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.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;
}
public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
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,
- ColumnSelection columnSelection, JalviewLite applet,
+ HiddenColumns hidden, JalviewLite applet,
String title, boolean embedded, boolean addToDisplay)
{
if (applet != null)
{
viewport.hideSequence(hiddenSeqs);
}
- if (columnSelection != null)
+ if (hidden != null)
{
- viewport.setColumnSelection(columnSelection);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
viewport.setScaleAboveWrapped(scaleAbove.getState());
}
case KeyEvent.VK_PAGE_UP:
- if (viewport.getWrapAlignment())
- {
- ranges.scrollUp(true);
- }
- else
- {
- ranges.pageUp();
- }
+ ranges.pageUp();
break;
case KeyEvent.VK_PAGE_DOWN:
- if (viewport.getWrapAlignment())
- {
- ranges.scrollUp(false);
- }
- else
- {
- ranges.pageDown();
- }
+ ranges.pageDown();
break;
case KeyEvent.VK_Z:
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(
static StringBuffer copiedSequences;
- static Vector copiedHiddenColumns;
+ static Vector<int[]> copiedHiddenColumns;
protected void copy_actionPerformed()
{
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);
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector();
+ copiedHiddenColumns = new Vector<>(viewport.getAlignment()
+ .getHiddenColumns().getHiddenColumnsCopy());
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
{
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]);
}
}
}
Frame frame = new Frame();
- OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel);
frame.add(overview);
// +50 must allow for applet frame window
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
@Override
public void windowClosing(WindowEvent e)
{
+ overview.dispose();
if (ap != null)
{
ap.setOverviewPanel(null);
{
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()));
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()
{
- NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+ newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
+ "Neighbour joining tree using PID");
}
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()
{
- 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))
* @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)