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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56 public void fastPaint(int horizontal, int vertical)
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58 if(horizontal==0 && vertical==0)
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64 if (img==null || paintFlag)
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70 gg.copyArea( 0,0, imgWidth, imgHeight, -horizontal*av.charWidth, -vertical*av.charHeight );
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72 int sr=av.startRes, er=av.endRes+1, ss = av.startSeq, es = av.endSeq, transX=0, transY = 0;
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73 if(horizontal>0) // scrollbar pulled right, image to the left
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75 transX = (er-sr-horizontal)*av.charWidth;
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76 sr = er - horizontal ;
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78 else if(horizontal<0)
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86 if(vertical>0) // scroll down
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88 transY = imgHeight - vertical*av.charHeight;
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98 gg.translate(transX, transY);
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100 drawPanel(gg, sr,er,ss,es,sr,ss,0);
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102 gg.translate( -transX, -transY );
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103 getGraphics().drawImage(img,0,0,this);
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108 * Definitions of startx and endx (hopefully):
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109 * SMJS This is what I'm working towards!
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110 * startx is the first residue (starting at 0) to display.
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111 * endx is the last residue to display (starting at 0).
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112 * starty is the first sequence to display (starting at 0).
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113 * endy is the last sequence to display (starting at 0).
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114 * NOTE 1: The av limits are set in setFont in this class and
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115 * in the adjustment listener in SeqPanel when the scrollbars move.
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118 public void paintComponent(Graphics g)
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120 // this draws the whole of the alignment
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122 imgWidth = getWidth();
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123 imgHeight = getHeight();
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125 imgWidth -= imgWidth%av.charWidth;
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126 imgHeight-= imgHeight%av.charHeight;
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128 img = createImage(imgWidth,imgHeight);
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129 gg = (Graphics2D)img.getGraphics();
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130 gg.setFont(av.getFont());
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131 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
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132 gg.setClip(0,0,imgWidth, imgHeight);
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136 chunkWidth = getWidth()/av.charWidth;
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137 chunkHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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139 av.setChunkHeight(chunkHeight);
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140 av.setChunkWidth(chunkWidth);
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142 g.setColor(Color.WHITE);
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143 g.fillRect(0,0,getWidth(), getHeight());
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145 if (av.getWrapAlignment())
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146 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
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148 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
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151 g.drawImage(img,0,0,this);
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155 public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
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157 AlignmentI da = av.getAlignment();
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159 int cWidth = canvasWidth/av.charWidth;
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160 int cHeight = (av.getAlignment().getHeight() + 2)*av.charHeight;
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162 int endx = startRes+cWidth-1;
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163 int ypos = 2*av.charHeight;
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165 while (ypos <= canvasHeight)
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167 drawScale(g, startRes, endx, ypos);
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168 drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
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171 startRes += cWidth;
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172 endx = startRes + cWidth - 1;
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174 if (endx > da.getWidth())
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175 endx = da.getWidth();
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181 public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
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184 Graphics2D g = (Graphics2D)g1;
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185 g.setFont(av.getFont());
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186 RendererI sr = av.getRenderer();
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188 /*Vector pid = av.getConsensus(false);
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189 Vector tmpseq = new Vector();
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190 for (int i = 0; i < av.getAlignment().getHeight(); i++)
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191 if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
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192 tmpseq.addElement(av.getAlignment().getSequenceAt(i));
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194 if (sr instanceof SequenceRenderer)
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195 pid = AAFrequency.calculate(tmpseq,x1,x2);
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197 else if (sr instanceof GraphRenderer)
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198 pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
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199 av.getAlignment().getSequences(),
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200 av.getPIDWindow(),x1,x2);
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204 /* if (y2 > starty && y1 < av.getEndSeq())
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208 (x1-startx)*charWidth,
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209 offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
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210 (x2-x1+1)*charWidth,
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211 offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
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216 /// First draw the sequences
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217 /////////////////////////////
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218 for (int i = y1 ; i < y2 ;i++)
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220 nextSeq = av.getAlignment().getSequenceAt(i);
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222 sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
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223 (x1 - startx) * av.charWidth,
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224 offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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225 av.charWidth,av.charHeight,null, i);
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227 if(av.showSequenceFeatures)
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229 fr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ), x1, x2,
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230 (x1 - startx) * av.charWidth,
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232 AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
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233 av.charWidth, av.charHeight, null, i);
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237 /////////////////////////////////////
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239 // Now outline any areas if necessary
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240 /////////////////////////////////////
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241 SequenceGroup group = av.getSelectionGroup();
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242 java.util.Vector groups = av.alignment.getGroups();
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244 int sx = -1, sy = -1, ex = -1;
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245 int groupIndex = -1;
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246 if (group == null && groups.size() > 0)
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248 group = (SequenceGroup) groups.elementAt(0);
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257 boolean inGroup = false;
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258 for (i = y1; i < y2; i++)
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260 sx = (group.getStartRes() - startx) * av.charWidth;
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261 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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262 ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
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264 if (group.sequences.contains(av.alignment.getSequenceAt(i))
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272 if (group == av.getSelectionGroup())
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274 // g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,2f,2f}, 0f ));
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275 g.setColor(Color.RED);
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279 g.setStroke(new BasicStroke());
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280 g.setColor(group.getOutlineColour());
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288 g.drawRect(sx, oldY, ex, (sy - oldY));
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295 sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
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296 g.drawRect(sx, oldY, ex, (sy - oldY));
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301 if (groupIndex >= groups.size())
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304 group = (SequenceGroup) groups.elementAt(groupIndex);
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307 while (groupIndex < groups.size());
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310 /// Highlight search Results once all sequences have been drawn
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311 //////////////////////////////////////////////////////////
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314 for(int r=0; r<searchResults.length; r+=3)
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316 int searchSeq = searchResults[r];
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317 int searchStart = searchResults[r+1];
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318 int searchEnd = searchResults[r+2];
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320 if (searchSeq >= y1 && searchSeq < y2)
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322 SequenceRenderer ssr = (SequenceRenderer) sr;
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323 ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
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326 (searchStart - startx) * av.charWidth,
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328 AlignmentUtil.getPixelHeight(starty, searchSeq,
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339 public int getChunkWidth() {
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343 public void highlightSearchResults(int [] results)
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345 // results are in the order sequence, startRes, endRes
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347 displaySearch = false;
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349 displaySearch = true;
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351 searchResults = results;
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