*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
+import jalview.analysis.TreeModel;
import jalview.api.AlignCalcManagerI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.QuitHandler;
+import jalview.project.Jalview2XML;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.IdColumns;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
protected Deque<CommandI> redoList = new ArrayDeque<>();
/**
+ * used to determine if quit should be confirmed
+ */
+ private boolean savedUpToDate = false;
+
+ /**
* alignment displayed in the viewport. Please use get/setter
*/
protected AlignmentI alignment;
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(cs);
+ sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
/**
* results of cDNA complement consensus visible portion of view
*/
- protected Hashtable[] hcomplementConsensus = null;
+ protected Hashtable<String, Object>[] hcomplementConsensus = null;
/**
* results of secondary structure base pair consensus for visible portion of
* view
*/
- protected Hashtable[] hStrucConsensus = null;
+ protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
}
@Override
- public void setComplementConsensusHash(Hashtable[] hconsensus)
+ public void setComplementConsensusHash(
+ Hashtable<String, Object>[] hconsensus)
{
this.hcomplementConsensus = hconsensus;
}
}
@Override
- public Hashtable[] getComplementConsensusHash()
+ public Hashtable<String, Object>[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
- public Hashtable[] getRnaStructureConsensusHash()
+ public Hashtable<String, Object>[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
- public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ public void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus)
{
this.hStrucConsensus = hStrucConsensus;
residueShading = null; // may hold a reference to Consensus
changeSupport = null;
ranges = null;
+ currentTree = null;
+ selectionGroup = null;
+ colSel = null;
setAlignment(null);
}
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
- changeSupport.removePropertyChangeListener(listener);
+ if (changeSupport != null)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
}
/**
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
+ isColSelChanged(true);
}
@Override
}
@Override
- public CigarArray getViewAsCigars(boolean selectedRegionOnly)
- {
- return new CigarArray(alignment, alignment.getHiddenColumns(),
- (selectedRegionOnly ? selectionGroup : null));
- }
-
- @Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
{
if (alignment.getHiddenColumns() != null
&& alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = alignment.getHiddenColumns()
- .getVisibleSequenceStrings(start, end, seqs);
+ for (i = 0; i < iSize; i++)
+ {
+ Iterator<int[]> blocks = alignment.getHiddenColumns()
+ .getVisContigsIterator(start, end + 1, false);
+ selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+ }
}
else
{
{
if (start == 0)
{
- start = hidden.adjustForHiddenColumns(start);
+ start = hidden.visibleToAbsoluteColumn(start);
}
- end = hidden.getHiddenBoundaryRight(start);
+ end = hidden.getNextHiddenBoundary(false, start);
if (start == end)
{
end = max;
if (hidden != null && hidden.hasHiddenColumns())
{
- start = hidden.adjustForHiddenColumns(end);
- start = hidden.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.visibleToAbsoluteColumn(end);
+ start = hidden.getNextHiddenBoundary(true, start) + 1;
}
} while (end < max);
- int[][] startEnd = new int[regions.size()][2];
+ // int[][] startEnd = new int[regions.size()][2];
return regions;
}
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- alignment.getHiddenColumns().makeVisibleAnnotation(
- selectionGroup.getStartRes(), selectionGroup.getEndRes(),
- clone);
+ clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ selectionGroup.getEndRes(), alignment.getHiddenColumns());
}
else
{
- alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+ clone.makeVisibleAnnotation(alignment.getHiddenColumns());
}
ala.add(clone);
}
* TODO reorder the annotation rows according to group/sequence ordering on
* alignment
*/
- boolean sortg = true;
+ // boolean sortg = true;
// remove old automatic annotation
// add any new annotation
public void clearSequenceColours()
{
sequenceColours.clear();
- };
+ }
@Override
public AlignViewportI getCodingComplement()
{
this.historyList.push(command);
broadcastCommand(command, false);
+ setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
}
}
viewStyle.setProteinFontAsCdna(b);
}
+ @Override
+ public void setShowComplementFeatures(boolean b)
+ {
+ viewStyle.setShowComplementFeatures(b);
+ }
+
+ @Override
+ public boolean isShowComplementFeatures()
+ {
+ return viewStyle.isShowComplementFeatures();
+ }
+
+ @Override
+ public void setShowComplementFeaturesOnTop(boolean b)
+ {
+ viewStyle.setShowComplementFeaturesOnTop(b);
+ }
+
+ @Override
+ public boolean isShowComplementFeaturesOnTop()
+ {
+ return viewStyle.isShowComplementFeaturesOnTop();
+ }
+
/**
* @return true if view should scroll to show the highlighted region of a
* sequence
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
for (int seqNo = ranges
- .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
*/
private SearchResultsI searchResults = null;
+ protected TreeModel currentTree = null;
+
@Override
public boolean hasSearchResults()
{
return searchResults;
}
+ @Override
+ public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+ {
+ return alignment.getContactListFor(_aa, column);
+ }
+
+ @Override
+ public ContactMatrixI getContactMatrix(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ return alignment.getContactMatrixFor(alignmentAnnotation);
+ }
+
+
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
+ ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
return sq;
}
+
+ @Override
+ public void setCurrentTree(TreeModel tree)
+ {
+ currentTree = tree;
+ }
+
+ @Override
+ public TreeModel getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ @Override
+ public AlignmentExportData getAlignExportData(
+ AlignExportSettingsI options)
+ {
+ AlignmentI alignmentToExport = null;
+ String[] omitHidden = null;
+ alignmentToExport = null;
+
+ if (hasHiddenColumns() && !options.isExportHiddenColumns())
+ {
+ omitHidden = getViewAsString(false,
+ options.isExportHiddenSequences());
+ }
+
+ int[] alignmentStartEnd = new int[2];
+ if (hasHiddenRows() && options.isExportHiddenSequences())
+ {
+ alignmentToExport = getAlignment().getHiddenSequences()
+ .getFullAlignment();
+ }
+ else
+ {
+ alignmentToExport = getAlignment();
+ }
+ alignmentStartEnd = getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
+ AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+ omitHidden, alignmentStartEnd);
+ return ed;
+ }
+
+ /**
+ * flag set to indicate if structure views might be out of sync with sequences
+ * in the alignment
+ */
+
+ private boolean needToUpdateStructureViews = false;
+
+ @Override
+ public boolean isUpdateStructures()
+ {
+ return needToUpdateStructureViews;
+ }
+
+ @Override
+ public void setUpdateStructures(boolean update)
+ {
+ needToUpdateStructureViews = update;
+ }
+
+ @Override
+ public boolean needToUpdateStructureViews()
+ {
+ boolean update = needToUpdateStructureViews;
+ needToUpdateStructureViews = false;
+ return update;
+ }
+
+ @Override
+ public void addSequenceGroup(SequenceGroup sequenceGroup)
+ {
+ alignment.addGroup(sequenceGroup);
+
+ Color col = sequenceGroup.idColour;
+ if (col != null)
+ {
+ col = col.brighter();
+
+ for (SequenceI sq : sequenceGroup.getSequences())
+ {
+ setSequenceColour(sq, col);
+ }
+ }
+
+ if (codingComplement != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils
+ .mapSequenceGroup(sequenceGroup, this, codingComplement);
+ if (mappedGroup.getSequences().size() > 0)
+ {
+ codingComplement.getAlignment().addGroup(mappedGroup);
+
+ if (col != null)
+ {
+ for (SequenceI seq : mappedGroup.getSequences())
+ {
+ codingComplement.setSequenceColour(seq, col);
+ }
+ }
+ }
+ // propagate the structure view update flag according to our own setting
+ codingComplement.setUpdateStructures(needToUpdateStructureViews);
+ }
+ }
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
+
+ /**
+ * ordered list of annotation values displayed per sequence in ID panel
+ */
+ private IdColumns id_columns = null;
+
+ /**
+ * available and currently visible columns for this view
+ */
+ @Override
+ public IdColumns getIdColumns()
+ {
+ if (alignment == null)
+ {
+ return null;
+ }
+ if (id_columns == null)
+ {
+ id_columns = new IdColumns(alignment);
+ }
+ return id_columns;
+ }
+
+ public void setSavedUpToDate(boolean s)
+ {
+ setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
+ }
+
+ public void setSavedUpToDate(boolean s, QuitHandler.Message m)
+ {
+ Console.debug(
+ "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+ savedUpToDate = s;
+ QuitHandler.setMessage(m);
+ }
+
+ public boolean savedUpToDate()
+ {
+ Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+ + savedUpToDate);
+ return savedUpToDate;
+ }
}