+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
public class AlignViewController implements AlignViewControllerI
{
- AlignViewportI viewport=null;
- AlignmentViewPanel alignPanel=null;
+ AlignViewportI viewport = null;
+
+ AlignmentViewPanel alignPanel = null;
+
/**
* the GUI container that is handling interactions with the user
*/
private AlignViewControllerGuiI avcg;
- @Override
- protected void finalize() throws Throwable {
- viewport = null;
- alignPanel = null;
- avcg = null;
- };
-
- public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
- AlignmentViewPanel alignPanel)
+
+ public AlignViewController(AlignViewControllerGuiI alignFrame,
+ 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(),
+ viewport.getAlignment().getHiddenColumns());
+ }
+ }
+ 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]);
+ if (colours != null)
+ {
+ gps[g].setColourScheme(colours.getInstance(viewport, 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))
- viewport.setSequenceColour(sq, col);
+ gps[g].idColour = col;
+ viewport.setUpdateStructures(true);
+ viewport.addSequenceGroup(gps[g]);
}
return true;
}
return false;
-}
+ }
+
@Override
public boolean createGroup()
{
SequenceGroup sg = viewport.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- viewport.getAlignment().addGroup(sg);
- return true;
- }
+ viewport.getAlignment().addGroup(sg);
+ return true;
+ }
return false;
}
+
@Override
public boolean unGroup()
{
SequenceGroup sg = viewport.getSelectionGroup();
- if (sg!=null)
+ if (sg != null)
{
- viewport.getAlignment().deleteGroup(sg);
- return true;
+ viewport.getAlignment().deleteGroup(sg);
+ return true;
}
return false;
}
+
@Override
public boolean deleteGroups()
{
- if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+ if (viewport.getAlignment().getGroups() != null
+ && viewport.getAlignment().getGroups().size() > 0)
{
- viewport.getAlignment().deleteAllGroups();
- viewport.clearSequenceColours();
- viewport.setSelectionGroup(null);
- return true;
+ viewport.getAlignment().deleteAllGroups();
+ viewport.clearSequenceColours();
+ viewport.setSelectionGroup(null);
+ return true;
}
return false;
}
-
+
@Override
- public boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean toggle, String featureType)
+ public boolean markColumnsContainingFeatures(boolean invert,
+ 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
BitSet bs = new BitSet();
- int alw,alStart;
- SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport.getAlignment() : viewport.getSelectionGroup());
- alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes()+1;
+ boolean searchSelection = viewport.getSelectionGroup() != null
+ && !extendCurrent;
+ SequenceCollectionI sqcol = searchSelection ? viewport
+ .getSelectionGroup() : viewport.getAlignment();
+
+ int nseq = findColumnsWithFeature(featureType, 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"),
+ featureType, Integer.valueOf(nseq).toString() }));
+ return true;
+ }
+ }
+ else
+ {
+ 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(false, false);
+ }
+ }
+ return false;
+ }
+
+ /**
+ * 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)
+ {
+ 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)
{
- 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.findPosition(sqcol.getStartRes());
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+ endColumn, featureType);
+
+ boolean found = false;
+ for (SequenceFeature sf : sfs)
{
- int ist = sq.findIndex(sq.getStart());
- int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist> alw)
+ if (fr.getColour(sf) == null)
{
- // sequence not in region
continue;
}
- for (SequenceFeature sfpos : sf)
+ if (!found)
+ {
+ nseq++;
+ }
+ found = true;
+
+ int sfStartCol = sq.findIndex(sf.getBegin());
+ int sfEndCol = sq.findIndex(sf.getEnd());
+
+ if (sf.isContactFeature())
{
- // future functionalty - featureType == null means mark columns
- // containing all displayed features
- if (sfpos != null && (featureType.equals(sfpos.getType())))
+ /*
+ * 'contact' feature - check for 'start' or 'end'
+ * position within the selected region
+ */
+ if (sfStartCol >= startColumn && sfStartCol <= endColumn)
+ {
+ bs.set(sfStartCol - 1);
+ }
+ if (sfEndCol >= startColumn && sfEndCol <= endColumn)
{
- 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);
- }
+ bs.set(sfEndCol - 1);
}
+ continue;
}
- }
- if (tfeat > 0)
- {
- nseq++;
+ /*
+ * contiguous feature - select feature positions (if any)
+ * within the selected region
+ */
+ if (sfStartCol < startColumn)
+ {
+ 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
+ }
}
}
}
- ColumnSelection cs = viewport.getColumnSelection();
- if (bs.cardinality() > 0 || invert)
+ return nseq;
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(List<String> typ)
+ {
+ String methodText = MessageManager.getString("label.sort_by_density");
+ sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ /**
+ * 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 (types == null && fr != null)
+ {
+ types = fr.getDisplayedFeatureTypes();
+ }
+ if (types.isEmpty())
+ {
+ return; // nothing to do
+ }
+ List<String> gps = null;
+ if (fr != null)
+ {
+ gps = fr.getDisplayedFeatureGroups();
+ }
+ AlignmentI al = viewport.getAlignment();
+
+ int start, stop;
+ SequenceGroup sg = viewport.getSelectionGroup();
+ if (sg != null)
+ {
+ start = sg.getStartRes();
+ stop = sg.getEndRes();
+ }
+ else
+ {
+ start = 0;
+ stop = al.getWidth();
+ }
+ SequenceI[] oldOrder = al.getSequencesArray();
+ 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 boolean parseFeaturesFile(String file, DataSourceType protocol,
+ boolean relaxedIdMatching)
+ {
+ 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)
{
- if (cs == null)
+ ex.printStackTrace();
+ }
+
+ if (featuresAdded)
+ {
+ avcg.refreshFeatureUI(true);
+ if (fr != null)
{
- cs = new ColumnSelection();
- } else {
- if (!extendCurrent)
- {
- cs.clear();
- }
+ // update the min/max ranges where necessary
+ fr.findAllFeatures(true);
}
- if (invert)
+ if (avcg.getFeatureSettingsUI() != null)
{
- // 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);
- }
- }
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
}
- else
+ 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)
{
- 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(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;
}
- viewport.setColumnSelection(cs);
- alignPanel.paintAlignment(true);
- avcg.setStatus((toggle ? "Toggled ": "Marked ")
- + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality())
- + " columns "+(invert ? "not " : "") + "containing features of type " + featureType
- + " across " + nseq + " sequence(s)");
- return true;
}
else
{
- avcg.setStatus("No features of type " + featureType + " found.");
- if (!extendCurrent && cs!=null)
+ avcg.setStatus(MessageManager
+ .formatMessage("No highlighted regions marked"));
+ if (!extendCurrent)
{
cs.clear();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
- return false;
}
+ return false;
}
+
}
git://source.jalview.org / jalview.git / blobdiff