import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.renderer.ResidueShaderI;
+import jalview.renderer.ResidueColourFinder;
import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.schemes.ColourSchemeI;
import jalview.util.Comparison;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
-public class SequenceRenderer implements jalview.api.SequenceRenderer
+public class SequenceRenderer implements jalview.api.SequenceRendererI
{
final static int CHAR_TO_UPPER = 'A' - 'a';
- AlignViewportI av;
+ private AlignViewportI av;
- FontMetrics fm;
+ private FontMetrics fm;
- boolean renderGaps = true;
+ private SequenceGroup[] allGroups = null;
- SequenceGroup currentSequenceGroup = null;
+ private Graphics graphics;
- SequenceGroup[] allGroups = null;
+ private boolean monospacedFont;
- Color resBoxColour;
-
- Graphics graphics;
-
- boolean monospacedFont;
-
- boolean forOverview = false;
+ private ResidueColourFinder resColourFinder;
/**
* Creates a new SequenceRenderer object
public SequenceRenderer(AlignViewportI viewport)
{
this.av = viewport;
+ resColourFinder = new ResidueColourFinder();
}
/**
- * DOCUMENT ME!
+ * Constructor given a choice of colour scheme. May be used to find colours
+ * for a structure that has a viewport colour scheme other than 'by sequence'
*
- * @param b
- * DOCUMENT ME!
+ * @param cs
*/
- public void prepare(Graphics g, boolean renderGaps)
+ public SequenceRenderer(AlignViewportI viewport, ColourSchemeI cs)
+ {
+ this.av = viewport;
+ resColourFinder = new ResidueColourFinder(viewport, cs);
+ }
+
+/**
+ * Sets the Graphics context to draw on, and also guesses whether we are using a monospaced font
+ *
+ * @param g
+ */
+ public void setGraphics(Graphics g)
{
graphics = g;
fm = g.getFontMetrics();
monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
&& av.getCharWidth() == dwidth);
-
- this.renderGaps = renderGaps;
- }
-
- protected Color getResidueBoxColour(SequenceI seq, int i)
- {
- // rate limiting step when rendering overview for lots of groups
- allGroups = av.getAlignment().findAllGroups(seq);
-
- if (inCurrentSequenceGroup(i))
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.getResidueShading(), seq, i);
- }
-
- return resBoxColour;
}
/**
public Color getResidueColour(final SequenceI seq, int position,
FeatureColourFinder finder)
{
- Color col = getResidueBoxColour(seq, position);
-
- if (finder != null)
- {
- col = finder.findFeatureColour(col, seq, position);
- }
- return col;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param shader
- * DOCUMENT ME!
- * @param seq
- * DOCUMENT ME!
- * @param i
- * DOCUMENT ME!
- */
- void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
- {
- if (shader.getColourScheme() != null)
- {
- resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
- }
- else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
- {
- resBoxColour = Color.lightGray;
- }
- else
- {
- resBoxColour = Color.white;
- }
+ allGroups = av.getAlignment().findAllGroups(seq);
+ return resColourFinder.getResidueColour(av.getShowBoxes(),
+ av.getResidueShading(),
+ allGroups, seq, position,
+ finder);
}
/**
- * DOCUMENT ME!
+ * Draws the sequence (box colour and residues) over the given range, at the
+ * specified y-offset on the Graphics context
*
- * @param g
- * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
+ * @param sg groups (if any) that the sequence is a member of (may have
+ * distinct group colouring)
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
+ * @param drawGaps
*/
public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
- int end, int y1)
+ int end, int y1, boolean drawGaps)
{
allGroups = sg;
if (av.isValidCharWidth())
{
- drawText(seq, start, end, y1);
+ drawText(seq, start, end, y1, drawGaps);
}
}
/**
- * DOCUMENT ME!
+ * Draws box colours on the given sequence residue range, at the specified
+ * y-offset on the Graphics context
*
* @param seq
- * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
*/
public synchronized void drawBoxes(SequenceI seq, int start, int end,
int y1)
{
+ Color resBoxColour = Color.white;
+
if (seq == null)
{
return; // fix for racecondition
if (i < length)
{
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
+ if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
}
}
else if (av.getShowBoxes())
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
}
}
/**
- * DOCUMENT ME!
+ * Draws residue letters on the given sequence residue range, at the specified
+ * y-offset on the Graphics context
*
* @param seq
- * DOCUMENT ME!
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
+ * @param drawGaps
*/
- public void drawText(SequenceI seq, int start, int end, int y1)
+ public void drawText(SequenceI seq, int start, int end, int y1, boolean drawGaps)
{
y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
int charOffset = 0;
boolean srep = av.isDisplayReferenceSeq();
boolean getboxColour = false;
boolean isarep = av.getAlignment().getSeqrep() == seq;
- boolean isgrep = currentSequenceGroup != null
- ? currentSequenceGroup.getSeqrep() == seq
- : false;
- char sr_c;
+ Color resBoxColour = Color.white;
+
for (int i = start; i <= end; i++)
{
getboxColour = false;
s = seq.getCharAt(i);
- if (!renderGaps && jalview.util.Comparison.isGap(s))
+ if (!drawGaps && Comparison.isGap(s))
{
continue;
}
- if (inCurrentSequenceGroup(i))
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(
+ allGroups, i);
+ if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq,
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq,
i);
if (currentSequenceGroup.getColourText())
{
graphics.setColor(currentSequenceGroup.textColour);
}
+ boolean isgrep = currentSequenceGroup != null
+ ? currentSequenceGroup.getSeqrep() == seq : false;
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize
{
// todo - use sequence group consensus
s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
-
}
-
}
else
{
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
{
if (!getboxColour)
{
- getBoxColour(av.getResidueShading(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
if (!isarep && av.getShowUnconserved())
{
s = getDisplayChar(srep, i, s, '.', null);
-
}
-
}
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
graphics.drawString(String.valueOf(s),
charOffset + av.getCharWidth() * (i - start), y1);
-
}
}
}
/**
* DOCUMENT ME!
*
- * @param res
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- boolean inCurrentSequenceGroup(int res)
- {
- if (allGroups == null)
- {
- return false;
- }
-
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- currentSequenceGroup = allGroups[i];
-
- return true;
- }
- }
-
- return false;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param seq
* DOCUMENT ME!
* @param start
}
}
- public void drawCursor(SequenceI seq, int res, int x1, int y1)
+ /**
+ * Draw a sequence canvas cursor
+ *
+ * @param g
+ * graphics context to draw on
+ * @param s
+ * character to draw at cursor
+ * @param x1
+ * x position of cursor in graphics context
+ * @param y1
+ * y position of cursor in graphics context
+ */
+ public void drawCursor(Graphics g, char s, int x1, int y1)
{
int pady = av.getCharHeight() / 5;
int charOffset = 0;
- graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+ g.setColor(Color.black);
+ g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
if (av.isValidCharWidth())
{
- graphics.setColor(Color.white);
-
- char s = seq.getCharAt(res);
-
+ g.setColor(Color.white);
charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1,
+ g.drawString(String.valueOf(s), charOffset + x1,
(y1 + av.getCharHeight()) - pady);
}
git://source.jalview.org / jalview.git / blobdiff