4 import javax.swing.*;
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5 import java.awt.event.*;
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6 import jalview.datamodel.*;
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7 import jalview.schemes.*;
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8 import jalview.analysis.*;
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11 public class SeqCanvas extends JPanel
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21 public boolean paintFlag = false;
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23 boolean showScores = false;
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24 boolean displaySearch = false;
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25 int [] searchResults = null;
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31 public SeqCanvas(AlignViewport av)
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34 fr = new FeatureRenderer(av);
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35 setLayout(new BorderLayout());
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36 PaintRefresher.Register(this);
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40 public void drawScale(Graphics g, int startx, int endx,int ypos) {
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41 int scalestartx = startx - startx%10 + 10;
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43 g.setColor(Color.black);
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45 for (int i=scalestartx;i < endx;i+= 10)
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47 String string = String.valueOf(i);
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48 g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
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50 g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,
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51 (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );
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59 * Definitions of startx and endx (hopefully):
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60 * SMJS This is what I'm working towards!
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61 * startx is the first residue (starting at 0) to display.
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62 * endx is the last residue to display (starting at 0).
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63 * starty is the first sequence to display (starting at 0).
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64 * endy is the last sequence to display (starting at 0).
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65 * NOTE 1: The av limits are set in setFont in this class and
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66 * in the adjustment listener in SeqPanel when the scrollbars move.
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69 public void paintComponent(Graphics g)
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72 if (img==null || imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
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74 imgWidth = getWidth();
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75 imgHeight = getHeight();
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76 img = createImage(imgWidth,imgHeight);
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77 gg = img.getGraphics();
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78 gg.setFont(av.getFont());
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83 chunkWidth = getWidth()/av.charWidth;
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84 chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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86 av.setChunkHeight(chunkHeight);
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87 av.setChunkWidth(chunkWidth);
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89 fillBackground(gg,Color.WHITE,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 g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
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130 g.setFont(av.getFont());
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131 int charWidth = av.getCharWidth();
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132 int charHeight = av.getCharHeight();
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133 RendererI sr = av.getRenderer();
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135 /*Vector pid = av.getConsensus(false);
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136 Vector tmpseq = new Vector();
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137 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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138 if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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139 tmpseq.addElement(av.getAlignment().getSequenceAt(i));
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141 if (sr instanceof SequenceRenderer)
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142 pid = AAFrequency.calculate(tmpseq,x1,x2);
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144 else if (sr instanceof GraphRenderer)
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145 pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
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146 av.getAlignment().getSequences(),
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147 av.getPIDWindow(),x1,x2);
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151 /* if (y2 > starty && y1 < av.getEndSeq())
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155 (x1-startx)*charWidth,
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156 offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
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157 (x2-x1+1)*charWidth,
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158 offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
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162 SequenceGroup group=null;
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163 SequenceGroup [] groups=null;
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164 boolean inGroup=false; // are we in a defined group?
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165 boolean inRB=false; //Are we in a rubberband group?
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166 int sx=-1, sy=-1, ex=-1, ey=-1;
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167 int oldStartX=0,oldEndX=0,oldY=0;
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168 int oldRStartX=0,oldREndX=0,oldRY=0;
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169 for (int i = y1 ; i < y2 ;i++)
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171 nextSeq = av.getAlignment().getSequenceAt(i);
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173 group = av.alignment.findGroup( nextSeq );
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174 groups = av.alignment.findAllGroups( nextSeq );
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176 sr.drawSequence(g, nextSeq, groups,x1,x2,
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177 (x1 - startx) * charWidth,
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178 offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
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179 charWidth,charHeight,null, i);
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181 if(av.showSequenceFeatures)
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183 fr.drawSequence(g, nextSeq, groups, x1, x2,
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184 (x1 - startx) * charWidth,
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186 AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
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187 charWidth, charHeight, null, i);
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196 g.setColor(Color.lightGray);
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198 sx = (group.getStartRes()-startx)*charWidth;
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199 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
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200 ex = (group.getEndRes()+1-startx)*charWidth;
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201 ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());
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206 g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
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210 g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side
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211 g.drawLine( ex,sy,ex,ey); // vertical line, right hand side
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212 if (i == y2 - 1)// last line of alignment, seal the box
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213 g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
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222 g.setColor(Color.lightGray);
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223 g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
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228 group = av.getRubberbandGroup();
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229 if( group != null && group.sequences.contains(nextSeq) )
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231 g.setColor(Color.RED.brighter());
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232 sx = (group.getStartRes() - startx) * charWidth;
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234 AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
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235 ex = (group.getEndRes() + 1 - startx) * charWidth;
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237 AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());
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242 g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
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246 g.drawLine(sx, sy, sx, ey); // vertical line, left hand side
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247 g.drawLine(ex, sy, ex, ey); // vertical line, right hand side
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248 if (i == y2 - 1) // last line of alignment, seal the box
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249 g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
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257 g.setColor(Color.RED.brighter());
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258 g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box
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266 /// Highlight search Results once all sequences have been drawn
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269 for(int r=0; r<searchResults.length; r+=3)
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271 int searchSeq = searchResults[r];
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272 int searchStart = searchResults[r+1];
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273 int searchEnd = searchResults[r+2];
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275 if (searchSeq >= y1 && searchSeq < y2)
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277 SequenceRenderer ssr = (SequenceRenderer) sr;
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278 ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
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281 (searchStart - startx) * charWidth,
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283 AlignmentUtil.getPixelHeight(starty, searchSeq,
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293 public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
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295 g.fillRect(x1,y1,width,height);
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298 public int getChunkWidth() {
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302 public void highlightSearchResults(int [] results)
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304 // results are in the order sequence, startRes, endRes
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306 displaySearch = false;
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308 displaySearch = true;
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310 searchResults = results;
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