/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.gui;
import java.awt.*;
import java.awt.image.*;
+import java.util.List;
+
import javax.swing.*;
import jalview.datamodel.*;
boolean fastPaint = false;
- java.util.Vector searchResults;
+ List<SequenceI> searchResults;
FontMetrics fm;
AnnotationPanel ap;
- Font idfont;
+ private Font idfont;
/**
* Creates a new IdCanvas object.
gg.setColor(Color.black);
}
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth
- fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, ypos);
}
{
if (av.seqNameItalics)
{
- idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
- .getSize());
+ setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+ .getSize()));
}
else
{
- idfont = av.getFont();
+ setIdfont(av.getFont());
}
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
fm = gg.getFontMetrics();
if (av.antiAlias)
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
int annotationHeight = 0;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
if (ap == null)
{
{
for (int i = starty; i < alheight; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
- if (av.hasHiddenRows)
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
{
setHiddenFont(s);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
drawIdString(gg, s, i, 0, ypos);
}
- if (labels != null && av.showAnnotation)
+ if (labels != null && av.isShowAnnotation())
{
gg.translate(0, ypos + (alheight * av.charHeight));
labels.drawComponent(gg, getWidth());
// Now draw the id strings
for (int i = starty; i < endy; i++)
{
- sequence = av.alignment.getSequenceAt(i);
+ sequence = av.getAlignment().getSequenceAt(i);
if (sequence == null)
{
continue;
}
- if (av.hasHiddenRows)
+ if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
{
setHiddenFont(sequence);
}
String string = sequence.getDisplayId(av.getShowJVSuffix());
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth - fm.stringWidth(string) - 4;
}
(((i - starty) * av.charHeight) + av.charHeight)
- (av.charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, 0);
}
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
}
else
{
- gg.setFont(idfont);
+ gg.setFont(getIdfont());
}
}
/**
* DOCUMENT ME!
*
- * @param found
+ * @param list
* DOCUMENT ME!
*/
- public void setHighlighted(java.util.Vector found)
+ public void setHighlighted(List<SequenceI> list)
{
- searchResults = found;
+ searchResults = list;
repaint();
}
+
+ public Font getIdfont()
+ {
+ return idfont;
+ }
+
+ public void setIdfont(Font idfont)
+ {
+ this.idfont = idfont;
+ }
}