*/\r
package jalview.gui;\r
\r
-import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
\r
import java.awt.*;\r
gg.setColor(Color.black);\r
}\r
\r
- String string = s.getName();\r
-\r
- if (av.getShowFullId())\r
- {\r
- string = s.getDisplayId();\r
- }\r
\r
- gg.drawString(string, 0,\r
- (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+ gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
+ 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
}\r
\r
/**\r
//Fill in the background\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, getWidth(), imgHeight);\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- gg.setFont(italic);\r
\r
drawIds(av.getStartSeq(), av.endSeq);\r
\r
*/\r
void drawIds(int starty, int endy)\r
{\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ gg.setFont(italic);\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 annotationHeight = 0;\r
+ AnnotationLabels labels = null;\r
+\r
+ if(av.showAnnotation)\r
+ {\r
+ AnnotationPanel ap = new AnnotationPanel(av);\r
+ annotationHeight = ap.adjustPanelHeight();\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
+ + hgap\r
+ + annotationHeight;\r
+\r
int rowSize = av.getEndRes() - av.getStartRes();\r
\r
// Draw the rest of the panels\r
- for (int ypos = 2 * av.charHeight, row = av.startRes;\r
+ for (int ypos = hgap, row = av.startRes;\r
(ypos <= getHeight()) && (row < av.alignment.getWidth());\r
- ypos += av.chunkHeight, row += rowSize)\r
+ ypos += cHeight, row += rowSize)\r
{\r
for (int i = starty; i < av.alignment.getHeight(); i++)\r
{\r
+\r
SequenceI s = av.alignment.getSequenceAt(i);\r
+ gg.setFont(italic);\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
+ labels.drawComponent(gg, getWidth());\r
+ gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));\r
+\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
+ }\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
{\r
- gg.setColor(Color.black);\r
currentColor = Color.black;\r
currentTextColor = Color.white;\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).getName();\r
-\r
- if (av.getShowFullId())\r
+ if (markHidden)\r
{\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\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
+\r
gg.drawString(string, 0,\r
(((i - starty) * av.charHeight) + av.charHeight) -\r
(av.charHeight / 5));\r
}\r
\r
// add a border\r
- gg.setColor(Color.white);\r
- gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r
+ // gg.setColor(Color.cyan);\r
+ // gg.fillRect(getWidth() - 4, 0, 4, getHeight());\r
}\r
}\r
\r