+ 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.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 = alheight * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
+\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 < maxwidth);\r
+ ypos += cHeight, row += rowSize)\r
+ {\r
+ for (int i = starty; i < alheight; i++)\r
+ {\r
+ if (av.hasHiddenRows)\r
+ {\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
+ {\r
+ gg.translate(0, ypos+(alheight * av.charHeight));\r
+ labels.drawComponent(gg, getWidth());\r
+ gg.translate(0, -ypos-(alheight * av.charHeight));\r
+ }\r
+\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ //Now draw the id strings\r
+\r
+ //Now draw the id strings\r
+ for (int i = starty; i < endy; i++)\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
+ {\r
+ currentColor = Color.black;\r
+ currentTextColor = Color.white;\r
+ }\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
+ }\r
+ else\r
+ {\r
+ currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
+ }\r
+\r
+ gg.setColor(currentColor);\r
+\r
+ gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
+ av.charHeight);\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
+ if(av.hasHiddenRows && av.showHiddenMarkers)\r
+ drawMarker(i, starty, 0);\r
+\r
+ }\r