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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignFrame.java
diff --git
a/src/jalview/appletgui/AlignFrame.java
b/src/jalview/appletgui/AlignFrame.java
index
3f02c33
..
fb1ee92
100644
(file)
--- a/
src/jalview/appletgui/AlignFrame.java
+++ b/
src/jalview/appletgui/AlignFrame.java
@@
-22,6
+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.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;
@@
-43,6
+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;
@@
-169,14
+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)
@@
-219,9
+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());
@@
-1434,6
+1438,17
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
return null;
}
return null;
}
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
@@
-1441,12
+1456,14
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
if (displayTextbox)
}
if (displayTextbox)
@@
-1794,7
+1811,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
synchronized void slideSequences(boolean right, int size)
{
synchronized void slideSequences(boolean right, int size)
{
- List<SequenceI> sg = new Vector<SequenceI>();
+ List<SequenceI> sg = new Vector<>();
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
if (viewport.cursorMode)
{
sg.add(viewport.getAlignment().getSequenceAt(
@@
-1896,7
+1913,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
static StringBuffer copiedSequences;
static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static Vector<int[]> copiedHiddenColumns;
protected void copy_actionPerformed()
{
protected void copy_actionPerformed()
{
@@
-1907,7
+1924,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
SequenceGroup sg = viewport.getSelectionGroup();
copiedSequences = new StringBuffer();
- Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
+ Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
for (int i = 0; i < sg.getSize(); i++)
{
SequenceI seq = sg.getSequenceAt(i);
@@
-1920,12
+1937,13
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector();
+ copiedHiddenColumns = new Vector<>(viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : viewport.getColumnSelection().getHiddenColumns())
+ for (int[] region : copiedHiddenColumns)
{
{
- copiedHiddenColumns.addElement(new int[] {
- region[0] - hiddenOffset, region[1] - hiddenOffset });
+ region[0] = region[0] - hiddenOffset;
+ region[1] = region[1] - hiddenOffset;
}
}
else
}
}
else
@@
-2040,7
+2058,7
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
{
for (int i = 0; i < copiedHiddenColumns.size(); i++)
{
- int[] region = (int[]) copiedHiddenColumns.elementAt(i);
+ int[] region = copiedHiddenColumns.elementAt(i);
af.viewport.hideColumns(region[0], region[1]);
}
}
af.viewport.hideColumns(region[0], region[1]);
}
}
@@
-2728,7
+2746,7
@@
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()));
@@
-2820,25
+2838,31
@@
public class AlignFrame extends EmbmenuFrame implements ActionListener,
public void averageDistanceTreeMenuItem_actionPerformed()
{
public void averageDistanceTreeMenuItem_actionPerformed()
{
- NewTreePanel("AV", "PID", "Average distance tree using PID");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
+ "Average distance tree using PID");
}
public void neighbourTreeMenuItem_actionPerformed()
{
}
public void neighbourTreeMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+ "Neighbour joining tree using PID");
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
}
protected void njTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
+ .getBlosum62().getName(),
+ "Neighbour joining tree using BLOSUM62");
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
}
protected void avTreeBlosumMenuItem_actionPerformed()
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+ newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
+ .getBlosum62().getName(),
+ "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))
@@
-4196,9
+4220,10
@@
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)