type, String pwType, String title)
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
{
// are the sequences aligned?
if (!viewport.getAlignment().isAligned(false))
@@
-3342,7
+3357,10
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
.getString("action.make_groups_selection"));
grpsFromSelection.addActionListener(this);
createGroup.setLabel(MessageManager.getString("action.create_group"));
+ createGroup.addActionListener(this);
unGroup.setLabel(MessageManager.getString("action.remove_group"));
unGroup.setLabel(MessageManager.getString("action.remove_group"));
+ unGroup.addActionListener(this);
+
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
annotationColumnSelection.setLabel(MessageManager
.getString("action.select_by_annotation"));
annotationColumnSelection.addActionListener(this);
@@
-4191,9
+4209,10
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
* @param csel
* - columns to be selected on the alignment
*/
* @param csel
* - columns to be selected on the alignment
*/
- public void select(SequenceGroup sel, ColumnSelection csel)
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
{
{
- alignPanel.seqPanel.selection(sel, csel, null);
+ alignPanel.seqPanel.selection(sel, csel, hidden, null);
}
public void scrollTo(int row, int column)
}
public void scrollTo(int row, int column)