+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
+import java.awt.*;\r
+\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
\r
-public class SequenceRenderer implements RendererI\r
+public class SequenceRenderer\r
{\r
AlignViewport av;\r
FontMetrics fm;\r
boolean renderGaps = true;\r
SequenceGroup currentSequenceGroup = null;\r
- Color color;\r
+ SequenceGroup[] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
\r
public SequenceRenderer(AlignViewport av)\r
{\r
this.av = av;\r
}\r
\r
-\r
public void renderGaps(boolean b)\r
{\r
renderGaps = b;\r
\r
public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
- Color c = Color.white;\r
- try{\r
- c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);\r
- }catch(Exception ex){}\r
+ getBoxColour(cs, seq, i);\r
\r
- return c;\r
+ return resBoxColour;\r
+ }\r
+\r
+ void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+ {\r
+ if (cs != null)\r
+ {\r
+ resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+ }\r
+ else\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
}\r
\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width,\r
+ int height)\r
{\r
- currentSequenceGroup = sg;\r
+ allGroups = sg;\r
\r
- drawBoxes(g, seq, start, end, x1, y1, (int) width, height, pid);\r
+ graphics = g;\r
\r
- fm = g.getFontMetrics();\r
- drawText(g,seq,start,end,x1,y1,(int)width,height);\r
+ drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
\r
+ fm = g.getFontMetrics();\r
+ drawText(seq, start, end, x1, y1, (int) width, height);\r
}\r
\r
- public void drawBoxes(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {\r
- int i = start;\r
+ public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
+ {\r
+ int i = start;\r
int length = seq.getLength();\r
\r
- Color currentColor = Color.WHITE;\r
-\r
- int curStart = x1;\r
+ int curStart = -1;\r
int curWidth = width;\r
\r
- // int threshold = 80;\r
+ Color tempColour = null;\r
\r
- while (i <= end && i < length)\r
+ while ( (i <= end) && (i < length))\r
{\r
- color = color.white;\r
-\r
- if(inCurrentSequenceGroup(i))\r
+ if (inCurrentSequenceGroup(i))\r
{\r
- if( currentSequenceGroup.getDisplayBoxes())\r
- color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ else\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
}\r
- else if(av.getShowBoxes())\r
- color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
-\r
-\r
- // Hashtable hash = (Hashtable)freq.elementAt(i-start);\r
- // String s = (String)hash.get("maxResidue");\r
- // int count = ((Integer)hash.get("maxCount")).intValue();\r
- // int max = ((Integer)hash.get("size")).intValue();\r
- // int nongap = ((Integer)hash.get("nongap")).intValue();\r
- // float frac = (float)(count*1.0/(1.0*nongap));\r
-\r
- //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);\r
- /* if (!seq.getSequence().substring(i,i+1).equals(s) ||\r
- s.equals("-") ||\r
- s.equals(".") ||\r
- s.equals(" "))\r
+ else if (av.getShowBoxes())\r
{\r
- c = Color.white;\r
- } else {\r
- if (frac > 0.9) {\r
- c = Color.red;\r
- } else if (frac > 0.8) {\r
- c = Color.orange;\r
- } else if (frac > 0.7) {\r
- c = Color.pink;\r
- } else if (frac > 0.5) {\r
- c = Color.yellow;\r
- } else if (frac> 0.3) {\r
- c = Color.lightGray;\r
- }\r
- }*/\r
-\r
- if (color != currentColor || color != null)\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+ }\r
+ else\r
{\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ resBoxColour = Color.white;\r
+ }\r
\r
- currentColor = color;\r
- g.setColor(color);\r
+ if (resBoxColour != tempColour)\r
+ {\r
+ if (tempColour != null)\r
+ {\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
+ curWidth, height);\r
+ }\r
+\r
+ graphics.setColor(resBoxColour);\r
\r
curStart = i;\r
curWidth = width;\r
+ tempColour = resBoxColour;\r
}\r
else\r
+ {\r
curWidth += width;\r
+ }\r
\r
i++;\r
}\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
+ height);\r
}\r
\r
- public void drawText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
+ int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
- g.setColor(Color.black);\r
-\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
char s;\r
+\r
// Need to find the sequence position here.\r
+ String sequence = seq.getSequence();\r
+\r
for (int i = start; i <= end; i++)\r
{\r
- if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
- else\r
- s = ' ';\r
+ graphics.setColor(Color.black);\r
\r
- if(!renderGaps && (s=='-' || s=='.' || s==' '))\r
- continue;\r
+ if (i < sequence.length())\r
+ {\r
+ s = sequence.charAt(i);\r
+ }\r
+ else\r
+ {\r
+ s = ' ';\r
+ }\r
\r
- g.setColor(Color.black);\r
+ if (!renderGaps && jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
- if (inCurrentSequenceGroup(i))\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (!currentSequenceGroup.getDisplayText())\r
{\r
- if(!currentSequenceGroup.getDisplayText())\r
- continue;\r
+ continue;\r
+ }\r
\r
- if(currentSequenceGroup.getColourText())\r
- g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());\r
+ if (currentSequenceGroup.getColourText())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ graphics.setColor(resBoxColour.darker());\r
}\r
- else\r
+ }\r
+ else\r
+ {\r
+ if (!av.getShowText())\r
{\r
- if(!av.getShowText())\r
- continue;\r
+ continue;\r
+ }\r
\r
- if(av.getColourText())\r
- g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());\r
+ if (av.getColourText())\r
+ {\r
+ getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+\r
+ if (av.getShowBoxes())\r
+ {\r
+ graphics.setColor(resBoxColour.darker());\r
+ }\r
+ else\r
+ {\r
+ graphics.setColor(resBoxColour);\r
+ }\r
}\r
+ }\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
}\r
-\r
-\r
}\r
\r
boolean inCurrentSequenceGroup(int res)\r
{\r
- if(currentSequenceGroup==null)\r
+ if (allGroups == null)\r
+ {\r
return false;\r
+ }\r
+\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ {\r
+ if ( (allGroups[i].getStartRes() <= res) &&\r
+ (allGroups[i].getEndRes() >= res))\r
+ {\r
+ currentSequenceGroup = allGroups[i];\r
\r
- return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;\r
+ return true;\r
+ }\r
+ }\r
+\r
+ return false;\r
}\r
\r
- public void drawHighlightedText(Graphics g, SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
+ int y1, int width, int height)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
- g.setColor(Color.BLACK);\r
- g.fillRect(x1,y1,width*(end-start+1),height);\r
- g.setColor(Color.white);\r
+ int pady = height / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.BLACK);\r
+ graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
+ graphics.setColor(Color.white);\r
+\r
+ char s = '~';\r
\r
- char s='~';\r
// Need to find the sequence position here.\r
for (int i = start; i <= end; i++)\r
{\r
- if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
+ if (i < seq.getLength())\r
+ {\r
+ s = seq.getSequence().charAt(i);\r
+ }\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
}\r
}\r
-\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff