private BaseFineEditor(
AnnotatedFeatureI editMe,
GuiCurationState curationState,
SeqFeatureI geneHolder,
Set<SeqFeatureI> selectedResults) {
super((editMe.isForwardStrand() ? "Forward" : "Reverse") + " Strand Exon Editor");
this.curationState = curationState;
curationState.getController().addListener(this);
curationState.getController().addListener(new BaseEditorDataListener());
szap = curationState.getSZAP();
transformer = szap.getScaleView().getTransform();
int seqStart = curationState.getCurationSet().getLow();
int seqEnd = curationState.getCurationSet().getHigh();
CurationSet s = curationState.getCurationSet();
// FeatureSetI annFeatSet=((DrawableFeatureSet)view.getDrawableSet()).getFeatureSet();
// REFACTOR BaseEditorPanel - (what allows for selection and modification of the annotations?)
// create BaseViewPanel -> have BaseEditorPanel extend it
// take the header outside of the editorPanel (is it really inside right now?)
// create a new panel using BaseViewPanel
/*
* The viewable components of the new BaseFineEditor (should this be renamed?):
*
* 1) The Genomic Strand
* 2) The Annotations (will these always be a copy of the genomic strand?)
* q1) Can annotations also be nucliotides? - A: Yes. Create a separate view for those.
* q2) Does it make sense to view both the forward and reverse strand at once?
* q3) How do we know what to load - A: highlight the region we want to look at?
* q4) Will we expect users to be able to view many annotations at once?
* q4) How will the user know which annotation they are looking at? - A: Display the name when hovering over?
* 3) The Results
* q1) See above questions.
* 4) Result Score information
* 5) An overview - Right now this is at the transcript (gene model?) level
* q1) What should be contained in this view?
*
*
*/
// I think that right now every base in the ede is a copy of the genomic, will that always be
// the case?
// is there ever sequence associated with an annotation.
editorPanel =
new BaseEditorPanel(
curationState, this, !editMe.isForwardStrand(), seqStart, seqEnd, geneHolder);
addResults(selectedResults);
initGui(editMe); // cant do til after editorPanel made
// cant do this til after initGui (editorPanel needs to know size)
editorPanel.displayAnnot(editMe);
attachListeners();
showEditRegion();
displayAnnot(getTransOrOneLevelAnn(editMe));
translationViewer.repaint();
setVisible(true);
// Might just be linux, but bofe gets iconified on close
if (getState() == Frame.ICONIFIED) setState(Frame.NORMAL);
}
private BaseFineEditor(
AnnotatedFeatureI editMe, GuiCurationState curationState, SeqFeatureI geneHolder) {
super((editMe.isForwardStrand() ? "Forward" : "Reverse") + " Strand Exon Editor");
this.curationState = curationState;
curationState.getController().addListener(this);
curationState.getController().addListener(new BaseEditorDataListener());
szap = curationState.getSZAP();
transformer = szap.getScaleView().getTransform();
int seqStart = curationState.getCurationSet().getLow();
int seqEnd = curationState.getCurationSet().getHigh();
// FeatureSetI annFeatSet=((DrawableFeatureSet)view.getDrawableSet()).getFeatureSet();
editorPanel =
new BaseEditorPanel(
curationState, this, !editMe.isForwardStrand(), seqStart, seqEnd, geneHolder);
initGui(editMe); // cant do til after editorPanel made
// cant do this til after initGui (editorPanel needs to know size)
editorPanel.displayAnnot(editMe);
attachListeners();
showEditRegion();
displayAnnot(getTransOrOneLevelAnn(editMe));
translationViewer.repaint();
setVisible(true);
// Might just be linux, but bofe gets iconified on close
if (getState() == Frame.ICONIFIED) setState(Frame.NORMAL);
}
private boolean isSequencingErrorPosition(int bp, SeqFeatureI feature, SequenceType type) {
boolean result = false;
if (type == SequenceType.DNA) {
result = curationState.getCurationSet().getRefSequence().isSequencingErrorPosition(bp);
} else {
result =
curationState.getCurationSet().getRefSequence().isSequencingErrorPosition(bp)
|| curationState
.getCurationSet()
.getRefSequence()
.isSequencingErrorPosition(bp + feature.getStrand())
|| curationState
.getCurationSet()
.getRefSequence()
.isSequencingErrorPosition(bp + (2 * feature.getStrand()));
}
return result;
}
/** Performs the update */
public void actionPerformed(ActionEvent e) {
// TODO check that the basepair is within the bounds of an exon
if (basepair < 0 || feature == null) {
throw new IllegalArgumentException("basepair:" + basepair + " feature:" + feature);
}
annotationEditor.setSelections(null, null, null, null);
annotationEditor.setTranslationStart((ExonI) feature, basepair);
curationState.getSZAP().repaint();
// TODO repaint all msa's
}
public SelectionManager getSelectionManager() {
return curationState.getSelectionManager(); // this.selection_manager;
}
public Controller getController() {
return curationState.getController();
}
private Controller getController() {
return curationState.getController();
}