package jalview.gui;\r
\r
import java.awt.*;\r
+import java.awt.image.*;\r
import javax.swing.*;\r
-import java.util.*;\r
import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
import jalview.analysis.*;\r
\r
\r
-public class SeqCanvas extends JPanel\r
+public class SeqCanvas extends JComponent\r
{\r
- Image img;\r
- Graphics gg;\r
+ FeatureRenderer fr;\r
+ SequenceRenderer sr;\r
+ BufferedImage img;\r
+ Graphics2D gg;\r
int imgWidth;\r
int imgHeight;\r
\r
AlignViewport av;\r
- int pady = 2;\r
- int oldstartx;\r
- int oldstarty;\r
- int oldendx;\r
- int oldendy;\r
- public boolean paintFlag = false;\r
\r
boolean showScores = false;\r
boolean displaySearch = false;\r
int chunkHeight;\r
int chunkWidth;\r
\r
- ColourSchemeI cs = new ZappoColourScheme();\r
+ boolean fastPaint = false;\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
- }\r
-\r
- public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) {\r
- int scalestartx = startx - startx%10 + 10;\r
-\r
- gg.setColor(Color.black);\r
-\r
- for (int i=scalestartx;i < endx;i+= 10) {\r
- String string = String.valueOf(i);\r
- gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));\r
- }\r
- }\r
-\r
+ PaintRefresher.Register(this);\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
- public void paintComponent(Graphics g) {\r
+ void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\r
+ int scalestartx = startx - startx % 10 + 10;\r
\r
- AlignmentI da = av.getAlignment();\r
+ g.setColor(Color.black);\r
\r
- if (img == null ||\r
- imgWidth != getWidth() ||\r
- imgHeight != getHeight()\r
- || paintFlag)\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
- imgWidth = (getWidth() > 0 ? getWidth() : 1);\r
- imgHeight = (getHeight() > 0 ? getHeight() : 1);\r
-\r
- img = createImage(imgWidth,imgHeight);\r
- gg = img.getGraphics();\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 - 2);\r
\r
- gg.setFont(av.getFont());\r
-\r
- oldstartx = -1;\r
- oldendx = -1;\r
- oldstarty = -1;\r
- oldendy = -1;\r
- paintFlag = false;\r
}\r
+ }\r
\r
- int startx = av.getStartRes();\r
- int starty = av.getStartSeq();\r
-\r
- int endx = av.getEndRes();\r
- int endy = av.getEndSeq();\r
-\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
-\r
- chunkWidth = (int)(getWidth()/charWidth);\r
- chunkHeight = (da.getHeight() + 2)*charHeight;\r
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)\r
+ {\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ ypos+= av.charHeight;\r
+ // EAST 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
+ while (index < endx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index++;\r
+ continue;\r
+ }\r
\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ break;\r
+ }\r
+ if(value!=-1)\r
+ {\r
+ int x = LABEL_WEST - fm.stringWidth(value+"");\r
+ g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5);\r
+ }\r
+ }\r
+ }\r
\r
- int offy = av.getStartSeq();\r
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
+{\r
+ ypos+= av.charHeight;\r
+ // EAST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
+ continue;\r
+ }\r
\r
- if (oldendx == -1) {\r
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
+ value = av.alignment.getSequenceAt(i).findPosition(index);\r
+ break;\r
+ }\r
+ if(value!=-1)\r
+ g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5);\r
+ }\r
\r
- if (av.getWrapAlignment()) {\r
- startx = (int)(offy/chunkWidth)*chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = offy%chunkHeight;\r
- endy = starty + da.getHeight();\r
+}\r
\r
- int ypos = 0;\r
- int rowstart = starty;\r
\r
- if (starty == 0) {\r
- ypos = 2*charHeight;\r
- } else if (starty == 1) {\r
- starty = 0;\r
- ypos = charHeight;\r
- }\r
\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
\r
- if (rowstart < 2) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- }\r
+public void fastPaint(int horizontal, int vertical)\r
+{\r
+ if (horizontal == 0 && vertical == 0 || gg==null)\r
+ return;\r
\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);\r
+ gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
+ -vertical * av.charHeight);\r
\r
- if (rowstart == 0) {\r
- ypos = ypos + chunkHeight;\r
- } else if (rowstart == 1) {\r
- ypos = ypos + chunkHeight;\r
- } else {\r
- ypos = ypos + chunkHeight - rowstart*charHeight;\r
- }\r
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
+ transX = 0, transY = 0;\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
+ er = sr - horizontal;\r
\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = 0;\r
+ else if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
+ if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ ss = av.startSeq;\r
+ else\r
+ transY = imgHeight - vertical * av.charHeight;\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
+ if(es > av.endSeq)\r
+ es = av.endSeq;\r
+ }\r
\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
- // Draw the rest of the panels\r
\r
- while (ypos <= getHeight()) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);\r
+ gg.translate(transX, transY);\r
\r
- ypos += chunkHeight;\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);\r
+ drawPanel(gg, sr, er, ss, es, sr, ss, 0);\r
+ gg.translate( -transX, -transY);\r
\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
+ fastPaint = true;\r
+ repaint();\r
\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
+}\r
\r
- }\r
- }\r
- else\r
- {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\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
- oldstartx = startx;\r
- oldendx = endx;\r
- oldstarty = starty;\r
- oldendy = endy;\r
+ public void paint(Graphics g)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0, 0, getWidth(), getHeight());\r
\r
- }\r
+ if (fastPaint)\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
}\r
\r
- else if (oldstartx < startx)\r
- {\r
- // This is dragging horizontal scrollbar to the right\r
+ // this draws the whole of the alignment\r
+ imgWidth = getWidth();\r
+ imgHeight = getHeight();\r
+ if(imgWidth==0 || imgHeight==0)\r
+ return;\r
\r
- int delx = (int)((startx - oldstartx) * charWidth);\r
- int delx2 = (int)((oldendx - startx + 1) * charWidth);\r
+ imgWidth -= imgWidth%av.charWidth;\r
+ imgHeight-= imgHeight%av.charHeight;\r
\r
- gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);\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,RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
- if (startx > oldendx)\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- else\r
- drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0,0,imgWidth,imgHeight);\r
\r
+ chunkWidth = getWrappedCanvasWidth( getWidth() );\r
+ chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
\r
- oldstartx = startx;\r
- oldendx = endx;\r
+ av.setChunkHeight(chunkHeight);\r
+ av.setChunkWidth(chunkWidth);\r
\r
- } else if (oldstartx > startx)\r
- {\r
- // Horizontal scrollbar pulled to the left\r
\r
- int delx = (int)((oldstartx - startx) * charWidth);\r
- int delx2 = (int)((endx - oldstartx +1) * charWidth);\r
+ if (av.getWrapAlignment())\r
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
+ else\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
\r
- gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);\r
+ g.drawImage(img, 0, 0, this);\r
\r
- if (oldstartx > endx) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0);\r
- }\r
+ }\r
\r
- oldstartx = startx;\r
- oldendx = endx;\r
+ int LABEL_WEST, LABEL_EAST;\r
+ public int getWrappedCanvasWidth(int cwidth)\r
+ {\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- } else if (oldstarty < starty) {\r
- // Vertical scrollbar down\r
- int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely);\r
+ if(av.scaleRightWrapped)\r
+ LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
\r
- if (starty > oldendy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0);\r
- }\r
+ if(av.scaleLeftWrapped)\r
+ LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );\r
\r
- oldstarty = starty;\r
- oldendy = endy;\r
+ return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+ }\r
\r
- } else if (oldstarty > starty) {\r
+ public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+ {\r
+ AlignmentI al = av.getAlignment();\r
\r
- // Vertical scrollbar up\r
- int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);\r
+ int LABEL_EAST = 0;\r
+ if(av.scaleRightWrapped)\r
+ LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );\r
+ int LABEL_WEST = 0;\r
+ if(av.scaleLeftWrapped)\r
+ LABEL_WEST = fm.stringWidth(al.getWidth()+"0");\r
\r
- if (oldstarty > endy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);\r
- }\r
\r
- oldstarty = starty;\r
- oldendy = endy;\r
- }\r
+ int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+ int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
\r
- if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {\r
- System.out.println("LIMITS ERROR LIMITS ERROR");\r
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
- }\r
+ int endx = startRes+cWidth-1;\r
+ int ypos = 2*av.charHeight;\r
\r
+ while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )\r
+ {\r
+ g.setColor(Color.black);\r
\r
- // gg.setColor(Color.red);\r
- // gg.drawRect( groupX, groupY, groupendX-groupX, groupendY-groupY );\r
- // gg.drawRect( groupX+1, groupY+1, groupendX-groupX-2, groupendY-groupY-2 );\r
+ if(av.scaleLeftWrapped)\r
+ drawWestScale(g, startRes, endx, ypos);\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.drawImage(img,0,0,this);\r
+ g.translate(LABEL_WEST,0);\r
+ if(av.scaleAboveWrapped)\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
+ if(clip==null)\r
+ g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);\r
+ else\r
+ g.setClip(0,\r
+ (int)clip.getBounds().getY(),\r
+ cWidth*av.charWidth,\r
+ (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
+ endx = al.getWidth();\r
+ }\r
\r
}\r
\r
\r
+ synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
\r
-\r
- public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
-\r
-/*\r
- System.out.println("drawPanel called with g = " + g);\r
- System.out.println(" x1 = " + x1);\r
- System.out.println(" x2 = " + x2);\r
- System.out.println(" y1 = " + y1);\r
- System.out.println(" y2 = " + y2);\r
- System.out.println(" startx = " + startx);\r
- System.out.println(" starty = " + starty);\r
-*/\r
-\r
+ Graphics2D g = (Graphics2D)g1;\r
g.setFont(av.getFont());\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
- RendererI sr = av.getRenderer();\r
+ sr.renderGaps(av.renderGaps);\r
+\r
\r
+ SequenceI nextSeq;\r
\r
- /*Vector pid = av.getConsensus(false);\r
- Vector tmpseq = new Vector();\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
- tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
+ for (int i = y1 ; i < y2 ;i++)\r
+ {\r
+ nextSeq = av.alignment.getSequenceAt(i);\r
\r
- if (sr instanceof SequenceRenderer)\r
- pid = AAFrequency.calculate(tmpseq,x1,x2);\r
+ sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,\r
+ (x1 - startx) * av.charWidth,\r
+ offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
+ av.charWidth,av.charHeight);\r
\r
- else if (sr instanceof GraphRenderer)\r
- pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
- av.getAlignment().getSequences(),\r
- av.getPIDWindow(),x1,x2);\r
+ if(av.showSequenceFeatures)\r
+ {\r
+ fr.drawSequence(g, nextSeq, 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
+ //\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
\r
- if (y2 > starty && y1 < av.getEndSeq())\r
+ int sx = -1, sy = -1, ex = -1;\r
+ int groupIndex = -1;\r
+ if (group == null && groups.size() > 0)\r
{\r
- fillBackground(g,\r
- Color.WHITE,\r
- (int)((x1-startx)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),\r
- (int)((x2-x1+1)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));\r
+ group = (SequenceGroup) groups.elementAt(0);\r
+ groupIndex = 0;\r
}\r
\r
- SequenceI nextSeq;\r
- SequenceGroup group;\r
- for (int i = y1 ; i < y2 ;i++)\r
- {\r
- /* if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
- r = fr;\r
- System.out.println("use feature renderer");\r
- } else if ( i == 0) {\r
- // r = br;\r
- } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
- r = cgr;\r
- System.out.println("cg renderer");\r
- }\r
-*/\r
- nextSeq = av.getAlignment().getSequenceAt(i);\r
- group = av.alignment.findGroup( nextSeq );\r
- if( group!=null )\r
- {\r
- sr.drawSequence(g, group.cs, nextSeq,\r
- x1,\r
- x2,\r
- (int) ( (x1 - startx) * charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth, charHeight,\r
- false, group.getDisplayBoxes(), group.getDisplayText(), group.getColourText(),\r
- null, i);\r
- }\r
- else\r
- {\r
- sr.drawSequence(g, cs, nextSeq,\r
- x1,\r
- x2,\r
- (int) ( (x1 - startx) * charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),\r
- charWidth,charHeight,\r
- showScores, av.getShowBoxes(), av.getShowText(), av.getColourText(),\r
- null, i);\r
+ if (group != null)\r
+ do\r
+ {\r
+ int oldY = -1;\r
+ int i = 0;\r
+ boolean inGroup = false;\r
+ int top=-1, bottom =-1;\r
+ for (i = y1; i < y2; i++)\r
+ {\r
+ sx = (group.getStartRes() - startx) * av.charWidth;\r
+ sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
+ ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;\r
+\r
+ if (sx < getWidth()\r
+ && ex > 0\r
+ && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
+ {\r
+ if (bottom == -1 &&\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))\r
+ bottom = sy + av.charHeight ;\r
+\r
+ if (!inGroup)\r
+ {\r
+ if (top == -1 && i==0 ||\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
+ top = sy;\r
+\r
+\r
+ oldY = sy;\r
+ inGroup = true;\r
+ if (group == av.getSelectionGroup())\r
+ {\r
+ g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, 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
+ if (bottom != -1)\r
+ {\r
+ g.drawLine(sx, bottom, sx + ex, bottom);\r
+ bottom = -1;\r
+ }\r
+\r
+\r
+ inGroup = false;\r
+ }\r
+ }\r
+ }\r
\r
- }\r
+ if (inGroup)\r
+ {\r
\r
+ if(top!=-1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top =-1;\r
+ }\r
+ if(bottom!=-1)\r
+ {\r
+ g.drawLine(sx, bottom-1, sx + ex, bottom-1);\r
+ bottom = -1;\r
+\r
+ }\r
+ sy = offset + 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
+ groupIndex++;\r
+ if (groupIndex >= groups.size())\r
+ break;\r
\r
- }\r
+ group = (SequenceGroup) groups.elementAt(groupIndex);\r
+\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
int searchStart = searchResults[r+1];\r
int searchEnd = searchResults[r+2];\r
\r
- if (searchSeq >= y1 && searchSeq <= y2)\r
+ if (searchSeq >= y1 && searchSeq < y2)\r
{\r
SequenceRenderer ssr = (SequenceRenderer) sr;\r
- ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),\r
+ if(searchStart<x1)\r
+ searchStart = x1;\r
+ if(searchEnd > x2)\r
+ searchEnd = x2;\r
+ ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
searchStart,\r
searchEnd,\r
- (int) ( (searchStart - startx) * charWidth),\r
+ (searchStart - startx) * av.charWidth,\r
offset +\r
AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- charHeight),\r
- (int) charWidth,\r
- charHeight);\r
-\r
+ av.charHeight),\r
+ av.charWidth,\r
+ av.charHeight);\r
}\r
}\r
}\r
\r
-\r
}\r
\r
- // public int groupX, groupY, groupendX, groupendY;\r
\r
- public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {\r
- g.setColor(c);\r
- g.fillRect(x1,y1,width,height);\r
- }\r
-\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
\r
public void highlightSearchResults(int [] results)\r
{\r
// results are in the order sequence, startRes, endRes\r
+ if(results==null)\r
+ displaySearch = false;\r
+ else\r
+ displaySearch = true;\r
+\r
searchResults = results;\r
- displaySearch = true;\r
- paintFlag = true;\r
+\r
repaint();\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff