/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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;
// calculation till later or to do all calculations in thread.
// via changecolour
globalColourScheme = cs;
- boolean recalc=false;
- if (cs!=null)
+ boolean recalc = false;
+ if (cs != null)
{
cs.setConservationApplied(recalc = getConservationSelected());
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme || cs instanceof Blosum62ColourScheme)
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
{
recalc = true;
cs.setThreshold(threshold, ignoreGapsInConsensusCalculation);
- } else {
+ }
+ else
+ {
cs.setThreshold(0, ignoreGapsInConsensusCalculation);
}
if (recalc)
|| cs instanceof Blosum62ColourScheme)
{
sg.cs.setThreshold(threshold, getIgnoreGapsConsensus());
- recalc=true;
+ recalc = true;
}
else
{
if (getConservationSelected())
{
sg.cs.setConservationApplied(true);
- recalc=true;
+ recalc = true;
}
else
{
sg.cs.setConservation(null);
// sg.cs.setThreshold(0, getIgnoreGapsConsensus());
}
- if (recalc) {
+ if (recalc)
+ {
sg.recalcConservation();
- } else {
+ }
+ else
+ {
sg.cs.alignmentChanged(sg, hiddenRepSequences);
}
}
* view
*/
protected Hashtable[] hStrucConsensus = null;
-
+
protected Conservation hconservation = null;
+
@Override
public void setConservation(Conservation cons)
{
hconservation = cons;
}
+
/**
* percentage gaps allowed in a column before all amino acid properties should
* be considered unconserved
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
public void setHiddenColumns(ColumnSelection colsel)
{
this.colSel = colsel;
- if (colSel.getHiddenColumns() != null)
- {
- hasHiddenColumns = true;
- }
}
@Override
return colSel;
}
+ @Override
public void setColumnSelection(ColumnSelection colSel)
{
this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
}
/**
this.hiddenRepSequences = hiddenRepSequences;
}
- protected boolean hasHiddenColumns = false;
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return colSel != null && colSel.hasHiddenColumns();
+ }
public void updateHiddenColumns()
{
- hasHiddenColumns = colSel.getHiddenColumns() != null;
+ // this method doesn't really do anything now. But - it could, since a
+ // column Selection could be in the process of modification
+ // hasHiddenColumns = colSel.hasHiddenColumns();
}
protected boolean hasHiddenRows = false;
+ @Override
public boolean hasHiddenRows()
{
return hasHiddenRows;
sequenceSetID = new String(newid);
}
+ @Override
public String getSequenceSetId()
{
if (sequenceSetID == null)
colSel.hideSelectedColumns();
setSelectionGroup(null);
- hasHiddenColumns = true;
}
public void hideColumns(int start, int end)
{
colSel.hideColumns(start, end);
}
-
- hasHiddenColumns = true;
}
public void showColumn(int col)
{
colSel.revealHiddenColumns(col);
- if (colSel.getHiddenColumns() == null)
- {
- hasHiddenColumns = false;
- }
+
}
public void showAllHiddenColumns()
{
colSel.revealAllHiddenColumns();
- hasHiddenColumns = false;
}
// common hide/show seq stuff
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();
: 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)
{
- return new jalview.datamodel.CigarArray(alignment,
- (hasHiddenColumns ? colSel : null),
+ return new jalview.datamodel.CigarArray(alignment, colSel,
(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)
{
return new AlignmentView(alignment, colSel, selectionGroup,
- hasHiddenColumns, selectedOnly, markGroups);
+ colSel != null && colSel.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)
{
}
selection = new String[iSize];
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
selection = colSel.getVisibleSequenceStrings(start, end, seqs);
}
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();
do
{
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
if (start == 0)
{
regions.addElement(new int[]
{ start, end });
- if (hasHiddenColumns)
+ if (colSel != null && colSel.hasHiddenColumns())
{
start = colSel.adjustForHiddenColumns(end);
start = colSel.getHiddenBoundaryLeft(start) + 1;
}
- /**
- * @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())
{
conservation = new AlignmentAnnotation("Conservation",
"Conservation of total alignment less than "
- + getConsPercGaps() + "% gaps",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ + getConsPercGaps() + "% gaps", new Annotation[1],
+ 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
conservation.hasText = true;
conservation.autoCalculated = true;
alignment.addAnnotation(conservation);
}
}
}
+
private void initQuality()
{
if (showQuality)
{
quality = new AlignmentAnnotation("Quality",
"Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
quality.hasText = true;
quality.autoCalculated = true;
alignment.addAnnotation(quality);
}
}
}
+
private void initRNAStructure()
{
- if (alignment.hasRNAStructure() && strucConsensus==null)
+ if (alignment.hasRNAStructure() && strucConsensus == null)
{
strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f,
- AlignmentAnnotation.BAR_GRAPH);
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
strucConsensus.hasText = true;
strucConsensus.autoCalculated = true;
}
}
}
+
/*
* (non-Javadoc)
*
* @see jalview.api.AlignViewportI#calcPanelHeight()
*/
+ @Override
public int calcPanelHeight()
{
// setHeight of panels
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.add(aan[an].groupRef);
- alignment.deleteAnnotation(aan[an],false);
+ alignment.deleteAnnotation(aan[an], false);
}
}
}
*/
private boolean colourByReferenceSeq=false;
+ @Override
public boolean isDisplayReferenceSeq()
{
return alignment.hasSeqrep() && displayReferenceSeq;
}
+ @Override
public void setDisplayReferenceSeq(boolean displayReferenceSeq)
{
this.displayReferenceSeq = displayReferenceSeq;
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc=Color.white;
+ Color sqc = Color.white;
if (sequenceColours != null)
{
sqc = (Color) sequenceColours.get(seq);
- if (sqc == null) {
+ if (sqc == null)
+ {
sqc = Color.white;
}
}
{
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