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Merge branch 'develop' into task/JAL-4001_migrate_googleanalytics_to_GA4
[jalview.git]
/
src
/
jalview
/
gui
/
IdCanvas.java
diff --git
a/src/jalview/gui/IdCanvas.java
b/src/jalview/gui/IdCanvas.java
index
484173c
..
c94dee0
100755
(executable)
--- a/
src/jalview/gui/IdCanvas.java
+++ b/
src/jalview/gui/IdCanvas.java
@@
-20,10
+20,6
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import jalview.datamodel.SequenceI;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
@@
-37,6
+33,10
@@
import java.util.List;
import javax.swing.JPanel;
import javax.swing.JPanel;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-55,7
+55,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
BufferedImage image;
BufferedImage image;
- Graphics2D gg;
+ // Graphics2D gg;
int imgHeight = 0;
int imgHeight = 0;
@@
-79,7
+79,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
av.getRanges().addPropertyChangeListener(this);
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
av.getRanges().addPropertyChangeListener(this);
- }
+ }
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-137,7
+137,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
- if (hiddenRows)
+ if (hiddenRows && av.getShowHiddenMarkers())
{
drawMarker(g, av, i, starty, ypos);
}
{
drawMarker(g, av, i, starty, ypos);
}
@@
-152,10
+152,11
@@
public class IdCanvas extends JPanel implements ViewportListenerI
*/
public void fastPaint(int vertical)
{
*/
public void fastPaint(int vertical)
{
+
/*
* for now, not attempting fast paint of wrapped ids...
*/
/*
* for now, not attempting fast paint of wrapped ids...
*/
- if (gg == null || av.getWrapAlignment())
+ if (image == null || av.getWrapAlignment())
{
repaint();
{
repaint();
@@
-164,6
+165,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
ViewportRanges ranges = av.getRanges();
ViewportRanges ranges = av.getRanges();
+ Graphics2D gg = image.createGraphics();
gg.copyArea(0, 0, getWidth(), imgHeight, 0,
-vertical * av.getCharHeight());
gg.copyArea(0, 0, getWidth(), imgHeight, 0,
-vertical * av.getCharHeight());
@@
-200,6
+202,8
@@
public class IdCanvas extends JPanel implements ViewportListenerI
gg.translate(0, -transY);
gg.translate(0, -transY);
+ gg.dispose();
+
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
@@
-217,66
+221,66
@@
public class IdCanvas extends JPanel implements ViewportListenerI
@Override
public void paintComponent(Graphics g)
{
@Override
public void paintComponent(Graphics g)
{
- super.paintComponent(g);
-
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
-
+
if (fastPaint)
{
fastPaint = false;
g.drawImage(image, 0, 0, this);
if (fastPaint)
{
fastPaint = false;
g.drawImage(image, 0, 0, this);
-
+
return;
}
return;
}
-
+
int oldHeight = imgHeight;
int oldHeight = imgHeight;
-
+
imgHeight = getHeight();
imgHeight -= (imgHeight % av.getCharHeight());
imgHeight = getHeight();
imgHeight -= (imgHeight % av.getCharHeight());
-
+
if (imgHeight < 1)
{
return;
}
if (imgHeight < 1)
{
return;
}
-
+
if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
{
if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
{
- image = new BufferedImage(getWidth(), imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
}
}
-
- gg = (Graphics2D) image.getGraphics();
-
+
+ Graphics2D gg = image.createGraphics();
+
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
-
- drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
-
+
+ drawIds(gg, av, av.getRanges().getStartSeq(),
+ av.getRanges().getEndSeq(), searchResults);
+
+ gg.dispose();
+
g.drawImage(image, 0, 0, this);
}
/**
g.drawImage(image, 0, 0, this);
}
/**
- * Draws sequence ids from sequence index starty to endy (inclusive), with the
- * font and other display settings configured on the viewport. Ids of
+ * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with
+ * the font and other display settings configured on the viewport. Ids of
* sequences included in the selection are coloured grey, otherwise the
* current id colour for the sequence id is used.
*
* @param g
* @param alignViewport
* sequences included in the selection are coloured grey, otherwise the
* current id colour for the sequence id is used.
*
* @param g
* @param alignViewport
- * @param starty
- * @param endy
+ * @param startSeq
+ * @param endSeq
* @param selection
*/
* @param selection
*/
- void drawIds(Graphics2D g, AlignViewport alignViewport, final int starty,
- final int endy, List<SequenceI> selection)
+ void drawIds(Graphics2D g, AlignViewport alignViewport,
+ final int startSeq, final int endSeq, List<SequenceI> selection)
{
Font font = alignViewport.getFont();
if (alignViewport.isSeqNameItalics())
{
{
Font font = alignViewport.getFont();
if (alignViewport.isSeqNameItalics())
{
- setIdfont(new Font(font.getName(), Font.ITALIC,
- font.getSize()));
+ setIdfont(new Font(font.getName(), Font.ITALIC, font.getSize()));
}
else
{
}
else
{
@@
-295,11
+299,11
@@
public class IdCanvas extends JPanel implements ViewportListenerI
Color currentColor = Color.white;
Color currentTextColor = Color.black;
Color currentColor = Color.white;
Color currentTextColor = Color.black;
- boolean hasHiddenRows = av.hasHiddenRows();
+ boolean hasHiddenRows = alignViewport.hasHiddenRows();
if (alignViewport.getWrapAlignment())
{
if (alignViewport.getWrapAlignment())
{
- drawIdsWrapped(starty, hasHiddenRows);
+ drawIdsWrapped(g, alignViewport, startSeq, getHeight());
return;
}
return;
}
@@
-308,7
+312,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
int xPos = 0;
// Now draw the id strings
int xPos = 0;
// Now draw the id strings
- for (int i = starty; i <= endy; i++)
+ for (int i = startSeq; i <= endSeq; i++)
{
SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
{
SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
@@
-320,6
+324,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
{
g.setFont(getHiddenFont(sequence, alignViewport));
if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
{
g.setFont(getHiddenFont(sequence, alignViewport));
+ fm = g.getFontMetrics();
}
// Selected sequence colours
}
// Selected sequence colours
@@
-328,8
+333,8
@@
public class IdCanvas extends JPanel implements ViewportListenerI
currentColor = Color.black;
currentTextColor = Color.white;
}
currentColor = Color.black;
currentTextColor = Color.white;
}
- else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
- .getSequences(null).contains(sequence))
+ else if ((alignViewport.getSelectionGroup() != null) && alignViewport
+ .getSelectionGroup().getSequences(null).contains(sequence))
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
@@
-343,8
+348,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
g.setColor(currentColor);
int charHeight = alignViewport.getCharHeight();
g.setColor(currentColor);
int charHeight = alignViewport.getCharHeight();
- g.fillRect(0, (i - starty) * charHeight,
- getWidth(), charHeight);
+ g.fillRect(0, (i - startSeq) * charHeight, getWidth(), charHeight);
g.setColor(currentTextColor);
g.setColor(currentTextColor);
@@
-356,56
+360,46
@@
public class IdCanvas extends JPanel implements ViewportListenerI
xPos = panelWidth - fm.stringWidth(string) - 4;
}
xPos = panelWidth - fm.stringWidth(string) - 4;
}
- g.drawString(string, xPos, (((i - starty) * charHeight) + charHeight)
- - (charHeight / 5));
+ g.drawString(string, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
- if (hasHiddenRows)
+ if (hasHiddenRows && av.getShowHiddenMarkers())
{
{
- drawMarker(g, alignViewport, i, starty, 0);
+ drawMarker(g, alignViewport, i, startSeq, 0);
}
}
}
/**
}
}
}
/**
- * Draws sequence ids in wrapped mode
+ * Draws sequence ids, and annotation labels if annotations are shown, in
+ * wrapped mode
*
*
- * @param starty
- * @param hasHiddenRows
+ * @param g
+ * @param alignViewport
+ * @param startSeq
*/
*/
- protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
+ void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
+ int startSeq, int pageHeight)
{
{
- int maxwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getHeight();
+ int alignmentWidth = alignViewport.getAlignment().getWidth();
+ final int alheight = alignViewport.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getAlignment().getHiddenColumns()
- .absoluteToVisibleColumn(maxwidth) - 1;
- }
+ /*
+ * assumption: SeqCanvas.calculateWrappedGeometry has been called
+ */
+ SeqCanvas seqCanvas = alignViewport.getAlignPanel()
+ .getSeqPanel().seqCanvas;
- int annotationHeight = 0;
+ final int charHeight = alignViewport.getCharHeight();
AnnotationLabels labels = null;
AnnotationLabels labels = null;
- if (av.isShowAnnotation())
- {
- if (ap == null)
- {
- ap = new AnnotationPanel(av);
- }
-
- annotationHeight = ap.adjustPanelHeight();
- labels = new AnnotationLabels(av);
- }
-
- int hgap = av.getCharHeight();
- if (av.getScaleAboveWrapped())
+ if (alignViewport.isShowAnnotation())
{
{
- hgap += av.getCharHeight();
+ labels = new AnnotationLabels(alignViewport);
}
}
- int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
-
- ViewportRanges ranges = av.getRanges();
+ ViewportRanges ranges = alignViewport.getRanges();
int rowSize = ranges.getViewportWidth();
int rowSize = ranges.getViewportWidth();
@@
-413,34
+407,34
@@
public class IdCanvas extends JPanel implements ViewportListenerI
* draw repeating sequence ids until out of sequence data or
* out of visible space, whichever comes first
*/
* draw repeating sequence ids until out of sequence data or
* out of visible space, whichever comes first
*/
- int ypos = hgap;
- int row = ranges.getStartRes();
- while ((ypos <= getHeight()) && (row < maxwidth))
+ boolean hasHiddenRows = alignViewport.hasHiddenRows();
+ int ypos = seqCanvas.wrappedSpaceAboveAlignment;
+ int rowStartRes = ranges.getStartRes();
+ while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth))
{
{
- for (int i = starty; i < alheight; i++)
+ for (int i = startSeq; i < alheight; i++)
{
{
- SequenceI s = av.getAlignment().getSequenceAt(i);
- if (hasHiddenRows || av.isDisplayReferenceSeq())
+ SequenceI s = alignViewport.getAlignment().getSequenceAt(i);
+ if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
{
{
- gg.setFont(getHiddenFont(s, av));
+ g.setFont(getHiddenFont(s, alignViewport));
}
else
{
}
else
{
- gg.setFont(getIdfont());
+ g.setFont(getIdfont());
}
}
-
- drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
+ drawIdString(g, hasHiddenRows, s, i, 0, ypos);
}
}
- if (labels != null && av.isShowAnnotation())
+ if (labels != null && alignViewport.isShowAnnotation())
{
{
- gg.translate(0, ypos + (alheight * av.getCharHeight()));
- labels.drawComponent(gg, getWidth());
- gg.translate(0, -ypos - (alheight * av.getCharHeight()));
+ g.translate(0, ypos + (alheight * charHeight));
+ labels.drawComponent(g, getWidth());
+ g.translate(0, -ypos - (alheight * charHeight));
}
}
- ypos += cHeight;
- row += rowSize;
+ ypos += seqCanvas.wrappedRepeatHeightPx;
+ rowStartRes += rowSize;
}
}
}
}
@@
-454,7
+448,8
@@
public class IdCanvas extends JPanel implements ViewportListenerI
* @param starty
* @param yoffset
*/
* @param starty
* @param yoffset
*/
- void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
+ void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex,
+ int starty, int yoffset)
{
SequenceI[] hseqs = alignViewport.getAlignment()
.getHiddenSequences().hiddenSequences;
{
SequenceI[] hseqs = alignViewport.getAlignment()
.getHiddenSequences().hiddenSequences;
@@
-497,8
+492,7
@@
public class IdCanvas extends JPanel implements ViewportListenerI
/*
* vertices of the triangle, below or above hidden seqs
*/
/*
* vertices of the triangle, below or above hidden seqs
*/
- int[] xPoints = new int[]
- { getWidth() - charHeight,
+ int[] xPoints = new int[] { getWidth() - charHeight,
getWidth() - charHeight, getWidth() };
int yShift = seqIndex - starty;
getWidth() - charHeight, getWidth() };
int yShift = seqIndex - starty;