import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.util.MessageManager;
-import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.Color;
import java.util.BitSet;
private AlignViewControllerGuiI avcg;
public AlignViewController(AlignViewControllerGuiI alignFrame,
- AlignViewportI viewport, AlignmentViewPanel alignPanel)
+ AlignViewportI vp, AlignmentViewPanel ap)
{
this.avcg = alignFrame;
- this.viewport = viewport;
- this.alignPanel = alignPanel;
+ this.viewport = vp;
+ this.alignPanel = ap;
}
@Override
- public void setViewportAndAlignmentPanel(AlignViewportI viewport,
- AlignmentViewPanel alignPanel)
+ public void setViewportAndAlignmentPanel(AlignViewportI vp,
+ AlignmentViewPanel ap)
{
- this.alignPanel = alignPanel;
- this.viewport = viewport;
-
+ this.alignPanel = ap;
+ this.viewport = vp;
}
@Override
/**
* Sets a bit in the BitSet for each column (base 0) in the sequence
- * collection which includes the specified feature type. Returns the number of
- * sequences which have the feature in the selected range.
+ * collection which includes a visible feature of the specified feature type.
+ * Returns the number of sequences which have the feature visible in the
+ * selected range.
*
* @param featureType
* @param sqcol
int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
- FeatureRendererModel fr = (FeatureRendererModel) alignPanel
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
.getFeatureRenderer();
- List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
List<SequenceFeature> sfs = sq.findFeatures(startColumn,
endColumn, featureType);
- if (!sfs.isEmpty())
- {
- nseq++;
- }
-
+ boolean found = false;
for (SequenceFeature sf : sfs)
{
- {
- if (!visibleFeatures.contains(sf.getType())
- || fr.getColour(sf) == null) // could pull up getColour to FeatureRenderer interface
- {
- continue;
- }
+ if (fr.getColour(sf) == null)
+ {
+ continue;
+ }
+ if (!found)
+ {
+ nseq++;
}
+ found = true;
+
int sfStartCol = sq.findIndex(sf.getBegin());
int sfEndCol = sq.findIndex(sf.getEnd());
}
@Override
- public boolean parseFeaturesFile(String file, DataSourceType protocol,
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
boolean relaxedIdMatching)
{
- boolean featuresFile = false;
+ boolean featuresAdded = false;
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
try
{
- featuresFile = new FeaturesFile(false, file, protocol).parse(
- viewport.getAlignment().getDataset(),
- alignPanel.getFeatureRenderer().getFeatureColours(), false,
- relaxedIdMatching);
+ featuresAdded = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+ fr.getFeatureFilters(), false, relaxedIdMatching);
} catch (Exception ex)
{
ex.printStackTrace();
}
- if (featuresFile)
+ if (featuresAdded)
{
avcg.refreshFeatureUI(true);
- if (alignPanel.getFeatureRenderer() != null)
+ if (fr != null)
{
// update the min/max ranges where necessary
- alignPanel.getFeatureRenderer().findAllFeatures(true);
+ fr.findAllFeatures(true);
}
if (avcg.getFeatureSettingsUI() != null)
{
alignPanel.paintAlignment(true, true);
}
- return featuresFile;
+ return featuresAdded;
}