import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
+import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
{
Font font;
- TreeModel currentTree = null;
-
boolean cursorMode = false;
boolean antiAlias = false;
}
/**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(TreeModel tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public TreeModel getCurrentTree()
- {
- return currentTree;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
* area
* @return
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- int[] viscontigs = null;
- int start = 0, end = 0;
+ int start = 0;
+ int end = 0;
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
{
end = alignment.getWidth();
}
- viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
- return viscontigs;
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
}
/**
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
{
if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(toAdd, title))
- {
- return;
- }
+ openLinkedAlignment(toAdd, title);
+ return;
}
}
+ alignmentDataAdded(toAdd);
+ }
+ private void alignmentDataAdded(AlignmentI toAdd)
+ {
/*
* No mappings, or offer declined - add sequences to this alignment
*/
* @param al
* @param title
*/
- protected boolean openLinkedAlignment(AlignmentI al, String title)
+ protected void openLinkedAlignment(AlignmentI al, String title)
{
String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+ final AlignViewport us = this;
+ JvOptionPane.newOptionDialog(Desktop.desktop)
+ .response(new RunResponse(1)
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, true);
+ }
+ }).response(new RunResponse(2)
+ {
+ @Override
+ public void run()
+ {
+ us.openLinkedAlignmentAs(al, title, false);
+ }
+ }).defaultResponse(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ alignmentDataAdded(al);
+ }
+ }).showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
+ }
- if (response != 1 && response != 2)
+ protected void openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane)
{
- return false;
- }
- final boolean openSplitPane = (response == 1);
- final boolean openInNewWindow = (response == 2);
-
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ AlignmentI thisAlignment = newWindowOrSplitPane
+ ? new Alignment(getAlignment())
: getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
// alignFrame.setFileName(file, format);
// }
- if (openInNewWindow)
+ if (!newWindowOrSplitPane)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
{
}
- if (openSplitPane)
+ if (newWindowOrSplitPane)
{
al.alignAs(thisAlignment);
protein = openSplitFrame(newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
}
fr.setTransparency(featureSettings.getTransparency());
}
-
}