-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-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
-\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 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
- boolean isOverview = false;\r
-\r
- /**\r
- * Creates a new SeqCanvas object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this, av.alignment);\r
- setBackground(Color.white);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param startx DOCUMENT ME!\r
- * @param endx DOCUMENT ME!\r
- * @param ypos DOCUMENT ME!\r
- */\r
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
- {\r
- int scalestartx = startx - (startx % 10) + 10;\r
-\r
- g.setColor(Color.black);\r
-\r
- // NORTH SCALE\r
- for (int i = scalestartx; i < endx; i += 10)\r
- {\r
- 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
- FontMetrics fm = getFontMetrics(av.getFont());\r
- ypos += av.charHeight;\r
-\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
-\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.alignment.getSequenceAt(i).findPosition(index);\r
-\r
- break;\r
- }\r
-\r
- if (value != -1)\r
- {\r
- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;\r
- g.drawString(value + "", x,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param startx DOCUMENT ME!\r
- * @param endx DOCUMENT ME!\r
- * @param ypos DOCUMENT ME!\r
- */\r
- void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
- {\r
- ypos += av.charHeight;\r
-\r
- // 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
-\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
-\r
- break;\r
- }\r
-\r
- if (value != -1)\r
- {\r
- g.drawString(String.valueOf(value), av.charWidth/2,\r
- (ypos + (i * av.charHeight)) - (av.charHeight / 5));\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param horizontal DOCUMENT ME!\r
- * @param vertical DOCUMENT ME!\r
- */\r
- public void fastPaint(int horizontal, int vertical)\r
- {\r
- if (gg == null)\r
- {\r
- return;\r
- }\r
-\r
- 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
-\r
- if (horizontal > 0) // scrollbar pulled right, image to the left\r
- {\r
- er ++;\r
- transX = (er - sr - horizontal) * av.charWidth;\r
- sr = er - horizontal;\r
- }\r
- else if (horizontal < 0)\r
- {\r
- er = sr - horizontal-1;\r
- }\r
- else if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
-\r
- 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
- if (es > av.endSeq)\r
- {\r
- es = av.endSeq;\r
- }\r
- }\r
-\r
- gg.translate(transX, transY);\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
- // Set this to false to force a full panel paint\r
- public void paintComponent(Graphics g)\r
- {\r
- sr.renderGaps(av.renderGaps);\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
- return;\r
- }\r
-\r
- // this draws the whole of the alignment\r
- imgWidth = getWidth();\r
- imgHeight = getHeight();\r
-\r
- imgWidth -= (imgWidth % av.charWidth);\r
- imgHeight -= (imgHeight % av.charHeight);\r
-\r
- if ((imgWidth < 1) || (imgHeight < 1))\r
- {\r
- return;\r
- }\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
- 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
- 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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cwidth DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getWrappedCanvasWidth(int cwidth)\r
- {\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
- LABEL_EAST = 0;\r
- LABEL_WEST = 0;\r
-\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(getMask()+"0");\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
- /**\r
- * Generates a string of zeroes.\r
- * @return String\r
- */\r
- String getMask()\r
- {\r
- String mask = "0";\r
- for (int i = av.alignment.getWidth(); i > 0; i /= 10)\r
- {\r
- mask += "0";\r
- }\r
- return mask;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param canvasWidth DOCUMENT ME!\r
- * @param canvasHeight DOCUMENT ME!\r
- * @param startRes DOCUMENT ME!\r
- */\r
- public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,\r
- int startRes)\r
- {\r
-\r
- AlignmentI al = av.getAlignment();\r
-\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
- int LABEL_EAST = 0;\r
-\r
- if (av.scaleRightWrapped)\r
- {\r
- LABEL_EAST = fm.stringWidth(getMask()+"0");\r
- }\r
-\r
- int LABEL_WEST = 0;\r
-\r
- if (av.scaleLeftWrapped)\r
- {\r
- LABEL_WEST = fm.stringWidth(getMask());\r
- }\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
-\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
- 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
-\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
- if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())\r
- {\r
- endx = av.vconsensus.size() - 2;\r
- }\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
- * 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
-\r
- SequenceI nextSeq;\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 + ((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
- //\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 ((group == null) && (groups.size() > 0))\r
- {\r
- group = (SequenceGroup) groups.elementAt(0);\r
- groupIndex = 0;\r
- }\r
-\r
-\r
- if (group != null && !isOverview)\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
- if(sx+ex<0 || sx>imgWidth)\r
- {\r
- continue;\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
- 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 >= (x2 - x1 + 1) * av.charWidth)\r
- ex = (x2 - x1 + 1) * av.charWidth;\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
-\r
- inGroup = false;\r
- }\r
- }\r
- }\r
-\r
- if (inGroup)\r
- {\r
- sy = offset + ( (i - starty) * av.charHeight);\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
- else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)\r
- ex = (x2 - x1 + 1) * av.charWidth;\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top = -1;\r
- }\r
-\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);\r
- bottom = -1;\r
- }\r
-\r
- inGroup = false;\r
- }\r
-\r
- groupIndex++;\r
-\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
- /// 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
-\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
-\r
- if (searchStart < x1)\r
- {\r
- searchStart = x1;\r
- }\r
-\r
- if (searchEnd > x2)\r
- {\r
- searchEnd = x2;\r
- }\r
-\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
- * DOCUMENT ME!\r
- *\r
- * @param results DOCUMENT ME!\r
- */\r
- public void highlightSearchResults(int[] results)\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
-\r
- repaint();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.gui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JComponent;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent
+{
+ final FeatureRenderer fr;
+
+ final SequenceRenderer sr;
+
+ BufferedImage img;
+
+ Graphics2D gg;
+
+ int imgWidth;
+
+ int imgHeight;
+
+ AlignViewport av;
+
+ SearchResults searchResults = null;
+
+ boolean fastPaint = false;
+
+ int LABEL_WEST;
+
+ int LABEL_EAST;
+
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ /**
+ * Creates a new SeqCanvas object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public SeqCanvas(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ updateViewport();
+ fr = new FeatureRenderer(ap);
+ sr = new SequenceRenderer(av);
+ setLayout(new BorderLayout());
+ PaintRefresher.Register(this, av.getSequenceSetId());
+ setBackground(Color.white);
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return sr;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return fr;
+ }
+
+ int charHeight = 0, charWidth = 0;
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ {
+ updateViewport();
+ 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) * charWidth,
+ ypos - (charHeight / 2));
+
+ g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
+ + (charWidth / 2), ypos - 2);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += 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))
+ - charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * charHeight))
+ - (charHeight / 5));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += 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 * charHeight))
+ - (charHeight / 5));
+ }
+ }
+ }
+
+ boolean fastpainting = false;
+
+ /**
+ * need to make this thread safe move alignment rendering in response to
+ * slider adjustment
+ *
+ * @param horizontal
+ * shift along
+ * @param vertical
+ * shift up or down in repaint
+ */
+ public void fastPaint(int horizontal, int vertical)
+ {
+ if (fastpainting || gg == null)
+ {
+ return;
+ }
+ fastpainting = true;
+ fastPaint = true;
+ updateViewport();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
+ int sr = av.startRes;
+ int er = av.endRes;
+ int ss = av.startSeq;
+ int es = av.endSeq;
+ int transX = 0;
+ int transY = 0;
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ er++;
+ transX = (er - sr - horizontal) * charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal - 1;
+ }
+ 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 * 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();
+ fastpainting = false;
+ }
+
+ /**
+ * 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.
+ */
+
+ // Set this to false to force a full panel paint
+ public void paintComponent(Graphics g)
+ {
+ updateViewport();
+ BufferedImage lcimg = img; // take reference since other threads may null
+ // img and call later.
+ super.paintComponent(g);
+
+ if (lcimg != null
+ && (fastPaint
+ || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
+ .getClipBounds().height)))
+ {
+ g.drawImage(lcimg, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ // this draws the whole of the alignment
+ imgWidth = getWidth();
+ imgHeight = getHeight();
+
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
+
+ if ((imgWidth < 1) || (imgHeight < 1))
+ {
+ return;
+ }
+
+ if (lcimg == null || imgWidth != lcimg.getWidth()
+ || imgHeight != lcimg.getHeight())
+ {
+ try
+ {
+ lcimg = img = new BufferedImage(imgWidth, imgHeight,
+ BufferedImage.TYPE_INT_RGB);
+ gg = (Graphics2D) img.getGraphics();
+ gg.setFont(av.getFont());
+ } catch (OutOfMemoryError er)
+ {
+ System.gc();
+ System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
+ new OOMWarning("Creating alignment image for display", er);
+
+ return;
+ }
+ }
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, imgHeight);
+
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+ }
+ else
+ {
+ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ }
+
+ g.drawImage(lcimg, 0, 0, this);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cwidth
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedCanvasWidth(int cwidth)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ }
+
+ /**
+ * Generates a string of zeroes.
+ *
+ * @return String
+ */
+ String getMask()
+ {
+ String mask = "00";
+ int maxWidth = 0;
+ int tmp;
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ tmp = av.getAlignment().getSequenceAt(i).getEnd();
+ if (tmp > maxWidth)
+ {
+ maxWidth = tmp;
+ }
+ }
+
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ mask += "0";
+ }
+ return mask;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param canvasWidth
+ * DOCUMENT ME!
+ * @param canvasHeight
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ */
+ public void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
+ {
+ updateViewport();
+ AlignmentI al = av.getAlignment();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ if (av.getScaleRightWrapped())
+ {
+ LABEL_EAST = fm.stringWidth(getMask());
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ LABEL_WEST = fm.stringWidth(getMask());
+ }
+
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * 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.setFont(av.getFont());
+ g.setColor(Color.black);
+
+ if (av.getScaleLeftWrapped())
+ {
+ drawWestScale(g, startRes, endx, ypos);
+ }
+
+ if (av.getScaleRightWrapped())
+ {
+ g.translate(canvasWidth - LABEL_EAST, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - LABEL_EAST), 0);
+ }
+
+ g.translate(LABEL_WEST, 0);
+
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ 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 * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[] { ypos - (charHeight / 2),
+ ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ 3);
+
+ }
+ }
+
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
+
+ if (clip == null)
+ {
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
+ (int) clip.getBounds().getHeight());
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1,
+ startRes, endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
+ }
+ g.setClip(clip);
+ g.translate(-LABEL_WEST, 0);
+
+ ypos += cHeight + getAnnotationHeight() + hgap;
+
+ startRes += cWidth;
+ }
+ }
+
+ AnnotationPanel annotations;
+
+ int getAnnotationHeight()
+ {
+ if (!av.isShowAnnotation())
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ * @param startSeq
+ * DOCUMENT ME!
+ * @param endSeq
+ * DOCUMENT ME!
+ * @param offset
+ * DOCUMENT ME!
+ */
+ public void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ updateViewport();
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, offset);
+ }
+ else
+ {
+ List<int[]> regions = av.getColumnSelection().getHiddenColumns();
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : regions)
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ blockEnd = hideStart - 1;
+
+ g1.translate(screenY * charWidth, 0);
+
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ if (av.getShowHiddenMarkers())
+ {
+ g1.setColor(Color.blue);
+
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq) * charHeight + offset);
+ }
+
+ g1.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+ }
+
+ if (screenY <= (endRes - startRes))
+ {
+ blockEnd = blockStart + (endRes - startRes) - screenY;
+ g1.translate(screenY * charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+ g1.translate(-screenY * 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,
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
+ {
+ g.setFont(av.getFont());
+ sr.prepare(g, av.isRenderGaps());
+
+ SequenceI nextSeq;
+
+ // / First draw the sequences
+ // ///////////////////////////
+ for (int i = startSeq; i < endSeq; i++)
+ {
+ nextSeq = av.getAlignment().getSequenceAt(i);
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ continue;
+ }
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
+
+ if (av.isShowSequenceFeatures())
+ {
+ fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ + ((i - startSeq) * 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)
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
+ }
+ }
+ }
+
+ if (av.cursorMode && cursorY == i && cursorX >= startRes
+ && cursorX <= endRes)
+ {
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
+ }
+ }
+
+ if (av.getSelectionGroup() != null
+ || av.getAlignment().getGroups().size() > 0)
+ {
+ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+ }
+
+ }
+
+ void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
+ {
+ Graphics2D g = (Graphics2D) g1;
+ //
+ // ///////////////////////////////////
+ // Now outline any areas if necessary
+ // ///////////////////////////////////
+ SequenceGroup group = av.getSelectionGroup();
+
+ int sx = -1;
+ int sy = -1;
+ int ex = -1;
+ int groupIndex = -1;
+ int visWidth = (endRes - startRes + 1) * charWidth;
+
+ 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;
+
+ for (i = startSeq; i < endSeq; i++)
+ {
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
+
+ if (sx + ex < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * charWidth)
+ && group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1)))
+ {
+ bottom = sy + 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.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+ 0f));
+ g.setColor(Color.RED);
+ }
+ else
+ {
+ g.setStroke(new BasicStroke());
+ g.setColor(group.getOutlineColour());
+ }
+ }
+ }
+ else
+ {
+ if (inGroup)
+ {
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < visWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > visWidth)
+ {
+ ex = visWidth;
+ }
+
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+ {
+ ex = (endRes - startRes + 1) * 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) * charHeight);
+ if (sx >= 0 && sx < visWidth)
+ {
+ g.drawLine(sx, oldY, sx, sy);
+ }
+
+ if (sx + ex < visWidth)
+ {
+ g.drawLine(sx + ex, oldY, sx + ex, sy);
+ }
+
+ if (sx < 0)
+ {
+ ex += sx;
+ sx = 0;
+ }
+
+ if (sx + ex > visWidth)
+ {
+ ex = visWidth;
+ }
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
+ {
+ ex = (endRes - startRes + 1) * 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++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.getAlignment().getGroups().size())
+ {
+ break;
+ }
+
+ group = av.getAlignment().getGroups().get(groupIndex);
+
+ } while (groupIndex < av.getAlignment().getGroups().size());
+
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param results
+ * DOCUMENT ME!
+ */
+ public void highlightSearchResults(SearchResults results)
+ {
+ img = null;
+
+ searchResults = results;
+
+ repaint();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff