*/
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
- * and end residues and sequences, hidden column/row adjustments, ratio of
- * viewport to alignment etc
+ * and end residues and sequences
*/
public class ViewportPositionProps extends ViewportProperties
{
// end sequence of viewport
private int endSeq;
- // character height
- private int charHeight;
-
- // character width
- private int charWidth;
-
// alignment
private AlignmentI al;
- // 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
+ *
+ * @param alignment
+ * the viewport's alignment
*/
- public ViewportPositionProps(AlignmentI alignment, ViewStyleI vstyle)
+ public ViewportPositionProps(AlignmentI alignment)
{
// initial values of viewport settings
this.startRes = 0;
this.startSeq = 0;
this.endSeq = alignment.getHeight() - 1;
this.al = alignment;
- this.viewstyle = vstyle;
- }
-
- public void setCharHeight(int h)
- {
- viewstyle.setCharHeight(h);
- }
-
- public void setCharWidth(int w)
- {
- viewstyle.setCharWidth(w);
}
// ways to update values
// ways to supply positional information
/**
- * Get alignment width
+ * Get alignment width in cols, including hidden cols
*/
- public int getAlignmentWidthInCols()
+ public int getAbsoluteAlignmentWidth()
{
return al.getWidth();
}
/**
- * Get alignment height
+ * Get alignment height in rows, including hidden rows
*/
- public int getAlignmentHeightInRows()
+ public int getAbsoluteAlignmentHeight()
{
- return al.getHeight();
+ return al.getHeight() + al.getHiddenSequences().getSize();
}
+ /**
+ * Set first residue visible in the viewport
+ *
+ * @param res
+ * residue position
+ */
public void setStartRes(int res)
{
if (res > al.getWidth() - 1)
this.startRes = res;
}
+ /**
+ * Set last residue visible in the viewport
+ *
+ * @param res
+ * residue position
+ */
public void setEndRes(int res)
{
- if (res > al.getWidth() - 1)
+ if (res >= al.getWidth())
{
res = al.getWidth() - 1;
}
- else if (res < 0)
+ else if (res < 1)
{
- res = 0;
+ res = 1;
}
this.endRes = res;
}
+ /**
+ * Set the first sequence visible in the viewport
+ *
+ * @param seq
+ * sequence position
+ */
public void setStartSeq(int seq)
{
- if (seq > al.getHeight())
+ if (seq > al.getHeight() - 1)
{
- seq = al.getHeight();
+ seq = al.getHeight() - 1;
}
else if (seq < 0)
{
this.startSeq = seq;
}
+ /**
+ * Set the last sequence visible in the viewport
+ *
+ * @param seq
+ * sequence position
+ */
public void setEndSeq(int seq)
{
- if (seq > al.getHeight())
+ if (seq >= al.getHeight())
{
- seq = al.getHeight();
+ seq = al.getHeight() - 1;
}
- else if (seq < 0)
+ else if (seq < 1)
{
- seq = 0;
+ seq = 1;
}
this.endSeq = seq;
}
{
return endSeq;
}
- /**
- * Get start residue of viewport
- */
- public int getStartRes(boolean countHidden)
- {
- if (countHidden)
- {
- return 0; // av.getColumnSelection().adjustForHiddenColumns(startRes);
- }
- else
- {
- return startRes;
- }
- }
-
- /**
- * Convert distance x in viewport pixels to a distance in number of residues
- *
- * @param x
- * number of pixels
- * @return number of residues
- */
- public int convertPixelsToResidues(int x)
- {
- return Math.round((float) x / viewstyle.getCharWidth());
- }
-
- /**
- * Convert distance y in viewport pixels to a distance in number of sequences
- *
- * @param y
- * number of pixels
- * @return number of sequences
- */
- public int convertPixelsToSequences(int y)
- {
- return Math.round((float) y / viewstyle.getCharHeight());
- }
-
- /**
- * Convert number of sequences s to a height in viewport pixels
- *
- * @param s
- * number of sequences
- * @return number of pixels
- */
- public int convertSequencesToPixels(int s)
- {
- return (s * viewstyle.getCharHeight());
- }
-
- /**
- * Convert number of residues r to a width in viewport pixels
- *
- * @param r
- * number of residues
- * @return number of pixels
- */
- public int convertResiduesToPixels(int r)
- {
- 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 / blobdiff