/*\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 SeqCanvas\r
extends JComponent\r
{\r
- FeatureRenderer fr;\r
- SequenceRenderer sr;\r
+ final FeatureRenderer fr;\r
+ final SequenceRenderer sr;\r
BufferedImage img;\r
Graphics2D gg;\r
int imgWidth;\r
int imgHeight;\r
AlignViewport av;\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int[] searchResults = null;\r
- int chunkHeight;\r
- int chunkWidth;\r
+ SearchResults searchResults = null;\r
boolean fastPaint = false;\r
int LABEL_WEST;\r
int LABEL_EAST;\r
\r
+ int cursorX = 0;\r
+ int cursorY = 0;\r
\r
- public SeqCanvas(AlignViewport av)\r
+ /**\r
+ * Creates a new SeqCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public SeqCanvas(AlignmentPanel ap)\r
{\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
+ this.av = ap.av;\r
+ fr = new FeatureRenderer(ap);\r
sr = new SequenceRenderer(av);\r
setLayout(new BorderLayout());\r
- PaintRefresher.Register(this, av.alignment);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
setBackground(Color.white);\r
}\r
\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
{\r
int scalestartx = startx - (startx % 10) + 10;\r
// NORTH SCALE\r
for (int i = scalestartx; i < endx; i += 10)\r
{\r
- String string = String.valueOf(i);\r
- g.drawString(string, (i - startx - 1) * av.charWidth,\r
+ int value = i;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+ }\r
+\r
+ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
ypos - (av.charHeight / 2));\r
\r
g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
ypos += av.charHeight;\r
\r
- // EAST SCALE\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ // WEST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
SequenceI seq = av.alignment.getSequenceAt(i);\r
\r
if (value != -1)\r
{\r
- int x = LABEL_WEST - fm.stringWidth(value + "");\r
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -\r
+ av.charWidth / 2;\r
g.drawString(value + "", x,\r
(ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
}\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param endx DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
{\r
ypos += av.charHeight;\r
\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ }\r
+\r
+ SequenceI seq;\r
// EAST SCALE\r
for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
+ seq = av.alignment.getSequenceAt(i);\r
int index = endx;\r
int value = -1;\r
\r
continue;\r
}\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ value = seq.findPosition(index);\r
\r
break;\r
}\r
\r
if (value != -1)\r
{\r
- g.drawString(value + "", 0,\r
+ g.drawString(String.valueOf(value), 0,\r
(ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
}\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param horizontal DOCUMENT ME!\r
+ * @param vertical DOCUMENT ME!\r
+ */\r
public void fastPaint(int horizontal, int vertical)\r
{\r
- if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))\r
+ if (gg == null)\r
{\r
return;\r
}\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
+ fastPaint = true;\r
+\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth,\r
+ imgHeight,\r
+ -horizontal * av.charWidth,\r
-vertical * av.charHeight);\r
\r
int sr = av.startRes;\r
\r
if (horizontal > 0) // scrollbar pulled right, image to the left\r
{\r
+ er++;\r
transX = (er - sr - horizontal) * av.charWidth;\r
sr = er - horizontal;\r
}\r
else if (horizontal < 0)\r
{\r
- er = sr - horizontal;\r
+ er = sr - horizontal - 1;\r
}\r
else if (vertical > 0) // scroll down\r
{\r
}\r
\r
gg.translate(transX, transY);\r
-\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, (er - sr + 1) * av.charWidth,\r
- (es - ss) * av.charHeight);\r
- drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
gg.translate( -transX, -transY);\r
\r
- fastPaint = true;\r
repaint();\r
}\r
\r
* in the adjustment listener in SeqPanel when the scrollbars move.\r
*/\r
\r
-\r
// Set this to false to force a full panel paint\r
public void paintComponent(Graphics g)\r
{\r
- if (img!=null\r
- && (fastPaint || getWidth() != g.getClipBounds().width\r
- || getHeight() != g.getClipBounds().height))\r
+ super.paintComponent(g);\r
+\r
+ if (img != null && (fastPaint\r
+ || (getVisibleRect().width != g.getClipBounds().width)\r
+ || (getVisibleRect().height != g.getClipBounds().height)))\r
{\r
g.drawImage(img, 0, 0, this);\r
fastPaint = false;\r
return;\r
}\r
\r
- img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) img.getGraphics();\r
- gg.setFont(av.getFont());\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())\r
+ {\r
+ try\r
+ {\r
+ img = new BufferedImage(imgWidth, imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ gg = (Graphics2D) img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }\r
+ catch (OutOfMemoryError er)\r
+ {\r
+ System.gc();\r
+ System.out.println(er + " making image, SeqCanvas");\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.\r
+ desktop,\r
+ "Out of memory creating alignment image!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, imgWidth, imgHeight);\r
+ return;\r
+ }\r
+ }\r
\r
- chunkWidth = getWrappedCanvasWidth(getWidth());\r
- chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\r
\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
if (av.getWrapAlignment())\r
{\r
}\r
else\r
{\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq,\r
- av.startRes, av.startSeq, 0);\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
+\r
+\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cwidth DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getWrappedCanvasWidth(int cwidth)\r
{\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
if (av.scaleLeftWrapped)\r
{\r
- LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * @return String\r
+ */\r
+ String getMask()\r
+ {\r
+ String mask = "00";\r
+ int maxWidth = 0;\r
+ int tmp;\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ tmp = av.alignment.getSequenceAt(i).getEnd();\r
+ if (tmp > maxWidth)\r
+ {\r
+ maxWidth = tmp;\r
+ }\r
+ }\r
+\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param canvasWidth DOCUMENT ME!\r
+ * @param canvasHeight DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ */\r
public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
int startRes)\r
{\r
\r
FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- int LABEL_EAST = 0;\r
-\r
if (av.scaleRightWrapped)\r
{\r
- LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
}\r
\r
- int LABEL_WEST = 0;\r
-\r
if (av.scaleLeftWrapped)\r
{\r
- LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
+ }\r
+\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ hgap += av.charHeight;\r
}\r
\r
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+\r
+ av.setWrappedWidth(cWidth);\r
\r
av.endRes = av.startRes + cWidth;\r
\r
- int endx = (startRes + cWidth) - 1;\r
- int ypos = 2 * av.charHeight;\r
+ int endx;\r
+ int ypos = hgap;\r
+ int maxwidth = av.alignment.getWidth() - 1;\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
- while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ while ( (ypos <= canvasHeight) && (startRes < maxwidth))\r
{\r
+ endx = startRes + cWidth - 1;\r
+\r
+ if (endx > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
+\r
+ g.setFont(av.getFont());\r
g.setColor(Color.black);\r
\r
if (av.scaleLeftWrapped)\r
\r
if (av.scaleRightWrapped)\r
{\r
- g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+ g.translate( - (canvasWidth - LABEL_EAST), 0);\r
}\r
\r
g.translate(LABEL_WEST, 0);\r
drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
+ if (av.hasHiddenColumns && av.showHiddenMarkers)\r
+ {\r
+ g.setColor(Color.blue);\r
+ int res;\r
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size();\r
+ i++)\r
+ {\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+ startRes;\r
+\r
+ if (res < 0 || res > endx - startRes)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ gg.fillPolygon(new int[]\r
+ {res * av.charWidth - av.charHeight / 4,\r
+ res * av.charWidth + av.charHeight / 4,\r
+ res * av.charWidth},\r
+ new int[]\r
+ {\r
+ ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2),\r
+ ypos - (av.charHeight / 2) + 8\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
// When printing we have an extra clipped region,\r
// the Printable page which we need to account for here\r
Shape clip = g.getClip();\r
cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
}\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 3);\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ annotations.drawComponent( (Graphics2D) g, startRes, endx + 1);\r
+ g.translate(0, -cHeight - ypos - 3);\r
+ }\r
g.setClip(clip);\r
g.translate( -LABEL_WEST, 0);\r
\r
- ypos += cHeight;\r
+ ypos += cHeight + getAnnotationHeight() + hgap;\r
+\r
startRes += cWidth;\r
- endx = (startRes + cWidth) - 1;\r
+ }\r
+ }\r
\r
- if (endx > al.getWidth())\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if (!av.showAnnotation)\r
+ {\r
+ return 0;\r
+ }\r
+\r
+ if (annotations == null)\r
+ {\r
+ annotations = new AnnotationPanel(av);\r
+ }\r
+\r
+ return annotations.adjustPanelHeight();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g1 DOCUMENT ME!\r
+ * @param startRes DOCUMENT ME!\r
+ * @param endRes DOCUMENT ME!\r
+ * @param startSeq DOCUMENT ME!\r
+ * @param endSeq DOCUMENT ME!\r
+ * @param offset DOCUMENT ME!\r
+ */\r
+ void drawPanel(Graphics g1, int startRes, int endRes,\r
+ int startSeq, int endSeq, int offset)\r
+ {\r
+ if (!av.hasHiddenColumns)\r
+ {\r
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+ else\r
+ {\r
+ java.util.Vector regions = av.getColumnSelection().getHiddenColumns();\r
+\r
+ int screenY = 0;\r
+ int blockStart = startRes;\r
+ int blockEnd = endRes;\r
+\r
+ for (int i = 0; i < regions.size(); i++)\r
+ {\r
+ int[] region = (int[]) regions.elementAt(i);\r
+ int hideStart = region[0];\r
+ int hideEnd = region[1];\r
+\r
+ if (hideStart <= blockStart)\r
+ {\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
+\r
+ blockEnd = hideStart - 1;\r
+\r
+ g1.translate(screenY * av.charWidth, 0);\r
+\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ if (av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\r
+\r
+ g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ 0 + offset,\r
+ (blockEnd - blockStart + 1) * av.charWidth - 1,\r
+ (endSeq - startSeq) * av.charHeight + offset);\r
+ }\r
+\r
+ g1.translate( -screenY * av.charWidth, 0);\r
+ screenY += blockEnd - blockStart + 1;\r
+ blockStart = hideEnd + 1;\r
+ }\r
+\r
+ if (screenY <= (endRes - startRes))\r
{\r
- endx = al.getWidth();\r
+ blockEnd = blockStart + (endRes - startRes) - screenY;\r
+ g1.translate(screenY * av.charWidth, 0);\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+\r
+ g1.translate( -screenY * av.charWidth, 0);\r
}\r
}\r
+\r
}\r
\r
- synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
- int y2, int startx, int starty, int offset)\r
+ //int startRes, int endRes, int startSeq, int endSeq, int x, int y,\r
+ // int x1, int x2, int y1, int y2, int startx, int starty,\r
+ void draw(Graphics g,\r
+ int startRes, int endRes,\r
+ int startSeq, int endSeq,\r
+ int offset)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
+ sr.prepare(g, av.renderGaps);\r
\r
SequenceI nextSeq;\r
\r
/// First draw the sequences\r
/////////////////////////////\r
- for (int i = y1; i < y2; i++)\r
+ for (int i = startSeq; i < endSeq; i++)\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
\r
- sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
- x1, x2, (x1 - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth, av.charHeight);\r
+ sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.drawSequence(g, nextSeq,\r
- av.alignment.findAllGroups(nextSeq), x1, x2,\r
- (x1 - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth, av.charHeight);\r
+ fr.drawSequence(g, nextSeq, startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
+ }\r
+\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (searchResults != null)\r
+ {\r
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
+ endRes);\r
+ if (visibleResults != null)\r
+ {\r
+ for (int r = 0; r < visibleResults.length; r += 2)\r
+ {\r
+ sr.drawHighlightedText(nextSeq, visibleResults[r],\r
+ visibleResults[r + 1],\r
+ (visibleResults[r] - startRes) *\r
+ av.charWidth,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
+ }\r
+ }\r
+ }\r
+\r
+ if (av.cursorMode && cursorY == i\r
+ && cursorX >= startRes && cursorX <= endRes)\r
+ {\r
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
}\r
}\r
\r
+ if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)\r
+ {\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
+\r
+ }\r
+\r
+ void drawGroupsBoundaries(Graphics g1,\r
+ int startRes, int endRes,\r
+ int startSeq, int endSeq,\r
+ int offset)\r
+ {\r
+ Graphics2D g = (Graphics2D) g1;\r
//\r
/////////////////////////////////////\r
// Now outline any areas if necessary\r
/////////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
int sx = -1;\r
int sy = -1;\r
int ex = -1;\r
int groupIndex = -1;\r
+ int visWidth = (endRes - startRes + 1) * av.charWidth;\r
\r
- if ( (group == null) && (groups.size() > 0))\r
+ if ( (group == null) && (av.alignment.getGroups().size() > 0))\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
groupIndex = 0;\r
}\r
\r
int top = -1;\r
int bottom = -1;\r
\r
- for (i = y1; i < y2; i++)\r
+ for (i = startSeq; i < endSeq; i++)\r
{\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ sx = (group.getStartRes() - startRes) * av.charWidth;\r
+ sy = offset + ( (i - startSeq) * av.charHeight);\r
ex = ( ( (group.getEndRes() + 1) - group.getStartRes()) *\r
av.charWidth) -\r
1;\r
\r
- if ( (sx < getWidth()) && (ex > 0) &&\r
- group.sequences.contains(av.alignment.getSequenceAt(\r
- i)))\r
+ if (sx + ex < 0 || sx > visWidth)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if ( (sx <= (endRes - startRes) * av.charWidth) &&\r
+ group.getSequences(null).\r
+ contains(av.alignment.getSequenceAt(i)))\r
{\r
if ( (bottom == -1) &&\r
- !group.sequences.contains(\r
+ !group.getSequences(null).contains(\r
av.alignment.getSequenceAt(i + 1)))\r
{\r
bottom = sy + av.charHeight;\r
if (!inGroup)\r
{\r
if ( ( (top == -1) && (i == 0)) ||\r
- !group.sequences.contains(\r
+ !group.getSequences(null).contains(\r
av.alignment.getSequenceAt(i - 1)))\r
{\r
top = sy;\r
{\r
if (inGroup)\r
{\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ if (sx >= 0 && sx < visWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < visWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > visWidth)\r
+ {\r
+ ex = visWidth;\r
+ }\r
+\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
\r
if (top != -1)\r
{\r
\r
if (inGroup)\r
{\r
+ sy = offset + ( (i - startSeq) * av.charHeight);\r
+ if (sx >= 0 && sx < visWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
+\r
+ if (sx + ex < visWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\r
+\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
+ }\r
+\r
+ if (sx + ex > visWidth)\r
+ {\r
+ ex = visWidth;\r
+ }\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ {\r
+ ex = (endRes - startRes + 1) * av.charWidth;\r
+ }\r
+\r
if (top != -1)\r
{\r
g.drawLine(sx, top, sx + ex, top);\r
bottom = -1;\r
}\r
\r
- sy = offset +\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
inGroup = false;\r
}\r
\r
groupIndex++;\r
\r
- if (groupIndex >= groups.size())\r
+ g.setStroke(new BasicStroke());\r
+\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
{\r
break;\r
}\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
- }\r
- while (groupIndex < groups.size());\r
- }\r
-\r
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if (displaySearch)\r
- {\r
- for (int r = 0; r < searchResults.length; r += 3)\r
- {\r
- int searchSeq = searchResults[r];\r
-\r
- if ( (searchSeq >= y1) && (searchSeq < y2))\r
- {\r
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\r
-\r
- int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
- int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
-\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
-\r
- if (searchStart < x1)\r
- {\r
- searchStart = x1;\r
- }\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
\r
- if (searchEnd > x2)\r
- {\r
- searchEnd = x2;\r
- }\r
-\r
- ssr.drawHighlightedText(seq, searchStart, searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty,\r
- searchSeq,\r
- av.charHeight), av.charWidth, av.charHeight);\r
- }\r
}\r
+ while (groupIndex < av.alignment.getGroups().size());\r
+\r
}\r
+\r
}\r
\r
- public void highlightSearchResults(int[] results)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(SearchResults results)\r
{\r
- // results are in the order sequence, startRes, endRes\r
- if (results == null)\r
- {\r
- displaySearch = false;\r
- }\r
- else\r
- {\r
- displaySearch = true;\r
- }\r
+ img = null;\r
\r
searchResults = results;\r
\r
git://source.jalview.org / jalview.git / blobdiff