/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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 jalview.api.FeatureRenderer;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
{
AlignViewport av;
* Creates a new SequenceRenderer object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public SequenceRenderer(AlignViewport av)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void prepare(Graphics g, boolean renderGaps)
{
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av.charWidth == dwidth);
this.renderGaps = renderGaps;
}
+ @Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
return resBoxColour;
}
/**
+ * Get the residue colour at the given sequence position - as determined by
+ * the sequence group colour (if any), else the colour scheme, possibly
+ * overridden by a feature colour.
+ *
+ * @param seq
+ * @param position
+ * @param fr
+ * @return
+ */
+ @Override
+ public Color getResidueColour(final SequenceI seq, int position,
+ FeatureRenderer fr)
+ {
+ // TODO replace 8 or so code duplications with calls to this method
+ // (refactored as needed)
+ Color col = getResidueBoxColour(seq, position);
+
+ if (fr != null)
+ {
+ col = fr.findFeatureColour(col, seq, position);
+ }
+ return col;
+ }
+
+ /**
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
{
if (cs != null)
{
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
}
else if (forOverview
&& !jalview.util.Comparison.isGap(seq.getCharAt(i)))
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
int end, int y1)
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public synchronized void drawBoxes(SequenceI seq, int start, int end,
int y1)
{
+ if (seq == null)
+ {
+ return; // fix for racecondition
+ }
int i = start;
int length = seq.getLength();
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
}
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawText(SequenceI seq, int start, int end, int y1)
{
}
else
{
+ boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
for (int i = start; i <= end; i++)
{
{
graphics.setColor(currentSequenceGroup.textColour);
}
+ if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+ {
+ // todo - use sequence group consensus
+ s = getDisplayChar(srep, i, s,
+ '.');
+
+ }
}
else
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
if (av.getShowBoxes())
{
{
if (!getboxColour)
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
graphics.setColor(av.textColour2);
}
}
+ if (av.getShowUnconserved())
+ {
+ s = getDisplayChar(srep, i, s,
+ '.');
+
+ }
}
}
}
+ private char getDisplayChar(final boolean usesrep, int position,
+ char s, char c)
+ {
+ // TODO - use currentSequenceGroup rather than alignemnt
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (conschar != '-' && s == conschar)
+ {
+ s = c;
+ }
+ return s;
+ }
+
/**
* DOCUMENT ME!
*
* @param res
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param x1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param width
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param height
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawHighlightedText(SequenceI seq, int start, int end,
int x1, int y1)
}
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics
- .drawString(String.valueOf(s), charOffset + x1
- + (av.charWidth * (i - start)),
- (y1 + av.charHeight) - pady);
+ graphics.drawString(String.valueOf(s), charOffset + x1
+ + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
}
}
}
git://source.jalview.org / jalview.git / blobdiff