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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20 public boolean paintFlag = false;
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22 boolean showScores = false;
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23 boolean displaySearch = false;
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24 int [] searchResults = null;
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30 public SeqCanvas(AlignViewport 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 = img.getGraphics();
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76 gg.setFont(av.getFont());
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81 chunkWidth = getWidth()/av.charWidth;
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82 chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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84 av.setChunkHeight(chunkHeight);
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85 av.setChunkWidth(chunkWidth);
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87 fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
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89 if (av.getWrapAlignment())
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90 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
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92 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
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95 g.drawImage(img,0,0,this);
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99 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
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101 AlignmentI da = av.getAlignment();
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103 int cWidth = canvasWidth/av.charWidth;
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104 int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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106 int endx = startRes+cWidth-1;
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107 int ypos = 2*av.charHeight;
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109 while (ypos <= canvasHeight)
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111 drawScale(g, startRes, endx, ypos);
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112 drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
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115 startRes += cWidth;
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116 endx = startRes + cWidth - 1;
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118 if (endx > da.getWidth())
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119 endx = da.getWidth();
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125 public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
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128 g.setFont(av.getFont());
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129 int charWidth = av.getCharWidth();
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130 int charHeight = av.getCharHeight();
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131 RendererI sr = av.getRenderer();
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133 /*Vector pid = av.getConsensus(false);
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134 Vector tmpseq = new Vector();
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135 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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136 if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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137 tmpseq.addElement(av.getAlignment().getSequenceAt(i));
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139 if (sr instanceof SequenceRenderer)
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140 pid = AAFrequency.calculate(tmpseq,x1,x2);
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142 else if (sr instanceof GraphRenderer)
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143 pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
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144 av.getAlignment().getSequences(),
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145 av.getPIDWindow(),x1,x2);
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149 /* if (y2 > starty && y1 < av.getEndSeq())
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153 (x1-startx)*charWidth,
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154 offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
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155 (x2-x1+1)*charWidth,
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156 offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
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160 SequenceGroup group=null;
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161 SequenceGroup [] groups=null;
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162 boolean inGroup=false; // are we in a defined group?
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163 boolean inRB=false; //Are we in a rubberband group?
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164 int sx=-1, sy=-1, ex=-1, ey=-1;
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165 int oldStartX=0,oldEndX=0,oldY=0;
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166 int oldRStartX=0,oldREndX=0,oldRY=0;
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167 for (int i = y1 ; i < y2 ;i++)
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169 nextSeq = av.getAlignment().getSequenceAt(i);
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171 group = av.alignment.findGroup( nextSeq );
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172 groups = av.alignment.findAllGroups( nextSeq );
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174 sr.drawSequence(g, nextSeq, groups,x1,x2,
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175 (x1 - startx) * charWidth,
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176 offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
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177 charWidth,charHeight,null, i);
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183 g.setColor(Color.lightGray);
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185 sx = (group.getStartRes()-startx)*charWidth;
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186 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
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187 ex = (group.getEndRes()+1-startx)*charWidth;
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188 ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());
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193 g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
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197 g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side
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198 g.drawLine( ex,sy,ex,ey); // vertical line, right hand side
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199 if (i == y2 - 1)// last line of alignment, seal the box
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200 g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
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209 g.setColor(Color.lightGray);
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210 g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
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215 group = av.getRubberbandGroup();
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216 if( group != null && group.sequences.contains(nextSeq) )
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218 g.setColor(Color.RED.brighter());
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219 sx = (group.getStartRes() - startx) * charWidth;
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221 AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
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222 ex = (group.getEndRes() + 1 - startx) * charWidth;
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224 AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());
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229 g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
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233 g.drawLine(sx, sy, sx, ey); // vertical line, left hand side
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234 g.drawLine(ex, sy, ex, ey); // vertical line, right hand side
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235 if (i == y2 - 1) // last line of alignment, seal the box
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236 g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
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244 g.setColor(Color.RED.brighter());
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245 g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box
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253 /// Highlight search Results once all sequences have been drawn
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256 for(int r=0; r<searchResults.length; r+=3)
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258 int searchSeq = searchResults[r];
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259 int searchStart = searchResults[r+1];
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260 int searchEnd = searchResults[r+2];
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262 if (searchSeq >= y1 && searchSeq < y2)
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264 SequenceRenderer ssr = (SequenceRenderer) sr;
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265 ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
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268 (searchStart - startx) * charWidth,
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270 AlignmentUtil.getPixelHeight(starty, searchSeq,
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280 public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
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282 g.fillRect(x1,y1,width,height);
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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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