-/*\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
-import java.awt.image.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
- Color resBoxColour;\r
- float transparency = 1.0f;\r
- FontMetrics fm;\r
- int charOffset;\r
- boolean drawText = true;\r
-\r
- // The following vector holds the features which are\r
- // to be added, in the correct order or rendering\r
- Vector featuresDisplayed = null;\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
- initColours();\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
- BufferedImage bi;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if (bi == null)\r
- bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);\r
-\r
- bi.setRGB(0,0, initialCol.getRGB());\r
-\r
- drawText = false;\r
-\r
- drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
- drawText = true;\r
-\r
- return new Color(bi.getRGB(0, 0));\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(Graphics g, SequenceI seq,\r
- int start, int end, int x1, int y1, int width, int height)\r
- {\r
-\r
-//System.out.println(start+" "+end+" "+x1+" "+y1);\r
- if (seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().size()==0)\r
- return;\r
-\r
- fm = g.getFontMetrics();\r
-\r
- if (transparency != 1)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
- }\r
-\r
- String type;\r
- SequenceFeature sf;\r
- if (featuresDisplayed == null)\r
- findAllFeatures();\r
-\r
- Enumeration e = featuresDisplayed.elements(), e2;\r
-\r
- // Loop through each visible feature\r
- while (e.hasMoreElements())\r
- {\r
-\r
- type = e.nextElement().toString();\r
- e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
- // loop through all features in sequence to find\r
- // current feature to render\r
- while (e2.hasMoreElements())\r
- {\r
-\r
- sf = (SequenceFeature) e2.nextElement();\r
- if (!type.equals(sf.getType()))\r
- continue;\r
-\r
- if (sf.getBegin() > seq.getEnd())\r
- continue;\r
-\r
- if (type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- type, start, end, x1, y1, width, height);\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sf.getBegin()) - 1,\r
- seq.findIndex(sf.getEnd()) - 1,\r
- type, start, end, x1, y1, width, height);\r
- }\r
- }\r
-\r
- if(transparency!=1.0f)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, 1.0f));\r
- }\r
- }\r
-\r
-\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
- {\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
- 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(getColour(type));\r
-\r
- g.fillRect( (i - start) * width, y1, width, height);\r
-\r
- if(drawText)\r
- {\r
- g.setColor(Color.white);\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + (width * (i - start)),\r
- (y1 + height) - height / 5); //pady = height / 5;\r
- }\r
- }\r
- }\r
- }\r
-\r
- void findAllFeatures()\r
- {\r
- Vector features = new Vector();\r
- SequenceFeature sf;\r
- featuresDisplayed = new Vector();\r
- Enumeration e;\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
- getSequenceFeatures();\r
- if (features == null)\r
- continue;\r
-\r
- e = features.elements();\r
- while (e.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- if (!featuresDisplayed.contains(sf.getType()))\r
- {\r
- featuresDisplayed.addElement(sf.getType());\r
- }\r
- }\r
- }\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- return (Color)featureColours.get(featureType);\r
- }\r
-\r
- public void addNewFeature(String name, Color col)\r
- {\r
- setColour(name, col);\r
- if(featuresDisplayed==null)\r
- featuresDisplayed = new Vector();\r
- featuresDisplayed.insertElementAt(name, 0);\r
- }\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\r
- }\r
-\r
- public void setTransparency(float value)\r
- {\r
- transparency = value;\r
- }\r
-\r
- public float getTransparency()\r
- {\r
- return transparency;\r
- }\r
-\r
- public void setFeaturePriority(Object [][] data)\r
- {\r
- // The feature table will display high priority\r
- // features at the top, but theses are the ones\r
- // we need to render last, so invert the data\r
- featuresDisplayed.clear();\r
- for(int i=data.length-1; i>-1; i--)\r
- {\r
- String type = data[i][0].toString();\r
- setColour(type, (Color)data[i][1]);\r
- if( ((Boolean)data[i][2]).booleanValue() )\r
- featuresDisplayed.addElement(type);\r
- }\r
- }\r
-\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
- {\r
- featureColours.put("active site", new Color(255, 75, 0));\r
- featureColours.put("binding site", new Color(245, 85, 0));\r
- featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
- featureColours.put("chain", new Color(225, 105, 0));\r
- featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
- featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
- featureColours.put("cross-link", new Color(195, 135, 0));\r
- featureColours.put("disulfide bond", new Color(230,230,0));\r
- featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
- featureColours.put("domain", new Color(165, 165, 0));\r
- featureColours.put("glycosylation site", new Color(155, 175, 0));\r
- featureColours.put("helix", new Color(145, 185, 0));\r
- featureColours.put("initiator methionine", new Color(135, 195, 5));\r
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
- featureColours.put("modified residue", new Color(105, 225, 35));\r
- featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
- featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
- featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
- featureColours.put("peptide", new Color(55, 235, 85));\r
- featureColours.put("propeptide", new Color(45, 225, 95));\r
- featureColours.put("region of interest", new Color(35, 215, 105));\r
- featureColours.put("repeat", new Color(25, 205, 115));\r
- featureColours.put("selenocysteine", new Color(15, 195, 125));\r
- featureColours.put("sequence conflict", new Color(5, 185, 135));\r
- featureColours.put("sequence variant", new Color(0, 175, 145));\r
- featureColours.put("short sequence motif", new Color(0, 165, 155));\r
- featureColours.put("signal peptide", new Color(0, 155, 165));\r
- featureColours.put("site", new Color(0, 145, 175));\r
- featureColours.put("splice variant", new Color(0, 135, 185));\r
- featureColours.put("strand", new Color(0, 125, 195));\r
- featureColours.put("topological domain", new Color(0, 115, 205));\r
- featureColours.put("transit peptide", new Color(0, 105, 215));\r
- featureColours.put("transmembrane region", new Color(0, 95, 225));\r
- featureColours.put("turn", new Color(0, 85, 235));\r
- featureColours.put("unsure residue", new Color(0, 75, 245));\r
- featureColours.put("zinc finger region", new Color(0, 65, 255));\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
+ implements jalview.api.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