/*
- * 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.appletgui;
-import java.awt.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueColourFinder;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
-public class SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRenderer
{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
AlignViewport av;
FontMetrics fm;
boolean renderGaps = true;
- SequenceGroup currentSequenceGroup = null;
-
SequenceGroup[] allGroups = null;
Color resBoxColour;
Graphics graphics;
- boolean forOverview = false;
+ ResidueColourFinder resColourFinder;
public SequenceRenderer(AlignViewport av)
{
this.av = av;
+ resColourFinder = new ResidueColourFinder();
}
/**
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void prepare(Graphics g, boolean renderGaps)
{
this.renderGaps = renderGaps;
}
- public Color getResidueBoxColour(SequenceI seq, int i)
- {
- allGroups = av.alignment.findAllGroups(seq);
-
- if (inCurrentSequenceGroup(i))
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.cs, seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.globalColourScheme, seq, i);
- }
-
- return resBoxColour;
- }
-
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ /**
+ * 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 finder
+ * @return
+ */
+ @Override
+ public Color getResidueColour(final SequenceI seq, int position,
+ FeatureColourFinder finder)
{
- if (cs != null)
- {
- resBoxColour = cs.findColour(seq.getCharAt(i), i);
- }
- else if (forOverview
- && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
- {
- resBoxColour = Color.lightGray;
- }
- else
- {
- resBoxColour = Color.white;
- }
-
+ // TODO replace 8 or so code duplications with calls to this method
+ // (refactored as needed)
+ return resColourFinder.getResidueColour(av.getShowBoxes(),
+ av.getResidueShading(), allGroups, seq, position, finder);
}
public Color findSequenceColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ allGroups = av.getAlignment().findAllGroups(seq);
drawBoxes(seq, i, i, 0);
return resBoxColour;
}
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(),
+ avCharHeight = av.getCharHeight();
+ Color resBoxColour = Color.white;
Color tempColour = null;
while (i <= end)
{
resBoxColour = Color.white;
if (i < length)
{
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
}
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avCharWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avCharWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
+ avCharHeight);
}
public void drawText(SequenceI seq, int start, int end, int y1)
{
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
Font boldFont = null;
boolean bold = false;
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
- boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
graphics.setFont(av.getFont());
}
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += avCharHeight - avCharHeight / 5; // height/5 replaces pady
int charOffset = 0;
}
char s = ' ';
-
+ boolean srep = av.isDisplayReferenceSeq();
for (int i = start; i <= end; i++)
{
graphics.setColor(Color.black);
continue;
}
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
if (currentSequenceGroup.getColourText())
{
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
graphics.setColor(resBoxColour.darker());
}
+ if (currentSequenceGroup.getShowNonconserved())
+ {
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+ }
}
else
{
if (av.getColourText())
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
graphics.setColor(resBoxColour.darker());
graphics.setColor(resBoxColour);
}
}
+ if (av.getShowUnconserved())
+ {
+ s = getDisplayChar(srep, i, s, '.', null);
+
+ }
}
- if (av.upperCasebold)
+ if (av.isUpperCasebold())
{
fm = graphics.getFontMetrics();
if ('A' <= s && s <= 'Z')
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
- * (i - start), y1);
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + avCharWidth * (i - start), y1);
}
}
- boolean inCurrentSequenceGroup(int res)
+ /**
+ * Returns 'conservedChar' to represent the given position if the sequence
+ * character at that position is equal to the consensus (ignoring case), else
+ * returns the sequence character
+ *
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
+ */
+ private char getDisplayChar(final boolean usesrep, int position,
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
{
- if (allGroups == null)
- {
- return false;
- }
-
- for (int i = 0; i < allGroups.length; i++)
+ // TODO - use currentSequenceGroup rather than alignment
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes()
+ ? av.getAlignment().getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null
+ ? currentGroup.getSeqrep().getCharAt(position)
+ : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes()
+ && currentGroup
+ .getConsensus().annotations.length > position)
+ ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (!jalview.util.Comparison.isGap(conschar)
+ && (sequenceChar == conschar
+ || sequenceChar + CHAR_TO_UPPER == conschar))
{
- if (allGroups[i].getStartRes() <= res
- && allGroups[i].getEndRes() >= res)
- {
- currentSequenceGroup = allGroups[i];
- return true;
- }
+ sequenceChar = conservedChar;
}
-
- return false;
+ return sequenceChar;
}
- public void drawHighlightedText(SequenceI seq, int start, int end,
- int x1, int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+ int y1)
{
- int pady = av.charHeight / 5;
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+ int pady = avCharHeight / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1),
+ avCharHeight);
graphics.setColor(Color.white);
char s = '~';
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1
- + av.charWidth * (i - start), y1 + av.charHeight - pady);
+ charOffset = (avCharWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + avCharWidth * (i - start),
+ y1 + avCharHeight - pady);
}
}
}
public void drawCursor(SequenceI seq, int res, int x1, int y1)
{
- int pady = av.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
graphics.setColor(Color.white);
graphics.setColor(Color.white);
if (av.validCharWidth)
{
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ (y1 + av.getCharHeight()) - pady);
}
}
git://source.jalview.org / jalview.git / blobdiff