+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+\r
package jalview.appletgui;\r
\r
import java.awt.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
\r
+import jalview.datamodel.*;\r
\r
-public class SeqCanvas extends Panel\r
+public class SeqCanvas\r
+ extends Panel\r
{\r
- FeatureRenderer fr;\r
- SequenceRenderer sr;\r
- Image img;\r
- Graphics gg;\r
- int imgWidth;\r
- int imgHeight;\r
+ FeatureRenderer fr;\r
+ SequenceRenderer sr;\r
+ Image img;\r
+ Graphics gg;\r
+ int imgWidth;\r
+ int imgHeight;\r
\r
- AlignViewport av;\r
+ AlignViewport av;\r
\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
+ SearchResults searchResults = null;\r
\r
- int chunkHeight;\r
- int chunkWidth;\r
+ boolean fastPaint = false;\r
\r
- boolean fastPaint = false;\r
\r
+ int cursorX = 0;\r
+ int cursorY = 0;\r
\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- PaintRefresher.Register(this);\r
\r
- }\r
+ public SeqCanvas(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ fr = new FeatureRenderer(av);\r
+ sr = new SequenceRenderer(av);\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ MCview.AppletPDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.AppletPDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
\r
- void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\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
// 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
+ int value = i;\r
+ if(av.hasHiddenColumns)\r
+ value = av.getColumnSelection().adjustForHiddenColumns(value);\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 - 2);\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
+ (ypos + 2) - (av.charHeight / 2),\r
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ypos -\r
+ 2);\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
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ ypos += av.charHeight;\r
+ if (av.hasHiddenColumns)\r
{\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = startx;\r
- int value = -1;\r
- while (index < endx)\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
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+\r
+ // WEST SCALE\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ SequenceI seq = av.alignment.getSequenceAt(i);\r
+ int index = startx;\r
+ int value = -1;\r
+\r
+ while (index < endx)\r
{\r
- index++;\r
- continue;\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
+\r
+ break;\r
}\r
\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
+ 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
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
+ ypos += av.charHeight;\r
\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
+ if(av.hasHiddenColumns)\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
+ seq = av.alignment.getSequenceAt(i);\r
+ int index = endx;\r
+ int value = -1;\r
\r
+ while (index > startx)\r
+ {\r
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
+ {\r
+ index--;\r
\r
+ continue;\r
+ }\r
\r
-public void fastPaint(int horizontal, int vertical)\r
-{\r
- if (horizontal == 0 && vertical == 0 || gg==null)\r
+ value = seq.findPosition(index);\r
+\r
+ break;\r
+ }\r
+\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
+ int lastsr=0;\r
+ void fastPaint(int horizontal, int vertical)\r
+ {\r
+ if ( fastPaint || gg == null)\r
+ {\r
return;\r
+ }\r
+\r
+\r
+ // Its possible on certain browsers that the call to fastpaint\r
+ // is faster than it can paint, so this check here catches\r
+ // this possibility\r
+ if(lastsr + horizontal != av.startRes)\r
+ {\r
+ horizontal = av.startRes - lastsr;\r
+ }\r
+\r
+ lastsr = av.startRes;\r
\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
+ fastPaint = true;\r
+ gg.copyArea(horizontal * av.charWidth,\r
+ vertical * av.charHeight,\r
+ imgWidth - horizontal * av.charWidth,\r
+ imgHeight - vertical * av.charHeight,\r
+ -horizontal * av.charWidth,\r
-vertical * av.charHeight);\r
\r
+\r
+\r
int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
transX = 0, 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
\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
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time\r
+ {\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(es > av.endSeq)\r
+ if (es > av.endSeq)\r
+ {\r
es = av.endSeq;\r
+ }\r
}\r
\r
-\r
gg.translate(transX, transY);\r
\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
+ drawPanel(gg, sr, er, ss, es, 0);\r
gg.translate( -transX, -transY);\r
\r
- fastPaint = true;\r
repaint();\r
\r
-}\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
+ * 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
public void update(Graphics g)\r
{\r
paint(g);\r
\r
public void paint(Graphics g)\r
{\r
+\r
+ if (img != null && (fastPaint\r
+ || (getSize().width != g.getClipBounds().width)\r
+ || (getSize().height != g.getClipBounds().height)))\r
+ {\r
+ g.drawImage(img, 0, 0, this);\r
+ fastPaint = false;\r
+ return;\r
+ }\r
+\r
if (fastPaint)\r
{\r
g.drawImage(img, 0, 0, this);\r
}\r
\r
// this draws the whole of the alignment\r
- imgWidth = this.getSize().width;\r
- imgHeight = this.getSize().height;\r
- if(imgWidth<1 || imgHeight<1)\r
- return;\r
-\r
- imgWidth -= imgWidth%av.charWidth;\r
- imgHeight-= imgHeight%av.charHeight;\r
+ imgWidth = this.getSize().width;\r
+ imgHeight = this.getSize().height;\r
\r
- if(img==null || imgWidth!=img.getWidth(this) || imgHeight!=img.getHeight(this))\r
- {\r
- img = createImage(imgWidth, imgHeight);\r
- gg = img.getGraphics();\r
- gg.setFont(av.getFont());\r
- }\r
+ imgWidth -= imgWidth % av.charWidth;\r
+ imgHeight -= imgHeight % av.charHeight;\r
\r
- gg.setColor(Color.white);\r
- gg.fillRect(0,0,imgWidth,imgHeight);\r
+ if (imgWidth < 1 || imgHeight < 1)\r
+ {\r
+ return;\r
+ }\r
\r
- chunkWidth = getWrappedCanvasWidth( getSize().width );\r
- chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
+ if (img == null || imgWidth != img.getWidth(this) ||\r
+ imgHeight != img.getHeight(this))\r
+ {\r
+ img = createImage(imgWidth, imgHeight);\r
+ gg = img.getGraphics();\r
+ gg.setFont(av.getFont());\r
+ }\r
\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
+ gg.setColor(Color.white);\r
+ gg.fillRect(0, 0, imgWidth, imgHeight);\r
\r
\r
if (av.getWrapAlignment())\r
- drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);\r
+ {\r
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
+ }\r
else\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
+ {\r
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
+ }\r
\r
g.drawImage(img, 0, 0, this);\r
\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
}\r
\r
int LABEL_WEST, LABEL_EAST;\r
public int getWrappedCanvasWidth(int cwidth)\r
{\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ cwidth -= cwidth % av.charWidth;\r
\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
\r
- if(av.scaleRightWrapped)\r
- LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
+ LABEL_EAST = 0;\r
+ LABEL_WEST = 0;\r
\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );\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
- return (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
}\r
\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)\r
+\r
+ /**\r
+ * Generates a string of zeroes.\r
+ * @return String\r
+ */\r
+ String getMask()\r
{\r
- AlignmentI al = av.getAlignment();\r
+ String mask = "0";\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
+ maxWidth = tmp;\r
+ }\r
\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
+ for (int i = maxWidth; i > 0; i /= 10)\r
+ {\r
+ mask += "0";\r
+ }\r
+ return mask;\r
+ }\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
+\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
+ hgap += av.charHeight;\r
+\r
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
\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
+ av.setWrappedWidth(cWidth);\r
\r
+ av.endRes = av.startRes + cWidth;\r
\r
- int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\r
\r
- av.endRes = av.startRes + cWidth;\r
+ int endx;\r
+ int ypos = hgap;\r
\r
- int endx = startRes+cWidth-1;\r
- int ypos = 2*av.charHeight;\r
+ int maxwidth = av.alignment.getWidth();\r
\r
- while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )\r
+ if(av.hasHiddenColumns)\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth)-1;\r
+\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.setColor(Color.black);\r
\r
- if(av.scaleLeftWrapped)\r
- drawWestScale(g, startRes, endx, ypos);\r
+ if (av.scaleLeftWrapped)\r
+ {\r
+ drawWestScale(g, startRes, endx, ypos);\r
+ }\r
\r
- if(av.scaleRightWrapped)\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
+ g.translate(canvasWidth - LABEL_EAST, 0);\r
+ drawEastScale(g, startRes, endx, ypos);\r
+ g.translate(-(canvasWidth - LABEL_EAST), 0);\r
}\r
\r
- g.translate(LABEL_WEST,0);\r
- if(av.scaleAboveWrapped)\r
+ g.translate(LABEL_WEST, 0);\r
+\r
+ if (av.scaleAboveWrapped)\r
+ {\r
drawNorthScale(g, startRes, endx, ypos);\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
+\r
+ }\r
+ }\r
\r
+ if(g.getClip()==null)\r
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\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().y,\r
- cWidth*av.charWidth,\r
- (int)clip.getBounds().height\r
- );\r
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
+ g.setClip(null);\r
+\r
+\r
+ if(av.showAnnotation)\r
+ {\r
+ g.translate(0, cHeight + ypos+4);\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
+\r
+ annotations.drawComponent( g, startRes, endx+1 );\r
+ g.translate(0, -cHeight - ypos-4);\r
+ }\r
+ g.translate(-LABEL_WEST, 0);\r
+\r
+ ypos += cHeight+getAnnotationHeight()+hgap;\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
\r
- if (endx > al.getWidth())\r
- endx = al.getWidth();\r
+ }\r
+\r
+ AnnotationPanel annotations;\r
+ int getAnnotationHeight()\r
+ {\r
+ if(!av.showAnnotation)\r
+ return 0;\r
+\r
+ if(annotations==null)\r
+ annotations = new AnnotationPanel(av);\r
+\r
+ return annotations.adjustPanelHeight();\r
+ }\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
- }\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
- synchronized public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
+ if (hideStart <= blockStart)\r
+ {\r
+ blockStart += (hideEnd - hideStart) + 1;\r
+ continue;\r
+ }\r
\r
- g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
+ blockEnd = hideStart - 1;\r
\r
- SequenceI nextSeq;\r
+ g1.translate(screenY * av.charWidth, 0);\r
\r
- /// First draw the sequences\r
- /////////////////////////////\r
- for (int i = y1 ; i < y2 ;i++)\r
- {\r
- nextSeq = av.alignment.getSequenceAt(i);\r
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
\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
+ if(av.getShowHiddenMarkers())\r
+ {\r
+ g1.setColor(Color.blue);\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
- 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
+ g1.translate( -screenY * av.charWidth, 0);\r
+ screenY += blockEnd - blockStart + 1;\r
+ blockStart = hideEnd + 1;\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 (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
- int sx = -1, sy = -1, ex = -1;\r
- int groupIndex = -1;\r
- if (group == null && groups.size() > 0)\r
- {\r
- group = (SequenceGroup) groups.elementAt(0);\r
- groupIndex = 0;\r
}\r
\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
+\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
+ SequenceI nextSeq;\r
+\r
+ /// First draw the sequences\r
+ /////////////////////////////\r
+ for (int i = startSeq; i < endSeq; 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
+ nextSeq = av.alignment.getSequenceAt(i);\r
\r
- if (sx < getSize().width\r
- && ex > 0\r
- && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- if (bottom == -1 && (i==av.alignment.getHeight()-1 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i + 1))))\r
- bottom = sy + av.charHeight ;\r
+ sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),\r
+ startRes, endRes,\r
+ offset + ( (i - startSeq) * av.charHeight));\r
\r
- if (!inGroup)\r
+ if (av.showSequenceFeatures)\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.setColor(new Color(255,0,0));\r
- }\r
- else\r
- {\r
- g.setColor(group.getOutlineColour());\r
- }\r
+ fr.drawSequence(g, nextSeq, startRes, endRes,\r
+ offset + ((i - startSeq) * av.charHeight));\r
}\r
- }\r
- else\r
- {\r
- if (inGroup)\r
+\r
+ /// Highlight search Results once all sequences have been drawn\r
+ //////////////////////////////////////////////////////////\r
+ if (searchResults != null)\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
+ 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
+\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
\r
- if (inGroup)\r
- {\r
+ if(av.getSelectionGroup()!=null || av.alignment.getGroups().size()>0)\r
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
\r
- if(top!=-1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
- }\r
- if(bottom!=-1)\r
+ }\r
+\r
+ void drawGroupsBoundaries(Graphics g,\r
+ int startRes, int endRes,\r
+ int startSeq, int endSeq,\r
+ int offset)\r
+ {\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
+\r
+ if ( (group == null) && (av.alignment.getGroups().size() > 0))\r
+ {\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
+ groupIndex = 0;\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
+ int alHeight = av.alignment.getHeight()-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 > imgWidth)\r
{\r
- g.drawLine(sx, bottom-1, sx + ex, bottom-1);\r
- bottom = -1;\r
+ continue;\r
+ }\r
\r
+ if ( (sx <= (endRes - startRes) * av.charWidth) &&\r
+ group.getSequences(false).\r
+ contains(av.alignment.getSequenceAt(i)))\r
+ {\r
+ if ( (bottom == -1) &&\r
+ (i >= alHeight ||\r
+ !group.getSequences(false).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(false).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.setColor(Color.red);\r
+ }\r
+ else\r
+ {\r
+ g.setColor(group.getOutlineColour());\r
+ }\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
+ else\r
+ {\r
+ if (inGroup)\r
+ {\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
+\r
+ if (sx + ex < imgWidth)\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 > imgWidth)\r
+ ex = imgWidth;\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
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ if (inGroup)\r
+ {\r
+ sy = offset + ( (i - startSeq) * av.charHeight);\r
+ if (sx >= 0 && sx < imgWidth)\r
+ g.drawLine(sx, oldY, sx, sy);\r
\r
- }\r
- while (groupIndex < groups.size());\r
+ if (sx + ex < imgWidth)\r
+ g.drawLine(sx + ex, oldY, sx + ex, sy);\r
\r
+ if (sx < 0)\r
+ {\r
+ ex += sx;\r
+ sx = 0;\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 (sx + ex > imgWidth)\r
+ ex = imgWidth;\r
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)\r
+ ex = (endRes - startRes + 1) * av.charWidth;\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
- if(searchStart<x1)\r
- searchStart = x1;\r
- if(searchEnd > x2)\r
- searchEnd = x2;\r
-\r
- ssr.drawHighlightedText(seq,\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- av.charHeight),\r
- av.charWidth,\r
- av.charHeight);\r
- }\r
- }\r
- }\r
+ if (top != -1)\r
+ {\r
+ g.drawLine(sx, top, sx + ex, top);\r
+ top = -1;\r
+ }\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
\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
+ if (groupIndex >= av.alignment.getGroups().size())\r
+ {\r
+ break;\r
+ }\r
\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
+ }\r
+ while (groupIndex < av.alignment.getGroups().size());\r
+\r
+ }\r
+ }\r
+\r
+ public void highlightSearchResults(SearchResults results)\r
+ {\r
searchResults = results;\r
\r
repaint();\r
}\r
\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff