import jalview.datamodel.Annotation;
import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SearchResultsI;
import jalview.util.Comparison;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
+ final protected ViewportRanges ranges;
+
protected ViewStyleI viewStyle = new ViewStyle();
/**
protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
/**
+ * alignment displayed in the viewport. Please use get/setter
+ */
+ protected AlignmentI alignment;
+
+ public AlignmentViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ ranges = new ViewportRanges(al);
+ }
+
+ /**
* @param name
* @see jalview.api.ViewStyleI#setFontName(java.lang.String)
*/
viewStyle.setSeqNameItalics(default1);
}
- /**
- * alignment displayed in the viewport. Please use get/setter
- */
- protected AlignmentI alignment;
+
@Override
public AlignmentI getAlignment()
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ResidueShaderI residueShading;
+ protected ResidueShaderI residueShading = new ResidueShader();
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
if (cs != null)
{
- // if (getConservationSelected() || getAbovePIDThreshold()
- // || cs instanceof PIDColourScheme
- // || cs instanceof Blosum62ColourScheme)
if (getConservationSelected())
{
residueShading.setConservation(hconservation);
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
}
/**
- * Set the selection group for this window.
+ * Set the selection group for this window. Also sets the current alignment as
+ * the context for the group, if it does not already have one.
*
* @param sg
* - group holding references to sequences in this alignment view
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
+ if (sg != null && sg.getContext() == null)
+ {
+ sg.setContext(alignment);
+ }
}
- public void setHiddenColumns(ColumnSelection colsel)
+ public void setHiddenColumns(HiddenColumns hidden)
{
- this.colSel = colsel;
+ this.alignment.setHiddenColumns(hidden);
+ // this.colSel = colsel;
}
@Override
@Override
public boolean hasHiddenColumns()
{
- return colSel != null && colSel.hasHiddenColumns();
+ return colSel != null
+ && alignment.getHiddenColumns().hasHiddenColumns();
}
public void updateHiddenColumns()
protected boolean showConsensus = true;
+ protected boolean showOccupancy = true;
+
private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
protected SequenceAnnotationOrder sortAnnotationsBy = null;
*/
private boolean followHighlight = true;
- // TODO private with getters and setters?
- public int startRes;
-
- public int endRes;
-
- public int startSeq;
-
- public int endSeq;
-
/**
* Property change listener for changes in alignment
*
return;
}
- colSel.hideSelectedColumns();
+ colSel.hideSelectedColumns(alignment);
setSelectionGroup(null);
isColSelChanged(true);
}
{
if (start == end)
{
- colSel.hideColumns(start);
+ colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
}
else
{
- colSel.hideColumns(start, end);
+ alignment.getHiddenColumns().hideColumns(start, end);
}
isColSelChanged(true);
}
public void showColumn(int col)
{
- colSel.revealHiddenColumns(col);
+ alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
isColSelChanged(true);
}
public void showAllHiddenColumns()
{
- colSel.revealAllHiddenColumns();
+ alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
isColSelChanged(true);
}
@Override
public void invertColumnSelection()
{
- colSel.invertColumnSelection(0, alignment.getWidth());
+ colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
}
@Override
@Override
public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
- return new CigarArray(alignment, colSel,
+ return new CigarArray(alignment, alignment.getHiddenColumns(),
(selectedRegionOnly ? selectionGroup : null));
}
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
- return new AlignmentView(alignment, colSel, selectionGroup,
- colSel != null && colSel.hasHiddenColumns(), selectedOnly,
+ return new AlignmentView(alignment, alignment.getHiddenColumns(),
+ selectionGroup, alignment.getHiddenColumns() != null
+ && alignment.getHiddenColumns().hasHiddenColumns(),
+ selectedOnly,
markGroups);
}
}
selection = new String[iSize];
- if (colSel != null && colSel.hasHiddenColumns())
+ if (alignment.getHiddenColumns() != null
+ && alignment.getHiddenColumns().hasHiddenColumns())
{
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+ selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
+ start, end, seqs);
}
else
{
do
{
- if (colSel != null && colSel.hasHiddenColumns())
+ HiddenColumns hidden = alignment.getHiddenColumns();
+ if (hidden != null && hidden.hasHiddenColumns())
{
if (start == 0)
{
- start = colSel.adjustForHiddenColumns(start);
+ start = hidden.adjustForHiddenColumns(start);
}
- end = colSel.getHiddenBoundaryRight(start);
+ end = hidden.getHiddenBoundaryRight(start);
if (start == end)
{
end = max;
regions.add(new int[] { start, end });
- if (colSel != null && colSel.hasHiddenColumns())
+ if (hidden != null && hidden.hasHiddenColumns())
{
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
+ start = hidden.adjustForHiddenColumns(end);
+ start = hidden.getHiddenBoundaryLeft(start) + 1;
}
} while (end < max);
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ alignment.getHiddenColumns().makeVisibleAnnotation(
+ selectionGroup.getStartRes(),
selectionGroup.getEndRes(), clone);
}
else
{
- colSel.makeVisibleAnnotation(clone);
+ alignment.getHiddenColumns().makeVisibleAnnotation(clone);
}
ala.add(clone);
}
{
initRNAStructure();
}
- consensus = new AlignmentAnnotation("Consensus", "PID",
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+ initGapCounts();
initComplementConsensus();
}
}
/**
- * If this is a protein alignment and there are mappings to cDNA, add the cDNA
- * consensus annotation.
+ * If this is a protein alignment and there are mappings to cDNA, adds the
+ * cDNA consensus annotation and returns true, else returns false.
*/
- public void initComplementConsensus()
+ public boolean initComplementConsensus()
{
if (!alignment.isNucleotide())
{
if (doConsensus)
{
complementConsensus = new AlignmentAnnotation("cDNA Consensus",
- "PID for cDNA", new Annotation[1], 0f, 100f,
+ MessageManager
+ .getString("label.complement_consensus_descr"),
+ new Annotation[1], 0f, 100f,
AlignmentAnnotation.BAR_GRAPH);
initConsensus(complementConsensus);
+ return true;
}
}
}
+ return false;
}
private void initConsensus(AlignmentAnnotation aa)
}
}
+ // these should be extracted from the view model - style and settings for
+ // derived annotation
+ private void initGapCounts()
+ {
+ if (showOccupancy)
+ {
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f,
+ alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ alignment.addAnnotation(gapcounts);
+ }
+ }
+
private void initConservation()
{
if (showConservation)
if (conservation == null)
{
conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps", new Annotation[1],
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()), new Annotation[1],
0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
if (quality == null)
{
quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
+ MessageManager.getString("label.quality_descr"),
new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
{
if (alignment.hasRNAStructure() && strucConsensus == null)
{
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
+ if (residueShading != null)
+ {
+ residueShading.setConservationApplied(settingsForView
+ .isConservationColourSelected());
+ }
}
@Override
viewStyle.setScaleProteinAsCdna(b);
}
+ @Override
+ public boolean isProteinFontAsCdna()
+ {
+ return viewStyle.isProteinFontAsCdna();
+ }
+
+ @Override
+ public void setProteinFontAsCdna(boolean b)
+ {
+ viewStyle.setProteinFontAsCdna(b);
+ }
+
/**
* @return true if view should scroll to show the highlighted region of a
* sequence
this.followHighlight = b;
}
- public int getStartRes()
- {
- return startRes;
- }
-
@Override
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
+ public ViewportRanges getRanges()
{
- this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- if (res > alignment.getWidth() - 1)
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
- if (res < 0)
- {
- res = 0;
- }
- this.endRes = res;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
+ return ranges;
}
/**
* locate 'middle' column (true middle if an odd number visible, left of
* middle if an even number visible)
*/
- int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+ int middleColumn = ranges.getStartRes()
+ + (ranges.getEndRes() - ranges.getStartRes()) / 2;
final HiddenSequences hiddenSequences = getAlignment()
.getHiddenSequences();
*/
int lastSeq = alignment.getHeight() - 1;
List<AlignedCodonFrame> seqMappings = null;
- for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+ for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
{
sequence = getAlignment().getSequenceAt(seqNo);
if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
*/
private boolean selectionIsDefinedGroup = false;
-
@Override
public boolean isSelectionDefinedGroup()
{
git://source.jalview.org / jalview.git / blobdiff