+/*
+ * 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 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.ColumnSelection;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.util.ArrayList;
+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 {
+ protected void finalize() throws Throwable
+ {
viewport = null;
alignPanel = null;
avcg = null;
};
-
- public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
- AlignmentViewPanel alignPanel)
+
+ public AlignViewController(AlignViewControllerGuiI alignFrame,
+ AlignViewportI viewport, AlignmentViewPanel alignPanel)
{
this.avcg = alignFrame;
- this.viewport=viewport;
+ this.viewport = viewport;
this.alignPanel = alignPanel;
}
+
@Override
- public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel)
{
this.alignPanel = alignPanel;
this.viewport = viewport;
-
+
}
+
@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()))
+ {
+ gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
+ .getSequenceSelection(), 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)
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
- viewport.getSequenceSelection(),
- viewport.getAlignmentView(true).getSequenceStrings(
- viewport.getGapCharacter()), viewport.getAlignment()
- .getGroups());
viewport.getAlignment().deleteAllGroups();
viewport.clearSequenceColours();
viewport.setSelectionGroup(null);
(int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
for (SequenceI sq : gps[g].getSequences(null))
+ {
viewport.setSequenceColour(sq, col);
+ }
}
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)
+ {
+ // 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)
+ {
+ SequenceFeature[] sf = sq.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);
+ }
+ }
+ }
+ }
+
+ if (tfeat > 0)
+ {
+ nseq++;
+ }
+ }
+ }
+ ColumnSelection cs = viewport.getColumnSelection();
+ if (bs.cardinality() > 0 || invert)
+ {
+ if (cs == null)
+ {
+ cs = new ColumnSelection();
+ }
+ else
+ {
+ if (!extendCurrent)
+ {
+ cs.clear();
+ }
+ }
+ 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)
+ {
+ cs.clear();
+ alignPanel.paintAlignment(true);
+ }
+ return false;
+ }
+ }
+
+ @Override
+ public void sortAlignmentByFeatureDensity(String[] typ)
+ {
+ sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+ }
+
+ protected void sortBy(String[] typ, String methodText, final String method)
+ {
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();
+ if (typ == null)
+ {
+ typ = fr == null ? null : fr.getDisplayedFeatureTypes();
+ }
+ String gps[] = null;
+ gps = fr == null ? null : fr.getDisplayedFeatureGroups();
+ if (typ != null)
+ {
+ List<String> types = new ArrayList<String>();
+ for (String displayed : typ)
+ {
+ if (displayed != null)
+ {
+ types.add(displayed);
+ }
+ }
+ typ = new String[types.size()];
+ types.toArray(typ);
+ }
+ if (gps != null)
+ {
+ List<String> grps = new ArrayList<String>();
+
+ for (int i = 0; i < gps.length; i++)
+ {
+ if (gps[i] != null)
+ {
+ grps.add(gps[i]);
+ }
+ }
+ gps = new String[grps.size()];
+ grps.toArray(gps);
+ }
+ 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(typ, gps, start, stop, al, method);
+ avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
+ .getAlignment()));
+ alignPanel.paintAlignment(true);
+
+ }
+
+ @Override
+ public void sortAlignmentByFeatureScore(String[] typ)
+ {
+ sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+ }
+
+ @Override
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching)
+ {
+ boolean featuresFile = false;
+ try
+ {
+ featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
+ .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+ .getFeatureColours(), false, relaxedIdMatching);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ if (featuresFile)
+ {
+ avcg.refreshFeatureUI(true);
+ if (alignPanel.getFeatureRenderer() != null)
+ {
+ // update the min/max ranges where necessary
+ alignPanel.getFeatureRenderer().findAllFeatures(true);
+ }
+ if (avcg.getFeatureSettingsUI() != null)
+ {
+ avcg.getFeatureSettingsUI().discoverAllFeatureData();
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ return featuresFile;
+
}
+}
git://source.jalview.org / jalview.git / blobdiff