/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.controller;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureRenderer;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
public class AlignViewController implements AlignViewControllerI
{
*/
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
public boolean makeGroupsFromSelection()
{
-
- if (viewport.getSelectionGroup() != null)
+ SequenceGroup sg = viewport.getSelectionGroup();
+ ColumnSelection cs = viewport.getColumnSelection();
+ SequenceGroup[] gps = null;
+ if (sg != null && (cs == null || cs.isEmpty()))
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ gps = jalview.analysis.Grouping.makeGroupsFrom(
viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
+ viewport.getAlignmentView(true)
+ .getSequenceStrings(viewport.getGapCharacter()),
+ viewport.getAlignment().getGroups());
+ }
+ else
+ {
+ if (cs != null)
+ {
+ gps = jalview.analysis.Grouping.makeGroupsFromCols(
+ (sg == null) ? viewport.getAlignment().getSequencesArray()
+ : sg.getSequences().toArray(new SequenceI[0]),
+ cs, viewport.getAlignment().getGroups());
+ }
+ }
+ if (gps != null)
+ {
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
+ ColourSchemeI colours = viewport.getGlobalColourScheme();
// set view properties for each group
for (int g = 0; g < gps.length; g++)
{
// gps[g].setShowunconserved(viewport.getShowUnconserved());
gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
viewport.getAlignment().addGroup(gps[g]);
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
- col = col.brighter();
- for (SequenceI sq : gps[g].getSequences(null))
+ if (colours != null)
{
- viewport.setSequenceColour(sq, col);
+ gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
}
+ Color col = new Color((int) (Math.random() * 255),
+ (int) (Math.random() * 255), (int) (Math.random() * 255));
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
}
return true;
}
// 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();
- int alw, alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
- .getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes() + 1;
- List<SequenceI> seqs = sqcol.getSequences();
- int nseq = 0;
- for (SequenceI sq : seqs)
- {
- int tfeat = 0;
- if (sq != null)
- {
- SequenceI dsq = sq.getDatasetSequence();
- while (dsq.getDatasetSequence() != null)
- {
- dsq = dsq.getDatasetSequence();
- }
- ;
- SequenceFeature[] sf = dsq.getSequenceFeatures();
- if (sf != null)
- {
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist > alw)
- {
- // sequence not in region
- continue;
- }
- for (SequenceFeature sfpos : sf)
- {
- // future functionalty - featureType == null means mark columns
- // containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
- {
- tfeat++;
- // optimisation - could consider 'spos,apos' like cursor argument
- // - findIndex wastes time by starting from first character and
- // counting
-
- int i = sq.findIndex(sfpos.getBegin());
- int j = sq.findIndex(sfpos.getEnd());
- if (j < alStart || i > alw)
- {
- // feature is outside selected region
- continue;
- }
- if (i < alStart)
- {
- i = alStart;
- }
- if (i < ist)
- {
- i = ist;
- }
- if (j > alw)
- {
- j = alw;
- }
- for (; i <= j; i++)
- {
- bs.set(i - 1);
- }
- }
- }
- }
+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection
+ ? viewport.getSelectionGroup()
+ : viewport.getAlignment();
+
+ int nseq = findColumnsWithFeature(featureType, sqcol, bs);
- if (tfeat > 0)
- {
- nseq++;
- }
- }
- }
ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
if (bs.cardinality() > 0 || invert)
{
- if (cs == null)
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
{
- cs = new ColumnSelection();
- }
- else
- {
- if (!extendCurrent)
- {
- cs.clear();
- }
+ viewport.setColumnSelection(cs);
+ 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"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
}
- if (invert)
- {
- // invert only in the currently selected sequence region
- for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
- && i < (alw);)
- {
- if (ibs < 0 || i < ibs)
- {
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- }
- else
- {
- cs.addElement(i++);
- }
- }
- else
- {
- i = bs.nextClearBit(ibs);
- ibs = bs.nextSetBit(i);
- }
- }
- }
- else
- {
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
- .nextSetBit(i + 1))
- {
- if (toggle && cs.contains(i))
- {
- cs.removeElement(i);
- }
- else
- {
- cs.addElement(i);
- }
- }
- }
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
- new String[]{
- (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
- (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
- featureType, Integer.valueOf(nseq).toString()
- }));
- return true;
}
else
{
- avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
- if (!extendCurrent && cs != null)
+ String key = searchSelection ? "label.no_feature_found_selection"
+ : "label.no_feature_of_type_found";
+ avcg.setStatus(
+ MessageManager.formatMessage(key, new String[]
+ { featureType }));
+ if (!extendCurrent)
{
cs.clear();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
- return false;
}
+ return false;
}
- public static boolean filterAnnotations(Annotation[] annotations,
- AnnotationFilterParameter filterParams, ColumnSelection cs)
+ /**
+ * 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.
+ *
+ * @param featureType
+ * @param sqcol
+ * @param bs
+ * @return
+ */
+ int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+ BitSet bs)
{
- cs.revealAllHiddenColumns();
- cs.clear();
- int count = 0;
- do
+ 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();
+ int nseq = 0;
+ for (SequenceI sq : seqs)
{
- if (annotations[count] != null)
+ if (sq != null)
{
+ // int ist = sq.findPosition(sqcol.getStartRes());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+ featureType);
- boolean itemMatched = false;
-
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
- && annotations[count].value > filterParams
- .getThresholdValue())
- {
- itemMatched = true;
- }
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
- && annotations[count].value < filterParams
- .getThresholdValue())
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterAlphaHelix()
- && annotations[count].secondaryStructure == 'H')
+ boolean found = false;
+ for (SequenceFeature sf : sfs)
{
- itemMatched = true;
- }
-
- if (filterParams.isFilterBetaSheet()
- && annotations[count].secondaryStructure == 'E')
- {
- itemMatched = true;
- }
+ if (fr.getColour(sf) == null)
+ {
+ continue;
+ }
+ if (!found)
+ {
+ nseq++;
+ }
+ found = true;
- if (filterParams.isFilterTurn()
- && annotations[count].secondaryStructure == 'S')
- {
- itemMatched = true;
- }
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
- String regexSearchString = filterParams.getRegexString();
- if (regexSearchString != null
- && !filterParams.getRegexSearchFields().isEmpty())
- {
- List<SearchableAnnotationField> fields = filterParams
- .getRegexSearchFields();
- try
+ if (sf.isContactFeature())
{
- if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
- && annotations[count].displayCharacter
- .matches(regexSearchString))
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
{
- itemMatched = true;
+ bs.set(sfStartCol - 1);
}
- } catch (java.util.regex.PatternSyntaxException pse)
- {
- if (annotations[count].displayCharacter
- .equals(regexSearchString))
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
{
- itemMatched = true;
+ bs.set(sfEndCol - 1);
}
+ continue;
}
- if (fields.contains(SearchableAnnotationField.DESCRIPTION)
- && annotations[count].description != null
- && annotations[count].description
- .matches(regexSearchString))
+
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
{
- itemMatched = true;
+ sfStartCol = startColumn;
+ }
+ // not sure what the point of this is
+ // if (sfStartCol < ist)
+ // {
+ // sfStartCol = ist;
+ // }
+ if (sfEndCol > endColumn)
+ {
+ sfEndCol = endColumn;
+ }
+ for (; sfStartCol <= sfEndCol; sfStartCol++)
+ {
+ bs.set(sfStartCol - 1); // convert to base 0
}
- }
-
- if (itemMatched)
- {
- cs.addElement(count);
}
}
- count++;
- } while (count < annotations.length);
- return false;
+ }
+ return nseq;
}
@Override
- public void sortAlignmentByFeatureDensity(String[] typ)
+ public void sortAlignmentByFeatureDensity(List<String> typ)
{
- sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ String methodText = MessageManager.getString("label.sort_by_density");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
}
- protected void sortBy(String[] typ, String methodText, final String method)
+ /**
+ * Sorts the alignment (or current selection) by either average score or
+ * density of the specified feature types, and adds to the command history. If
+ * {@code types} is null, all visible feature types are used for the sort. If
+ * no feature types apply, does nothing.
+ *
+ * @param types
+ * @param methodText
+ * - text shown in Undo/Redo command
+ * @param method
+ * - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
+ */
+ protected void sortByFeatures(List<String> types, String methodText,
+ final String method)
{
FeatureRenderer fr = alignPanel.getFeatureRenderer();
- if (typ == null)
+ if (types == null && fr != null)
{
- typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+ types = fr.getDisplayedFeatureTypes();
}
- String gps[] = null;
- gps = fr==null ? null : fr.getDisplayedFeatureGroups();
- if (typ != null)
+ if (types.isEmpty())
{
- ArrayList types = new ArrayList();
- for (int i = 0; i < typ.length; i++)
- {
- if (typ[i] != null)
- {
- types.add(typ[i]);
- }
- typ = new String[types.size()];
- types.toArray(typ);
- }
+ return; // nothing to do
}
- if (gps != null)
+ List<String> gps = null;
+ if (fr != null)
{
- ArrayList grps = new ArrayList();
-
- for (int i = 0; i < gps.length; i++)
- {
- if (gps[i] != null)
- {
- grps.add(gps[i]);
- }
- }
- gps = new String[grps.size()];
- grps.toArray(gps);
+ gps = fr.getDisplayedFeatureGroups();
}
AlignmentI al = viewport.getAlignment();
stop = al.getWidth();
}
SequenceI[] oldOrder = al.getSequencesArray();
- AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
- avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
- .getAlignment()));
- alignPanel.paintAlignment(true);
+ AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+ viewport.getAlignment()));
+ alignPanel.paintAlignment(true, false);
+
+ }
+ @Override
+ public void sortAlignmentByFeatureScore(List<String> typ)
+ {
+ String methodText = MessageManager.getString("label.sort_by_score");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
}
@Override
- public void sortAlignmentByFeatureScore(String[] typ)
+ public boolean parseFeaturesFile(Object file, DataSourceType protocol,
+ boolean relaxedIdMatching)
{
- sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ boolean featuresAdded = false;
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ try
+ {
+ featuresAdded = new FeaturesFile(false, file, protocol).parse(
+ viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+ fr.getFeatureFilters(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresAdded)
+ {
+ avcg.refreshFeatureUI(true);
+ if (fr != null)
+ {
+ // update the min/max ranges where necessary
+ fr.findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true, true);
+ }
+
+ return featuresAdded;
+
+ }
+
+ @Override
+ public boolean markHighlightedColumns(boolean invert,
+ boolean extendCurrent, boolean toggle)
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+ // JBPNote this routine could also mark rows, not just columns.
+ BitSet bs = new BitSet();
+ 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.
+ int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+
+ if (bs.cardinality() > 0 || invert)
+ {
+ boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+ sqcol.getEndRes(), invert, extendCurrent, toggle);
+ if (changed)
+ {
+ viewport.setColumnSelection(cs);
+ 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"),
+ String.valueOf(columnCount),
+ invert ? MessageManager
+ .getString("label.not_containing")
+ : MessageManager.getString("label.containing"),
+ "Highlight", Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ avcg.setStatus(MessageManager
+ .getString("label.no_highlighted_regions_marked"));
+ if (!extendCurrent)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(false, false);
+ }
+ }
+ return false;
+ }
+
+ @Override
+ public boolean copyHighlightedRegionsToClipboard()
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+
+ SearchResultsI searchResults = viewport.getSearchResults();
+ if (searchResults.isEmpty())
+ {
+ return false; // shouldn't happen
+ }
+ List<SequenceI> seqs = searchResults.getMatchingSubSequences();
+
+ // TODO: pass in hiddenColumns according to intersection of searchResults
+ // and visible columns. Currently this isn't done, since each contig becomes
+ // a single subsequence
+ Desktop.jalviewClipboard = new Object[] {
+ seqs.toArray(new SequenceI[0]),
+ alignPanel.getAlignment().getDataset(), null };
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", seqs.size()));
+ // Technically we should return false, since view has not changed
+ return false;
+ }
+
+ @Override
+ public boolean justify_Region(boolean left)
+ {
+ AlignmentI al = viewport.getAlignment();
+ SequenceGroup reg = viewport.getSelectionGroup();
+ int from, to;
+ List<SequenceI> seqs;
+
+ from = 0;
+ to = al.getWidth() - 1;
+ seqs = al.getSequences();
+ if (reg != null)
+ {
+ seqs = reg.getSequences();
+ from = reg.getStartRes();
+ to = reg.getEndRes();
+ }
+
+ if ((to - from) < 1)
+ {
+ return false;
+ }
+
+ al.padGaps();
+ jalview.commands.JustifyLeftOrRightCommand finalEdit = new jalview.commands.JustifyLeftOrRightCommand(
+ "Justify " + (left ? "Left" : "Right"), left, seqs, from, to,
+ al);
+ avcg.addHistoryItem(finalEdit);
+ viewport.notifyAlignmentChanged();
+ return true;
}
}