-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)\r
- * Copyright (C) 2014 The Jalview Authors\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3\r
- * of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- * The Jalview Authors are detailed in the 'AUTHORS' file.\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.SearchResults;\r
-import jalview.datamodel.SequenceGroup;\r
-import jalview.datamodel.SequenceI;\r
-\r
-import java.awt.Color;\r
-import java.awt.FontMetrics;\r
-import java.awt.Graphics;\r
-import java.awt.Image;\r
-import java.awt.Panel;\r
-\r
-public class SeqCanvas extends Panel\r
-{\r
- FeatureRenderer fr;\r
-\r
- SequenceRenderer sr;\r
-\r
- Image img;\r
-\r
- Graphics gg;\r
-\r
- int imgWidth;\r
-\r
- int imgHeight;\r
-\r
- AlignViewport av;\r
-\r
- SearchResults searchResults = null;\r
-\r
- boolean fastPaint = false;\r
-\r
- int cursorX = 0;\r
-\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, 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
- public SequenceRenderer getSequenceRenderer()\r
- {\r
- return sr;\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
- {\r
- int value = i;\r
- if (av.hasHiddenColumns())\r
- {\r
- value = av.getColumnSelection().adjustForHiddenColumns(value);\r
- }\r
-\r
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,\r
- ypos - (av.charHeight / 2));\r
-\r
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
- (ypos + 2) - (av.charHeight / 2),\r
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),\r
- ypos - 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
- if (av.hasHiddenColumns())\r
- {\r
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);\r
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
- }\r
-\r
- int maxwidth = av.getAlignment().getWidth();\r
- if (av.hasHiddenColumns())\r
- {\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
- }\r
-\r
- // WEST SCALE\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- SequenceI seq = av.getAlignment().getSequenceAt(i);\r
- int index = startx;\r
- int value = -1;\r
-\r
- while (index < endx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index++;\r
-\r
- continue;\r
- }\r
-\r
- value = av.getAlignment().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, (ypos + (i * av.charHeight))\r
- - (av.charHeight / 5));\r
- }\r
- }\r
- }\r
-\r
- void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
- {\r
- ypos += av.charHeight;\r
-\r
- if (av.hasHiddenColumns())\r
- {\r
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);\r
- }\r
-\r
- SequenceI seq;\r
- // EAST SCALE\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- {\r
- seq = av.getAlignment().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
- value = seq.findPosition(index);\r
-\r
- break;\r
- }\r
-\r
- if (value != -1)\r
- {\r
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))\r
- - (av.charHeight / 5));\r
- }\r
- }\r
- }\r
-\r
- int lastsr = 0;\r
-\r
- void fastPaint(int horizontal, int vertical)\r
- {\r
- if (fastPaint || gg == null)\r
- {\r
- return;\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
- fastPaint = true;\r
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,\r
- imgWidth - horizontal * av.charWidth, imgHeight - vertical\r
- * av.charHeight, -horizontal * av.charWidth, -vertical\r
- * av.charHeight);\r
-\r
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, 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
- {\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
- {\r
- es = av.endSeq;\r
- }\r
- }\r
-\r
- gg.translate(transX, transY);\r
-\r
- drawPanel(gg, sr, er, ss, es, 0);\r
- gg.translate(-transX, -transY);\r
-\r
- repaint();\r
-\r
- }\r
-\r
- /**\r
- * Definitions of startx and endx (hopefully): SMJS This is what I'm working\r
- * towards! startx is the first residue (starting at 0) to display. endx is\r
- * the last residue to display (starting at 0). starty is the first sequence\r
- * to display (starting at 0). endy is the last sequence to display (starting\r
- * at 0). NOTE 1: The av limits are set in setFont in this class and in the\r
- * adjustment listener in SeqPanel when the scrollbars move.\r
- */\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
-\r
- if (img != null\r
- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g\r
- .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
- fastPaint = false;\r
- return;\r
- }\r
-\r
- // this draws the whole of the alignment\r
- imgWidth = this.getSize().width;\r
- imgHeight = this.getSize().height;\r
-\r
- imgWidth -= imgWidth % av.charWidth;\r
- imgHeight -= imgHeight % av.charHeight;\r
-\r
- if (imgWidth < 1 || imgHeight < 1)\r
- {\r
- return;\r
- }\r
-\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
- gg.setColor(Color.white);\r
- gg.fillRect(0, 0, imgWidth, imgHeight);\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);\r
- }\r
- else\r
- {\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);\r
- }\r
-\r
- g.drawImage(img, 0, 0, this);\r
-\r
- }\r
-\r
- int LABEL_WEST, LABEL_EAST;\r
-\r
- public int getWrappedCanvasWidth(int cwidth)\r
- {\r
- cwidth -= cwidth % av.charWidth;\r
-\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\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
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- }\r
-\r
- /**\r
- * Generates a string of zeroes.\r
- * \r
- * @return String\r
- */\r
- String getMask()\r
- {\r
- String mask = "0";\r
- int maxWidth = 0;\r
- int tmp;\r
- AlignmentI alignment = av.getAlignment();\r
- for (int i = 0; i < alignment.getHeight(); i++)\r
- {\r
- tmp = alignment.getSequenceAt(i).getEnd();\r
- if (tmp > maxWidth)\r
- {\r
- maxWidth = tmp;\r
- }\r
- }\r
-\r
- for (int i = maxWidth; i > 0; i /= 10)\r
- {\r
- mask += "0";\r
- }\r
- return mask;\r
- }\r
-\r
- public void drawWrappedPanel(Graphics g, int canvasWidth,\r
- int canvasHeight, 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
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight;\r
-\r
- av.setWrappedWidth(cWidth);\r
-\r
- av.endRes = av.startRes + cWidth;\r
-\r
- int endx;\r
- int ypos = hgap;\r
-\r
- int maxwidth = av.getAlignment().getWidth() - 1;\r
-\r
- if (av.hasHiddenColumns())\r
- {\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
- }\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
- {\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
- 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()\r
- .size(); i++)\r
- {\r
- res = av.getColumnSelection().findHiddenRegionPosition(i)\r
- - startRes;\r
-\r
- if (res < 0 || res > endx - startRes)\r
- {\r
- continue;\r
- }\r
-\r
- gg.fillPolygon(new int[]\r
- { res * av.charWidth - av.charHeight / 4,\r
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },\r
- new int[]\r
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),\r
- ypos - (av.charHeight / 2) + 8 }, 3);\r
-\r
- }\r
- }\r
-\r
- if (g.getClip() == null)\r
- {\r
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);\r
- }\r
-\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);\r
- g.setClip(null);\r
-\r
- if (av.showAnnotation)\r
- {\r
- g.translate(0, cHeight + ypos + 4);\r
- if (annotations == null)\r
- {\r
- annotations = new AnnotationPanel(av);\r
- }\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
- startRes += cWidth;\r
- }\r
-\r
- }\r
-\r
- AnnotationPanel annotations;\r
-\r
- int getAnnotationHeight()\r
- {\r
- if (!av.showAnnotation)\r
- {\r
- return 0;\r
- }\r
-\r
- if (annotations == null)\r
- {\r
- annotations = new AnnotationPanel(av);\r
- }\r
-\r
- return annotations.adjustPanelHeight();\r
- }\r
-\r
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,\r
- int endSeq, int offset)\r
- {\r
-\r
-\r
- if (!av.hasHiddenColumns())\r
- {\r
- draw(g1, startRes, endRes, startSeq, endSeq, offset);\r
- }\r
- else\r
- {\r
-\r
- int screenY = 0;\r
- int blockStart = startRes;\r
- int blockEnd = endRes;\r
-\r
- if (av.hasHiddenColumns())\r
- {\r
- for (int[] region : av.getColumnSelection().getHiddenColumns())\r
- {\r
- int hideStart = region[0];\r
- int hideEnd = region[1];\r
-\r
- if (hideStart <= blockStart)\r
- {\r
- blockStart += (hideEnd - hideStart) + 1;\r
- continue;\r
- }\r
-\r
- blockEnd = hideStart - 1;\r
-\r
- g1.translate(screenY * av.charWidth, 0);\r
-\r
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
-\r
- if (av.getShowHiddenMarkers())\r
- {\r
- g1.setColor(Color.blue);\r
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,\r
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth\r
- - 1, (endSeq - startSeq) * av.charHeight\r
- + offset);\r
- }\r
-\r
- g1.translate(-screenY * av.charWidth, 0);\r
- screenY += blockEnd - blockStart + 1;\r
- blockStart = hideEnd + 1;\r
- }\r
- }\r
- if (screenY <= (endRes - startRes))\r
- {\r
- blockEnd = blockStart + (endRes - startRes) - screenY;\r
- g1.translate(screenY * av.charWidth, 0);\r
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);\r
-\r
- g1.translate(-screenY * av.charWidth, 0);\r
- }\r
- }\r
-\r
- }\r
-\r
- // 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, int startRes, int endRes, 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
- nextSeq = av.getAlignment().getSequenceAt(i);\r
-\r
- if (nextSeq == null)\r
- {\r
- continue;\r
- }\r
-\r
- sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),\r
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));\r
-\r
- if (av.isShowSequenceFeatures())\r
- {\r
- fr.drawSequence(g, nextSeq, startRes, endRes, offset\r
- + ((i - startSeq) * av.charHeight));\r
- }\r
-\r
- // / Highlight search Results once all sequences have been drawn\r
- // ////////////////////////////////////////////////////////\r
- if (searchResults != null)\r
- {\r
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,\r
- endRes);\r
- if (visibleResults != null)\r
- {\r
- for (int r = 0; r < visibleResults.length; r += 2)\r
- {\r
- sr.drawHighlightedText(nextSeq, visibleResults[r],\r
- visibleResults[r + 1], (visibleResults[r] - startRes)\r
- * av.charWidth, offset\r
- + ((i - startSeq) * av.charHeight));\r
- }\r
- }\r
- }\r
-\r
- if (av.cursorMode && cursorY == i && cursorX >= startRes\r
- && cursorX <= endRes)\r
- {\r
- sr.drawCursor(nextSeq, cursorX,\r
- (cursorX - startRes) * av.charWidth, offset\r
- + ((i - startSeq) * av.charHeight));\r
- }\r
- }\r
-\r
- if (av.getSelectionGroup() != null\r
- || av.getAlignment().getGroups().size() > 0)\r
- {\r
- drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);\r
- }\r
-\r
- }\r
-\r
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,\r
- int startSeq, int endSeq, 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.getAlignment().getGroups().size() > 0))\r
- {\r
- group = av.getAlignment().getGroups().get(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.getAlignment().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) - 1;\r
-\r
- if (sx + ex < 0 || sx > imgWidth)\r
- {\r
- continue;\r
- }\r
-\r
- if ((sx <= (endRes - startRes) * av.charWidth)\r
- && group.getSequences(null).contains(\r
- av.getAlignment().getSequenceAt(i)))\r
- {\r
- if ((bottom == -1)\r
- && (i >= alHeight || !group.getSequences(null)\r
- .contains(\r
- av.getAlignment().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.getAlignment().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
- else\r
- {\r
- if (inGroup)\r
- {\r
- if (sx >= 0 && sx < imgWidth)\r
- {\r
- g.drawLine(sx, oldY, sx, sy);\r
- }\r
-\r
- if (sx + ex < imgWidth)\r
- {\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
- }\r
-\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
-\r
- if (sx + ex > imgWidth)\r
- {\r
- ex = imgWidth;\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
- 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 < imgWidth)\r
- {\r
- g.drawLine(sx, oldY, sx, sy);\r
- }\r
-\r
- if (sx + ex < imgWidth)\r
- {\r
- g.drawLine(sx + ex, oldY, sx + ex, sy);\r
- }\r
-\r
- if (sx < 0)\r
- {\r
- ex += sx;\r
- sx = 0;\r
- }\r
-\r
- if (sx + ex > imgWidth)\r
- {\r
- ex = imgWidth;\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 (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
- if (groupIndex >= av.getAlignment().getGroups().size())\r
- {\r
- break;\r
- }\r
-\r
- group = av.getAlignment().getGroups()\r
- .get(groupIndex);\r
- } while (groupIndex < av.getAlignment().getGroups().size());\r
-\r
- }\r
- }\r
-\r
- public void highlightSearchResults(SearchResults results)\r
- {\r
- searchResults = results;\r
-\r
- repaint();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+
+public class SeqCanvas extends Panel
+{
+ FeatureRenderer fr;
+
+ SequenceRenderer sr;
+
+ Image img;
+
+ Graphics gg;
+
+ int imgWidth;
+
+ int imgHeight;
+
+ AlignViewport av;
+
+ SearchResults searchResults = null;
+
+ boolean fastPaint = false;
+
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ public SeqCanvas(AlignViewport av)
+ {
+ this.av = av;
+ fr = new FeatureRenderer(av);
+ sr = new SequenceRenderer(av);
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ }
+
+ public AlignViewport getViewport()
+ {
+ return av;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return fr;
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return sr;
+ }
+
+ void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ {
+ int scalestartx = startx - startx % 10 + 10;
+
+ g.setColor(Color.black);
+
+ // NORTH SCALE
+ for (int i = scalestartx; i < endx; i += 10)
+ {
+ int value = i;
+ if (av.hasHiddenColumns())
+ {
+ value = av.getColumnSelection().adjustForHiddenColumns(value);
+ }
+
+ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
+ ypos - (av.charHeight / 2));
+
+ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ (ypos + 2) - (av.charHeight / 2),
+ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ ypos - 2);
+ }
+ }
+
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += av.charHeight;
+ if (av.hasHiddenColumns())
+ {
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ // WEST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
+ int index = startx;
+ int value = -1;
+
+ while (index < endx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index++;
+
+ continue;
+ }
+
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+ - av.charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * av.charHeight))
+ - (av.charHeight / 5));
+ }
+ }
+ }
+
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += av.charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ int index = endx;
+ int value = -1;
+
+ while (index > startx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index--;
+
+ continue;
+ }
+
+ value = seq.findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
+ - (av.charHeight / 5));
+ }
+ }
+ }
+
+ int lastsr = 0;
+
+ void fastPaint(int horizontal, int vertical)
+ {
+ if (fastPaint || gg == null)
+ {
+ return;
+ }
+
+ // Its possible on certain browsers that the call to fastpaint
+ // is faster than it can paint, so this check here catches
+ // this possibility
+ if (lastsr + horizontal != av.startRes)
+ {
+ horizontal = av.startRes - lastsr;
+ }
+
+ lastsr = av.startRes;
+
+ fastPaint = true;
+ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
+ imgWidth - horizontal * av.charWidth, imgHeight - vertical
+ * av.charHeight, -horizontal * av.charWidth, -vertical
+ * av.charHeight);
+
+ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * av.charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+
+ else if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ {
+ ss = av.startSeq;
+ }
+ else
+ {
+ transY = imgHeight - vertical * av.charHeight;
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(transX, transY);
+
+ drawPanel(gg, sr, er, ss, es, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
+
+ }
+
+ /**
+ * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+ * towards! startx is the first residue (starting at 0) to display. endx is
+ * the last residue to display (starting at 0). starty is the first sequence
+ * to display (starting at 0). endy is the last sequence to display (starting
+ * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+ * adjustment listener in SeqPanel when the scrollbars move.
+ */
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+
+ if (img != null
+ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
+ .getClipBounds().height)))
+ {
+ g.drawImage(img, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ if (fastPaint)
+ {
+ g.drawImage(img, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ // this draws the whole of the alignment
+ imgWidth = this.getSize().width;
+ imgHeight = this.getSize().height;
+
+ imgWidth -= imgWidth % av.charWidth;
+ imgHeight -= imgHeight % av.charHeight;
+
+ if (imgWidth < 1 || imgHeight < 1)
+ {
+ return;
+ }
+
+ if (img == null || imgWidth != img.getWidth(this)
+ || imgHeight != img.getHeight(this))
+ {
+ img = createImage(imgWidth, imgHeight);
+ gg = img.getGraphics();
+ gg.setFont(av.getFont());
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, imgHeight);
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ }
+ else
+ {
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ }
+
+ g.drawImage(img, 0, 0, this);
+
+ }
+
+ int LABEL_WEST, LABEL_EAST;
+
+ public int getWrappedCanvasWidth(int cwidth)
+ {
+ cwidth -= cwidth % av.charWidth;
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.scaleRightWrapped)
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.scaleLeftWrapped)
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ }
+
+ /**
+ * Generates a string of zeroes.
+ *
+ * @return String
+ */
+ String getMask()
+ {
+ String mask = "0";
+ int maxWidth = 0;
+ int tmp;
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ tmp = alignment.getSequenceAt(i).getEnd();
+ if (tmp > maxWidth)
+ {
+ maxWidth = tmp;
+ }
+ }
+
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ mask += "0";
+ }
+ return mask;
+ }
+
+ public void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ AlignmentI al = av.getAlignment();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ if (av.scaleRightWrapped)
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.scaleLeftWrapped)
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+ av.setWrappedWidth(cWidth);
+
+ av.endRes = av.startRes + cWidth;
+
+ int endx;
+ int ypos = hgap;
+
+ int maxwidth = av.getAlignment().getWidth() - 1;
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
+ {
+ endx = startRes + cWidth - 1;
+
+ if (endx > maxwidth)
+ {
+ endx = maxwidth;
+ }
+
+ g.setColor(Color.black);
+
+ if (av.scaleLeftWrapped)
+ {
+ drawWestScale(g, startRes, endx, ypos);
+ }
+
+ if (av.scaleRightWrapped)
+ {
+ g.translate(canvasWidth - LABEL_EAST, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ if (av.scaleAboveWrapped)
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)
+ {
+ g.setColor(Color.blue);
+ int res;
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+ .size(); i++)
+ {
+ res = av.getColumnSelection().findHiddenRegionPosition(i)
+ - startRes;
+
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
+ }
+
+ gg.fillPolygon(new int[]
+ { res * av.charWidth - av.charHeight / 4,
+ res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ new int[]
+ { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
+ ypos - (av.charHeight / 2) + 8 }, 3);
+
+ }
+ }
+
+ if (g.getClip() == null)
+ {
+ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ g.setClip(null);
+
+ if (av.showAnnotation)
+ {
+ g.translate(0, cHeight + ypos + 4);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.drawComponent(g, startRes, endx + 1);
+ g.translate(0, -cHeight - ypos - 4);
+ }
+ g.translate(-LABEL_WEST, 0);
+
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ startRes += cWidth;
+ }
+
+ }
+
+ AnnotationPanel annotations;
+
+ int getAnnotationHeight()
+ {
+ if (!av.showAnnotation)
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
+ {
+
+
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ }
+ else
+ {
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ if (av.hasHiddenColumns())
+ {
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g1.translate(screenY * av.charWidth, 0);
+
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ if (av.getShowHiddenMarkers())
+ {
+ g1.setColor(Color.blue);
+ g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
+ - 1, (endSeq - startSeq) * av.charHeight
+ + offset);
+ }
+
+ g1.translate(-screenY * av.charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+ }
+ }
+ if (screenY <= (endRes - startRes))
+ {
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g1.translate(screenY * av.charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g1.translate(-screenY * av.charWidth, 0);
+ }
+ }
+
+ }
+
+ // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+ // int x1, int x2, int y1, int y2, int startx, int starty,
+ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
+ int offset)
+ {
+ g.setFont(av.getFont());
+ sr.prepare(g, av.renderGaps);
+
+ SequenceI nextSeq;
+
+ // / First draw the sequences
+ // ///////////////////////////
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ nextSeq = av.getAlignment().getSequenceAt(i);
+
+ if (nextSeq == null)
+ {
+ continue;
+ }
+
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ + ((i - startSeq) * av.charHeight));
+ }
+
+ // / Highlight search Results once all sequences have been drawn
+ // ////////////////////////////////////////////////////////
+ if (searchResults != null)
+ {
+ int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+ endRes);
+ if (visibleResults != null)
+ {
+ for (int r = 0; r < visibleResults.length; r += 2)
+ {
+ sr.drawHighlightedText(nextSeq, visibleResults[r],
+ visibleResults[r + 1], (visibleResults[r] - startRes)
+ * av.charWidth, offset
+ + ((i - startSeq) * av.charHeight));
+ }
+ }
+ }
+
+ if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
+ {
+ sr.drawCursor(nextSeq, cursorX,
+ (cursorX - startRes) * av.charWidth, offset
+ + ((i - startSeq) * av.charHeight));
+ }
+ }
+
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+ SequenceGroup group = av.getSelectionGroup();
+
+ int sx = -1;
+ int sy = -1;
+ int ex = -1;
+ int groupIndex = -1;
+
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))
+ {
+ group = av.getAlignment().getGroups().get(0);
+ groupIndex = 0;
+ }
+
+ if (group != null)
+ {
+ do
+ {
+ int oldY = -1;
+ int i = 0;
+ boolean inGroup = false;
+ int top = -1;
+ int bottom = -1;
+ int alHeight = av.getAlignment().getHeight() - 1;
+
+ for (i = startSeq; i < endSeq; i++)
+ {
+ sx = (group.getStartRes() - startRes) * av.charWidth;
+ sy = offset + ((i - startSeq) * av.charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+
+ if (sx + ex < 0 || sx > imgWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * av.charWidth)
+ && group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && (i >= alHeight || !group.getSequences(null)
+ .contains(
+ av.getAlignment().getSequenceAt(i + 1))))
+ {
+ bottom = sy + av.charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0))
+ || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i - 1)))
+ {
+ top = sy;
+ }
+
+ oldY = sy;
+ inGroup = true;
+
+ if (group == av.getSelectionGroup())
+ {
+ g.setColor(Color.red);
+ }
+ else
+ {
+ g.setColor(group.getOutlineColour());
+ }
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ if (sx >= 0 && sx < imgWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < imgWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > imgWidth)
+ {
+ ex = imgWidth;
+ }
+
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ {
+ ex = (endRes - startRes + 1) * av.charWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + ex, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom, sx + ex, bottom);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+ }
+ }
+
+ if (inGroup)
+ {
+ sy = offset + ((i - startSeq) * av.charHeight);
+ if (sx >= 0 && sx < imgWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < imgWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > imgWidth)
+ {
+ ex = imgWidth;
+ }
+ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ {
+ ex = (endRes - startRes + 1) * av.charWidth;
+ }
+
+ if (top != -1)
+ {
+ g.drawLine(sx, top, sx + ex, top);
+ top = -1;
+ }
+
+ if (bottom != -1)
+ {
+ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+ bottom = -1;
+ }
+
+ inGroup = false;
+ }
+
+ groupIndex++;
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups()
+ .get(groupIndex);
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+ }
+
+ public void highlightSearchResults(SearchResults results)
+ {
+ searchResults = results;
+
+ repaint();
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff