-/*\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
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\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
- /**\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
- if (sf.getStart() > seq.getEnd())\r
- {\r
- continue;\r
- }\r
-\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
- int fend = seq.findIndex(sf.getEnd()) - 1;\r
-\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
- if (fend >= end)\r
- {\r
- fend = end;\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
- 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
+{
+ Color resBoxColour;
+
+ AlignmentPanel ap;
+
+ /**
+ * Creates a new FeatureRenderer object
+ *
+ * @param alignPanel
+ */
+ public FeatureRenderer(AlignmentPanel alignPanel)
+ {
+ super(alignPanel.av);
+ this.ap = alignPanel;
+ if (alignPanel.getSeqPanel() != null
+ && alignPanel.getSeqPanel().seqCanvas != null
+ && alignPanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff