-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.image.*;\r
-import javax.swing.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-\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
-\r
- AlignViewport av;\r
-\r
- boolean showScores = false;\r
- boolean displaySearch = false;\r
- int [] searchResults = null;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
-\r
- boolean fastPaint = false;\r
-\r
-\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- fr = new FeatureRenderer(av);\r
- sr = new SequenceRenderer(av);\r
- setLayout(new BorderLayout());\r
- PaintRefresher.Register(this);\r
-\r
- }\r
-\r
- void drawNorthScale(Graphics g, int startx, int endx,int ypos) {\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 - 2);\r
-\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
- {\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = startx;\r
- int value = -1;\r
- while (index < endx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index++;\r
- continue;\r
- }\r
-\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
- break;\r
- }\r
- if(value!=-1)\r
- {\r
- int x = LABEL_WEST - fm.stringWidth(value+"");\r
- g.drawString(value + "", x, ypos + i*av.charHeight - av.charHeight/5);\r
- }\r
- }\r
- }\r
-\r
- void drawEastScale(Graphics g, int startx, int endx, int ypos)\r
-{\r
- ypos+= av.charHeight;\r
- // EAST SCALE\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI seq = av.alignment.getSequenceAt(i);\r
- int index = endx;\r
- int value = -1;\r
- while (index > startx)\r
- {\r
- if (jalview.util.Comparison.isGap(seq.getCharAt(index)))\r
- {\r
- index--;\r
- continue;\r
- }\r
-\r
- value = av.alignment.getSequenceAt(i).findPosition(index);\r
- break;\r
- }\r
- if(value!=-1)\r
- g.drawString(value + "", 0, ypos + i*av.charHeight - av.charHeight/5);\r
- }\r
-\r
-}\r
-\r
-\r
-\r
-\r
-\r
-public void fastPaint(int horizontal, int vertical)\r
-{\r
- if (horizontal == 0 && vertical == 0 || gg==null)\r
- return;\r
-\r
- gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,\r
- -vertical * av.charHeight);\r
-\r
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,\r
- transX = 0, transY = 0;\r
- if (horizontal > 0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er - sr - horizontal) * av.charWidth;\r
- sr = er - horizontal;\r
- }\r
- else if (horizontal < 0)\r
- er = sr - horizontal;\r
-\r
- else if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- else\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if(es > av.endSeq)\r
- es = av.endSeq;\r
- }\r
-\r
-\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
- gg.translate( -transX, -transY);\r
-\r
- fastPaint = true;\r
- repaint();\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
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getWidth(), getHeight());\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 = getWidth();\r
- imgHeight = getHeight();\r
- if(imgWidth==0 || imgHeight==0)\r
- return;\r
-\r
- imgWidth -= imgWidth%av.charWidth;\r
- imgHeight-= imgHeight%av.charHeight;\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,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
-\r
- if (av.getWrapAlignment())\r
- drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);\r
- else\r
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);\r
-\r
- g.drawImage(img, 0, 0, this);\r
-\r
- }\r
-\r
- int LABEL_WEST, LABEL_EAST;\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
- LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );\r
-\r
- if(av.scaleLeftWrapped)\r
- LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );\r
-\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
- AlignmentI al = av.getAlignment();\r
-\r
- FontMetrics fm = getFontMetrics(av.getFont());\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
-\r
-\r
- int cWidth = (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;\r
- int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;\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
- drawWestScale(g, startRes, endx, ypos);\r
-\r
- if(av.scaleRightWrapped)\r
- {\r
- g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);\r
- drawEastScale(g, startRes, endx, ypos);\r
- g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);\r
- }\r
-\r
- g.translate(LABEL_WEST,0);\r
- if(av.scaleAboveWrapped)\r
- drawNorthScale(g, startRes, endx, ypos);\r
-\r
-\r
- // When printing we have an extra clipped region,\r
- // the Printable page which we need to account for here\r
- Shape clip = g.getClip();\r
- if(clip==null)\r
- g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);\r
- else\r
- g.setClip(0,\r
- (int)clip.getBounds().getY(),\r
- cWidth*av.charWidth,\r
- (int)clip.getBounds().getHeight()\r
- );\r
-\r
- drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);\r
- g.setClip(clip);\r
- g.translate(-LABEL_WEST,0);\r
-\r
- ypos += cHeight;\r
- startRes += cWidth;\r
- endx = startRes + cWidth - 1;\r
-\r
- if (endx > al.getWidth())\r
- endx = al.getWidth();\r
- }\r
-\r
- }\r
-\r
-\r
- synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
-\r
- Graphics2D g = (Graphics2D)g1;\r
- g.setFont(av.getFont());\r
- sr.renderGaps(av.renderGaps);\r
-\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 ),x1,x2,\r
- (x1 - startx) * av.charWidth,\r
- offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- av.charWidth,av.charHeight);\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
-\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, 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
- sx = (group.getStartRes() - startx) * av.charWidth;\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;\r
-\r
- if (sx < getWidth()\r
- && ex > 0\r
- && group.sequences.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- if (bottom == -1 &&\r
- !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))\r
- bottom = sy + av.charHeight ;\r
-\r
- if (!inGroup)\r
- {\r
- if (top == -1 && i==0 ||\r
- !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))\r
- top = sy;\r
-\r
-\r
- oldY = sy;\r
- inGroup = true;\r
- if (group == av.getSelectionGroup())\r
- {\r
- g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f ));\r
- g.setColor(Color.RED);\r
- }\r
- else\r
- {\r
- g.setStroke(new BasicStroke());\r
- g.setColor(group.getOutlineColour());\r
- }\r
- }\r
- }\r
- else\r
- {\r
- if (inGroup)\r
- {\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
-\r
- if (top != -1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
- }\r
- if (bottom != -1)\r
- {\r
- g.drawLine(sx, bottom, sx + ex, bottom);\r
- bottom = -1;\r
- }\r
-\r
-\r
- inGroup = false;\r
- }\r
- }\r
- }\r
-\r
- if (inGroup)\r
- {\r
-\r
- if(top!=-1)\r
- {\r
- g.drawLine(sx, top, sx + ex, top);\r
- top =-1;\r
- }\r
- if(bottom!=-1)\r
- {\r
- g.drawLine(sx, bottom-1, sx + ex, bottom-1);\r
- bottom = -1;\r
-\r
- }\r
- sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);\r
- g.drawLine(sx, oldY, sx, sy );\r
- g.drawLine(sx+ex, oldY, sx+ex, sy );\r
- inGroup = false;\r
- }\r
- groupIndex++;\r
- if (groupIndex >= groups.size())\r
- break;\r
-\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
-\r
- }\r
- while (groupIndex < groups.size());\r
-\r
-\r
- /// Highlight search Results once all sequences have been drawn\r
- //////////////////////////////////////////////////////////\r
- if(displaySearch)\r
- {\r
- for(int r=0; r<searchResults.length; r+=3)\r
- {\r
- int searchSeq = searchResults[r];\r
- int searchStart = searchResults[r+1];\r
- int searchEnd = searchResults[r+2];\r
-\r
- if (searchSeq >= y1 && searchSeq < y2)\r
- {\r
- SequenceRenderer ssr = (SequenceRenderer) sr;\r
- if(searchStart<x1)\r
- searchStart = x1;\r
- if(searchEnd > x2)\r
- searchEnd = x2;\r
- ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),\r
- searchStart,\r
- searchEnd,\r
- (searchStart - startx) * av.charWidth,\r
- offset +\r
- AlignmentUtil.getPixelHeight(starty, searchSeq,\r
- av.charHeight),\r
- av.charWidth,\r
- av.charHeight);\r
- }\r
- }\r
- }\r
-\r
- }\r
-\r
-\r
-\r
- public void highlightSearchResults(int [] results)\r
- {\r
- // results are in the order sequence, startRes, endRes\r
- if(results==null)\r
- displaySearch = false;\r
- else\r
- displaySearch = true;\r
-\r
- searchResults = results;\r
-\r
- repaint();\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+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.beans.PropertyChangeEvent;
+import java.util.List;
+
+import javax.swing.JComponent;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqCanvas extends JComponent implements ViewportListenerI
+{
+ private static String ZEROS = "0000000000";
+
+ final FeatureRenderer fr;
+
+ final SequenceRenderer sr;
+
+ BufferedImage img;
+
+ Graphics2D gg;
+
+ int imgWidth;
+
+ int imgHeight;
+
+ AlignViewport av;
+
+ boolean fastPaint = false;
+
+ int labelWidthWest;
+
+ int labelWidthEast;
+
+ 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);
+
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ 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();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
+ {
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
+ {
+ continue;
+ }
+ String mstring = mark.text;
+
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
+ }
+ g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
+ - (charHeight / 2), (mpos * 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.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .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 = labelWidthWest - 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.getAlignment().getHiddenColumns()
+ .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();
+
+ ViewportRanges ranges = av.getRanges();
+ int startRes = ranges.getStartRes();
+ int endRes = ranges.getEndRes();
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
+ int transX = 0;
+ int transY = 0;
+
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (endRes - startRes - horizontal) * charWidth;
+ startRes = endRes - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ endRes = startRes - horizontal;
+ }
+ else if (vertical > 0) // scroll down
+ {
+ startSeq = endSeq - vertical;
+
+ if (startSeq < ranges.getStartSeq())
+ { // ie scrolling too fast, more than a page at a time
+ startSeq = ranges.getStartSeq();
+ }
+ else
+ {
+ transY = imgHeight - ((vertical + 1) * charHeight);
+ }
+ }
+ else if (vertical < 0)
+ {
+ endSeq = startSeq - vertical;
+
+ if (endSeq > ranges.getEndSeq())
+ {
+ endSeq = ranges.getEndSeq();
+ }
+ }
+
+ gg.translate(transX, transY);
+ drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+ gg.translate(-transX, -transY);
+
+ repaint();
+ fastpainting = false;
+ }
+
+ @Override
+ 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);
+
+ ViewportRanges ranges = av.getRanges();
+ if (av.getWrapAlignment())
+ {
+ drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+ }
+ else
+ {
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
+ }
+
+ g.drawImage(lcimg, 0, 0, this);
+
+ }
+
+ /**
+ * Returns the visible width of the canvas in residues, after allowing for
+ * East or West scales (if shown)
+ *
+ * @param canvasWidth
+ * the width in pixels (possibly including scales)
+ *
+ * @return
+ */
+ public int getWrappedCanvasWidth(int canvasWidth)
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ labelWidthEast = 0;
+ labelWidthWest = 0;
+
+ if (av.getScaleRightWrapped())
+ {
+ labelWidthEast = getLabelWidth(fm);
+ }
+
+ if (av.getScaleLeftWrapped())
+ {
+ labelWidthWest = labelWidthEast > 0 ? labelWidthEast
+ : getLabelWidth(fm);
+ }
+
+ return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
+ }
+
+ /**
+ * Returns a pixel width suitable for showing the largest sequence coordinate
+ * (end position) in the alignment. Returns 2 plus the number of decimal
+ * digits to be shown (3 for 1-10, 4 for 11-99 etc).
+ *
+ * @param fm
+ * @return
+ */
+ protected int getLabelWidth(FontMetrics fm)
+ {
+ /*
+ * find the biggest sequence end position we need to show
+ * (note this is not necessarily the sequence length)
+ */
+ int maxWidth = 0;
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
+ }
+
+ int length = 2;
+ for (int i = maxWidth; i > 0; i /= 10)
+ {
+ length++;
+ }
+
+ return fm.stringWidth(ZEROS.substring(0, length));
+ }
+
+ /**
+ * 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();
+
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+ {
+ FontMetrics fm = getFontMetrics(av.getFont());
+ labelWidth = getLabelWidth(fm);
+ }
+
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += charHeight;
+ }
+
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
+
+ av.setWrappedWidth(cWidth);
+
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
+
+ int endx;
+ int ypos = hgap;
+ int maxwidth = av.getAlignment().getWidth();
+
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
+ }
+
+ int annotationHeight = getAnnotationHeight();
+
+ 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 - labelWidthEast, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - labelWidthEast), 0);
+ }
+
+ g.translate(labelWidthWest, 0);
+
+ if (av.getScaleAboveWrapped())
+ {
+ drawNorthScale(g, startRes, endx, ypos);
+ }
+
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
+ {
+ g.setColor(Color.blue);
+ int res;
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
+ {
+ res = pos - 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() - 1, 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(-labelWidthWest, 0);
+
+ ypos += cHeight + annotationHeight + hgap;
+
+ startRes += cWidth;
+ }
+ }
+
+ AnnotationPanel annotations;
+
+ int getAnnotationHeight()
+ {
+ if (!av.isShowAnnotation())
+ {
+ return 0;
+ }
+
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ return annotations.adjustPanelHeight();
+ }
+
+ /**
+ * Draws the visible region of the alignment on the graphics context. If there
+ * are hidden column markers in the visible region, then each sub-region
+ * between the markers is drawn separately, followed by the hidden column
+ * marker.
+ *
+ * @param g1
+ * @param startRes
+ * offset of the first column in the visible region (0..)
+ * @param endRes
+ * offset of the last column in the visible region (0..)
+ * @param startSeq
+ * offset of the first sequence in the visible region (0..)
+ * @param endSeq
+ * offset of the last sequence in the visible region (0..)
+ * @param yOffset
+ * vertical offset at which to draw (for wrapped alignments)
+ */
+ public void drawPanel(Graphics g1, final int startRes, final int endRes,
+ final int startSeq, final int endSeq, final int yOffset)
+ {
+ updateViewport();
+ if (!av.hasHiddenColumns())
+ {
+ draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
+ }
+ else
+ {
+ int screenY = 0;
+ final int screenYMax = endRes - startRes;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int[] region : av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy())
+ {
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
+
+ /*
+ * draw up to just before the next hidden region, or the end of
+ * the visible region, whichever comes first
+ */
+ blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
+ - screenY);
+
+ g1.translate(screenY * charWidth, 0);
+
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
+
+ /*
+ * draw the downline of the hidden column marker (ScalePanel draws the
+ * triangle on top) if we reached it
+ */
+ if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+ {
+ g1.setColor(Color.blue);
+
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + yOffset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq + 1) * charHeight + yOffset);
+ }
+
+ g1.translate(-screenY * charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+
+ if (screenY > screenYMax)
+ {
+ // already rendered last block
+ return;
+ }
+ }
+
+ if (screenY <= screenYMax)
+ {
+ // remaining visible region to render
+ blockEnd = blockStart + screenYMax - screenY;
+ g1.translate(screenY * charWidth, 0);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
+
+ g1.translate(-screenY * charWidth, 0);
+ }
+ }
+
+ }
+
+ /**
+ * Draws a region of the visible alignment
+ *
+ * @param g1
+ * @param startRes
+ * offset of the first column in the visible region (0..)
+ * @param endRes
+ * offset of the last column in the visible region (0..)
+ * @param startSeq
+ * offset of the first sequence in the visible region (0..)
+ * @param endSeq
+ * offset of the last sequence in the visible region (0..)
+ * @param yOffset
+ * vertical offset at which to draw (for wrapped alignments)
+ */
+ 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), false);
+ }
+
+ /*
+ * highlight search Results once sequence has been drawn
+ */
+ if (av.hasSearchResults())
+ {
+ SearchResultsI searchResults = av.getSearchResults();
+ 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());
+
+ }
+
+ }
+
+ /**
+ * Highlights search results in the visible region by rendering as white text
+ * on a black background. Any previous highlighting is removed. Answers true
+ * if any highlight was left on the visible alignment (so status bar should be
+ * set to match), else false.
+ * <p>
+ * Currently fastPaint is not implemented for wrapped alignments. If a wrapped
+ * alignment had to be scrolled to show the highlighted region, then it should
+ * be fully redrawn, otherwise a fast paint can be performed. This argument
+ * could be removed if fast paint of scrolled wrapped alignment is coded in
+ * future (JAL-2609).
+ *
+ * @param results
+ * @param noFastPaint
+ * @return
+ */
+ public boolean highlightSearchResults(SearchResultsI results,
+ boolean noFastPaint)
+ {
+ if (fastpainting)
+ {
+ return false;
+ }
+ boolean wrapped = av.getWrapAlignment();
+
+ try
+ {
+ fastPaint = !noFastPaint;
+ fastpainting = fastPaint;
+
+ updateViewport();
+
+ /*
+ * to avoid redrawing the whole visible region, we instead
+ * redraw just the minimal regions to remove previous highlights
+ * and add new ones
+ */
+ SearchResultsI previous = av.getSearchResults();
+ av.setSearchResults(results);
+ boolean redrawn = false;
+ boolean drawn = false;
+ if (wrapped)
+ {
+ redrawn = drawMappedPositionsWrapped(previous);
+ drawn = drawMappedPositionsWrapped(results);
+ redrawn |= drawn;
+ }
+ else
+ {
+ redrawn = drawMappedPositions(previous);
+ drawn = drawMappedPositions(results);
+ redrawn |= drawn;
+ }
+
+ /*
+ * if highlights were either removed or added, repaint
+ */
+ if (redrawn)
+ {
+ repaint();
+ }
+
+ /*
+ * return true only if highlights were added
+ */
+ return drawn;
+
+ } finally
+ {
+ fastpainting = false;
+ }
+ }
+
+ /**
+ * Redraws the minimal rectangle in the visible region (if any) that includes
+ * mapped positions of the given search results. Whether or not positions are
+ * highlighted depends on the SearchResults set on the Viewport. This allows
+ * this method to be called to either clear or set highlighting. Answers true
+ * if any positions were drawn (in which case a repaint is still required),
+ * else false.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawMappedPositions(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ /*
+ * calculate the minimal rectangle to redraw that
+ * includes both new and existing search results
+ */
+ int firstSeq = Integer.MAX_VALUE;
+ int lastSeq = -1;
+ int firstCol = Integer.MAX_VALUE;
+ int lastCol = -1;
+ boolean matchFound = false;
+
+ ViewportRanges ranges = av.getRanges();
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getEndRes();
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region -
+ * remember the first and last sequence matched, and the first
+ * and last visible columns in the matched positions
+ */
+ matchFound = true;
+ firstSeq = Math.min(firstSeq, seqNo);
+ lastSeq = Math.max(lastSeq, seqNo);
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+ firstCol = Math.min(firstCol, firstMatchedColumn);
+ lastCol = Math.max(lastCol, lastMatchedColumn);
+ }
+ }
+ }
+ }
+
+ if (matchFound)
+ {
+ if (av.hasHiddenColumns())
+ {
+ firstCol = alignment.getHiddenColumns()
+ .findColumnPosition(firstCol);
+ lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+ }
+ int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
+ int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
+ gg.translate(transX, transY);
+ drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
+ gg.translate(-transX, -transY);
+ }
+
+ return matchFound;
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (av.getWrapAlignment())
+ {
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ repaint();
+ }
+ }
+ else
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ ViewportRanges vpRanges = av.getRanges();
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else if (scrollX < -range)
+ {
+ scrollX = -range;
+ }
+ }
+
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
+ }
+
+ /**
+ * Redraws any positions in the search results in the visible region of a
+ * wrapped alignment. Any highlights are drawn depending on the search results
+ * set on the Viewport, not the <code>results</code> argument. This allows
+ * this method to be called either to clear highlights (passing the previous
+ * search results), or to draw new highlights.
+ *
+ * @param results
+ * @return
+ */
+ protected boolean drawMappedPositionsWrapped(SearchResultsI results)
+ {
+ if (results == null)
+ {
+ return false;
+ }
+
+ boolean matchFound = false;
+
+ int wrappedWidth = av.getWrappedWidth();
+ int wrappedHeight = getRepeatHeightWrapped();
+
+ ViewportRanges ranges = av.getRanges();
+ int canvasHeight = getHeight();
+ int repeats = canvasHeight / wrappedHeight;
+ if (canvasHeight / wrappedHeight > 0)
+ {
+ repeats++;
+ }
+
+ int firstVisibleColumn = ranges.getStartRes();
+ int lastVisibleColumn = ranges.getStartRes() + repeats
+ * ranges.getViewportWidth() - 1;
+
+ AlignmentI alignment = av.getAlignment();
+ if (av.hasHiddenColumns())
+ {
+ firstVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(firstVisibleColumn);
+ lastVisibleColumn = alignment.getHiddenColumns()
+ .adjustForHiddenColumns(lastVisibleColumn);
+ }
+
+ int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
+ .getEndSeq(); seqNo++)
+ {
+ SequenceI seq = alignment.getSequenceAt(seqNo);
+
+ int[] visibleResults = results.getResults(seq, firstVisibleColumn,
+ lastVisibleColumn);
+ if (visibleResults != null)
+ {
+ for (int i = 0; i < visibleResults.length - 1; i += 2)
+ {
+ int firstMatchedColumn = visibleResults[i];
+ int lastMatchedColumn = visibleResults[i + 1];
+ if (firstMatchedColumn <= lastVisibleColumn
+ && lastMatchedColumn >= firstVisibleColumn)
+ {
+ /*
+ * found a search results match in the visible region
+ */
+ firstMatchedColumn = Math.max(firstMatchedColumn,
+ firstVisibleColumn);
+ lastMatchedColumn = Math.min(lastMatchedColumn,
+ lastVisibleColumn);
+
+ /*
+ * draw each mapped position separately (as contiguous positions may
+ * wrap across lines)
+ */
+ for (int mappedPos = firstMatchedColumn; mappedPos <= lastMatchedColumn; mappedPos++)
+ {
+ int displayColumn = mappedPos;
+ if (av.hasHiddenColumns())
+ {
+ displayColumn = alignment.getHiddenColumns()
+ .findColumnPosition(displayColumn);
+ }
+
+ /*
+ * transX: offset from left edge of canvas to residue position
+ */
+ int transX = labelWidthWest
+ + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
+ * av.getCharWidth();
+
+ /*
+ * transY: offset from top edge of canvas to residue position
+ */
+ int transY = gapHeight;
+ transY += (displayColumn - ranges.getStartRes())
+ / wrappedWidth * wrappedHeight;
+ transY += (seqNo - ranges.getStartSeq()) * av.getCharHeight();
+
+ /*
+ * yOffset is from graphics origin to start of visible region
+ */
+ int yOffset = 0;// (displayColumn / wrappedWidth) * wrappedHeight;
+ if (transY < getHeight())
+ {
+ matchFound = true;
+ gg.translate(transX, transY);
+ drawPanel(gg, displayColumn, displayColumn, seqNo, seqNo,
+ yOffset);
+ gg.translate(-transX, -transY);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return matchFound;
+ }
+
+ /**
+ * Answers the height in pixels of a repeating section of the wrapped
+ * alignment, including space above, scale above if shown, sequences, and
+ * annotation panel if shown
+ *
+ * @return
+ */
+ protected int getRepeatHeightWrapped()
+ {
+ // gap (and maybe scale) above
+ int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ // add sequences
+ repeatHeight += av.getRanges().getViewportHeight() * charHeight;
+
+ // add annotations panel height if shown
+ repeatHeight += getAnnotationHeight();
+
+ return repeatHeight;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff