-/*\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.appletgui;\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
- float transparency = .4f;\r
-\r
- // The following vector holds the features which are\r
- // to be added, in the correct order or rendering\r
- Vector featuresDisplayed;\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
- String version = System.getProperty("java.version");\r
- if (version.indexOf("1.1") == 0)\r
- highlightTransparent = false;\r
-\r
- }\r
-\r
-boolean highlightTransparent = true;\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
-\r
- if(seq.getSequenceFeatures()==null)\r
- return;\r
-\r
- Enumeration e = null, e2;\r
- String type;\r
- if(featuresDisplayed!=null)\r
- e = featuresDisplayed.elements();\r
- else\r
- e = seq.getSequenceFeatures().elements();\r
-\r
- if(highlightTransparent)\r
- {\r
- // MyGraphics.SetTransparency(g, transparency);\r
- }\r
-\r
-\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf=null;\r
- if(featuresDisplayed!=null)\r
- {\r
- e2 = seq.getSequenceFeatures().elements();\r
- type = e.nextElement().toString();\r
- while(e2.hasMoreElements())\r
- {\r
- sf = (SequenceFeature) e2.nextElement();\r
- if(sf.getType().equals(type))\r
- break;\r
- else\r
- sf = null;\r
- }\r
- }\r
- else\r
- {\r
- sf = (SequenceFeature) e.nextElement();\r
- type = sf.getType();\r
- }\r
-\r
- if(sf==null)\r
- continue;\r
-\r
-\r
- if (sf.getBegin() > seq.getEnd())\r
- {\r
- continue;\r
- }\r
-\r
- int fstart = seq.findIndex(sf.getBegin()) - 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(getColour(type));\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(getColour(type));\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
- if (highlightTransparent)\r
- {\r
- // MyGraphics.SetTransparency(g, 1.0f);\r
- }\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- return (Color)featureColours.get(featureType);\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 = new Vector();\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(185, 145, 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",\r
- 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
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+ AlignViewport av;
+
+ Hashtable featureColours = new Hashtable();
+
+ // A higher level for grouping features of a
+ // particular type
+ Hashtable featureGroups = null;
+
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
+ // This is actually an Integer held in the hashtable,
+ // Retrieved using the key feature type
+ Object currentColour;
+
+ String[] renderOrder;
+
+ FontMetrics fm;
+ int charOffset;
+
+ float transparency = 1f;
+
+ TransparencySetter transparencySetter = null;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public FeatureRenderer(AlignViewport av)
+ {
+ this.av = av;
+
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ transparencySetter = new TransparencySetter();
+ }
+ }
+
+ public void transferSettings(FeatureRenderer fr)
+ {
+ renderOrder = fr.renderOrder;
+ featureGroups = fr.featureGroups;
+ featureColours = fr.featureColours;
+ transparency = fr.transparency;
+ }
+
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
+ {
+ overview = true;
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
+ }
+
+ lastSequence = seq;
+ sequenceFeatures = lastSequence.getSequenceFeatures();
+ if (sequenceFeatures == null)
+ {
+ return initialCol;
+ }
+
+ sfSize = sequenceFeatures.length;
+
+ if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
+ {
+ return Color.white;
+ }
+
+ currentColour = null;
+
+ drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
+
+ if (currentColour == null)
+ {
+ return initialCol;
+ }
+
+ return new Color( ( (Integer) currentColour).intValue());
+ }
+
+ /**
+ * This is used by the Molecule Viewer to get the accurate colour
+ * of the rendered sequence
+ */
+ boolean overview = false;
+
+ int white = Color.white.getRGB();
+ public int findFeatureColour(int initialCol, int seqIndex, int column)
+ {
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
+ }
+
+ if (seqIndex != lastSequenceIndex)
+ {
+ lastSequence = av.alignment.getSequenceAt(seqIndex);
+ lastSequenceIndex = seqIndex;
+ sequenceFeatures = lastSequence.getSequenceFeatures();
+ if (sequenceFeatures == null)
+ {
+ return initialCol;
+ }
+
+ sfSize = sequenceFeatures.length;
+ }
+
+ if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
+ {
+ return Color.white.getRGB();
+ }
+
+ currentColour = null;
+
+ drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
+
+ if (currentColour == null)
+ {
+ return initialCol;
+ }
+
+ return ( (Integer) currentColour).intValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ * @param sg DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ // String type;
+ // SequenceFeature sf;
+ int lastSequenceIndex = -1;
+ SequenceI lastSequence;
+ SequenceFeature[] sequenceFeatures;
+ int sfSize, sfindex, spos, epos;
+
+ public void drawSequence(Graphics g, SequenceI seq,
+ int start, int end, int y1)
+ {
+ if (seq.getSequenceFeatures() == null
+ || seq.getSequenceFeatures().length == 0)
+ {
+ return;
+ }
+
+ if (transparencySetter != null && g != null)
+ {
+ transparencySetter.setTransparency(g, transparency);
+ }
+
+ if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures())
+ {
+ lastSequence = seq;
+ sequenceFeatures = seq.getSequenceFeatures();
+ sfSize = sequenceFeatures.length;
+ }
+
+ if (av.featuresDisplayed == null || renderOrder == null)
+ {
+ findAllFeatures();
+ if (av.featuresDisplayed.size() < 1)
+ {
+ return;
+ }
+
+ sequenceFeatures = seq.getSequenceFeatures();
+ sfSize = sequenceFeatures.length;
+ }
+ if (!overview)
+ {
+ spos = lastSequence.findPosition(start);
+ epos = lastSequence.findPosition(end);
+ if (g != null)
+ {
+ fm = g.getFontMetrics();
+ }
+ }
+ String type;
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+ {
+ type = renderOrder[renderIndex];
+ if (!av.featuresDisplayed.containsKey(type))
+ {
+ continue;
+ }
+
+ // loop through all features in sequence to find
+ // current feature to render
+ for (sfindex = 0; sfindex < sfSize; sfindex++)
+ {
+ if (!sequenceFeatures[sfindex].type.equals(type))
+ {
+ continue;
+ }
+
+ if (featureGroups != null
+ && sequenceFeatures[sfindex].featureGroup != null
+ &&
+ featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+ &&
+ ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+ featureGroup)).
+ booleanValue())
+ {
+ continue;
+ }
+
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
+ || sequenceFeatures[sfindex].getEnd() < spos))
+ {
+ continue;
+ }
+
+ if (overview)
+ {
+ if (sequenceFeatures[sfindex].begin <= start &&
+ sequenceFeatures[sfindex].end >= start)
+ {
+ currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
+ type);
+ }
+
+ }
+ else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
+ {
+
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ new Color( ( (Integer) av.featuresDisplayed.get(
+ sequenceFeatures[sfindex].type)).intValue()),
+ start, end, y1);
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ new Color( ( (Integer) av.featuresDisplayed.get(
+ sequenceFeatures[sfindex].type)).intValue()),
+ start, end, y1);
+
+ }
+ else
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex].type),
+ start, end, y1);
+ }
+
+ }
+ }
+
+ if (transparencySetter != null && g != null)
+ {
+ transparencySetter.setTransparency(g, 1.0f);
+ }
+ }
+
+ char s;
+ int i;
+ void renderFeature(Graphics g, SequenceI seq,
+ int fstart, int fend, Color featureColour, int start,
+ int end, int y1)
+ {
+
+ if ( ( (fstart <= end) && (fend >= start)))
+ {
+ if (fstart < start)
+ { // fix for if the feature we have starts before the sequence start,
+ fstart = start; // but the feature end is still valid!!
+ }
+
+ if (fend >= end)
+ {
+ fend = end;
+ }
+
+ for (i = fstart; i <= fend; i++)
+ {
+ s = seq.getCharAt(i);
+
+ if (jalview.util.Comparison.isGap(s))
+ {
+ continue;
+ }
+
+ g.setColor(featureColour);
+
+ g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
+
+ if (!av.validCharWidth)
+ {
+ continue;
+ }
+
+ g.setColor(Color.white);
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s),
+ charOffset + (av.charWidth * (i - start)),
+ (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
+
+ }
+ }
+ }
+
+ void findAllFeatures()
+ {
+ jalview.schemes.UserColourScheme ucs = new
+ jalview.schemes.UserColourScheme();
+
+ av.featuresDisplayed = new Hashtable();
+ Vector allfeatures = new Vector();
+ for (int i = 0; i < av.alignment.getHeight(); i++)
+ {
+ SequenceFeature[] features = av.alignment.getSequenceAt(i).
+ getSequenceFeatures();
+
+ if (features == null)
+ {
+ continue;
+ }
+
+ int index = 0;
+ while (index < features.length)
+ {
+ if (!av.featuresDisplayed.containsKey(features[index].getType()))
+ {
+ if (getColour(features[index].getType()) == null)
+ {
+ featureColours.put(features[index].getType(),
+ ucs.createColourFromName(features[index].
+ getType()));
+ }
+
+ av.featuresDisplayed.put(features[index].getType(),
+ new Integer(getColour(features[index].
+ getType()).getRGB()));
+ allfeatures.addElement(features[index].getType());
+ }
+ index++;
+ }
+ }
+
+ renderOrder = new String[allfeatures.size()];
+ Enumeration en = allfeatures.elements();
+ int i = allfeatures.size() - 1;
+ while (en.hasMoreElements())
+ {
+ renderOrder[i] = en.nextElement().toString();
+ i--;
+ }
+ }
+
+ public Color getColour(String featureType)
+ {
+ return (Color) featureColours.get(featureType);
+ }
+
+ public void addNewFeature(String name, Color col)
+ {
+
+ setColour(name, col);
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable();
+ }
+
+ av.featuresDisplayed.put(name, "NOGROUP");
+ }
+
+ public void setColour(String featureType, Color col)
+ {
+ featureColours.put(featureType, col);
+ }
+
+ public void setFeaturePriority(Object[][] data)
+ {
+ // The feature table will display high priority
+ // features at the top, but theses are the ones
+ // we need to render last, so invert the data
+ if (av.featuresDisplayed != null)
+ {
+ av.featuresDisplayed.clear();
+ }
+
+ renderOrder = new String[data.length];
+
+ if (data.length > 0)
+ {
+ for (int i = 0; i < data.length; i++)
+ {
+ String type = data[i][0].toString();
+ setColour(type, (Color) data[i][1]);
+ if ( ( (Boolean) data[i][2]).booleanValue())
+ {
+ av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
+ }
+
+ renderOrder[data.length - i - 1] = type;
+ }
+ }
+ }
+
+ public void featuresAdded()
+ {
+ findAllFeatures();
+ }
+}
+
+class TransparencySetter
+{
+ void setTransparency(Graphics g, float value)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(
+ AlphaComposite.getInstance(
+ AlphaComposite.SRC_OVER, value));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff