/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
{
int xPos = 0;
int panelWidth = getWidth();
- int charHeight = av.charHeight;
+ int charHeight = av.getCharHeight();
if ((searchResults != null) && searchResults.contains(s))
{
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.getShowHiddenMarkers())
{
drawMarker(i, starty, ypos);
}
return;
}
- gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+ -vertical * av.getCharHeight());
int ss = av.startSeq;
int es = av.endSeq;
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - (vertical * av.getCharHeight());
}
}
else if (vertical < 0)
int oldHeight = imgHeight;
imgHeight = getHeight();
- imgHeight -= (imgHeight % av.charHeight);
+ imgHeight -= (imgHeight % av.getCharHeight());
if (imgHeight < 1)
{
*/
void drawIds(int starty, int endy)
{
- if (av.seqNameItalics)
+ if (av.isSeqNameItalics())
{
- 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)
{
}
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = alheight * av.charHeight + hgap + annotationHeight;
+ int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
{
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));
+ gg.translate(0, ypos + (alheight * av.getCharHeight()));
labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * av.getCharHeight()));
}
}
}
// 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);
}
currentTextColor = Color.white;
}
else if ((av.getSelectionGroup() != null)
- && av.getSelectionGroup().getSequences(null).contains(
- sequence))
+ && av.getSelectionGroup().getSequences(null)
+ .contains(sequence))
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
gg.setColor(currentColor);
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
- av.charHeight);
+ gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+ av.getCharHeight());
gg.setColor(currentTextColor);
String string = sequence.getDisplayId(av.getShowJVSuffix());
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
xPos = panelWidth - fm.stringWidth(string) - 4;
}
gg.drawString(string, xPos,
- (((i - starty) * av.charHeight) + av.charHeight)
- - (av.charHeight / 5));
+ (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.getShowHiddenMarkers())
{
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;
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(),
getWidth() }, new int[]
{
- (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight
- / 4, (i - starty) * av.charHeight + yoffset }, 3);
+ (i - starty) * av.getCharHeight() + yoffset,
+ (i - starty) * av.getCharHeight() + yoffset
+ + av.getCharHeight() / 4,
+ (i - starty) * av.getCharHeight() + yoffset }, 3);
}
if (above)
{
gg.fillPolygon(
new int[]
- { getWidth() - av.charHeight, getWidth() - av.charHeight,
+ { getWidth() - av.getCharHeight(),
+ getWidth() - av.getCharHeight(),
getWidth() }, new int[]
{
- (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset
- - av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset }, 3);
+ (i - starty + 1) * av.getCharHeight() + yoffset,
+ (i - starty + 1) * av.getCharHeight() + yoffset
+ - av.getCharHeight() / 4,
+ (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
}
}
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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff