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
Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
av.getFont().getSize());\r
+\r
gg.setFont(italic);\r
\r
if (av.antiAlias)\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
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
-\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- gg.setFont(italic);\r
- drawIdString(gg, s, i, 0, ypos);\r
+ setHiddenFont(i, starty);\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
{\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
-\r
+ gg.translate(0, -ypos-(alheight * av.charHeight));\r
}\r
}\r
}\r
else\r
{\r
//Now draw the id strings\r
- int tmp, hiddenIndex = starty;\r
- boolean markHidden = false;\r
for (int i = starty; i < endy; i++)\r
{\r
if (av.hasHiddenRows)\r
{\r
- tmp = av.adjustForHiddenSeqs(i);\r
- if(hiddenIndex != tmp)\r
- {\r
- hiddenIndex = tmp;\r
- markHidden = true;\r
- }\r
- else\r
- markHidden = false;\r
-\r
- hiddenIndex++;\r
+ setHiddenFont(i, starty);\r
}\r
\r
- if(av.hasHiddenRows && av.alignment.getSequenceAt(i).getHiddenSequences()!=null)\r
- {\r
- currentTextColor = Color.blue;\r
- }\r
- else\r
// Selected sequence colours\r
- if ((searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ if ( (searchResults != null) &&\r
+ searchResults.contains(av.alignment.getSequenceAt(i)))\r
{\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
+ av.alignment.getSequenceAt(i)))\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.alignment.getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
}\r
\r
gg.setColor(currentColor);\r
gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
av.charHeight);\r
\r
- if (markHidden)\r
- {\r
- gg.setColor(Color.blue);\r
- // gg.drawLine(0, (i-starty)*av.charHeight, getWidth(),(i-starty)*av.charHeight);\r
- gg.fillPolygon(new int[] { getWidth() - av.charHeight,\r
- getWidth() - av.charHeight,\r
- getWidth() },\r
- new int[]\r
- {\r
- (i-starty)*av.charHeight -av.charHeight/4,\r
- (i-starty)*av.charHeight +av.charHeight/4,\r
- (i-starty)*av.charHeight\r
- }, 3);\r
-\r
- }\r
-\r
gg.setColor(currentTextColor);\r
\r
String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());\r
(av.charHeight / 5));\r
}\r
\r
- // add a border\r
- // gg.setColor(Color.cyan);\r
- // gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r
}\r
}\r
\r
+ void setHiddenFont(int i, int starty)\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
+ int tmp, hiddenIndex = starty;\r
+ tmp = av.adjustForHiddenSeqs(i);\r
+\r
+ if (av.adjustForHiddenSeqs(i - 1) == tmp - 1)\r
+ {\r
+ hiddenIndex = tmp;\r
+ }\r
+\r
+ if (hiddenIndex != tmp)\r
+ {\r
+ hiddenIndex = tmp;\r
+ }\r
+\r
+ hiddenIndex++;\r
+\r
+ if (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