/*
- * 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.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.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.getSelected() == null || cs.size() == 0))
{
- SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
+ 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) {
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)
+ 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());
+ int alw, alStart;
+ SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
+ .getAlignment() : viewport.getSelectionGroup());
alStart = sqcol.getStartRes();
- alw = sqcol.getEndRes()+1;
+ 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();
+ SequenceFeature[] sf = sq.getSequenceFeatures();
if (sf != null)
{
int ist = sq.findIndex(sq.getStart());
int iend = sq.findIndex(sq.getEnd());
- if (iend < alStart || ist> alw)
+ if (iend < alStart || ist > alw)
{
// sequence not in region
continue;
int i = sq.findIndex(sfpos.getBegin());
int j = sq.findIndex(sfpos.getEnd());
- if (j<alStart || i>alw)
+ if (j < alStart || i > alw)
{
// feature is outside selected region
continue;
{
i = alStart;
}
- if (i< ist) {
+ if (i < ist)
+ {
i = ist;
}
if (j > alw)
if (cs == null)
{
cs = new ColumnSelection();
- } else {
+ }
+ else
+ {
if (!extendCurrent)
{
cs.clear();
if (ibs < 0 || i < ibs)
{
if (toggle && cs.contains(i))
- {
- cs.removeElement(i++);
- } else
- {
- cs.addElement(i++);
- }
+ {
+ cs.removeElement(i++);
+ }
+ else
+ {
+ cs.addElement(i++);
+ }
}
else
{
}
else
{
- for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs.nextSetBit(i + 1))
+ for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
+ .nextSetBit(i + 1))
{
if (toggle && cs.contains(i))
{
cs.removeElement(i);
- } else
+ }
+ else
{
cs.addElement(i);
}
}
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)");
+ 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("No features of type " + featureType + " found.");
- if (!extendCurrent && cs!=null)
+ 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)
+ {
+ 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);
+ }
+ }
+ if (gps != 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);
+ }
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff