+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class SequenceRenderer implements RendererI\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceRenderer\r
{\r
+ AlignViewport av;\r
FontMetrics fm;\r
+ boolean renderGaps = true;\r
+ SequenceGroup currentSequenceGroup = null;\r
+ SequenceGroup[] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
+ boolean monospacedFont;\r
+ boolean forOverview = false;\r
+\r
+ /**\r
+ * Creates a new SequenceRenderer object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public SequenceRenderer(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void prepare(Graphics g, boolean renderGaps)\r
+ {\r
+ graphics = g;\r
+ fm = g.getFontMetrics();\r
+\r
+ // If EPS graphics, stringWidth will be a double, not an int\r
+ double dwidth = fm.getStringBounds("M", g).getWidth();\r
\r
- Color c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);\r
- return c;\r
+ monospacedFont =\r
+ (dwidth == fm.getStringBounds("|", g).getWidth()\r
+ && (float) av.charWidth == dwidth);\r
\r
+ this.renderGaps = renderGaps;\r
}\r
\r
+ public Color getResidueBoxColour(SequenceI seq, int i)\r
+ {\r
+ allGroups = av.alignment.findAllGroups(seq);\r
\r
- public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText, boolean colourText,Vector freq, int seqnum) {\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r
\r
+ return resBoxColour;\r
+ }\r
\r
- if (displayBoxes)\r
- drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+ {\r
+ if (cs != null)\r
+ {\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);\r
+ }\r
+ else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
+ {\r
+ resBoxColour = Color.lightGray;\r
+ }\r
+ else\r
+ {\r
+ resBoxColour = Color.white;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int y1)\r
+ {\r
+ allGroups = sg;\r
\r
- if (displayText)\r
+ drawBoxes(seq, start, end, y1);\r
+\r
+ if (av.validCharWidth)\r
{\r
- fm = g.getFontMetrics();\r
- drawText(g,cs,colourText,seq,start,end,x1,y1,(int)width,height);\r
+ drawText(seq, start, end, y1);\r
}\r
}\r
\r
- public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {\r
- int i = start;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)\r
+ {\r
+ int i = start;\r
int length = seq.getLength();\r
\r
- Color currentColor = Color.WHITE;\r
+ int curStart = -1;\r
+ int curWidth = av.charWidth;\r
\r
- int curStart = x1;\r
- int curWidth = width;\r
+ Color tempColour = null;\r
\r
- // int threshold = 80;\r
+ while (i <= end)\r
+ {\r
+ resBoxColour = Color.white;\r
\r
- while (i <= end && i < length) {\r
- Color c = getResidueBoxColour(cs,seq,i);\r
+ if (i < length)\r
+ {\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, 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
\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
- {\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 (c != currentColor || c != null)\r
+ if (resBoxColour != tempColour)\r
{\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+ if (tempColour != null)\r
+ {\r
+ graphics.fillRect(av.charWidth * (curStart - start), y1,\r
+ curWidth, av.charHeight);\r
+ }\r
\r
- currentColor = c;\r
- g.setColor(c);\r
+ graphics.setColor(resBoxColour);\r
\r
curStart = i;\r
- curWidth = width;\r
+ curWidth = av.charWidth;\r
+ tempColour = resBoxColour;\r
}\r
else\r
- curWidth += width;\r
+ {\r
+ curWidth += av.charWidth;\r
+ }\r
\r
i++;\r
}\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
+\r
+ graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,\r
+ av.charHeight);\r
+\r
}\r
\r
- public void drawText(Graphics g, ColourSchemeI cs, boolean colText, SequenceI seq,int start, int end, int x1, int y1, int width, int height)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void drawText(SequenceI seq, int start, int end, int y1)\r
{\r
- int pady = height/5;\r
- int charOffset=0;\r
- g.setColor(Color.black);\r
-\r
+ y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady\r
+ int charOffset = 0;\r
char s;\r
- // Need to find the sequence position here.\r
- for (int i = start; i <= end; i++)\r
+\r
+ if (end + 1 >= seq.getLength())\r
{\r
- if (i < end && i < seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
- else if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
- else\r
- s = ' ';\r
+ end = seq.getLength() - 1;\r
+ }\r
+ graphics.setColor(av.textColour);\r
\r
- if (colText)\r
+ if (monospacedFont\r
+ && av.showText\r
+ && allGroups.length == 0\r
+ && !av.getColourText()\r
+ && av.thresholdTextColour == 0)\r
+ {\r
+ if (av.renderGaps)\r
+ {\r
+ graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);\r
+ }\r
+ else\r
+ {\r
+ char gap = av.getGapCharacter();\r
+ graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,\r
+ ' '), 0, y1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ boolean getboxColour = false;\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ graphics.setColor(av.textColour);\r
+ getboxColour = false;\r
+ s = seq.getCharAt(i);\r
+ if (!renderGaps && jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (!currentSequenceGroup.getDisplayText())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (currentSequenceGroup.thresholdTextColour > 0\r
+ || currentSequenceGroup.getColourText())\r
+ {\r
+ getboxColour = true;\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+\r
+ if (currentSequenceGroup.getColourText())\r
+ {\r
+ graphics.setColor(resBoxColour.darker());\r
+ }\r
+\r
+ if (currentSequenceGroup.thresholdTextColour > 0)\r
+ {\r
+ if (resBoxColour.getRed() +\r
+ resBoxColour.getBlue() +\r
+ resBoxColour.getGreen() <\r
+ currentSequenceGroup.thresholdTextColour)\r
+ {\r
+ graphics.setColor(currentSequenceGroup.textColour2);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ graphics.setColor(currentSequenceGroup.textColour);\r
+ }\r
+\r
+ }\r
+ else\r
{\r
- Color c = getResidueBoxColour(cs, seq, i);\r
- g.setColor(c.darker());\r
+ if (!av.getShowText())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (av.getColourText())\r
+ {\r
+ getboxColour = true;\r
+ getBoxColour(av.globalColourScheme, 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
+ if (av.thresholdTextColour > 0)\r
+ {\r
+ if (!getboxColour)\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r
+\r
+ if (resBoxColour.getRed() +\r
+ resBoxColour.getBlue() +\r
+ resBoxColour.getGreen() < av.thresholdTextColour)\r
+ {\r
+ graphics.setColor(av.textColour2);\r
+ }\r
+ }\r
+\r
}\r
\r
- charOffset = (width - fm.charWidth(s))/2;\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + av.charWidth * (i - start),\r
+ y1);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param res DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ boolean inCurrentSequenceGroup(int res)\r
+ {\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 true;\r
+ }\r
+ }\r
\r
+ return false;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
+ int y1)\r
+ {\r
+ int pady = av.charHeight / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.BLACK);\r
+ graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);\r
+ graphics.setColor(Color.white);\r
+\r
+ char s = '~';\r
+\r
+ // Need to find the sequence position here.\r
+ if (av.validCharWidth)\r
+ {\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ if (i < seq.getLength())\r
+ {\r
+ s = seq.getCharAt(i);\r
+ }\r
\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1 + (av.charWidth * (i - start)),\r
+ (y1 + av.charHeight) - pady);\r
+ }\r
}\r
}\r
\r
+ public void drawCursor(SequenceI seq, int res, int x1, int y1)\r
+ {\r
+ int pady = av.charHeight / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.black);\r
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);\r
+\r
+ if (av.validCharWidth)\r
+ {\r
+ graphics.setColor(Color.white);\r
+\r
+ char s = seq.getCharAt(res);\r
+\r
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s),\r
+ charOffset + x1,\r
+ (y1 + av.charHeight) - pady);\r
+ }\r
+\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff