-/*\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
-\r
- Hashtable featureColours = new Hashtable();\r
-\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
- // This is actually an Integer held in the hashtable,\r
- // Retrieved using the key feature type\r
- Object currentColour;\r
-\r
- String [] renderOrder;\r
-\r
- boolean newFeatureAdded = false;\r
-\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
- public void transferSettings(FeatureRenderer fr)\r
- {\r
- renderOrder = fr.renderOrder;\r
- featureGroups = fr.featureGroups;\r
- featureColours = fr.featureColours;\r
- transparency = fr.transparency;\r
- }\r
-\r
- BufferedImage offscreenImage;\r
- boolean offscreenRender = false;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
- {\r
- return new Color( findFeatureColour (initialCol.getRGB(),\r
- seq, res ));\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer and Overview to\r
- * get the accurate colourof the rendered sequence\r
- */\r
- public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
- return Color.white.getRGB();\r
-\r
-\r
- //Only bother making an offscreen image if transparency is applied\r
- if(transparency!=1.0f && offscreenImage==null)\r
- {\r
- offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
- }\r
-\r
- currentColour = null;\r
-\r
- offscreenRender = true;\r
-\r
- if(offscreenImage!=null)\r
- {\r
- offscreenImage.setRGB(0,0,initialCol);\r
- drawSequence(offscreenImage.getGraphics(),\r
- lastSeq,\r
- column,column,0);\r
-\r
- return offscreenImage.getRGB(0,0);\r
- }\r
- else\r
- {\r
- drawSequence(null,\r
- lastSeq,\r
- lastSeq.findPosition(column),\r
- -1, -1);\r
-\r
- if (currentColour == null)\r
- return initialCol;\r
- else\r
- return ((Integer)currentColour).intValue();\r
- }\r
-\r
-\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
- // String type;\r
- // SequenceFeature sf;\r
- SequenceI lastSeq;\r
- SequenceFeature [] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
-\r
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1)\r
- {\r
- if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
- return;\r
-\r
- if(g!=null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- if (av.featuresDisplayed == null\r
- || renderOrder==null\r
- || newFeatureAdded)\r
- {\r
- findAllFeatures();\r
- newFeatureAdded = false;\r
- if(av.featuresDisplayed.size()<1)\r
- return;\r
-\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(lastSeq==null || seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if (transparency != 1 && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
- }\r
-\r
- if(!offscreenRender)\r
- {\r
- spos = lastSeq.findPosition(start);\r
- epos = lastSeq.findPosition(end);\r
- }\r
-\r
-\r
- String type;\r
- for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
-\r
- if(!av.featuresDisplayed.containsKey(type))\r
- continue;\r
-\r
- // loop through all features in sequence to find\r
- // current feature to render\r
- for (sfindex = 0; sfindex < sfSize; sfindex++)\r
- {\r
- if(sequenceFeatures.length<=sfindex)\r
- {\r
- continue;\r
- }\r
- if (!sequenceFeatures[sfindex].type.equals(type))\r
- continue;\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
-\r
- if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
-\r
- if (offscreenRender && offscreenImage==null)\r
- {\r
- if (sequenceFeatures[sfindex].begin <= start &&\r
- sequenceFeatures[sfindex].end >= start)\r
- {\r
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
- type);\r
- }\r
- }\r
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1);\r
-\r
-\r
- }\r
-\r
- }\r
-\r
- if(transparency!=1.0f && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, 1.0f));\r
- }\r
- }\r
-\r
-\r
- char s;\r
- int i;\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start, int end, int y1)\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
- int pady = (y1 + av.charHeight) - av.charHeight / 5;\r
- for (i = fstart; i <= fend; i++)\r
- {\r
- s = seq.getSequence().charAt(i);\r
-\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- g.setColor(featureColour);\r
-\r
- g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);\r
-\r
- if(offscreenRender || !av.validCharWidth)\r
- continue;\r
-\r
- g.setColor(Color.white);\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + (av.charWidth * (i - start)),\r
- pady);\r
-\r
- }\r
- }\r
- }\r
-\r
-\r
- public void featuresAdded()\r
- {\r
- newFeatureAdded = true;\r
- findAllFeatures();\r
- }\r
-\r
- boolean findingFeatures = false;\r
- synchronized void findAllFeatures()\r
- {\r
-\r
- if(findingFeatures)\r
- return;\r
-\r
- findingFeatures = true;\r
- jalview.schemes.UserColourScheme ucs = new\r
- jalview.schemes.UserColourScheme();\r
-\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- av.featuresDisplayed.clear();\r
-\r
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features\r
- = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
-\r
- if (features == null)\r
- continue;\r
-\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
- {\r
- if(!(features[index].begin == 0 && features[index].end ==0))\r
- {\r
- // If beginning and end are 0, the feature is for the whole sequence\r
- // and we don't want to render the feature in the normal way\r
-\r
- if (getColour(features[index].getType()) == null)\r
- {\r
- featureColours.put(features[index].getType(),\r
- ucs.createColourFromName(features[index].\r
- getType()));\r
- }\r
-\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer(getColour(features[index].\r
- getType()).getRGB()));\r
- allfeatures.addElement(features[index].getType());\r
- }\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- renderOrder = new String[allfeatures.size()];\r
- Enumeration en = allfeatures.elements();\r
- int i = allfeatures.size()-1;\r
- while(en.hasMoreElements())\r
- {\r
- renderOrder[i] = en.nextElement().toString();\r
- i--;\r
- }\r
-\r
- findingFeatures = false;\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- Color colour = (Color)featureColours.get(featureType);\r
- return colour;\r
- }\r
-\r
-\r
- public void addNewFeature(String name, Color col, String group)\r
- {\r
-\r
- setColour(name, col);\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- if(group == null)\r
- group = "NOGROUP";\r
-\r
- av.featuresDisplayed.put(name, new Integer(col.getRGB()));\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
- if(av.featuresDisplayed!=null)\r
- av.featuresDisplayed.clear();\r
- else\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- renderOrder = new String[data.length];\r
-\r
- if (data.length > 0)\r
- for (int i = 0; i < data.length; i++)\r
- {\r
- String type = data[i][0].toString();\r
- setColour(type, (Color) data[i][1]);\r
- if ( ( (Boolean) data[i][2]).booleanValue())\r
- {\r
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
- }\r
-\r
- renderOrder[data.length - i - 1] = type;\r
- }\r
-\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;
+
+/**
+ * A class that manages drawing of sequence features for the Swing gui
+ */
+public class FeatureRenderer
+ extends jalview.renderer.seqfeatures.FeatureRenderer
+{
+ 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