/*\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
import java.awt.image.*;\r
import javax.swing.*;\r
\r
-import jalview.analysis.*;\r
import jalview.datamodel.*;\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class IdCanvas\r
extends JPanel\r
{\r
int imgHeight = 0;\r
boolean fastPaint = false;\r
java.util.Vector searchResults;\r
-\r
+ FontMetrics fm;\r
+ AnnotationLabels labels = null;\r
+ AnnotationPanel ap;\r
+ Font idfont;\r
+\r
+ /**\r
+ * Creates a new IdCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
public IdCanvas(AlignViewport av)\r
{\r
setLayout(new BorderLayout());\r
this.av = av;\r
- PaintRefresher.Register(this);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gg DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ * @param i DOCUMENT ME!\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
{\r
- int charHeight = av.getCharHeight();\r
+ int xPos = 0;\r
+ int panelWidth = getWidth();\r
+ int charHeight = av.charHeight;\r
\r
if ( (searchResults != null) && searchResults.contains(s))\r
{\r
gg.setColor(Color.black);\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
- getWidth(), charHeight);\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),\r
+ 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,\r
- AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
- getWidth(), charHeight);\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),\r
+ charHeight);\r
gg.setColor(Color.white);\r
}\r
else\r
{\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos,\r
- getWidth(), charHeight);\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
- String string = s.getName();\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
+ xPos,\r
+ ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
\r
- if (av.getShowFullId())\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
{\r
- string = s.getDisplayId();\r
+ drawMarker(i, starty, ypos);\r
}\r
\r
- gg.drawString(string, 0,\r
- (AlignmentUtil.getPixelHeight(starty, i, charHeight) + ypos +\r
- charHeight) - (charHeight / 5));\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param vertical DOCUMENT ME!\r
+ */\r
public void fastPaint(int vertical)\r
{\r
if (gg == null)\r
{\r
repaint();\r
+\r
return;\r
}\r
\r
repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\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
- 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
g.drawImage(image, 0, 0, this);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param starty DOCUMENT ME!\r
+ * @param endy DOCUMENT ME!\r
+ */\r
void drawIds(int starty, int endy)\r
{\r
- if(gg==null)\r
- return;\r
+ if (av.seqNameItalics)\r
+ {\r
+ idfont = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ }\r
+ else\r
+ {\r
+ idfont = av.getFont();\r
+ }\r
\r
+ gg.setFont(idfont);\r
+ fm = gg.getFontMetrics();\r
+\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\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
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ int annotationHeight = 0;\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ if (ap == null)\r
+ {\r
+ ap = new AnnotationPanel(av);\r
+ }\r
+\r
+ annotationHeight = ap.adjustPanelHeight();\r
+ if (labels == null)\r
+ {\r
+ labels = new AnnotationLabels(av);\r
+ }\r
+ }\r
+\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ hgap += av.charHeight;\r
+ }\r
+\r
+ int cHeight = alheight * 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
- (ypos <= getHeight()) && (row < av.alignment.getWidth());\r
- ypos += av.chunkHeight, row += rowSize)\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 < av.alignment.getHeight(); i++)\r
+ for (int i = starty; i < alheight; i++)\r
{\r
SequenceI s = av.alignment.getSequenceAt(i);\r
+ if (av.hasHiddenRows)\r
+ {\r
+ setHiddenFont(s);\r
+ }\r
+ else\r
+ {\r
+ gg.setFont(idfont);\r
+ }\r
+\r
drawIdString(gg, s, i, 0, ypos);\r
}\r
+\r
+ if (labels != null && av.showAnnotation)\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
else\r
{\r
+ //No need to hang on to labels if we're not wrapped\r
+ labels = null;\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
+ {\r
+ continue;\r
+ }\r
+\r
+ if (av.hasHiddenRows)\r
+ {\r
+ setHiddenFont(sequence);\r
+ }\r
+\r
// Selected sequence colours\r
if ( (searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ searchResults.contains(sequence))\r
{\r
- gg.setColor(Color.black);\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
+ av.getSelectionGroup().getSequences(null).contains(\r
+ sequence))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentColor = av.getSequenceColour(sequence);\r
currentTextColor = Color.black;\r
}\r
\r
gg.setColor(currentColor);\r
\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- getWidth(), av.charHeight);\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).getName();\r
+ String string = sequence.getDisplayId(av.getShowJVSuffix());\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.getShowFullId())\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
{\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\r
+ drawMarker(i, starty, 0);\r
}\r
\r
- gg.drawString(string, 0,\r
- (AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
- av.charHeight) - (av.charHeight / 5));\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
+ {\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
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex + 1);\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 -\r
+ av.charHeight / 4,\r
+ (i - starty + 1) * av.charHeight + yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(SequenceI seq)\r
+ {\r
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize());\r
+\r
+ if (av.hiddenRepSequences != null &&\r
+ av.hiddenRepSequences.containsKey(seq))\r
+ {\r
+ gg.setFont(bold);\r
+ }\r
+ else\r
+ {\r
+ gg.setFont(idfont);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param found DOCUMENT ME!\r
+ */\r
public void setHighlighted(java.util.Vector found)\r
{\r
searchResults = found;\r
git://source.jalview.org / jalview.git / blobdiff