X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=64fe053e2cce4a05570c32114cf7a2c825a5a263;hb=0d74306f282be2d15eeb5d8de53a949c0124a0a5;hp=e94fba41742996b73fb37829f07c4d36d14d42c3;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e94fba4..64fe053 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -1,35 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.*;
+import jalview.api.FeatureRenderer;
+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 implements jalview.api.SequenceRenderer
{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
AlignViewport av;
FontMetrics fm;
@@ -73,14 +76,17 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
// 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
+ .getCharWidth() == dwidth);
this.renderGaps = renderGaps;
}
+ @Override
public Color getResidueBoxColour(SequenceI seq, int i)
{
- allGroups = av.alignment.findAllGroups(seq);
+ // rate limiting step when rendering overview for lots of groups
+ allGroups = av.getAlignment().findAllGroups(seq);
if (inCurrentSequenceGroup(i))
{
@@ -91,13 +97,38 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
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
@@ -111,7 +142,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
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)))
@@ -181,12 +212,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
int y1)
{
if (seq == null)
+ {
return; // fix for racecondition
+ }
int i = start;
int length = seq.getLength();
int curStart = -1;
- int curWidth = av.charWidth;
+ int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av
+ .getCharHeight();
Color tempColour = null;
@@ -205,7 +239,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else if (av.getShowBoxes())
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
}
@@ -214,26 +248,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+ avHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
}
@@ -257,7 +290,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
*/
public void drawText(SequenceI seq, int start, int end, int y1)
{
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
int charOffset = 0;
char s;
@@ -265,12 +298,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
end = seq.getLength() - 1;
}
- graphics.setColor(av.textColour);
+ graphics.setColor(av.getTextColour());
- if (monospacedFont && av.showText && allGroups.length == 0
- && !av.getColourText() && av.thresholdTextColour == 0)
+ if (monospacedFont && av.getShowText() && allGroups.length == 0
+ && !av.getColourText() && av.getThresholdTextColour() == 0)
{
- if (av.renderGaps)
+ if (av.isRenderGaps())
{
graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
}
@@ -283,12 +316,19 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
else
{
+ boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
+ boolean isarep = av.getAlignment().getSeqrep() == seq;
+ boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
+ .getSeqrep() == seq : false;
+ char sr_c;
for (int i = start; i <= end; i++)
{
- graphics.setColor(av.textColour);
+
+ graphics.setColor(av.getTextColour());
getboxColour = false;
s = seq.getCharAt(i);
+
if (!renderGaps && jalview.util.Comparison.isGap(s))
{
continue;
@@ -325,10 +365,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
{
graphics.setColor(currentSequenceGroup.textColour);
}
- if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+ if (!isarep && !isgrep
+ && currentSequenceGroup.getShowNonconserved()) // todo
+ // optimize
{
// todo - use sequence group consensus
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
@@ -343,7 +385,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
if (av.getShowBoxes())
{
@@ -355,45 +397,72 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
}
}
- if (av.thresholdTextColour > 0)
+ if (av.getThresholdTextColour() > 0)
{
if (!getboxColour)
{
- getBoxColour(av.globalColourScheme, seq, i);
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
- + resBoxColour.getGreen() < av.thresholdTextColour)
+ + resBoxColour.getGreen() < av.getThresholdTextColour())
{
- graphics.setColor(av.textColour2);
+ graphics.setColor(av.getTextColour2());
}
}
- if (av.showUnconserved)
+ if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(av.consensus, i, s, '.');
+ s = getDisplayChar(srep, i, s, '.', null);
}
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
- * (i - start), y1);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + av.getCharWidth() * (i - start), y1);
}
}
}
- private char getDisplayChar(AlignmentAnnotation consensus, int position,
- char s, char c)
+ /**
+ * 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)
{
- char conschar = consensus.annotations[position].displayCharacter
- .charAt(0);
- if (conschar != '-' && s == conschar)
+ // 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))
{
- s = c;
+ sequenceChar = conservedChar;
}
- return s;
+ return sequenceChar;
}
/**
@@ -446,17 +515,17 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
public void drawHighlightedText(SequenceI seq, int start, int end,
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 * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+ av.getCharHeight());
graphics.setColor(Color.white);
char s = '~';
// Need to find the sequence position here.
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
for (int i = start; i <= end; i++)
{
@@ -465,29 +534,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
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 = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + (av.getCharWidth() * (i - start)),
+ (y1 + av.getCharHeight()) - 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());
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
graphics.setColor(Color.white);
char s = seq.getCharAt(res);
- 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);
}
}