/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
-
package jalview.appletgui;
import java.awt.*;
import java.awt.event.*;
+import java.util.Hashtable;
+import java.util.Vector;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.*;
+import jalview.structure.StructureSelectionManager;
-public class AlignmentPanel
- extends Panel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
{
public AlignViewport av;
+
OverviewPanel overviewPanel;
+
SeqPanel seqPanel;
+
IdPanel idPanel;
+
IdwidthAdjuster idwidthAdjuster;
+
public AlignFrame alignFrame;
+
ScalePanel scalePanel;
+
AnnotationPanel annotationPanel;
+
AnnotationLabels alabels;
// this value is set false when selection area being dragged
boolean fastPaint = true;
-
+
+ public void finalize() {
+ alignFrame=null;
+ av=null;
+ seqPanel=null;
+ seqPanelHolder=null;
+ sequenceHolderPanel=null;
+ scalePanel=null;
+ scalePanelHolder=null;
+ annotationPanel=null;
+ annotationPanelHolder=null;
+ annotationSpaceFillerHolder=null;
+ }
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
scalePanel = new ScalePanel(av, this);
idwidthAdjuster = new IdwidthAdjuster(this);
annotationPanel = new AnnotationPanel(this);
+ annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
- sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
+ sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
alabels = new AnnotationLabels(this);
fontChanged();
setScrollValues(0, 0);
+ apvscroll.addAdjustmentListener(this);
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
public void componentResized(ComponentEvent evt)
{
setScrollValues(av.getStartRes(), av.getStartSeq());
+ if (getSize().height>0 && annotationPanelHolder.getSize().height>0) {
+ validateAnnotationDimensions(false);
+ }
repaint();
}
+
});
Dimension d = calculateIdWidth();
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
annotationSpaceFillerHolder.setSize(d.width,
- annotationPanel.getSize().height);
+ annotationPanel.getSize().height);
alabels.setSize(d.width, annotationPanel.getSize().height);
-
final AlignmentPanel ap = this;
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
{
if (evt.getPropertyName().equals("alignment"))
{
- PaintRefresher.Refresh(ap,
- av.getSequenceSetId(),
- true,
- true);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
alignmentChanged();
}
}
FontMetrics fm = getFontMetrics(av.getFont());
scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
+ idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+ + fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
- int ap = annotationPanel.adjustPanelHeight();
- annotationPanel.repaint();
+ int ap = annotationPanel.adjustPanelHeight(false);
Dimension d = calculateIdWidth();
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
alabels.setSize(d.width + 4, ap);
+
idPanel.idCanvas.setSize(d);
hscrollFillerPanel.setSize(d);
-
+
+ validateAnnotationDimensions(false);
+ annotationPanel.repaint();
validate();
repaint();
{
idPanel.idCanvas.setSize(w, h);
idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+ annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
alabels.setSize(w, alabels.getSize().height);
validate();
}
return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
}
+ /**
+ * Highlight the given results on the alignment.
+ *
+ */
public void highlightSearchResults(SearchResults results)
{
+ scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(results);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
+ * @param results
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results)
+ {
+ return scrollToPosition(results, true);
+ }
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview)
+ {
+
// do we need to scroll the panel?
- if (results != null)
+ if (results != null && results.getSize() > 0)
{
- SequenceI seq = results.getResultSequence(0);
- int seqIndex = av.alignment.findIndex(seq);
- int start = seq.findIndex(results.getResultStart(0)) - 1;
- int end = seq.findIndex(results.getResultEnd(0)) - 1;
+ int seqIndex = av.alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+ int[] r = results.getResults(seq, 0,av.alignment.getWidth());
+ if (r == null)
+ {
+ if (av.applet.debug) {// DEBUG
+ System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+ }
+ return false;
+ }
+ if (av.applet.debug) {
+ // DEBUG
+ /*System.out.println("DEBUG: scroll: start=" + r[0]
+ + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
+ + " seq.end=" + seq.getEnd() + " av.getEndRes()="
+ + av.getEndRes() + " hextent=" + hextent);
+ */
+ }
+ int start = r[0];
+ int end = r[1];
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ return scrollTo(start, end, seqIndex, false, redrawOverview);
+ }
+ return true;
+ }
+ public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
- if (!av.wrapAlignment)
+ int start=-1;
+ if (av.hasHiddenColumns)
+ {
+ start = av.getColumnSelection().findColumnPosition(ostart);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start == end)
{
- if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
- ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ if (!scrollToNearest && !av.colSel.isVisible(ostart))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+ else
+ {
+ start = ostart;
+ }
+ if (!av.wrapAlignment)
+ {
+ /*
+ int spos=av.getStartRes(),sqpos=av.getStartSeq();
+ if ((startv = av.getStartRes()) >= start)
+ {
+ spos=start-1;
+// seqIn
+// setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
+ {
+// setScrollValues(spos=startv + 1 + end - endv, seqIndex);
+ spos=startv + 1 + end - endv;
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
+ {
+ setScrollValues(av.getStartRes(), seqIndex);
+ }
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
+
+ /* */
+ if ((av.getStartRes() > end)
+ || (av.getEndRes() < start)
+ || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
{
if (start > av.alignment.getWidth() - hextent)
{
{
start = 0;
}
+
}
if (seqIndex > av.alignment.getHeight() - vextent)
{
seqIndex = 0;
}
}
+ // System.out.println("trying to scroll to: "+start+" "+seqIndex);
setScrollValues(start, seqIndex);
- }
+ }/**/
}
else
{
scrollToWrappedVisible(start);
}
+ if (redrawOverview && overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
}
-
- repaint();
+ paintAlignment(redrawOverview);
+ return true;
}
void scrollToWrappedVisible(int res)
{
- int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
- getSize().width);
+ int cwidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
if (!av.wrapAlignment)
{
annotationSpaceFillerHolder.setVisible(b);
- annotationPanel.setVisible(b);
+ annotationPanelHolder.setVisible(b);
}
validate();
repaint();
}
-
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getSize().height == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ fontChanged();
+ validateAnnotationDimensions(true);
+ apvscroll.addNotify();
+ hscroll.addNotify();
+ validate();
+ paintAlignment(true);
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ boolean modified=false;
+ int height = annotationPanel.calcPanelHeight();
+ int minsize=0;
+ if (hscroll.isVisible())
+ {
+ height += (minsize=hscroll.getPreferredSize().height);
+ }
+ if (apvscroll.isVisible()) {
+ minsize+=apvscroll.getPreferredSize().height;
+ }
+ int mheight = height;
+ Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize();
+ int seqandannot=d.height-scalePanelHolder.getSize().height;
+ // sets initial preferred height
+ if ((height+40) > seqandannot / 2)
+ {
+ height = seqandannot / 2;
+ }
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=annotationPanelHolder.getSize().height;
+ }
+
+ if (seqandannot-height<5)
+ {
+ height = seqandannot;
+ }
+ annotationPanel.setSize(new Dimension(d.width,height));
+ alabels.setSize(new Dimension(e.width,height));
+ annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
+ annotationPanelHolder.setSize(new Dimension(d.width, height));
+ seqPanelHolder.setSize(d.width,seqandannot-height);
+ seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ int s=apvscroll.getValue();
+ if (s>mheight-height)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(s, height, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ }
+
public void setWrapAlignment(boolean wrap)
{
av.startSeq = 0;
if (wrap)
{
- annotationPanel.setVisible(false);
+ annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
else if (av.showAnnotation)
{
- annotationPanel.setVisible(true);
+ annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
}
idSpaceFillerPanel1.setVisible(!wrap);
- fontChanged(); //This is so that the scalePanel is resized correctly
+ fontChanged(); // This is so that the scalePanel is resized correctly
validate();
repaint();
}
int hextent = 0;
+
int vextent = 0;
// return value is true if the scroll is valid
{
width = av.getColumnSelection().findColumnPosition(width);
}
-
- av.setStartRes(x);
- av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ if (x<0) { x = 0; };
hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-
+
if (hextent > width)
{
hextent = width;
vextent = height;
}
- if ( (hextent + x) > width)
+ if ((hextent + x) > width)
{
+ System.err.println("hextent was "+hextent+" and x was "+x);
+
x = width - hextent;
}
- if ( (vextent + y) > height)
+ if ((vextent + y) > height)
{
y = height - vextent;
}
if (x < 0)
{
+ System.err.println("x was "+x);
x = 0;
}
}
av.setEndSeq(endSeq);
+ av.setStartRes(x);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
{
overviewPanel.setBoxPosition();
}
+ sendViewPosition();
+
}
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
+ if (evt == null || evt.getSource() == apvscroll)
+ {
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ // annotationPanel.image=null;
+ // alabels.image=null;
+ // alabels.repaint();
+ // annotationPanel.repaint();
+ }
if (evt == null || evt.getSource() == hscroll)
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -
- 1);
+ av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+ / av.getCharWidth() - 1);
}
if (evt == null || evt.getSource() == vscroll)
int offy = vscroll.getValue();
if (av.getWrapAlignment())
{
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getSize().width);
+ int rowSize = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
av.setStartRes(vscroll.getValue() * rowSize);
- av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+ av.setEndRes((vscroll.getValue() + 1) * rowSize);
}
else
{
av.setStartSeq(offy);
- av.setEndSeq(offy +
- seqPanel.seqCanvas.getSize().height / av.getCharHeight());
+ av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+ / av.getCharHeight());
}
}
}
idPanel.idCanvas.fastPaint(scrollY);
- seqPanel.seqCanvas.fastPaint(scrollX,
- scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
if (av.getShowAnnotation())
annotationPanel.fastPaint(av.getStartRes() - oldX);
}
}
+ sendViewPosition();
}
+ private void sendViewPosition()
+ {
+ StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
+ }
public void paintAlignment(boolean updateOverview)
{
repaint();
- if(updateOverview)
+ if (updateOverview)
{
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .sequenceColoursChanged(this);
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
if (overviewPanel != null)
{
invalidate();
Dimension d = idPanel.idCanvas.getSize();
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
- annotationSpaceFillerHolder.setSize(d.width,
- annotationPanel.getSize().height);
-
- alabels.setSize(d.width, annotationPanel.getSize().height);
-
+
if (av.getWrapAlignment())
{
int maxwidth = av.alignment.getWidth();
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth
- (seqPanel.seqCanvas.getSize().width);
+ int canvasWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
if (canvasWidth > 0)
{
int max = maxwidth / canvasWidth;
- vscroll.setMaximum(max);
+ vscroll.setMaximum(1 + max);
vscroll.setUnitIncrement(1);
vscroll.setVisibleAmount(1);
}
}
protected Panel sequenceHolderPanel = new Panel();
+
protected Scrollbar vscroll = new Scrollbar();
+
protected Scrollbar hscroll = new Scrollbar();
+
protected Panel seqPanelHolder = new Panel();
+
BorderLayout borderLayout1 = new BorderLayout();
+
BorderLayout borderLayout3 = new BorderLayout();
+
protected Panel scalePanelHolder = new Panel();
+
protected Panel idPanelHolder = new Panel();
+
BorderLayout borderLayout5 = new BorderLayout();
+
protected Panel idSpaceFillerPanel1 = new Panel();
+
public Panel annotationSpaceFillerHolder = new Panel();
+
BorderLayout borderLayout6 = new BorderLayout();
+
BorderLayout borderLayout7 = new BorderLayout();
+
Panel hscrollHolder = new Panel();
+
BorderLayout borderLayout10 = new BorderLayout();
+
protected Panel hscrollFillerPanel = new Panel();
+
BorderLayout borderLayout11 = new BorderLayout();
+
BorderLayout borderLayout4 = new BorderLayout();
+
BorderLayout borderLayout2 = new BorderLayout();
- private void jbInit()
- throws Exception
+ Panel annotationPanelHolder = new Panel();
+
+ protected Scrollbar apvscroll = new Scrollbar();
+
+ BorderLayout borderLayout12 = new BorderLayout();
+
+ private void jbInit() throws Exception
{
- // idPanelHolder.setPreferredSize(new Dimension(70, 10));
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));
this.setLayout(borderLayout7);
- // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+ //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
sequenceHolderPanel.setLayout(borderLayout3);
seqPanelHolder.setLayout(borderLayout1);
scalePanelHolder.setBackground(Color.white);
idPanelHolder.setLayout(borderLayout5);
idSpaceFillerPanel1.setBackground(Color.white);
- // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
idSpaceFillerPanel1.setLayout(borderLayout11);
annotationSpaceFillerHolder.setBackground(Color.white);
- // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
annotationSpaceFillerHolder.setLayout(borderLayout4);
hscroll.setOrientation(Scrollbar.HORIZONTAL);
hscrollHolder.setLayout(borderLayout10);
hscrollFillerPanel.setBackground(Color.white);
-
- // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+ apvscroll.setOrientation(Scrollbar.VERTICAL);
+ apvscroll.setVisible(true);
+ apvscroll.addAdjustmentListener(this);
+
+ annotationPanelHolder.setBackground(Color.white);
+ annotationPanelHolder.setLayout(borderLayout12);
+ annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
+ // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
hscrollHolder.setBackground(Color.white);
- // annotationScroller.setPreferredSize(new Dimension(10, 80));
- // this.setPreferredSize(new Dimension(220, 166));
+ // annotationScroller.setPreferredSize(new Dimension(10, 80));
+ // this.setPreferredSize(new Dimension(220, 166));
seqPanelHolder.setBackground(Color.white);
idPanelHolder.setBackground(Color.white);
sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
seqPanelHolder.add(vscroll, BorderLayout.EAST);
- // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
+ // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
this.add(idPanelHolder, BorderLayout.WEST);
idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
this.add(sequenceHolderPanel, BorderLayout.CENTER);
}
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
+ boolean updateCalcs = false;
+ boolean conv = av.isShowGroupConservation();
+ boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
+ }
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(av.applet);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff