*/
package jalview.viewmodel;
-import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeaturesDisplayedI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
return colSel;
}
+ @Override
public void setColumnSelection(ColumnSelection colSel)
{
this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
}
/**
public void updateHiddenColumns()
{
- hasHiddenColumns = colSel.getHiddenColumns() != null;
+ hasHiddenColumns = colSel.hasHiddenColumns();
}
protected boolean hasHiddenRows = false;
sequenceSetID = new String(newid);
}
+ @Override
public String getSequenceSetId()
{
if (sequenceSetID == null)
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(
+ List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
hasHiddenRows = false;
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+ index,
hiddenRepSequences);
if (tmp.size() > 0)
{
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
// JBPNote: refactor: only update flag if we modified visiblity (used to
// do this regardless)
for (int i = 0; i < seq.length; i++)
{
alignment.getHiddenSequences().hideSequence(seq[i]);
+ setSequenceAnnotationsVisible(seq[i], false);
}
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ /**
+ * Set visibility for any annotations for the given sequence.
+ *
+ * @param sequenceI
+ */
+ protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+ boolean visible)
+ {
+ for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
+ }
+ }
+
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
{
int sSize = sg.getSize();
public boolean isHiddenRepSequence(SequenceI seq)
{
- return hiddenRepSequences != null
- && hiddenRepSequences.containsKey(seq);
+ return alignment.getSeqrep()==seq || (hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(seq));
}
public SequenceGroup getRepresentedSequences(SequenceI seq)
: hiddenRepSequences.get(seq));
}
+ @Override
public int adjustForHiddenSeqs(int alignmentIndex)
{
return alignment.getHiddenSequences().adjustForHiddenSeqs(
alignmentIndex);
}
- // Selection manipulation
- /**
- * broadcast selection to any interested parties
- */
+ @Override
public abstract void sendSelection();
+ @Override
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
}
- /**
- * This method returns an array of new SequenceI objects derived from the
- * whole alignment or just the current selection with start and end points
- * adjusted
- *
- * @note if you need references to the actual SequenceI objects in the
- * alignment or currently selected then use getSequenceSelection()
- * @return selection as new sequenceI objects
- */
+
+ @Override
public SequenceI[] getSelectionAsNewSequence()
{
SequenceI[] sequences;
return sequences;
}
- /**
- * get the currently selected sequence objects or all the sequences in the
- * alignment.
- *
- * @return array of references to sequence objects
- */
+
@Override
public SequenceI[] getSequenceSelection()
{
return sequences;
}
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
+
@Override
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
(selectedRegionOnly ? selectionGroup : null));
}
- /**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
- *
- * @param selectedOnly
- * boolean true to just return the selected view
- * @return AlignmentView
- */
+
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly)
return getAlignmentView(selectedOnly, false);
}
- /**
- * return a compact representation of the current alignment selection to pass
- * to an analysis function
- *
- * @param selectedOnly
- * boolean true to just return the selected view
- * @param markGroups
- * boolean true to annotate the alignment view with groups on the
- * alignment (and intersecting with selected region if selectedOnly
- * is true)
- * @return AlignmentView
- */
+
@Override
public jalview.datamodel.AlignmentView getAlignmentView(
boolean selectedOnly, boolean markGroups)
hasHiddenColumns, selectedOnly, markGroups);
}
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
+
@Override
public String[] getViewAsString(boolean selectedRegionOnly)
{
return selection;
}
- /**
- * return visible region boundaries within given column range
- *
- * @param min
- * first column (inclusive, from 0)
- * @param max
- * last column (exclusive)
- * @return int[][] range of {start,end} visible positions
- */
+
+ @Override
public int[][] getVisibleRegionBoundaries(int min, int max)
{
Vector regions = new Vector();
}
- /**
- * @return the padGaps
- */
+ @Override
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ {
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] aa;
+ if ((aa=alignment.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;
+ }
+
+
+ @Override
public boolean isPadGaps()
{
return padGaps;
}
- /**
- * @param padGaps
- * the padGaps to set
- */
+
+ @Override
public void setPadGaps(boolean padGaps)
{
this.padGaps = padGaps;
*
* @param ap
*/
+ @Override
public void alignmentChanged(AlignmentViewPanel ap)
{
if (isPadGaps())
*
* @see jalview.api.AlignViewportI#calcPanelHeight()
*/
+ @Override
public int calcPanelHeight()
{
// setHeight of panels
}
oldrfs.clear();
}
+ /**
+ * show the reference sequence in the alignment view
+ */
+ private boolean displayReferenceSeq=false;
+ /**
+ * colour according to the reference sequence defined on the alignment
+ */
+ private boolean colourByReferenceSeq=false;
+
+ @Override
+ public boolean isDisplayReferenceSeq()
+ {
+ return alignment.hasSeqrep() && displayReferenceSeq;
+ }
+
+ @Override
+ public void setDisplayReferenceSeq(boolean displayReferenceSeq)
+ {
+ this.displayReferenceSeq = displayReferenceSeq;
+ }
+
+ public boolean isColourByReferenceSeq()
+ {
+ return alignment.hasSeqrep() && colourByReferenceSeq;
+ }
+
+ public void setColourByReferenceSeq(boolean colourByReferenceSeq)
+ {
+ this.colourByReferenceSeq = colourByReferenceSeq;
+ }
@Override
public Color getSequenceColour(SequenceI seq)
{
sequenceColours = null;
};
+
+ FeaturesDisplayedI featuresDisplayed = null;
+
+ @Override
+ public FeaturesDisplayedI getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ @Override
+ public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
+ {
+ featuresDisplayed = featuresDisplayedI;
+ }
+
+ @Override
+ public boolean areFeaturesDisplayed()
+ {
+ return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
+ }
+
+ /**
+ * display setting for showing/hiding sequence features on alignment view
+ */
+ boolean showSequenceFeatures = false;
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ @Override
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+ @Override
+ public boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ boolean showSeqFeaturesHeight;
+
+ @Override
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ @Override
+ public boolean isShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ private boolean showAnnotation = true;
+
+ private boolean rightAlignIds = false;
+
+
+ @Override
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ @Override
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ @Override
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ @Override
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff