import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
-import jalview.analysis.AnnotationSorter.SortOrder;
import jalview.analysis.Conservation;
import jalview.analysis.CrossRef;
import jalview.analysis.NJTree;
import jalview.datamodel.SequenceI;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BioJsHTMLOutput;
import jalview.io.FeaturesFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
}
/**
- * Make a new AlignFrame from exisiting alignmentPanels
+ * Make a new AlignFrame from existing alignmentPanels
*
* @param ap
* AlignmentPanel
scaleRight.setVisible(av.wrapAlignment);
annotationPanelMenuItem.setState(av.showAnnotation);
/*
- * Show/hide all annotations only enabled if annotation panel is shown
+ * Show/hide annotations only enabled if annotation panel is shown
*/
- showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
viewBoxesMenuItem.setSelected(av.showBoxes);
viewTextMenuItem.setSelected(av.showText);
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
}
+ @Override
+ public void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+ new BioJsHTMLOutput(alignPanel,
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+ }
public void createImageMap(File file, String image)
{
alignPanel.makePNGImageMap(file, image);
alignPanel.makeEPS(f);
}
+ public void createSVG(File f)
+ {
+ alignPanel.makeSVG(f);
+ }
@Override
public void pageSetup_actionPerformed(ActionEvent e)
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
alignPanel.setAnnotationVisible(setVisible);
- this.showAllAnnotations.setEnabled(setVisible);
- this.hideAllAnnotations.setEnabled(setVisible);
+ this.showAllSeqAnnotations.setEnabled(setVisible);
+ this.hideAllSeqAnnotations.setEnabled(setVisible);
+ this.showAllAlAnnotations.setEnabled(setVisible);
+ this.hideAllAlAnnotations.setEnabled(setVisible);
}
@Override
{
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
- (String) fm[1], toassoc, false);
+ (String) fm[1], toassoc, false,
+ Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
}
/**
- * Action on selection of menu option to Show or Hide all annotations.
+ * Action on selection of menu options to Show or Hide annotations.
*
- * @param visibile
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
*/
@Override
- protected void setAllAnnotationsVisibility(boolean visible)
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
{
for (AlignmentAnnotation aa : alignPanel.getAlignment()
.getAlignmentAnnotation())
{
- aa.visible = visible;
+ boolean apply = (aa.sequenceRef == null && forAlignment)
+ || (aa.sequenceRef != null && forSequences);
+ if (apply)
+ {
+ aa.visible = visible;
+ }
}
this.alignPanel.paintAlignment(true);
}
* Store selected annotation sort order for the view and repaint.
*/
@Override
- protected void sortAnnotations_actionPerformed(SortOrder sortOrder)
+ protected void sortAnnotations_actionPerformed()
{
- this.alignPanel.av.setSortAnnotationsBy(sortOrder);
- alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
}
}