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);
}
}
}
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
// 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);
+ }
- regions.add(new int[] { start, end });
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ {
+ end = max;
+ }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
- if (posProps.hasHiddenColumns())
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
+ regions.add(new int[] { start, end });
+
+ 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();
}
*/
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);
}
- }*/
+ }
}
/**
package jalview.viewmodel;
import jalview.api.ViewStyleI;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
/**
* Supplies and updates viewport properties relating to position such as: start
// viewstyle
private ViewStyleI viewstyle;
- // hidden column data
- protected ColumnSelection colSel = new ColumnSelection();
-
- private long colselhash = -1;
-
- // hidden sequence data
- private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
/**
* Constructor
* @param alignment TODO
public int convertPixelsToResidues(int x)
{
return Math.round((float) x / viewstyle.getCharWidth());
+ // return (int) ((float) x / viewstyle.getCharWidth());
}
/**
public int convertPixelsToSequences(int y)
{
return Math.round((float) y / viewstyle.getCharHeight());
+ // return (int) ((float) y / viewstyle.getCharHeight());
}
/**
{
return (r * viewstyle.getCharWidth());
}
-
- public void setHiddenColumns(ColumnSelection colsel)
- {
- this.colSel = colsel;
- }
-
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- public void setColumnSelection(ColumnSelection colSel)
- {
- this.colSel = colSel;
- if (colSel != null)
- {
- // updateHiddenColumns(); - does nothing
- }
- isColSelChanged(true);
- }
-
- public boolean hasHiddenColumns()
- {
- return colSel != null && colSel.hasHiddenColumns();
- }
-
- /**
- * checks current colsel against record of last hash value, and optionally
- * updates record.
- *
- * @param b
- * update the record of last hash value
- * @return true if colsel changed since last call (when b is true)
- */
- public boolean isColSelChanged(boolean b)
- {
- int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
- if (hc != -1 && hc != colselhash)
- {
- if (b)
- {
- colselhash = hc;
- }
- return true;
- }
- return false;
- }
-
- 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);
- }
-
- public void invertColumnSelection()
- {
- colSel.invertColumnSelection(0, al.getWidth());
- }
-
- public List<int[]> getVisibleRegionBoundaries(int min, int max)
- {
- ArrayList<int[]> regions = new ArrayList<int[]>();
- int start = min;
- int end = max;
-
- do
- {
- if (hasHiddenColumns())
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
-
- regions.add(new int[] { start, end });
-
- if (hasHiddenColumns())
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- return regions;
- }
-
- /**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
- *
- * @param sg
- * @param wholewidth
- */
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
- {
- int sgs, sge;
- if (sg != null && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes()))
- {
- if (!wholewidth && al.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
- }
- }
-
- public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
- boolean selectedOnly, SequenceGroup selectionGroup)
- {
- ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
- AlignmentAnnotation[] aa;
- if ((aa = al.getAlignmentAnnotation()) != null)
- {
- for (AlignmentAnnotation annot : aa)
- {
- AlignmentAnnotation clone = new AlignmentAnnotation(annot);
- if (selectedOnly && selectionGroup != null)
- {
- colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
- selectionGroup.getEndRes(), clone);
- }
- else
- {
- colSel.makeVisibleAnnotation(clone);
- }
- ala.add(clone);
- }
- }
- return ala;
- }
-
- public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
- {
- return colSel.getVisibleSequenceStrings(start, end, seqs);
- }
-
- /**
- * Set visibility for any annotations for the given sequence.
- *
- * @param sequenceI
- */
- protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
- boolean visible)
- {
- AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
- if (anns != null)
- {
- for (AlignmentAnnotation ann : anns)
- {
- if (ann.sequenceRef == sequenceI)
- {
- ann.visible = visible;
- }
- }
- }
- }
-
- public void setHiddenRepSequences(
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
- {
- this.hiddenRepSequences = hiddenRepSequences;
- }
-
- public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
- {
- return hiddenRepSequences;
- }
-
- // common hide/show seq stuff
- public SequenceGroup showAllHiddenSeqs(SequenceGroup selectionGroup)
- {
- if (al.getHiddenSequences().getSize() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(al.getWidth() - 1);
- }
- List<SequenceI> tmp = al.getHiddenSequences().showAll(
- hiddenRepSequences);
- for (SequenceI seq : tmp)
- {
- selectionGroup.addSequence(seq, false);
- setSequenceAnnotationsVisible(seq, true);
- }
-
- hiddenRepSequences = null;
-
- firePropertyChange("alignment", null, al.getSequences());
- // used to set hasHiddenRows/hiddenRepSequences here, after the property
- // changed event
- sendSelection();
- }
- }
-
- public void showSequence(int index, SequenceGroup selectionGroup)
- {
- List<SequenceI> tmp = al.getHiddenSequences().showSequence(index,
- hiddenRepSequences);
- if (tmp.size() > 0)
- {
- if (selectionGroup == null)
- {
- selectionGroup = new SequenceGroup();
- selectionGroup.setEndRes(al.getWidth() - 1);
- }
-
- for (SequenceI seq : tmp)
- {
- selectionGroup.addSequence(seq, false);
- setSequenceAnnotationsVisible(seq, true);
- }
- firePropertyChange("alignment", null, al.getSequences());
- sendSelection();
- }
- }
-
- public void hideAllSelectedSeqs(SequenceGroup selectionGroup)
- {
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- return;
- }
-
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(al);
-
- hideSequence(seqs);
-
- setSelectionGroup(null);
- }
-
- public void hideSequence(SequenceI[] seq)
- {
- if (seq != null)
- {
- for (int i = 0; i < seq.length; i++)
- {
- al.getHiddenSequences().hideSequence(seq[i]);
- setSequenceAnnotationsVisible(seq[i], false);
- }
- firePropertyChange("alignment", null, al.getSequences());
- }
- }
-
- /**
- * Hides the specified sequence, or the sequences it represents
- *
- * @param sequence
- * the sequence to hide, or keep as representative
- * @param representGroup
- * if true, hide the current selection group except for the
- * representative sequence
- */
- public void hideSequences(SequenceI sequence, boolean representGroup,
- SequenceGroup selectionGroup)
- {
- if (selectionGroup == null || selectionGroup.getSize() < 1)
- {
- hideSequence(new SequenceI[] { sequence });
- return;
- }
-
- if (representGroup)
- {
- hideRepSequences(sequence, selectionGroup);
- setSelectionGroup(null);
- return;
- }
-
- int gsize = selectionGroup.getSize();
- SequenceI[] hseqs = selectionGroup.getSequences().toArray(
- new SequenceI[gsize]);
-
- hideSequence(hseqs);
- setSelectionGroup(null);
- sendSelection();
- }
-
- public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
- {
- int sSize = sg.getSize();
- if (sSize < 2)
- {
- return;
- }
-
- if (hiddenRepSequences == null)
- {
- hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
- }
-
- hiddenRepSequences.put(repSequence, sg);
-
- // Hide all sequences except the repSequence
- SequenceI[] seqs = new SequenceI[sSize - 1];
- int index = 0;
- for (int i = 0; i < sSize; i++)
- {
- if (sg.getSequenceAt(i) != repSequence)
- {
- if (index == sSize - 1)
- {
- return;
- }
-
- seqs[index++] = sg.getSequenceAt(i);
- }
- }
- sg.setSeqrep(repSequence); // note: not done in 2.7applet
- sg.setHidereps(true); // note: not done in 2.7applet
- hideSequence(seqs);
-
- }
-
- /**
- *
- * @param seq
- * @return true if there are sequences represented by this sequence that are
- * currently hidden
- */
- public boolean isHiddenRepSequence(SequenceI seq)
- {
- return (hiddenRepSequences != null && hiddenRepSequences
- .containsKey(seq));
- }
-
- /**
- *
- * @param seq
- * @return null or a sequence group containing the sequences that seq
- * represents
- */
- public SequenceGroup getRepresentedSequences(SequenceI seq)
- {
- return (SequenceGroup) (hiddenRepSequences == null ? null
- : hiddenRepSequences.get(seq));
- }
-
- public int adjustForHiddenSeqs(int alignmentIndex)
- {
- return al.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
- }
}
git://source.jalview.org / jalview.git / commitdiff