/*\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) 2007 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
{\r
setLayout(null);\r
this.av = av;\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
public void drawIdString(Graphics gg, SequenceI s, int i, int starty,\r
if (searchResults != null && searchResults.contains(s))\r
{\r
gg.setColor(Color.black);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.white);\r
}\r
else if (av.getSelectionGroup() != null &&\r
- av.getSelectionGroup().sequences.contains(s))\r
+ av.getSelectionGroup().getSequences(null).contains(s))\r
{\r
gg.setColor(Color.lightGray);\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.white);\r
}\r
else\r
{\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos,\r
+ gg.setColor(av.getSequenceColour(s));\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos,\r
getSize().width, charHeight);\r
gg.setColor(Color.black);\r
}\r
\r
-\r
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,\r
- ((i - starty) * charHeight) + ypos +\r
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,\r
+ ( (i - starty) * charHeight) + ypos +\r
charHeight - (charHeight / 5));\r
\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ {\r
+ drawMarker(i, starty, ypos);\r
+ }\r
+\r
}\r
\r
public void fastPaint(int vertical)\r
gg.setFont(italic);\r
\r
gg.fillRect(0, 0, getSize().width, getSize().height);\r
- drawIds(av.getStartSeq(), av.endSeq);\r
+ drawIds(av.startSeq, av.endSeq);\r
g.drawImage(image, 0, 0, this);\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
+\r
+ gg.setFont(italic);\r
+\r
Color currentColor = Color.white;\r
Color currentTextColor = Color.black;\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
\r
if (av.getWrapAlignment())\r
{\r
+ int maxwidth = av.alignment.getWidth();\r
+ int alheight = av.alignment.getHeight();\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
int annotationHeight = 0;\r
AnnotationLabels labels = null;\r
\r
- if(av.showAnnotation)\r
+ if (av.showAnnotation)\r
{\r
AnnotationPanel ap = new AnnotationPanel(av);\r
annotationHeight = ap.adjustPanelHeight();\r
\r
int hgap = av.charHeight;\r
if (av.scaleAboveWrapped)\r
+ {\r
hgap += av.charHeight;\r
+ }\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
- // Draw the rest of the panels\r
- for (int ypos = hgap, row = av.startRes;\r
- (ypos <= getSize().height) && (row < av.alignment.getWidth());\r
- ypos += cHeight, row += rowSize)\r
+ // Draw the rest of the panels\r
+ for (int ypos = hgap, row = av.startRes;\r
+ (ypos <= getSize().height) && (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
+ {\r
+ gg.setFont(italic);\r
+ }\r
+\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ drawIdString(gg, s, i, 0, ypos);\r
+ }\r
+\r
+ if (labels != null)\r
{\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
-\r
- if(labels!=null)\r
- {\r
- gg.setFont(av.getFont());\r
- gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));\r
- labels.drawComponent(gg, getSize().width);\r
- gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));\r
- gg.setFont(italic);\r
- }\r
+ gg.translate(0, ypos + (alheight * av.charHeight));\r
+ labels.drawComponent(gg, getSize().width);\r
+ gg.translate(0, -ypos - (alheight * av.charHeight));\r
}\r
\r
+ }\r
}\r
else\r
{\r
+ //Now draw the id strings\r
\r
//Now draw the id strings\r
+ SequenceI seq;\r
for (int i = starty; i < endy; i++)\r
{\r
- // Selected sequence colours\r
+ if (av.hasHiddenRows)\r
+ {\r
+ setHiddenFont(i);\r
+ }\r
\r
- if (searchResults != null &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ seq = av.alignment.getSequenceAt(i);\r
+ if (seq == null)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ // Selected sequence colours\r
+ if ( (searchResults != null) &&\r
+ searchResults.contains(seq))\r
{\r
- gg.setColor(Color.black);\r
currentColor = Color.black;\r
currentTextColor = Color.white;\r
}\r
- else if (av.getSelectionGroup() != null\r
- &&\r
- av.getSelectionGroup().sequences.contains(av.alignment.\r
- getSequenceAt(i)))\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().getSequences(null).contains(seq))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentColor = av.getSequenceColour(seq);\r
currentTextColor = Color.black;\r
}\r
\r
gg.setColor(currentColor);\r
\r
- gg.fillRect(0,\r
- ((i - starty) * av.charHeight),\r
- getSize().width,\r
+ gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,\r
av.charHeight);\r
\r
gg.setColor(currentTextColor);\r
\r
- gg.drawString(av.alignment.getSequenceAt(i)\r
- .getDisplayId(av.getShowJVSuffix()), 0,\r
- ((i - starty) * av.charHeight) +\r
- av.charHeight - (av.charHeight / 5));\r
- }\r
+ gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),\r
+ 0,\r
+ ( ( (i - starty) * av.charHeight) + av.charHeight) -\r
+ (av.charHeight / 5));\r
\r
- // add a border\r
- gg.setColor(Color.white);\r
- gg.fillRect(getSize().width - 4, 0, 4, getSize().height);\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ {\r
+ drawMarker(i, starty, 0);\r
+ }\r
+ }\r
}\r
-\r
}\r
\r
public void setHighlighted(java.util.Vector found)\r
searchResults = found;\r
repaint();\r
}\r
+\r
+ void drawMarker(int i, int starty, int yoffset)\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
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex + 1);\r
+\r
+ for (int j = 0; j < hSize; j++)\r
+ {\r
+ if (hseqs[j] != null)\r
+ {\r
+ if (j - 1 < hiddenIndex)\r
+ {\r
+ hiddenIndex++;\r
+ }\r
+ if (j - 1 < lastIndex)\r
+ {\r
+ lastIndex++;\r
+ }\r
+ if (j - 1 < nextIndex)\r
+ {\r
+ nextIndex++;\r
+ }\r
+ }\r
+ }\r
+\r
+ gg.setColor(Color.blue);\r
+ if (below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getSize().width - av.charHeight,\r
+ getSize().width - av.charHeight,\r
+ getSize().width},\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
+ {getSize().width - av.charHeight,\r
+ getSize().width - av.charHeight,\r
+ getSize().width},\r
+ new int[]\r
+ {\r
+ (i - starty + 1) * av.charHeight + yoffset,\r
+ (i - starty + 1) * av.charHeight + yoffset -\r
+ av.charHeight / 4,\r
+ (i - starty + 1) * av.charHeight + yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(int i)\r
+ {\r
+ /* System.out.println(i+" "+av.alignment.getHeight());\r
+ if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+ gg.setFont(new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize()));\r
+ else\r
+ gg.setFont(new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize()));*/\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff