+/*\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 jalview.datamodel.*;\r
-import jalview.schemes.*;\r
+\r
import java.awt.*;\r
+\r
import java.util.*;\r
\r
-public class FeatureRenderer implements RendererI\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class FeatureRenderer\r
{\r
- AlignViewport av;\r
+ AlignViewport av;\r
+ SequenceGroup currentSequenceGroup = null;\r
+ SequenceGroup[] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
+ /**\r
+ * Creates a new FeatureRenderer object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public FeatureRenderer(AlignViewport av)\r
+ {\r
+ this.av = av;\r
+ }\r
\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\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(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width, int height)\r
+ {\r
+ Vector features = seq.getSequenceFeatures();\r
+ Enumeration e = features.elements();\r
\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\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
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
- {\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
+ if (sf.getStart() > seq.getEnd())\r
+ {\r
+ continue;\r
+ }\r
\r
- if( (fstart<=end && fend>=start) )\r
- {\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
+ int fstart = seq.findIndex(sf.getStart()) - 1;\r
+ int fend = seq.findIndex(sf.getEnd()) - 1;\r
\r
- if(fstart==fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
- g.setColor(Color.white);\r
+ if (((fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
\r
- }\r
- else\r
- {\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
- char s = seq.getSequence().charAt(i);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\r
- }\r
- }\r
- }\r
+ if (fstart == fend)\r
+ {\r
+ g.setColor(Color.red);\r
+ g.fillRoundRect((fstart - start) * width, y1, width,\r
+ height, 4, 4);\r
+ g.setColor(Color.white);\r
\r
- }\r
- }\r
+ char s = seq.getSequence().charAt(fstart);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (fstart - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ else\r
+ {\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
\r
+ g.setColor(Color.blue);\r
+ g.fillRect((i - start) * width, y1, width, height);\r
+\r
+ g.setColor(Color.white);\r
+\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff