X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=21c401a447ee1d0cbf52a97dd56deedb57b65cc8;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=291ce5fbc944d3b99daa97765ef3362be34c344f;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index 291ce5f..21c401a 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -16,94 +16,394 @@ * 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 jalview.datamodel.*; import java.awt.*; -import jalview.datamodel.*; +import java.util.*; +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ public class FeatureRenderer { - AlignViewport av; - - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; - Color resBoxColour; - Graphics graphics; - - public FeatureRenderer(AlignViewport av) - { - this.av = av; - } - - public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg, - int start, int end, int x1, int y1, int width, - int height) - { - Vector features = seq.getSequenceFeatures(); - Enumeration e = features.elements(); - while (e.hasMoreElements()) + AlignViewport av; + + + // A higher level for grouping features of a + // particular type + Hashtable featureGroups = null; + + // This is actually an Integer held in the hashtable, + // Retrieved using the key feature type + Object currentColour; + + String [] renderOrder; + + boolean drawText = true; + FontMetrics fm; + int charOffset; + + /** + * Creates a new FeatureRenderer object. + * + * @param av DOCUMENT ME! + */ + public FeatureRenderer(AlignViewport av) { - SequenceFeature sf = (SequenceFeature) e.nextElement(); - if (sf.getStart() > seq.getEnd()) + this.av = av; + initColours(); + } + + + public Color findFeatureColour(Color initialCol, SequenceI seq, int i) + { + 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, -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) { - continue; + lastSequence = av.alignment.getSequenceAt(seqIndex); + lastSequenceIndex = seqIndex; + sequenceFeatures = lastSequence.getSequenceFeatures(); + if(sequenceFeatures==null) + return initialCol; + + sfSize = sequenceFeatures.length; } - int fstart = seq.findIndex(sf.getStart()) - 1; - int fend = seq.findIndex(sf.getEnd()) - 1; - if ( (fstart <= end && fend >= start)) + if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) + return Color.white.getRGB(); + + currentColour = null; + + drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -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, int width, int height) + { + if ( seq.getSequenceFeatures() == null + || seq.getSequenceFeatures().length==0) + return; + + + if(g!=null) + fm = g.getFontMetrics(); + + if (av.featuresDisplayed == null || renderOrder==null) + { + findAllFeatures(); + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + if(lastSequence==null || seq!=lastSequence) + { + lastSequence = seq; + sequenceFeatures = seq.getSequenceFeatures(); + sfSize = sequenceFeatures.length; + } + if(!overview) { - if (fstart < 0) // fix for if the feature we have starts before the sequence start, + spos = lastSequence.findPosition(start); + epos = lastSequence.findPosition(end); + } + String type; + for(int renderIndex=0; renderIndex epos + || sequenceFeatures[sfindex].getEnd() < spos)) + continue; + + if (overview) + { + + if (sequenceFeatures[sfindex].begin - 1 <= start && + sequenceFeatures[sfindex].end + 1 >= 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, width, height); + 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, width, height); + + } + else + renderFeature(g, seq, + seq.findIndex(sequenceFeatures[sfindex].begin) - 1, + seq.findIndex(sequenceFeatures[sfindex].end) - 1, + getColour(sequenceFeatures[sfindex].type), + start, end, y1, width, height); + + } - if (fstart == fend) - { - g.setColor(Color.red); - g.fillRoundRect( (fstart - start) * width, y1, width, height, 4, 4); - g.setColor(Color.white); - - char s = seq.getSequence().charAt(fstart); - FontMetrics fm = g.getFontMetrics(); - int charOffset = (width - fm.charWidth(s)) / 2; - int pady = height / 5; - g.drawString(String.valueOf(s), - charOffset + x1 + width * (fstart - start), - y1 + height - pady); + } + } + + char s; + int i; + void renderFeature(Graphics g, SequenceI seq, + int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height) + { + + 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!! } - else + + if (fend >= end) { - for (int i = fstart; i <= fend; i++) + fend = end; + } + + for (i = fstart; i <= fend; i++) { - char s = seq.getSequence().charAt(i); + s = seq.getSequence().charAt(i); + if (jalview.util.Comparison.isGap(s)) { continue; } - g.setColor(Color.blue); + g.setColor(featureColour); + g.fillRect( (i - start) * width, y1, width, height); g.setColor(Color.white); - - FontMetrics fm = g.getFontMetrics(); - int charOffset = (width - fm.charWidth(s)) / 2; - int pady = height / 5; + charOffset = (width - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), - charOffset + x1 + width * (i - start), - y1 + height - pady); + charOffset + (width * (i - start)), + (y1 + height) - height / 5); //pady = height / 5; + + } + } + } + + void findAllFeatures() + { + av.featuresDisplayed = new Hashtable(); + 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())) + { + av.featuresDisplayed.put(features[index].getType(), + new Integer( getColour(features[index].getType()).getRGB()) ); } + index++; } } + renderOrder = new String[av.featuresDisplayed.size()]; + Enumeration en = av.featuresDisplayed.keys(); + int i = 0; + 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 + av.featuresDisplayed.clear(); + + renderOrder = new String[data.length]; + + if(data.length>0) + for(int i=0; i