*/
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.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
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
public abstract class AlignmentViewport implements AlignViewportI,
CommandListener, VamsasSource
{
- protected ViewportPositionProps posProps;
+ protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
return isDataset;
}
+ private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
- // protected ColumnSelection colSel = new ColumnSelection();
+ protected ColumnSelection colSel = new ColumnSelection();
public boolean autoCalculateConsensus = true;
{
residueShading.setConservation(hconservation);
}
- residueShading.alignmentChanged(alignment, getHiddenRepSequences());
+ residueShading.alignmentChanged(alignment, hiddenRepSequences);
}
/*
if (cs != null)
{
sg.getGroupColourScheme()
-.alignmentChanged(sg,
- getHiddenRepSequences());
+ .alignmentChanged(sg, hiddenRepSequences);
}
}
}
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
{
return;
}
public void setHiddenColumns(ColumnSelection colsel)
{
- posProps.setHiddenColumns(colsel);
- // this.colSel = colsel;
+ this.colSel = colsel;
}
@Override
public ColumnSelection getColumnSelection()
{
- return posProps.getColumnSelection();
- // return colSel;
+ return colSel;
}
@Override
public void setColumnSelection(ColumnSelection colSel)
{
- posProps.setColumnSelection(colSel);
- /*this.colSel = colSel;
+ this.colSel = colSel;
if (colSel != null)
{
updateHiddenColumns();
}
- isColSelChanged(true);*/
+ isColSelChanged(true);
}
/**
@Override
public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
{
- return posProps.getHiddenRepSequences();
+ return hiddenRepSequences;
}
@Override
public void setHiddenRepSequences(
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- posProps.getHiddenRepSequences();
+ this.hiddenRepSequences = hiddenRepSequences;
}
@Override
@Override
public boolean hasHiddenColumns()
{
- return posProps.hasHiddenColumns();
- // return colSel != null && colSel.hasHiddenColumns();
+ return colSel != null && colSel.hasHiddenColumns();
}
public void updateHiddenColumns()
}
- private long sgrouphash = -1;
+ private long sgrouphash = -1, colselhash = -1;
/**
* checks current SelectionGroup against record of last hash value, and
*/
public boolean isColSelChanged(boolean b)
{
- return posProps.isColSelChanged(b);
- /*int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
+ int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
if (hc != -1 && hc != colselhash)
{
if (b)
}
return true;
}
- return false;*/
+ return false;
}
@Override
*/
private boolean followHighlight = true;
- /*private int startRes;
-
- private int endRes;
-
- private int startSeq;
-
- private int endSeq;*/
-
/**
* Property change listener for changes in alignment
*
// common hide/show column stuff
- public void hideColumns(int start, int end)
- {
- posProps.hideColumns(start, end);
- }
-
- public void showColumn(int col)
- {
- posProps.showColumn(col);
- }
-
- public void showAllHiddenColumns()
- {
- posProps.showAllHiddenColumns();
- }
-
public void hideSelectedColumns()
{
if (colSel.isEmpty())
isColSelChanged(true);
}
+ public void hideColumns(int start, int end)
+ {
+ if (start == end)
+ {
+ colSel.hideColumns(start);
+ }
+ else
+ {
+ colSel.hideColumns(start, end);
+ }
+ isColSelChanged(true);
+ }
+ public void showColumn(int col)
+ {
+ colSel.revealHiddenColumns(col);
+ isColSelChanged(true);
+ }
+
+ public void showAllHiddenColumns()
+ {
+ colSel.revealAllHiddenColumns();
+ isColSelChanged(true);
+ }
// common hide/show seq stuff
public void showAllHiddenSeqs()
{
- selectionGroup = posProps.showAllHiddenSeqs(selectionGroup);
-
- /* if (alignment.getHiddenSequences().getSize() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(alignment.getWidth() - 1);
- }
- List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
- hiddenRepSequences);
- for (SequenceI seq : tmp)
- {
- selectionGroup.addSequence(seq, false);
- setSequenceAnnotationsVisible(seq, true);
- }
+ if (alignment.getHiddenSequences().getSize() > 0)
+ {
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
+ List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
+ hiddenRepSequences);
+ for (SequenceI seq : tmp)
+ {
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
+ }
- hiddenRepSequences = null;
+ hiddenRepSequences = null;
- firePropertyChange("alignment", null, alignment.getSequences());
- // used to set hasHiddenRows/hiddenRepSequences here, after the property
- // changed event
- sendSelection();
- }*/
+ firePropertyChange("alignment", null, alignment.getSequences());
+ // used to set hasHiddenRows/hiddenRepSequences here, after the property
+ // changed event
+ sendSelection();
+ }
}
public void showSequence(int index)
{
- posProps.showSequence(index, selectionGroup);
- /*List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
index, hiddenRepSequences);
if (tmp.size() > 0)
{
}
firePropertyChange("alignment", null, alignment.getSequences());
sendSelection();
- }*/
+ }
}
public void hideAllSelectedSeqs()
{
- posProps.hideAllSelectedSeqs(selectionGroup);
- /*if (selectionGroup == null || selectionGroup.getSize() < 1)
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
{
return;
}
hideSequence(seqs);
- setSelectionGroup(null);*/
+ setSelectionGroup(null);
}
public void hideSequence(SequenceI[] seq)
{
- posProps.hideSequence(seq);
- /*if (seq != null)
+ if (seq != null)
{
for (int i = 0; i < seq.length; i++)
{
setSequenceAnnotationsVisible(seq[i], false);
}
firePropertyChange("alignment", null, alignment.getSequences());
- }*/
+ }
}
/**
*/
public void hideSequences(SequenceI sequence, boolean representGroup)
{
- posProps.hideSequences(sequence, representGroup, selectionGroup);
- /*if (selectionGroup == null || selectionGroup.getSize() < 1)
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
{
hideSequence(new SequenceI[] { sequence });
return;
hideSequence(hseqs);
setSelectionGroup(null);
- sendSelection();*/
+ sendSelection();
}
+ /**
+ * Set visibility for any annotations for the given sequence.
+ *
+ * @param sequenceI
+ */
+ protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+ boolean visible)
+ {
+ AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+ if (anns != null)
+ {
+ for (AlignmentAnnotation ann : anns)
+ {
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
+ }
+ }
+ }
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
{
- posProps.hideRepSequences(repSequence, sg);
- /*int sSize = sg.getSize();
+ int sSize = sg.getSize();
if (sSize < 2)
{
return;
}
sg.setSeqrep(repSequence); // note: not done in 2.7applet
sg.setHidereps(true); // note: not done in 2.7applet
- hideSequence(seqs);*/
+ hideSequence(seqs);
}
*/
public boolean isHiddenRepSequence(SequenceI seq)
{
- return posProps.isHiddenRepSequence(seq);
- // return (hiddenRepSequences != null && hiddenRepSequences
- // .containsKey(seq));
+ return (hiddenRepSequences != null && hiddenRepSequences
+ .containsKey(seq));
}
/**
*/
public SequenceGroup getRepresentedSequences(SequenceI seq)
{
- return posProps.getRepresentedSequences(seq);
- // return (SequenceGroup) (hiddenRepSequences == null ? null
- // : hiddenRepSequences.get(seq));
+ return (SequenceGroup) (hiddenRepSequences == null ? null
+ : hiddenRepSequences.get(seq));
}
@Override
public int adjustForHiddenSeqs(int alignmentIndex)
{
- return posProps.adjustForHiddenSeqs(alignmentIndex);
- // return alignment.getHiddenSequences().adjustForHiddenSeqs(
- // alignmentIndex);
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(
+ alignmentIndex);
}
@Override
public void invertColumnSelection()
{
- posProps.invertColumnSelection();
- // colSel.invertColumnSelection(0, alignment.getWidth());
+ colSel.invertColumnSelection(0, alignment.getWidth());
}
@Override
@Override
public CigarArray getViewAsCigars(boolean selectedRegionOnly)
{
- return new CigarArray(alignment, posProps.getColumnSelection(),
+ return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
{
- return new AlignmentView(alignment, posProps.getColumnSelection(),
- selectionGroup, posProps.hasHiddenColumns(), selectedOnly,
+ return new AlignmentView(alignment, colSel, selectionGroup,
+ colSel != null && colSel.hasHiddenColumns(), selectedOnly,
markGroups);
}
}
selection = new String[iSize];
- if (posProps.hasHiddenColumns())
+ if (colSel != null && colSel.hasHiddenColumns())
{
- selection = posProps.getVisibleSequenceStrings(start, end, seqs);
+ selection = colSel.getVisibleSequenceStrings(start, end, seqs);
}
else
{
@Override
public List<int[]> getVisibleRegionBoundaries(int min, int max)
{
- return posProps.getVisibleRegionBoundaries(min, max);
- /* ArrayList<int[]> regions = new ArrayList<int[]>();
- int start = min;
- int end = max;
+ ArrayList<int[]> regions = new ArrayList<int[]>();
+ int start = min;
+ int end = max;
- do
+ do
+ {
+ if (colSel != null && colSel.hasHiddenColumns())
+ {
+ if (start == 0)
{
- if (colSel != null && colSel.hasHiddenColumns())
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
+ start = colSel.adjustForHiddenColumns(start);
+ }
+
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ {
+ end = max;
+ }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
- regions.add(new int[] { start, end });
+ regions.add(new int[] { start, end });
- if (posProps.hasHiddenColumns())
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
+ if (colSel != null && colSel.hasHiddenColumns())
+ {
+ start = colSel.adjustForHiddenColumns(end);
+ start = colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ } while (end < max);
- int[][] startEnd = new int[regions.size()][2];
+ int[][] startEnd = new int[regions.size()][2];
- return regions;*/
+ return regions;
}
@Override
public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
boolean selectedOnly)
{
- return posProps.getVisibleAlignmentAnnotation(selectedOnly,
- selectionGroup);
- /*ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
AlignmentAnnotation[] aa;
if ((aa = alignment.getAlignmentAnnotation()) != null)
{
ala.add(clone);
}
}
- return ala;*/
+ return ala;
}
@Override
ResidueShaderI rs = residueShading;
if (rs != null)
{
- rs.alignmentChanged(alignment, posProps.getHiddenRepSequences());
+ rs.alignmentChanged(alignment, hiddenRepSequences);
rs.setConsensus(hconsensus);
if (rs.conservationApplied())
{
if (sg.cs != null)
{
- sg.cs.alignmentChanged(sg, posProps.getHiddenRepSequences());
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
sg.recalcConservation();
}
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ "Number of aligned positions",
+ new Annotation[1], 0f, alignment.getHeight(),
+ AlignmentAnnotation.BAR_GRAPH);
+ initGapCounts(gapcounts);
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())
{
"PID for cDNA", 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(AlignmentAnnotation counts)
+ {
+ counts.hasText = false;
+ counts.autoCalculated = true;
+ counts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(counts);
+ }
+ }
+
private void initConservation()
{
if (showConservation)
}
@Override
- public ViewportPositionProps getPosProps()
+ public ViewportRanges getRanges()
{
- return posProps;
- }
-
- @Override
- public int getStartRes()
- {
- return posProps.getStartRes();
- }
-
- @Override
- public int getEndRes()
- {
- return posProps.getEndRes();
- }
-
- @Override
- public int getStartSeq()
- {
- return posProps.getStartSeq();
- }
-
- public void setStartRes(int res)
- {
- posProps.setStartRes(res);
- // this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- posProps.setStartSeq(seq);
- // this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- posProps.setEndRes(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)
- {
- posProps.setEndSeq(seq);
- /*if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;*/
- }
-
- @Override
- public int getEndSeq()
- {
- return posProps.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))
*/
public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- if (!this.hasSelectedColumns())
- {
- posProps.expandColSelection(sg, wholewidth);
- }
- /*int sgs, sge;
+ int sgs, sge;
if (sg != null && (sgs = sg.getStartRes()) >= 0
&& sg.getStartRes() <= (sge = sg.getEndRes())
&& !this.hasSelectedColumns())
{
colSel.addElement(cspos);
}
- }*/
+ }
}
/**
*/
private boolean selectionIsDefinedGroup = false;
-
@Override
public boolean isSelectionDefinedGroup()
{
git://source.jalview.org / jalview.git / blobdiff