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
@Override
public boolean markColumnsContainingFeatures(boolean invert,
- boolean extendCurrent, boolean toggle, String featureType)
+ boolean extendCurrent, boolean toggle, String... featureType)
{
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
|| extendCurrent) ? viewport.getAlignment()
: viewport.getSelectionGroup();
- int nseq = findColumnsWithFeature(featureType, sqcol, bs);
+ int nseq = findColumnsWithFeature(sqcol, bs, featureType);
ColumnSelection cs = viewport.getColumnSelection();
if (cs == null)
cs = new ColumnSelection();
}
+ String featureTypeString = featureType.length == 1 ? featureType[0]
+ : featureType.toString();
+
if (bs.cardinality() > 0 || invert)
{
boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
invert ? MessageManager
.getString("label.not_containing")
: MessageManager.getString("label.containing"),
- featureType, Integer.valueOf(nseq).toString() }));
+ featureTypeString, Integer.valueOf(nseq).toString() }));
return true;
}
}
{
avcg.setStatus(MessageManager
.formatMessage("label.no_feature_of_type_found", new String[]
- { featureType }));
+ { featureTypeString }));
if (!extendCurrent)
{
cs.clear();
/**
* Sets a bit in the BitSet for each column (base 0) in the sequence
- * 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.
+ * collection which includes a visible feature of the specified feature
+ * type(s). Returns the number of sequences which have the feature(s) visible
+ * in the selected range.
*
- * @param featureType
* @param sqcol
* @param bs
+ * @param featureType
+ *
* @return
*/
- int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol, BitSet bs)
+ int findColumnsWithFeature(SequenceCollectionI sqcol,
+ BitSet bs, String... featureType)
{
- FeatureRendererModel fr = alignPanel == null ? null
- : (FeatureRendererModel) alignPanel.getFeatureRenderer();
- List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
+ .getFeatureRenderer();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
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)
{
public boolean parseFeaturesFile(String 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;
}