viewer.setXpos(panel.getX());
viewer.setYpos(panel.getY());
viewer.setTitle(panel.getTitle());
- PCAModel pcaModel = panel.pcaModel;
+ PCAModel pcaModel = panel.getPcaModel();
viewer.setScoreModelName(pcaModel.getScoreModelName());
viewer.setXDim(panel.getSelectedDimensionIndex(X));
viewer.setYDim(panel.getSelectedDimensionIndex(Y));
viewer.setZDim(panel.getSelectedDimensionIndex(Z));
- viewer.setBgColour(panel.rc.getBackgroundColour().getRGB());
- viewer.setScaleFactor(panel.rc.scaleFactor);
- float[] spMin = panel.rc.getSeqMin();
+ viewer.setBgColour(panel.getRotatableCanvas().getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+ float[] spMin = panel.getRotatableCanvas().getSeqMin();
SeqPointMin spmin = new SeqPointMin();
spmin.setXPos(spMin[0]);
spmin.setYPos(spMin[1]);
spmin.setZPos(spMin[2]);
viewer.setSeqPointMin(spmin);
- float[] spMax = panel.rc.getSeqMax();
+ float[] spMax = panel.getRotatableCanvas().getSeqMax();
SeqPointMax spmax = new SeqPointMax();
spmax.setXPos(spMax[0]);
spmax.setYPos(spMax[1]);
spmax.setZPos(spMax[2]);
viewer.setSeqPointMax(spmax);
- viewer.setShowLabels(panel.rc.showLabels);
- viewer.setLinkToAllViews(panel.rc.applyToAllViews);
+ viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+ viewer.setLinkToAllViews(panel.getRotatableCanvas().isApplyToAllViews());
SimilarityParamsI sp = pcaModel.getSimilarityParameters();
viewer.setIncludeGaps(sp.includeGaps());
viewer.setMatchGaps(sp.matchGaps());
/*
* (end points of) axes on display
*/
- for (Point p : panel.rc.axisEndPoints)
+ for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
{
Axis axis = new Axis();
axis.setXPos(p.x);
boolean showLabels = viewer.isShowLabels();
panel.setShowLabels(showLabels);
- panel.rc.showLabels = showLabels;
- panel.rc.bgColour = new Color(viewer.getBgColour());
- panel.rc.applyToAllViews = viewer.isLinkToAllViews();
+ panel.getRotatableCanvas().setShowLabels(showLabels);
+ panel.getRotatableCanvas().setBgColour(new Color(viewer.getBgColour()));
+ panel.getRotatableCanvas().setApplyToAllViews(viewer.isLinkToAllViews());
/*
* load PCA output data
MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix());
pca.setEigenmatrix(result);
- panel.pcaModel.setPCA(pca);
+ panel.getPcaModel().setPCA(pca);
/*
* we haven't saved the input data! (JAL-2647 to do)
seq, pt);
seqPoints.add(seqPoint);
}
- panel.rc.setPoints(seqPoints, seqPoints.size());
+ panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size());
/*
* set min-max ranges and scale after setPoints (which recomputes them)
*/
- panel.rc.scaleFactor = viewer.getScaleFactor();
+ panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor());
SeqPointMin spMin = viewer.getSeqPointMin();
float[] min = new float[] { spMin.getXPos(), spMin.getYPos(),
spMin.getZPos() };
SeqPointMax spMax = viewer.getSeqPointMax();
float[] max = new float[] { spMax.getXPos(), spMax.getYPos(),
spMax.getZPos() };
- panel.rc.setSeqMinMax(min, max);
+ panel.getRotatableCanvas().setSeqMinMax(min, max);
// todo: hold points list in PCAModel only
- panel.pcaModel.setSequencePoints(seqPoints);
+ panel.getPcaModel().setSequencePoints(seqPoints);
panel.setSelectedDimensionIndex(viewer.getXDim(), X);
panel.setSelectedDimensionIndex(viewer.getYDim(), Y);
panel.setSelectedDimensionIndex(viewer.getZDim(), Z);
// is this duplication needed?
- panel.top = seqPoints.size() - 1;
- panel.pcaModel.setTop(seqPoints.size() - 1);
+ panel.setTop(seqPoints.size() - 1);
+ panel.getPcaModel().setTop(seqPoints.size() - 1);
/*
* add the axes' end points for the display
for (int i = 0; i < 3; i++)
{
Axis axis = viewer.getAxis(i);
- panel.rc.axisEndPoints[i] = new Point(axis.getXPos(),
+ panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point(axis.getXPos(),
axis.getYPos(), axis.getZPos());
}