*/\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.analysis.*;\r
-import jalview.datamodel.*;\r
\r
-public class SeqCanvas\r
- extends JComponent\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SeqCanvas extends JComponent\r
{\r
- FeatureRenderer fr;\r
- 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
- boolean fastPaint = false;\r
- int LABEL_WEST;\r
- int LABEL_EAST;\r
-\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.alignment);\r
- setBackground(Color.white);\r
- }\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
+ FeatureRenderer fr;\r
+ 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
+ boolean fastPaint = false;\r
+ int LABEL_WEST;\r
+ int LABEL_EAST;\r
+\r
+ /**\r
+ * Creates a new SeqCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public SeqCanvas(AlignViewport av)\r
{\r
- String string = String.valueOf(i);\r
- g.drawString(string, (i - startx - 1) * av.charWidth,\r
- ypos - (av.charHeight / 2));\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
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ setLayout(new BorderLayout());\r
+ PaintRefresher.Register(this, av.alignment);\r
+ setBackground(Color.white);\r
}\r
- }\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
+ * 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
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\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
+ ypos - (av.charHeight / 2));\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
+ }\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
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = startx;\r
- int value = -1;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ ypos += av.charHeight;\r
\r
- while (index < endx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- index++;\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
\r
- continue;\r
- }\r
+ while (index < endx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index++;\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ continue;\r
+ }\r
\r
- break;\r
- }\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
\r
- if (value != -1)\r
- {\r
- int x = LABEL_WEST - fm.stringWidth(value + "");\r
- g.drawString(value + "", x,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\r
- }\r
- }\r
+ break;\r
+ }\r
\r
- void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
- {\r
- ypos += av.charHeight;\r
+ if (value != -1)\r
+ {\r
+ int x = LABEL_WEST - fm.stringWidth(value + "");\r
+ g.drawString(value + "", x,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
+ }\r
+ }\r
+ }\r
\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\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
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = endx;\r
- int value = -1;\r
+ ypos += av.charHeight;\r
\r
- while (index > startx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- index--;\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
\r
- continue;\r
- }\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+\r
+ continue;\r
+ }\r
\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
\r
- break;\r
- }\r
+ break;\r
+ }\r
\r
- if (value != -1)\r
- {\r
- g.drawString(value + "", 0,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\r
+ if (value != -1)\r
+ {\r
+ g.drawString(value + "", 0,\r
+ (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
+ }\r
+ }\r
}\r
- }\r
\r
- public void fastPaint(int horizontal, int vertical)\r
- {\r
- if ( ( (horizontal == 0) && (vertical == 0)) || (gg == null))\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
- return;\r
- }\r
+ if (((horizontal == 0) && (vertical == 0)) || (gg == null))\r
+ {\r
+ return;\r
+ }\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
+ gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\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
+ 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 (horizontal > 0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er - sr - horizontal) * av.charWidth;\r
- sr = er - horizontal;\r
- }\r
- else if (horizontal < 0)\r
- {\r
- er = sr - horizontal;\r
- }\r
- else if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\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
+ if (horizontal > 0) // scrollbar pulled right, image to the left\r
+ {\r
+ transX = (er - sr - horizontal) * av.charWidth;\r
+ sr = er - horizontal;\r
+ }\r
+ else if (horizontal < 0)\r
+ {\r
+ er = sr - horizontal;\r
+ }\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
\r
- if (es > av.endSeq)\r
- {\r
- es = av.endSeq;\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
- 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
- gg.translate( -transX, -transY);\r
-\r
- fastPaint = true;\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
-\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
- {\r
- g.drawImage(img, 0, 0, this);\r
- fastPaint = false;\r
- return;\r
- }\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
\r
- // this draws the whole of the alignment\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
+ gg.translate(transX, transY);\r
\r
- imgWidth -= (imgWidth % av.charWidth);\r
- imgHeight -= (imgHeight % av.charHeight);\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
+ gg.translate(-transX, -transY);\r
\r
- if ( (imgWidth < 1) || (imgHeight < 1))\r
- {\r
- return;\r
+ fastPaint = true;\r
+ repaint();\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
+ /**\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
+ if ((img != null) &&\r
+ (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
+ (getHeight() != g.getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, imgWidth, imgHeight);\r
+ return;\r
+ }\r
\r
- chunkWidth = getWrappedCanvasWidth(getWidth());\r
- chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ // this draws the whole of the alignment\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
+ imgWidth -= (imgWidth % av.charWidth);\r
+ imgHeight -= (imgHeight % av.charHeight);\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,\r
- av.startRes, av.startSeq, 0);\r
- }\r
+ if ((imgWidth < 1) || (imgHeight < 1))\r
+ {\r
+ return;\r
+ }\r
\r
- g.drawImage(img, 0, 0, this);\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
\r
- public int getWrappedCanvasWidth(int cwidth)\r
- {\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
+ chunkWidth = getWrappedCanvasWidth(getWidth());\r
+ chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
+ av.setChunkHeight(chunkHeight);\r
+ av.setChunkWidth(chunkWidth);\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,\r
+ av.startRes, av.startSeq, 0);\r
+ }\r
+\r
+ g.drawImage(img, 0, 0, this);\r
}\r
\r
- if (av.scaleLeftWrapped)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cwidth DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getWrappedCanvasWidth(int cwidth)\r
{\r
- LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
- }\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- }\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
- int startRes)\r
- {\r
- AlignmentI al = av.getAlignment();\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");\r
+ }\r
\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");\r
+ }\r
\r
- int LABEL_EAST = 0;\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ }\r
\r
- if (av.scaleRightWrapped)\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
- LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
- }\r
+ AlignmentI al = av.getAlignment();\r
\r
- int LABEL_WEST = 0;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
- }\r
+ int LABEL_EAST = 0;\r
\r
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ LABEL_EAST = fm.stringWidth(al.getWidth() + "000");\r
+ }\r
\r
- av.endRes = av.startRes + cWidth;\r
+ int LABEL_WEST = 0;\r
\r
- int endx = (startRes + cWidth) - 1;\r
- int ypos = 2 * av.charHeight;\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ LABEL_WEST = fm.stringWidth(al.getWidth() + "0");\r
+ }\r
\r
- while ( (ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
- {\r
- g.setColor(Color.black);\r
-\r
- if (av.scaleLeftWrapped)\r
- {\r
- drawWestScale(g, startRes, endx, ypos);\r
- }\r
-\r
- if (av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 0);\r
- }\r
-\r
- g.translate(LABEL_WEST, 0);\r
-\r
- if (av.scaleAboveWrapped)\r
- {\r
- drawNorthScale(g, startRes, endx, ypos);\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
- 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
-\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
- g.translate( -LABEL_WEST, 0);\r
-\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = (startRes + cWidth) - 1;\r
-\r
- if (endx > al.getWidth())\r
- {\r
- endx = al.getWidth();\r
- }\r
- }\r
- }\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
\r
- synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
- int y2, int startx, int starty, int offset)\r
- {\r
- Graphics2D g = (Graphics2D) g1;\r
- g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
+ av.endRes = av.startRes + cWidth;\r
\r
- SequenceI nextSeq;\r
+ int endx = (startRes + cWidth) - 1;\r
+ int ypos = 2 * av.charHeight;\r
\r
- /// First draw the sequences\r
- /////////////////////////////\r
- for (int i = y1; i < y2; 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
-\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
- }\r
- }\r
+ while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
+ {\r
+ g.setColor(Color.black);\r
\r
- //\r
- /////////////////////////////////////\r
- // Now outline any areas if necessary\r
- /////////////////////////////////////\r
- SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- int sx = -1;\r
- int sy = -1;\r
- int ex = -1;\r
- int groupIndex = -1;\r
+ if (av.scaleRightWrapped)\r
+ {\r
+ g.translate(canvasWidth - LABEL_EAST + av.charWidth, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST + av.charWidth), 0);\r
+ }\r
\r
- if ( (group == null) && (groups.size() > 0))\r
- {\r
- group = (SequenceGroup) groups.elementAt(0);\r
- groupIndex = 0;\r
- }\r
+ g.translate(LABEL_WEST, 0);\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 = y1; i < y2; i++)\r
- {\r
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset +\r
- AlignmentUtil.getPixelHeight(starty, i, 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
- {\r
- if ( (bottom == -1) &&\r
- !group.sequences.contains(\r
- av.alignment.getSequenceAt(i + 1)))\r
+ if (av.scaleAboveWrapped)\r
{\r
- bottom = sy + av.charHeight;\r
+ drawNorthScale(g, startRes, endx, ypos);\r
}\r
\r
- if (!inGroup)\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
+ if (clip == null)\r
{\r
- if ( ( (top == -1) && (i == 0)) ||\r
- !group.sequences.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[]\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
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
}\r
- }\r
- else\r
- {\r
- if (inGroup)\r
+ else\r
{\r
- g.drawLine(sx, oldY, sx, sy);\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\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
+ g.setClip(0, (int) clip.getBounds().getY(),\r
+ cWidth * av.charWidth, (int) clip.getBounds().getHeight());\r
+ }\r
+\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
+ g.setClip(clip);\r
+ g.translate(-LABEL_WEST, 0);\r
+\r
+ ypos += cHeight;\r
+ startRes += cWidth;\r
+ endx = (startRes + cWidth) - 1;\r
+\r
+ if (endx > al.getWidth())\r
+ {\r
+ endx = al.getWidth();\r
}\r
- }\r
}\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g1 DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param x2 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param y2 DOCUMENT ME!\r
+ * @param startx DOCUMENT ME!\r
+ * @param starty DOCUMENT ME!\r
+ * @param offset DOCUMENT ME!\r
+ */\r
+ synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
+ int y2, int startx, int starty, int offset)\r
+ {\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
+ sr.renderGaps(av.renderGaps);\r
\r
- if (inGroup)\r
+ SequenceI nextSeq;\r
+\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
+ for (int i = y1; i < y2; i++)\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
- 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
+ nextSeq = av.alignment.getSequenceAt(i);\r
+\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ x1, x2, (x1 - startx) * av.charWidth,\r
+ offset + ((i - starty) * av.charHeight), av.charWidth,\r
+ 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 + ((i - starty) * av.charHeight), av.charWidth,\r
+ av.charHeight);\r
+ }\r
}\r
\r
- groupIndex++;\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
\r
- if (groupIndex >= groups.size())\r
+ if ((group == null) && (groups.size() > 0))\r
{\r
- break;\r
+ group = (SequenceGroup) groups.elementAt(0);\r
+ groupIndex = 0;\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
+ 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 = y1; i < y2; i++)\r
+ {\r
+ sx = (group.getStartRes() - startx) * av.charWidth;\r
+ sy = offset + ((i - starty) * av.charHeight);\r
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -\r
+ 1;\r
+\r
+\r
+ if ((sx < (x2-x1)*av.charWidth) &&\r
+ group.sequences.contains(av.alignment.getSequenceAt(\r
+ i)))\r
+ {\r
+ if ((bottom == -1) &&\r
+ !group.sequences.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.sequences.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
+ g.drawLine(sx, oldY, sx, sy);\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\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
+\r
+ if (inGroup)\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
+ sy = offset + ((i - starty) * 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
+ {\r
+ break;\r
+ }\r
+\r
+ group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ }\r
+ while (groupIndex < groups.size());\r
+ }\r
\r
- if ( (searchSeq >= y1) && (searchSeq < y2))\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (displaySearch)\r
{\r
- SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);\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
+ int searchStart = seq.findIndex(searchResults[r + 1]) - 1;\r
+ int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;\r
\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
+ SequenceRenderer ssr = (SequenceRenderer) sr;\r
\r
- if (searchStart < x1)\r
- {\r
- searchStart = x1;\r
- }\r
+ if (searchStart < x1)\r
+ {\r
+ searchStart = x1;\r
+ }\r
\r
- if (searchEnd > x2)\r
- {\r
- searchEnd = x2;\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
+ ssr.drawHighlightedText(seq, searchStart, searchEnd,\r
+ (searchStart - startx) * av.charWidth,\r
+ offset + ((searchSeq - starty) * av.charHeight),\r
+ av.charWidth, av.charHeight);\r
+ }\r
+ }\r
}\r
- }\r
}\r
- }\r
\r
- public void highlightSearchResults(int[] results)\r
- {\r
- // results are in the order sequence, startRes, endRes\r
- if (results == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(int[] results)\r
{\r
- displaySearch = false;\r
- }\r
- else\r
- {\r
- displaySearch = true;\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
\r
- searchResults = results;\r
+ searchResults = results;\r
\r
- repaint();\r
- }\r
+ repaint();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff