/*
- * 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.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
public class AlignmentPanel extends Panel implements AdjustmentListener,
sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
alabels = new AnnotationLabels(this);
- setAnnotationVisible(av.showAnnotation);
+ setAnnotationVisible(av.isShowAnnotation());
idPanelHolder.add(idPanel, BorderLayout.CENTER);
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
});
}
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
public SequenceRenderer getSequenceRenderer()
{
return seqPanel.seqCanvas.sr;
idPanel.idCanvas.image = null;
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+ scalePanel.setSize(new Dimension(10, av.getCharHeight()
+ + fm.getDescent()));
+ idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
{
start = ostart;
}
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
/*
* int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationPanelHolder.setVisible(b);
}
+ else
+ {
+ annotationSpaceFillerHolder.setVisible(false);
+ annotationPanelHolder.setVisible(false);
+ }
validate();
repaint();
}
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out.println("NEEDS FIXING");
+ System.out
+ .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
}
fontChanged();
validateAnnotationDimensions(true);
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
+ // NOTE: this logic is different in the application. Need a better
+ // algorithm to define behaviour
// sets initial preferred height
// try and set height according to alignment
- float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
+ float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
+ .getHeight()) / (1.0 * mheight));
if (sscaling > 0.5)
{
// if the alignment is too big then
}
else
{
- // otherwise just set the panel so that one row of sequence is visible
+ // otherwise just set the panel so that one row of sequence is visible
height = -av.getCharHeight() * 1
+ (int) (seqandannot * (1 - sscaling));
}
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);
+ // seqPanelHolder.setSize(d.width, seqandannot - height);
seqPanel.seqCanvas
.setSize(d.width, seqPanel.seqCanvas.getSize().height);
int s = apvscroll.getValue();
s = 0;
}
apvscroll.setValues(s, height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
}
public void setWrapAlignment(boolean wrap)
annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
fontChanged(); // This is so that the scalePanel is resized correctly
validate();
+ sequenceHolderPanel.validate();
repaint();
}
}
;
- hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
- vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
+ hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+ vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
if (hextent > width)
{
av.setEndSeq(endSeq);
av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+ .getCharWidth())) - 1);
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
if (evt == null || evt.getSource() == apvscroll)
{
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
// annotationPanel.image=null;
// alabels.image=null;
// alabels.repaint();
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.isShowAnnotation())
{
annotationPanel.fastPaint(av.getStartRes() - oldX);
}
av.endSeq);
}
+ /**
+ * Repaint the alignment and annotations, and, optionally, any overview window
+ */
public void paintAlignment(boolean updateOverview)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
if (updateOverview)
setScrollValues(av.getStartRes(), av.getStartSeq());
}
- alabels.repaint();
-
seqPanel.seqCanvas.repaint();
- scalePanel.repaint();
- annotationPanel.repaint();
idPanel.idCanvas.repaint();
+ if (!av.getWrapAlignment())
+ {
+ if (av.isShowAnnotation())
+ {
+ alabels.repaint();
+ annotationPanel.repaint();
+ }
+ scalePanel.repaint();
+ }
+
}
protected Panel sequenceHolderPanel = new Panel();
}
@Override
+ public String getViewName()
+ {
+ return getName();
+ }
+
+ @Override
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
git://source.jalview.org / jalview.git / blobdiff