/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-\r
import java.awt.*;\r
import java.awt.image.*;\r
-\r
import javax.swing.*;\r
\r
+import jalview.datamodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class SeqCanvas extends JComponent\r
+public class SeqCanvas\r
+ extends JComponent\r
{\r
- final FeatureRenderer fr;\r
- final SequenceRenderer sr;\r
- BufferedImage img;\r
- Graphics2D gg;\r
- int imgWidth;\r
- int imgHeight;\r
- AlignViewport av;\r
- SearchResults searchResults = null;\r
- boolean fastPaint = false;\r
- int LABEL_WEST;\r
- int LABEL_EAST;\r
-\r
-\r
- int cursorX = 0;\r
- int cursorY = 0;\r
-\r
-\r
- /**\r
- * Creates a new SeqCanvas object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public SeqCanvas(AlignViewport av)\r
+ final FeatureRenderer fr;\r
+ final SequenceRenderer sr;\r
+ BufferedImage img;\r
+ Graphics2D gg;\r
+ int imgWidth;\r
+ int imgHeight;\r
+ AlignViewport av;\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
+ /**\r
+ * Creates a new SeqCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ setLayout(new BorderLayout());\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+ setBackground(Color.white);\r
+ }\r
+\r
+ MCview.PDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.PDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\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
+\r
+ g.setColor(Color.black);\r
+\r
+ // NORTH SCALE\r
+ for (int i = scalestartx; i < endx; i += 10)\r
{\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this, av.getSequenceSetId());\r
- setBackground(Color.white);\r
- }\r
+ int value = i;\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\r
+ }\r
\r
- MCview.PDBCanvas pdbCanvas;\r
- public SequenceRenderer getSequenceRenderer()\r
- {\r
- return sr;\r
- }\r
+ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
+ ypos - (av.charHeight / 2));\r
\r
- public FeatureRenderer getFeatureRenderer()\r
- {\r
- return fr;\r
+ g.drawLine( ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
+ (ypos + 2) - (av.charHeight / 2),\r
+ ( (i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -\r
+ 2);\r
}\r
-\r
- public void setPDBCanvas(MCview.PDBCanvas pc)\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
+ if (av.hasHiddenColumns)\r
{\r
- pdbCanvas = pc;\r
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
}\r
\r
- public AlignViewport getViewport()\r
+ int maxwidth = av.alignment.getWidth();\r
+ if (av.hasHiddenColumns)\r
{\r
- return av;\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\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
+ // WEST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- int scalestartx = startx - (startx % 10) + 10;\r
-\r
- g.setColor(Color.black);\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
\r
- // NORTH SCALE\r
- for (int i = scalestartx; i < endx; i += 10)\r
+ while (index < endx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
{\r
- int value = i;\r
- if(av.hasHiddenColumns)\r
- value = av.getColumnSelection().adjustForHiddenColumns(value);\r
-\r
- g.drawString( String.valueOf(value), (i - startx - 1) * av.charWidth,\r
- ypos - (av.charHeight / 2));\r
+ index++;\r
\r
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
- (ypos + 2) - (av.charHeight / 2),\r
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -\r
- 2);\r
+ continue;\r
}\r
+\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
+\r
+ break;\r
+ }\r
+\r
+ if (value != -1)\r
+ {\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
- /**\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
+ SequenceI seq;\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- ypos += av.charHeight;\r
+ seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
\r
- if(av.hasHiddenColumns)\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
{\r
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ index--;\r
+\r
+ continue;\r
}\r
\r
- int maxwidth = av.alignment.getWidth();\r
- if (av.hasHiddenColumns)\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ value = seq.findPosition(index);\r
\r
- // WEST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = startx;\r
- int value = -1;\r
+ break;\r
+ }\r
\r
- while (index < endx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index++;\r
+ if (value != -1)\r
+ {\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 (gg == null)\r
+ {\r
+ return;\r
+ }\r
\r
- continue;\r
- }\r
+ fastPaint = true;\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth,\r
+ imgHeight,\r
+ -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\r
\r
- break;\r
- }\r
+ int sr = av.startRes;\r
+ int er = av.endRes;\r
+ int ss = av.startSeq;\r
+ int es = av.endSeq;\r
+ int transX = 0;\r
+ int transY = 0;\r
\r
- if (value != -1)\r
- {\r
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
- g.drawString(value + "", x,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\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
-\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
+ else if (horizontal < 0)\r
{\r
- ypos += av.charHeight;\r
-\r
- if(av.hasHiddenColumns)\r
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
+ er = sr - horizontal - 1;\r
+ }\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
\r
- SequenceI seq;\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- seq = av.alignment.getSequenceAt(i);\r
- int index = endx;\r
- int value = -1;\r
+ if (ss < av.startSeq)\r
+ { // ie scrolling too fast, more than a page at a time\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - (vertical * av.charHeight);\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
\r
- while (index > startx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index--;\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
\r
- continue;\r
- }\r
+ gg.translate(transX, transY);\r
+ drawPanel(gg, sr, er, ss, es, 0);\r
+ gg.translate( -transX, -transY);\r
+\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * Definitions of startx and endx (hopefully):\r
+ * SMJS This is what I'm working towards!\r
+ * startx is the first residue (starting at 0) to display.\r
+ * endx is the last residue to display (starting at 0).\r
+ * starty is the first sequence to display (starting at 0).\r
+ * endy is the last sequence to display (starting at 0).\r
+ * NOTE 1: The av limits are set in setFont in this class and\r
+ * in the adjustment listener in SeqPanel when the scrollbars move.\r
+ */\r
+\r
+ // Set this to false to force a full panel paint\r
+ public void paintComponent(Graphics g)\r
+ {\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
- value = seq.findPosition(index);\r
+ // this draws the whole of the alignment\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
\r
- break;\r
- }\r
+ imgWidth -= (imgWidth % av.charWidth);\r
+ imgHeight -= (imgHeight % av.charHeight);\r
\r
- if (value != -1)\r
- {\r
- g.drawString(String.valueOf(value), 0,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\r
- }\r
+ if ( (imgWidth < 1) || (imgHeight < 1))\r
+ {\r
+ return;\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
+ if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())\r
{\r
- if (gg == null)\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
- return;\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
+ return;\r
+ }\r
+ }\r
\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\r
\r
- fastPaint = true;\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- gg.copyArea(horizontal * av.charWidth,\r
- vertical * av.charHeight,\r
- imgWidth,\r
- imgHeight,\r
- -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ if (av.getWrapAlignment())\r
+ {\r
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+ }\r
+ else\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
+ }\r
\r
- int sr = av.startRes;\r
- int er = av.endRes;\r
- int ss = av.startSeq;\r
- int es = av.endSeq;\r
- int transX = 0;\r
- int transY = 0;\r
+ g.drawImage(img, 0, 0, this);\r
\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\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-1;\r
- }\r
- else if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
+ }\r
\r
- if (ss < av.startSeq)\r
- { // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- }\r
- else\r
- {\r
- transY = imgHeight - (vertical * av.charHeight);\r
- }\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\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 (es > av.endSeq)\r
- {\r
- es = av.endSeq;\r
- }\r
- }\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- gg.translate(transX, transY);\r
- drawPanel(gg, sr, er, ss, es, 0);\r
- gg.translate(-transX, -transY);\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
\r
- repaint();\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(getMask());\r
}\r
\r
- /**\r
- * Definitions of startx and endx (hopefully):\r
- * SMJS This is what I'm working towards!\r
- * startx is the first residue (starting at 0) to display.\r
- * endx is the last residue to display (starting at 0).\r
- * starty is the first sequence to display (starting at 0).\r
- * endy is the last sequence to display (starting at 0).\r
- * NOTE 1: The av limits are set in setFont in this class and\r
- * in the adjustment listener in SeqPanel when the scrollbars move.\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
- // Set this to false to force a full panel paint\r
- public void paintComponent(Graphics g)\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
{\r
- super.paintComponent(g);\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
+ AlignmentI al = av.getAlignment();\r
+\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(getMask());\r
+ }\r
\r
+ if (av.scaleLeftWrapped)\r
+ {\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
- 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
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
\r
+ av.setWrappedWidth(cWidth);\r
\r
- // this draws the whole of the alignment\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
+ av.endRes = av.startRes + cWidth;\r
\r
- imgWidth -= (imgWidth % av.charWidth);\r
- imgHeight -= (imgHeight % av.charHeight);\r
+ int endx;\r
+ int ypos = hgap;\r
+ int maxwidth = av.alignment.getWidth() - 1;\r
\r
- if ((imgWidth < 1) || (imgHeight < 1))\r
- {\r
- return;\r
- }\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
\r
- if (img == null || imgWidth != img.getWidth() || imgHeight != img.getHeight())\r
- {\r
- try{\r
- img = new BufferedImage(imgWidth, imgHeight,\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) img.getGraphics();\r
- gg.setFont(av.getFont());\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
+ while ( (ypos <= canvasHeight) && (startRes < maxwidth))\r
+ {\r
+ endx = startRes + cWidth - 1;\r
\r
- return;\r
- }\r
- }\r
+ if (endx > maxwidth)\r
+ {\r
+ endx = maxwidth;\r
+ }\r
\r
- if (av.antiAlias)\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ g.setFont(av.getFont());\r
+ g.setColor(Color.black);\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, imgWidth, imgHeight);\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate( - (canvasWidth - LABEL_EAST), 0);\r
+ }\r
\r
- if (av.getWrapAlignment())\r
- {\r
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
- }\r
- else\r
- {\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
- }\r
+ g.translate(LABEL_WEST, 0);\r
\r
- g.drawImage(img, 0, 0, this);\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ drawNorthScale(g, startRes, endx, ypos);\r
+ }\r
\r
- if (pdbCanvas != null)\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
- pdbCanvas.updateSeqColours();\r
- }\r
+ res = av.getColumnSelection().findHiddenRegionPosition(i) -\r
+ startRes;\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
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
+ if (res < 0 || res > endx - startRes)\r
+ {\r
+ continue;\r
+ }\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(getMask());\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
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(getMask());\r
}\r
+ }\r
\r
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\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
\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
+ if (clip == null)\r
{\r
- tmp = av.alignment.getSequenceAt(i).getEnd();\r
- if(tmp>maxWidth)\r
- maxWidth = tmp;\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
}\r
-\r
- for (int i = maxWidth; i > 0; i /= 10)\r
+ else\r
{\r
- mask += "0";\r
+ g.setClip(0, (int) clip.getBounds().getY(),\r
+ cWidth * av.charWidth, (int) clip.getBounds().getHeight());\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
- AlignmentI al = av.getAlignment();\r
\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
\r
-\r
- if (av.scaleRightWrapped)\r
+ if (av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos + 3);\r
+ if (annotations == null)\r
{\r
- LABEL_EAST = fm.stringWidth(getMask());\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
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(getMask());\r
- }\r
-\r
- int hgap = av.charHeight;\r
- if(av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
+ ypos += cHeight + getAnnotationHeight() + hgap;\r
\r
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
+ startRes += cWidth;\r
+ }\r
+ }\r
\r
- av.setWrappedWidth(cWidth);\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if (!av.showAnnotation)\r
+ {\r
+ return 0;\r
+ }\r
\r
- av.endRes = av.startRes + cWidth;\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 endx;\r
- int ypos = hgap;\r
- int maxwidth = av.alignment.getWidth()-1;\r
+ int screenY = 0;\r
+ int blockStart = startRes;\r
+ int blockEnd = endRes;\r
\r
- if(av.hasHiddenColumns)\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\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
- while ((ypos <= canvasHeight) && (startRes < maxwidth))\r
+ if (hideStart <= blockStart)\r
{\r
- endx = startRes + cWidth -1;\r
-\r
- if (endx > maxwidth)\r
- {\r
- endx = maxwidth;\r
- }\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
\r
- g.setFont(av.getFont());\r
- g.setColor(Color.black);\r
+ blockEnd = hideStart - 1;\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- drawWestScale(g, startRes, endx, ypos);\r
- }\r
+ g1.translate(screenY * av.charWidth, 0);\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate(-(canvasWidth - LABEL_EAST), 0);\r
- }\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
\r
- g.translate(LABEL_WEST, 0);\r
-\r
- if (av.scaleAboveWrapped)\r
- {\r
- drawNorthScale(g, startRes, endx, ypos);\r
- }\r
+ if (av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\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
- continue;\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
+ 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
- }\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
+ 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
- // 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
+ }\r
\r
- if (clip == null)\r
- {\r
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
- }\r
- else\r
- {\r
- g.setClip(0, (int) clip.getBounds().getY(),\r
- cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
- }\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
+ g.setFont(av.getFont());\r
+ sr.prepare(g, av.renderGaps);\r
\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+ SequenceI nextSeq;\r
\r
- if(av.showAnnotation)\r
- {\r
- g.translate(0, cHeight + ypos + 3);\r
- if(annotations==null)\r
- annotations = new AnnotationPanel(av);\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ nextSeq = av.alignment.getSequenceAt(i);\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
+ sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
\r
- ypos += cHeight+getAnnotationHeight()+hgap;\r
+ if (av.showSequenceFeatures)\r
+ {\r
+ fr.drawSequence(g, nextSeq, startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
+ }\r
\r
- startRes += cWidth;\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
- AnnotationPanel annotations;\r
- int getAnnotationHeight()\r
+ if (av.getSelectionGroup() != null || av.alignment.getGroups().size() > 0)\r
{\r
- if(!av.showAnnotation)\r
- return 0;\r
-\r
- if(annotations==null)\r
- annotations = new AnnotationPanel(av);\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
+ }\r
\r
- return annotations.adjustPanelHeight();\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
+\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) && (av.alignment.getGroups().size() > 0))\r
+ {\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
+ groupIndex = 0;\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
+ if (group != null)\r
{\r
- if(!av.hasHiddenColumns)\r
- {\r
- draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
- }\r
- else\r
+ do\r
{\r
- java.util.Vector regions = av.getColumnSelection().getHiddenColumns();\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top = -1;\r
+ int bottom = -1;\r
\r
- int screenY = 0;\r
- int blockStart = startRes;\r
- int blockEnd = endRes;\r
-\r
- for (int i = 0; i < regions.size(); i++)\r
+ for (i = startSeq; i < endSeq; i++)\r
{\r
- int[] region = (int[]) regions.elementAt(i);\r
- int hideStart = region[0];\r
- int hideEnd = region[1];\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 (hideStart <= blockStart)\r
+ if (sx + ex < 0 || sx > visWidth)\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
+ if ( (sx <= (endRes - startRes) * av.charWidth) &&\r
+ group.getSequences(null).\r
+ contains(av.alignment.getSequenceAt(i)))\r
{\r
- g1.setColor(Color.blue);\r
+ if ( (bottom == -1) &&\r
+ !group.getSequences(null).contains(\r
+ av.alignment.getSequenceAt(i + 1)))\r
+ {\r
+ bottom = sy + av.charHeight;\r
+ }\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
+ if (!inGroup)\r
+ {\r
+ if ( ( (top == -1) && (i == 0)) ||\r
+ !group.getSequences(null).contains(\r
+ av.alignment.getSequenceAt(i - 1)))\r
+ {\r
+ top = sy;\r
+ }\r
\r
- g1.translate( -screenY * av.charWidth, 0);\r
- screenY += blockEnd - blockStart + 1;\r
- blockStart = hideEnd + 1;\r
- }\r
+ oldY = sy;\r
+ inGroup = true;\r
\r
- if (screenY <= (endRes - startRes))\r
- {\r
- blockEnd = blockStart + (endRes - startRes) - screenY;\r
- g1.translate(screenY * av.charWidth, 0);\r
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(1,\r
+ BasicStroke.CAP_BUTT,\r
+ BasicStroke.JOIN_ROUND, 3f,\r
+ new float[]\r
+ {5f, 3f}, 0f));\r
+ g.setColor(Color.RED);\r
+ }\r
+ else\r
+ {\r
+ g.setStroke(new BasicStroke());\r
+ g.setColor(group.getOutlineColour());\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < visWidth)\r
+ {\r
+ g.drawLine(sx, oldY, sx, sy);\r
+ }\r
\r
- g1.translate( -screenY * av.charWidth, 0);\r
- }\r
- }\r
+ if (sx + ex < visWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
+ }\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
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\r
\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
- g.setFont(av.getFont());\r
- sr.prepare(g, av.renderGaps);\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
\r
- SequenceI nextSeq;\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
\r
- /// First draw the sequences\r
- /////////////////////////////\r
- for (int i = startSeq; i < endSeq; i++)\r
+ if (inGroup)\r
{\r
- nextSeq = av.alignment.getSequenceAt(i);\r
-\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, startRes, endRes,\r
- offset + ((i - startSeq) * av.charHeight));\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
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if (searchResults != null)\r
- {\r
- int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);\r
- if (visibleResults != null)\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) * av.charWidth,\r
- offset + ( (i - startSeq) * av.charHeight));\r
- }\r
- }\r
+ if (sx + ex < visWidth)\r
+ {\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\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
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\r
}\r
\r
- if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)\r
- drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\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
-\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) && (av.alignment.getGroups().size() > 0))\r
- {\r
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
- groupIndex = 0;\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
+ top = -1;\r
+ }\r
\r
- if (group != null)\r
- {\r
- do\r
- {\r
- int oldY = -1;\r
- int i = 0;\r
- boolean inGroup = false;\r
- int top = -1;\r
- int bottom = -1;\r
-\r
- for (i = startSeq; i < endSeq; i++)\r
- {\r
- sx = (group.getStartRes() - startRes) * av.charWidth;\r
- sy = offset + ((i - startSeq) * av.charHeight);\r
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
- 1;\r
-\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.getSequences(null).contains(\r
- av.alignment.getSequenceAt(i + 1)))\r
- {\r
- bottom = sy + av.charHeight;\r
- }\r
-\r
- if (!inGroup)\r
- {\r
- if (((top == -1) && (i == 0)) ||\r
- !group.getSequences(null).contains(\r
- av.alignment.getSequenceAt(i - 1)))\r
- {\r
- top = sy;\r
- }\r
-\r
- oldY = sy;\r
- inGroup = true;\r
-\r
- if (group == av.getSelectionGroup())\r
- {\r
- g.setStroke(new BasicStroke(1,\r
- BasicStroke.CAP_BUTT,\r
- BasicStroke.JOIN_ROUND, 3f,\r
- new float[] { 5f, 3f }, 0f));\r
- g.setColor(Color.RED);\r
- }\r
- else\r
- {\r
- g.setStroke(new BasicStroke());\r
- g.setColor(group.getOutlineColour());\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (inGroup)\r
- {\r
- if (sx >= 0 && sx < visWidth)\r
- g.drawLine(sx, oldY, sx, sy);\r
-\r
- if (sx + ex < visWidth)\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
-\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
-\r
- if (sx + ex > visWidth)\r
- ex = visWidth;\r
-\r
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
- ex = (endRes - startRes + 1) * av.charWidth;\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
-\r
- inGroup = false;\r
- }\r
- }\r
- }\r
-\r
- if (inGroup)\r
- {\r
- sy = offset + ( (i - startSeq) * av.charHeight);\r
- if (sx >= 0 && sx < visWidth)\r
- g.drawLine(sx, oldY, sx, sy);\r
-\r
- if (sx + ex < visWidth)\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
-\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
-\r
- if (sx + ex > visWidth)\r
- ex = visWidth;\r
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
- ex = (endRes - startRes + 1) * av.charWidth;\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
- }\r
-\r
- inGroup = false;\r
- }\r
-\r
- groupIndex++;\r
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
+ bottom = -1;\r
+ }\r
\r
- g.setStroke(new BasicStroke());\r
+ inGroup = false;\r
+ }\r
\r
- if (groupIndex >= av.alignment.getGroups().size())\r
- {\r
- break;\r
- }\r
+ groupIndex++;\r
\r
- group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+ g.setStroke(new BasicStroke());\r
\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
+ {\r
+ break;\r
+ }\r
\r
- }\r
- while (groupIndex < av.alignment.getGroups().size());\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
\r
- }\r
+ }\r
+ while (groupIndex < av.alignment.getGroups().size());\r
\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param results DOCUMENT ME!\r
- */\r
- public void highlightSearchResults(SearchResults results)\r
- {\r
- img = null;\r
+ }\r
\r
- searchResults = results;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(SearchResults results)\r
+ {\r
+ img = null;\r
\r
- repaint();\r
- }\r
+ searchResults = results;\r
+\r
+ repaint();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff