*/
private AlignViewControllerGuiI avcg;
- @Override
- protected void finalize() throws Throwable
- {
- viewport = null;
- alignPanel = null;
- avcg = null;
- };
-
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
SequenceGroup[] gps = null;
if (sg != null && (cs == null || cs.isEmpty()))
{
- gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
- .getSequenceSelection(), viewport.getAlignmentView(true)
- .getSequenceStrings(viewport.getGapCharacter()), viewport
- .getAlignment().getGroups());
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
+ viewport.getSequenceSelection(),
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
}
else
{
{
gps = jalview.analysis.Grouping.makeGroupsFromCols(
(sg == null) ? viewport.getAlignment().getSequencesArray()
- : sg.getSequences().toArray(new SequenceI[0]), cs,
- viewport.getAlignment().getGroups());
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
}
}
if (gps != null)
// JBPNote this routine could also mark rows, not just columns.
// need a decent query structure to allow all types of feature searches
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
if (changed)
{
viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
}
else
{
- avcg.setStatus(MessageManager.formatMessage(
- "label.no_feature_of_type_found",
- new String[] { featureType }));
+ avcg.setStatus(MessageManager
+ .formatMessage("label.no_feature_of_type_found", new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
}
return false;
/**
* 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
* @param bs
* @return
*/
- static int findColumnsWithFeature(String featureType,
+ int findColumnsWithFeature(String featureType,
SequenceCollectionI sqcol, BitSet bs)
{
+ FeatureRenderer fr = alignPanel == null ? null : alignPanel
+ .getFeatureRenderer();
+
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
List<SequenceI> seqs = sqcol.getSequences();
List<SequenceFeature> sfs = sq.findFeatures(startColumn,
endColumn, featureType);
- if (!sfs.isEmpty())
- {
- nseq++;
- }
-
+ boolean found = false;
for (SequenceFeature sf : sfs)
{
+ if (fr.getColour(sf) == null)
+ {
+ continue;
+ }
+ if (!found)
+ {
+ nseq++;
+ }
+ found = true;
+
int sfStartCol = sq.findIndex(sf.getBegin());
int sfEndCol = sq.findIndex(sf.getEnd());
}
SequenceI[] oldOrder = al.getSequencesArray();
AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
- alignPanel.paintAlignment(true);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
}
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)
{
avcg.getFeatureSettingsUI().discoverAllFeatureData();
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
- return featuresFile;
+ return featuresAdded;
}
}
// JBPNote this routine could also mark rows, not just columns.
BitSet bs = new BitSet();
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
- .getAlignment() : viewport.getSelectionGroup();
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+ || extendCurrent) ? viewport.getAlignment()
+ : viewport.getSelectionGroup();
// this could be a lambda... - the remains of the method is boilerplate,
// except for the different messages for reporting selection.
if (changed)
{
viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
- - bs.cardinality()
+ alignPanel.paintAlignment(false, false);
+ int columnCount = invert
+ ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+ - bs.cardinality()
: bs.cardinality();
avcg.setStatus(MessageManager.formatMessage(
- "label.view_controller_toggled_marked",
- new String[] {
- toggle ? MessageManager.getString("label.toggled")
- : MessageManager.getString("label.marked"),
+ "label.view_controller_toggled_marked", new String[]
+ { toggle ? MessageManager.getString("label.toggled")
+ : MessageManager.getString("label.marked"),
String.valueOf(columnCount),
invert ? MessageManager
.getString("label.not_containing")
if (!extendCurrent)
{
cs.clear();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
}
return false;
git://source.jalview.org / jalview.git / blobdiff