/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
int imgHeight = 0;\r
boolean fastPaint = false;\r
java.util.Vector searchResults;\r
+ FontMetrics fm;\r
+ AnnotationLabels labels = null;\r
+ AnnotationPanel ap;\r
\r
/**\r
* Creates a new IdCanvas object.\r
{\r
setLayout(new BorderLayout());\r
this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
/**\r
* @param starty DOCUMENT ME!\r
* @param ypos DOCUMENT ME!\r
*/\r
- public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,\r
- int ypos)\r
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)\r
{\r
+ int xPos = 0;\r
+ int panelWidth = getWidth();\r
int charHeight = av.charHeight;\r
\r
if ((searchResults != null) && searchResults.contains(s))\r
gg.setColor(Color.white);\r
}\r
else if ((av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().sequences.contains(s))\r
+ av.getSelectionGroup().getSequences(false).contains(s))\r
{\r
gg.setColor(Color.lightGray);\r
gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),\r
}\r
else\r
{\r
- gg.setColor(s.getColor());\r
+ gg.setColor(av.getSequenceColour(s));\r
gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),\r
charHeight);\r
gg.setColor(Color.black);\r
}\r
\r
+ if (av.rightAlignIds)\r
+ {\r
+ xPos = panelWidth - fm.stringWidth(\r
+ s.getDisplayId(av.getShowJVSuffix())\r
+ ) - 4;\r
+ }\r
\r
gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
- 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+ xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ drawMarker(i, starty, ypos);\r
+\r
+\r
}\r
\r
/**\r
return;\r
}\r
\r
+ int oldHeight = imgHeight;\r
+\r
imgHeight = getHeight();\r
imgHeight -= (imgHeight % av.charHeight);\r
\r
return;\r
}\r
\r
- image = new BufferedImage(getWidth(), imgHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
+ if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())\r
+ {\r
+ image = new BufferedImage(getWidth(), imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ }\r
+\r
gg = (Graphics2D) image.getGraphics();\r
\r
//Fill in the background\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, getWidth(), imgHeight);\r
\r
-\r
drawIds(av.getStartSeq(), av.endSeq);\r
\r
g.drawImage(image, 0, 0, this);\r
{\r
Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
av.getFont().getSize());\r
+\r
gg.setFont(italic);\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ fm = gg.getFontMetrics();\r
+\r
+ if (av.antiAlias)\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
Color currentColor = Color.white;\r
Color currentTextColor = Color.black;\r
\r
if (av.getWrapAlignment())\r
{\r
+ int maxwidth = av.alignment.getWidth();\r
+ int alheight = av.alignment.getHeight();\r
+\r
+ if (av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
int annotationHeight = 0;\r
- AnnotationLabels labels = null;\r
+\r
\r
if(av.showAnnotation)\r
{\r
- AnnotationPanel ap = new AnnotationPanel(av);\r
+ if (ap == null)\r
+ ap = new AnnotationPanel(av);\r
+\r
annotationHeight = ap.adjustPanelHeight();\r
- labels = new AnnotationLabels(av);\r
+ if (labels == null)\r
+ labels = new AnnotationLabels(av);\r
}\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\r
hgap += av.charHeight;\r
\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ int cHeight = alheight * av.charHeight\r
+ hgap\r
+ annotationHeight;\r
\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
+ int rowSize = av.getEndRes() - av.getStartRes();\r
+\r
\r
// Draw the rest of the panels\r
for (int ypos = hgap, row = av.startRes;\r
- (ypos <= getHeight()) && (row < av.alignment.getWidth());\r
+ (ypos <= getHeight()) && (row < maxwidth);\r
ypos += cHeight, row += rowSize)\r
{\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
+ for (int i = starty; i < alheight; i++)\r
+ {\r
+ if (av.hasHiddenRows)\r
{\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
+ setHiddenFont(i);\r
}\r
+ else\r
+ gg.setFont(italic);\r
+\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ drawIdString(gg, s, i, 0, ypos);\r
+ }\r
\r
- if(labels!=null)\r
+ if(labels!=null && av.showAnnotation)\r
{\r
- gg.setFont(av.getFont());\r
- gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));\r
+ gg.translate(0, ypos+(alheight * av.charHeight));\r
labels.drawComponent(gg, getWidth());\r
- gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));\r
- gg.setFont(italic);\r
+ gg.translate(0, -ypos-(alheight * av.charHeight));\r
}\r
}\r
}\r
else\r
{\r
+ //Now draw the id strings\r
+ int panelWidth = getWidth();\r
+ int xPos = 0;\r
+\r
+ SequenceI sequence;\r
//Now draw the id strings\r
for (int i = starty; i < endy; i++)\r
{\r
+ sequence = av.alignment.getSequenceAt(i);\r
+\r
+ if(sequence==null)\r
+ continue;\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ setHiddenFont(i);\r
+ }\r
+\r
// Selected sequence colours\r
- if ((searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ if ( (searchResults != null) &&\r
+ searchResults.contains(sequence))\r
{\r
- gg.setColor(Color.black);\r
- currentColor = Color.black;\r
- currentTextColor = Color.white;\r
+ currentColor = Color.black;\r
+ currentTextColor = Color.white;\r
}\r
- else if ((av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().sequences.contains(\r
- av.alignment.getSequenceAt(i)))\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().getSequences(false).contains(\r
+ sequence))\r
{\r
- currentColor = Color.lightGray;\r
- currentTextColor = Color.black;\r
+ currentColor = Color.lightGray;\r
+ currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
+ currentColor = av.getSequenceColour(sequence);\r
+ currentTextColor = Color.black;\r
}\r
\r
gg.setColor(currentColor);\r
\r
gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
- av.charHeight);\r
+ av.charHeight);\r
\r
gg.setColor(currentTextColor);\r
\r
- String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());\r
+ String string = sequence.getDisplayId( av.getShowJVSuffix());\r
\r
- gg.drawString(string, 0,\r
+\r
+ if(av.rightAlignIds)\r
+ {\r
+ xPos = panelWidth - fm.stringWidth(string) - 4;\r
+ }\r
+\r
+ gg.drawString(string, xPos,\r
(((i - starty) * av.charHeight) + av.charHeight) -\r
(av.charHeight / 5));\r
+\r
+ if(av.hasHiddenRows && av.showHiddenMarkers)\r
+ drawMarker(i, starty, 0);\r
+\r
}\r
\r
- // add a border\r
- gg.setColor(Color.white);\r
- gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r
}\r
}\r
\r
+ void drawMarker(int i, int starty, int yoffset)\r
+ {\r
+\r
+ SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+ //Use this method here instead of calling hiddenSeq adjust\r
+ //3 times.\r
+ int hSize = hseqs.length;\r
+\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r
+\r
+ for(int j=0; j<hSize; j++)\r
+ {\r
+ if (hseqs[j] != null)\r
+ {\r
+ if(j-1<hiddenIndex)\r
+ hiddenIndex++;\r
+ if(j-1<lastIndex)\r
+ lastIndex++;\r
+ if(j-1<nextIndex)\r
+ nextIndex++;\r
+ }\r
+ }\r
+\r
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex+1);\r
+\r
+\r
+ gg.setColor(Color.blue);\r
+ if(below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth()- av.charHeight,\r
+ getWidth()- av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty) * av.charHeight +yoffset,\r
+ (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,\r
+ (i - starty) * av.charHeight+yoffset\r
+ }, 3);\r
+ }\r
+ if(above)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth()- av.charHeight,\r
+ getWidth()- av.charHeight,\r
+ getWidth() },\r
+ new int[]\r
+ {\r
+ (i - starty+1) * av.charHeight +yoffset,\r
+ (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,\r
+ (i - starty+1) * av.charHeight +yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(int i)\r
+ {\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize());\r
+\r
+\r
+ if (av.alignment.getSequenceAt(i)!=null\r
+ && av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+ gg.setFont(bold);\r
+ else\r
+ gg.setFont(italic);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
git://source.jalview.org / jalview.git / blobdiff