4 import javax.swing.*;
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5 import jalview.datamodel.*;
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6 import jalview.analysis.*;
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9 public class SeqCanvas extends JPanel
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19 public boolean paintFlag = false;
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21 boolean showScores = false;
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22 boolean displaySearch = false;
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23 int [] searchResults = null;
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29 public SeqCanvas(AlignViewport av)
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32 fr = new FeatureRenderer(av);
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33 setLayout(new BorderLayout());
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34 PaintRefresher.Register(this);
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38 public void drawScale(Graphics g, int startx, int endx,int ypos) {
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39 int scalestartx = startx - startx%10 + 10;
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41 g.setColor(Color.black);
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43 for (int i=scalestartx;i < endx;i+= 10)
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45 String string = String.valueOf(i);
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46 g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
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48 g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,
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49 (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );
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57 * Definitions of startx and endx (hopefully):
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58 * SMJS This is what I'm working towards!
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59 * startx is the first residue (starting at 0) to display.
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60 * endx is the last residue to display (starting at 0).
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61 * starty is the first sequence to display (starting at 0).
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62 * endy is the last sequence to display (starting at 0).
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63 * NOTE 1: The av limits are set in setFont in this class and
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64 * in the adjustment listener in SeqPanel when the scrollbars move.
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67 public void paintComponent(Graphics g)
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70 if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
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72 imgWidth = getWidth();
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73 imgHeight = getHeight();
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74 img = createImage(imgWidth,imgHeight);
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75 gg = (Graphics2D)img.getGraphics();
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76 gg.setFont(av.getFont());
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77 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
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82 chunkWidth = getWidth()/av.charWidth;
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83 chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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85 av.setChunkHeight(chunkHeight);
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86 av.setChunkWidth(chunkWidth);
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88 gg.setColor(Color.WHITE);
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89 gg.fillRect(0,0,imgWidth,imgHeight);
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91 if (av.getWrapAlignment())
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92 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
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94 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
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97 g.drawImage(img,0,0,this);
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101 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
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103 AlignmentI da = av.getAlignment();
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105 int cWidth = canvasWidth/av.charWidth;
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106 int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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108 int endx = startRes+cWidth-1;
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109 int ypos = 2*av.charHeight;
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111 while (ypos <= canvasHeight)
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113 drawScale(g, startRes, endx, ypos);
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114 drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
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117 startRes += cWidth;
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118 endx = startRes + cWidth - 1;
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120 if (endx > da.getWidth())
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121 endx = da.getWidth();
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127 public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
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130 Graphics2D g = (Graphics2D)g1;
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131 g.setFont(av.getFont());
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132 RendererI sr = av.getRenderer();
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134 /*Vector pid = av.getConsensus(false);
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135 Vector tmpseq = new Vector();
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136 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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137 if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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138 tmpseq.addElement(av.getAlignment().getSequenceAt(i));
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140 if (sr instanceof SequenceRenderer)
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141 pid = AAFrequency.calculate(tmpseq,x1,x2);
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143 else if (sr instanceof GraphRenderer)
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144 pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
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145 av.getAlignment().getSequences(),
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146 av.getPIDWindow(),x1,x2);
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150 /* if (y2 > starty && y1 < av.getEndSeq())
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154 (x1-startx)*charWidth,
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155 offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
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156 (x2-x1+1)*charWidth,
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157 offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
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162 /// First draw the sequences
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163 /////////////////////////////
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164 for (int i = y1 ; i < y2 ;i++)
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166 nextSeq = av.getAlignment().getSequenceAt(i);
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168 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
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169 (x1 - startx) * av.charWidth,
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170 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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171 av.charWidth,av.charHeight,null, i);
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173 if(av.showSequenceFeatures)
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175 fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
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176 (x1 - startx) * av.charWidth,
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178 AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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179 av.charWidth, av.charHeight, null, i);
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183 /////////////////////////////////////
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185 // Now outline any areas if necessary
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186 /////////////////////////////////////
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187 SequenceGroup group = av.getSelectionGroup();
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188 java.util.Vector groups = av.alignment.getGroups();
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190 int sx = -1, sy = -1, ex = -1;
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191 int groupIndex = -1;
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192 if (group == null && groups.size() > 0)
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194 group = (SequenceGroup) groups.elementAt(0);
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203 boolean inGroup = false;
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204 for (i = y1; i < y2; i++)
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206 sx = (group.getStartRes() - startx) * av.charWidth;
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207 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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208 ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
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210 if (group.sequences.contains(av.alignment.getSequenceAt(i))
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218 if (group == av.getSelectionGroup())
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220 g.setStroke(new BasicStroke(2, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,2f,2f}, 0f ));
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221 g.setColor(Color.RED);
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225 g.setStroke(new BasicStroke());
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226 g.setColor(group.getOutlineColour());
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234 g.drawRect(sx, oldY, ex, (sy - oldY));
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241 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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242 g.drawRect(sx, oldY, ex, (sy - oldY));
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247 if (groupIndex >= groups.size())
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250 group = (SequenceGroup) groups.elementAt(groupIndex);
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253 while (groupIndex < groups.size());
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256 /// Highlight search Results once all sequences have been drawn
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257 //////////////////////////////////////////////////////////
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260 for(int r=0; r<searchResults.length; r+=3)
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262 int searchSeq = searchResults[r];
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263 int searchStart = searchResults[r+1];
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264 int searchEnd = searchResults[r+2];
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266 if (searchSeq >= y1 && searchSeq < y2)
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268 SequenceRenderer ssr = (SequenceRenderer) sr;
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269 ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
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272 (searchStart - startx) * av.charWidth,
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274 AlignmentUtil.getPixelHeight(starty, searchSeq,
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285 public int getChunkWidth() {
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289 public void highlightSearchResults(int [] results)
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291 // results are in the order sequence, startRes, endRes
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293 displaySearch = false;
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295 displaySearch = true;
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297 searchResults = results;
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