-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-\r
-\r
-public class SeqCanvas extends JPanel\r
-{\r
- Image img;\r
- Graphics gg;\r
- int imgWidth;\r
- int imgHeight;\r
-\r
- AlignViewport av;\r
- int pady = 2;\r
- int oldstartx;\r
- int oldstarty;\r
- int oldendx;\r
- int oldendy;\r
-\r
- public boolean paintFlag = false;\r
- boolean showScores = false;\r
-\r
- int chunkHeight;\r
- int chunkWidth;\r
-\r
- Graphics debugG;\r
- FeatureRenderer fr = new FeatureRenderer();\r
- BlockRenderer br = new BlockRenderer();\r
- CpGRenderer cgr = new CpGRenderer();\r
-\r
- ColourSchemeI cs = new ZappoColourScheme();\r
-\r
- public SeqCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- setLayout(new BorderLayout());\r
- }\r
-\r
- public void drawScale(int startx, int endx,double charWidth, int charHeight,int ypos) {\r
- int scalestartx = startx - startx%10 + 10;\r
-\r
- gg.setColor(Color.black);\r
-\r
- for (int i=scalestartx;i < endx;i+= 10) {\r
- String string = String.valueOf(i);\r
- gg.drawString(string,(int)((i-startx-1)*charWidth),ypos+15 - charHeight*(2));\r
- }\r
- }\r
-\r
-\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 paintComponent(Graphics g) {\r
- debugG = g;\r
-\r
- AlignmentI da = av.getAlignment();\r
-\r
- if (img == null ||\r
- imgWidth != getWidth() ||\r
- imgHeight != getHeight() ||\r
- paintFlag == true) {\r
-\r
- imgWidth = (getWidth() > 0 ? getWidth() : 1);\r
- imgHeight = (getHeight() > 0 ? getHeight() : 1);\r
-\r
- img = createImage(imgWidth,imgHeight);\r
- gg = img.getGraphics();\r
-\r
- // SMJS I added this in to update the AV when the size changes\r
- // until I figure out how this should be done\r
- setFont(av.getFont());\r
-\r
- gg.setFont(av.getFont());\r
-\r
- paintFlag = false;\r
-\r
- oldstartx = -1;\r
- oldendx = -1;\r
- oldstarty = -1;\r
- oldendy = -1;\r
- }\r
-\r
- int startx = av.getStartRes();\r
- int starty = av.getStartSeq();\r
-\r
- int endx = av.getEndRes();\r
- int endy = av.getEndSeq();\r
-\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
-\r
- chunkWidth = (int)(getWidth()/charWidth);\r
- chunkHeight = (da.getHeight() + 2)*charHeight;\r
-\r
- av.setChunkHeight(chunkHeight);\r
- av.setChunkWidth(chunkWidth);\r
-\r
- int offy = av.getStartSeq();\r
-\r
- if (oldendx == -1) {\r
- fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);\r
-\r
- /* if (av.getWrapAlignment() == true) {\r
- startx = (int)(offy/chunkWidth)*chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = offy%chunkHeight;\r
- endy = starty + da.getHeight();\r
-\r
- int ypos = 0;\r
- int rowstart = starty;\r
-\r
- if (starty == 0) {\r
- ypos = 2*charHeight;\r
- } else if (starty == 1) {\r
- starty = 0;\r
- ypos = charHeight;\r
- }\r
-\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
-\r
- if (rowstart < 2) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- }\r
-\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,ypos);\r
-\r
- if (rowstart == 0) {\r
- ypos = ypos + chunkHeight;\r
- } else if (rowstart == 1) {\r
- ypos = ypos + chunkHeight;\r
- } else {\r
- ypos = ypos + chunkHeight - rowstart*charHeight;\r
- }\r
-\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
- starty = 0;\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
- // Draw the rest of the panels\r
-\r
- while (ypos <= getHeight()) {\r
- drawScale(startx,endx,charWidth,charHeight,ypos);\r
- drawPanel(gg,startx,endx,0,da.getHeight(),startx,starty,ypos);\r
-\r
- ypos += chunkHeight;\r
- startx += chunkWidth;\r
- endx = startx + chunkWidth;\r
-\r
- if (endy > da.getHeight()) {\r
- endy = da.getHeight();\r
- }\r
-\r
- if (endx > da.getWidth()) {\r
- endx = da.getWidth();\r
- }\r
-\r
- }\r
- } else*/ {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
- oldstarty = starty;\r
- oldendy = endy;\r
-\r
- }\r
- }\r
-\r
- else if (oldstartx < startx)\r
- {\r
- // This is dragging horizontal scrollbar to the right\r
-\r
- int delx = (int)((startx - oldstartx) * charWidth);\r
- int delx2 = (int)((oldendx - startx + 1) * charWidth);\r
-\r
- gg.copyArea(delx,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),-delx,0);\r
-\r
- if (startx > oldendx)\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- else\r
- drawPanel(gg,oldendx+1,endx,starty,endy,startx,starty,0);\r
-\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
-\r
- } else if (oldstartx > startx)\r
- {\r
- // Horizontal scrollbar pulled to the left\r
-\r
- int delx = (int)((oldstartx - startx) * charWidth);\r
- int delx2 = (int)((endx - oldstartx +1) * charWidth);\r
-\r
- gg.copyArea(0,0,delx2,AlignmentUtil.getPixelHeight(starty,endy,charHeight),delx,0);\r
-\r
- if (oldstartx > endx) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,oldstartx-1,starty,endy,startx,starty,0);\r
- }\r
-\r
- oldstartx = startx;\r
- oldendx = endx;\r
-\r
- } else if (oldstarty < starty) {\r
- // Vertical scrollbar down\r
- int dely = AlignmentUtil.getPixelHeight(oldstarty,starty,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(starty,oldendy,charHeight);\r
-\r
- gg.copyArea(0,dely,(int)((endx-startx+1)*charWidth),dely2,0,-dely);\r
-\r
- if (starty > oldendy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,oldendy,endy,startx,starty,0);\r
- }\r
-\r
- oldstarty = starty;\r
- oldendy = endy;\r
-\r
- } else if (oldstarty > starty) {\r
-\r
- // Vertical scrollbar up\r
- int dely = AlignmentUtil.getPixelHeight(endy,oldendy,charHeight);\r
- int dely2 = AlignmentUtil.getPixelHeight(oldstarty,endy,charHeight);\r
-\r
- gg.copyArea(0,0,(int)((endx-startx+1)*charWidth),dely2,0,dely);\r
-\r
- if (oldstarty > endy) {\r
- drawPanel(gg,startx,endx,starty,endy,startx,starty,0);\r
- } else {\r
- drawPanel(gg,startx,endx,starty,oldstarty,startx,starty,0);\r
- }\r
-\r
- oldstarty = starty;\r
- oldendy = endy;\r
- }\r
-\r
- if ((oldendy -oldstarty) > (int)((getWidth() / av.getCharWidth()))) {\r
- System.out.println("LIMITS ERROR LIMITS ERROR");\r
- System.out.println("Corrds " + (oldendy-oldstarty) + " " + (int)(getWidth()/av.getCharWidth()) + " " + getWidth() + " " + av.getCharWidth());\r
- }\r
-\r
-\r
- g.drawImage(img,0,0,this);\r
-\r
- }\r
-\r
-\r
-\r
-\r
- public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {\r
-\r
-/*\r
- System.out.println("drawPanel called with g = " + g);\r
- System.out.println(" x1 = " + x1);\r
- System.out.println(" x2 = " + x2);\r
- System.out.println(" y1 = " + y1);\r
- System.out.println(" y2 = " + y2);\r
- System.out.println(" startx = " + startx);\r
- System.out.println(" starty = " + starty);\r
-*/\r
-\r
- g.setFont(av.getFont());\r
- double charWidth = av.getCharWidth();\r
- int charHeight = av.getCharHeight();\r
- RendererI sr = av.getRenderer();\r
-\r
-\r
- /*Vector pid = av.getConsensus(false);\r
-\r
- Vector tmpseq = new Vector();\r
-\r
- for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
- if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
- tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
-\r
-\r
-\r
- if (sr instanceof SequenceRenderer)\r
- pid = AAFrequency.calculate(tmpseq,x1,x2);\r
-\r
- else if (sr instanceof GraphRenderer)\r
- pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
- av.getAlignment().getSequences(),\r
- av.getPIDWindow(),x1,x2);\r
-\r
-*/\r
-\r
- if (y2 > starty && y1 < av.getEndSeq()) {\r
-\r
- fillBackground(g,\r
- Color.white,\r
- (int)((x1-startx)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),\r
- (int)((x2-x1+1)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));\r
- }\r
-\r
- for (int i = y1 ; i < y2 ;i++) {\r
-\r
- RendererI r = sr;\r
-/*\r
- if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
- r = fr;\r
- System.out.println("use feature renderer");\r
- } else if ( i == 0) {\r
- // r = br;\r
- } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
- r = cgr;\r
- System.out.println("cg renderer");\r
- }\r
-*/\r
-\r
- r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),\r
- x1,\r
- x2,\r
- (int)((x1-startx)*charWidth),\r
- offset + AlignmentUtil.getPixelHeight(starty,i,av.getCharHeight()),\r
- charWidth,\r
- charHeight,showScores,av.getShowBoxes(),av.getShowText(),null,i,av);\r
-\r
- }\r
- }\r
-\r
-\r
-\r
- public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {\r
- g.setColor(c);\r
- g.fillRect(x1,y1,width,height);\r
- }\r
-\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.image.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * 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;
+ 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ 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);
+ }
+ }
+
+ /**
+ * 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 += av.charHeight;
+
+ if (av.hasHiddenColumns)
+ {
+ startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ int maxwidth = av.alignment.getWidth();
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ // WEST SCALE
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ SequenceI seq = av.alignment.getSequenceAt(i);
+ int index = startx;
+ int value = -1;
+
+ while (index < endx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+ {
+ index++;
+
+ continue;
+ }
+
+ value = av.alignment.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));
+ }
+ }
+ }
+
+ /**
+ * 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 += av.charHeight;
+
+ if (av.hasHiddenColumns)
+ {
+ endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ seq = av.alignment.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));
+ }
+ }
+ }
+
+ 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)
+ {
+ return;
+ }
+ fastpainting = true;
+ if (gg == null)
+ {
+ return;
+ }
+
+ fastPaint = true;
+
+ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
+ imgWidth, imgHeight, -horizontal * av.charWidth, -vertical
+ * av.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) * av.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 * 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();
+ 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)
+ {
+ 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 % av.charWidth);
+ imgHeight -= (imgHeight % av.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.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 = "00";
+ int maxWidth = 0;
+ int tmp;
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ tmp = av.alignment.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)
+ {
+ 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.alignment.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.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);
+
+ }
+ }
+
+ // 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 * av.charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
+ (int) clip.getBounds().getHeight());
+ }
+
+ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+
+ if (av.showAnnotation)
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.drawComponent((Graphics2D) g, 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.showAnnotation)
+ {
+ 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!
+ */
+ 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
+ {
+ java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+ int screenY = 0;
+ int blockStart = startRes;
+ int blockEnd = endRes;
+
+ for (int i = 0; regions != null && i < regions.size(); i++)
+ {
+ int[] region = (int[]) regions.elementAt(i);
+ 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.alignment.getSequenceAt(i);
+ if (nextSeq == null)
+ {
+ // occasionally, a race condition occurs such that the alignment row is
+ // empty
+ continue;
+ }
+ sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+
+ if (av.showSequenceFeatures)
+ {
+ 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.alignment.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) * av.charWidth;
+
+ if ((group == null) && (av.alignment.getGroups().size() > 0))
+ {
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(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) * av.charWidth;
+ sy = offset + ((i - startSeq) * av.charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+
+ if (sx + ex < 0 || sx > visWidth)
+ {
+ continue;
+ }
+
+ if ((sx <= (endRes - startRes) * av.charWidth)
+ && group.getSequences(null).contains(
+ av.alignment.getSequenceAt(i)))
+ {
+ if ((bottom == -1)
+ && !group.getSequences(null).contains(
+ av.alignment.getSequenceAt(i + 1)))
+ {
+ bottom = sy + av.charHeight;
+ }
+
+ if (!inGroup)
+ {
+ if (((top == -1) && (i == 0))
+ || !group.getSequences(null).contains(
+ av.alignment.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) * 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 < 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) * 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++;
+
+ g.setStroke(new BasicStroke());
+
+ if (groupIndex >= av.alignment.getGroups().size())
+ {
+ break;
+ }
+
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(
+ groupIndex);
+
+ } while (groupIndex < av.alignment.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