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.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
-import java.awt.EventQueue;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
public void setFeatureGroupStateOn(final AlignFrameI alf,
final String groups, boolean state)
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
public void scrollViewToIn(final AlignFrameI alf, final String topRow,
final String leftHandColumn)
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
public void scrollViewToRowIn(final AlignFrameI alf, final String topRow)
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
public void scrollViewToColumnIn(final AlignFrameI alf,
final String leftHandColumn)
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
if (alignedPosition != null && (alignedPosition.trim().length() == 0
|| alignedPosition.toLowerCase().indexOf("false") > -1))
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
}
else
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
}
sel.setStartRes(start);
sel.setEndRes(end);
- EventQueue.invokeLater(new Runnable()
+ Jalview.execRunnable(new Runnable()
{
@Override
public void run()
{
return "";
}
- ;
final AlignmentOrder aorder = new AlignmentOrder(sqs);
if (undoName != null && undoName.trim().length() == 0)
}
}
+ public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+ {
+ if (new AnnotationFile().annotateAlignmentView(
+ ((AlignFrame) alf).getViewport(), annotation,
+ DataSourceType.PASTE))
+ {
+ ((AlignFrame) alf).alignPanel.fontChanged();
+ ((AlignFrame) alf).alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ ((AlignFrame) alf).parseFeaturesFile(annotation,
+ DataSourceType.PASTE);
+ }
+ }
+
+ public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ boolean autoenabledisplay)
+ {
+ boolean ret = ((AlignFrame) alf).parseFeaturesFile(features,
+ DataSourceType.PASTE);
+ if (!ret)
+ {
+ return false;
+ }
+ if (autoenabledisplay)
+ {
+ ((AlignFrame) alf).getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ }
+ return true;
+ }
+
+ public String getFeaturesFrom(AlignFrameI alf, String format,
+ boolean includeNonpositionsFeatures, boolean includeComplement)
+ {
+ AlignFrame f = ((AlignFrame) alf);
+
+ String features;
+ FeaturesFile formatter = new FeaturesFile();
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ features = formatter.printJalviewFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(),
+ includeNonpositionsFeatures, includeComplement);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ f.getViewport().getAlignment().getSequencesArray(),
+ f.alignPanel.getFeatureRenderer(),
+ includeNonpositionsFeatures, includeComplement);
+ }
+
+ if (features == null)
+ {
+ features = "";
+ }
+ return features;
+
+ }
+
+ public String getAnnotationFrom(AlignFrameI alf)
+ {
+ AlignFrame f = (AlignFrame) alf;
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(f.getViewport());
+ return annotation;
+ }
+
+ public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+ {
+ return (AlignFrameI) ((AlignFrame) alf).newView(name, true);
+ }
+
+ public String[] separatorListToArray(String list)
+ {
+ return separatorListToArray(list, separator);
+ }
+
+ public Object[] getSelectionForListener(AlignFrameI currentFrame,
+ SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof AlignViewport
+ && ((AlignFrame) currentFrame).getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = (AlignFrame) currentFrame;
+
+ }
+ }
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (src == null) ? -1
+ : src.alignPanel.av.getAlignment().getWidth();
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ seqs = new String[seqsel.getSize()];
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = seqsel.getSequenceAt(i).getName();
+ }
+ if (strt < seqsel.getStartRes())
+ {
+ strt = seqsel.getStartRes();
+ }
+ if (end == -1 || end > seqsel.getEndRes())
+ {
+ end = seqsel.getEndRes();
+ }
+ }
+ if (colsel != null && !colsel.isEmpty())
+ {
+ if (end == -1)
+ {
+ end = colsel.getMax() + 1;
+ }
+ cols = new String[colsel.getSelected().size()];
+ for (int i = 0; i < cols.length; i++)
+ {
+ cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ }
+ }
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[2];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ return new Object[] { src, setid, arrayToSeparatorList(seqs),
+ arrayToSeparatorList(cols) };
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff