X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=6fbdee858b359fdd7321ef94a7b8efd49734baf7;hb=add2f44022857817d1bb9a502f0e37627a34c5d8;hp=405fe9871999c467a6520e040d3a26affc52bf4b;hpb=d360d66235b8e99766ace8330175bd0258a8c07c;p=jalview.git diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 405fe98..6fbdee8 100755 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -24,6 +24,8 @@ import java.awt.*; import java.util.*; +import java.awt.image.*; + /** * DOCUMENT ME! @@ -62,39 +64,28 @@ public class FeatureRenderer initColours(); } - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) + public void transferSettings(FeatureRenderer fr) { - if(!av.showSequenceFeatures) - return initialCol; - - lastSequence = seq; - sequenceFeatures = lastSequence.getDatasetSequence().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); + renderOrder = fr.renderOrder; + featureGroups = fr.featureGroups; + featureColours = fr.featureColours; + transparency = fr.transparency; + } - if(currentColour==null) - return initialCol; + BufferedImage offscreenImage; + boolean offscreenRender = false; + public Color findFeatureColour(Color initialCol, SequenceI seq, int res) + { + int seqindex = av.alignment.findIndex(seq); - return new Color( ((Integer)currentColour).intValue() ); + return new Color( findFeatureColour (initialCol.getRGB(), + seqindex, res )); } + /** * 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) @@ -111,18 +102,43 @@ public class FeatureRenderer sfSize = sequenceFeatures.length; } - if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) return Color.white.getRGB(); + + //Only bother making an offscreen image if transparency is applied + if(transparency!=1.0f && offscreenImage==null) + { + offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB); + } + currentColour = null; - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1); + offscreenRender = true; + + if(offscreenImage!=null) + { + offscreenImage.setRGB(0,0,initialCol); + drawSequence(offscreenImage.getGraphics(), + lastSequence, + column,column,0); + + return offscreenImage.getRGB(0,0); + } + else + { + drawSequence(null, + lastSequence, + lastSequence.findPosition(column), + -1, -1); + + if (currentColour == null) + return initialCol; + else + return ((Integer)currentColour).intValue(); + } - if(currentColour==null) - return initialCol; - return ((Integer)currentColour).intValue(); } @@ -147,9 +163,9 @@ public class FeatureRenderer int sfSize, sfindex, spos, epos; public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1, int width, int height) + int start, int end, int y1) { - if ( seq.getDatasetSequence().getSequenceFeatures() == null + if ( seq.getDatasetSequence().getSequenceFeatures() == null || seq.getDatasetSequence().getSequenceFeatures().length==0) return; @@ -161,6 +177,9 @@ public class FeatureRenderer if (av.featuresDisplayed == null || renderOrder==null) { findAllFeatures(); + if(av.featuresDisplayed.size()<1) + return; + sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures(); sfSize = sequenceFeatures.length; } @@ -181,21 +200,28 @@ public class FeatureRenderer AlphaComposite.SRC_OVER, transparency)); } - if(!overview) + if(!offscreenRender) { spos = lastSequence.findPosition(start); epos = lastSequence.findPosition(end); } + String type; for(int renderIndex=0; renderIndex epos + if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex].getEnd() < spos)) continue; - if (overview) + if (offscreenRender && offscreenImage==null) { - - if (sequenceFeatures[sfindex].begin - 1 <= start && - sequenceFeatures[sfindex].end + 1 >= start) + if (sequenceFeatures[sfindex].begin <= start && + sequenceFeatures[sfindex].end >= start) { currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); + type); } - } else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) { @@ -233,13 +257,13 @@ public class FeatureRenderer seq.findIndex(sequenceFeatures[sfindex].begin) - 1, new Color( ( (Integer) av.featuresDisplayed.get( sequenceFeatures[sfindex].type)).intValue()), - start, end, y1, width, height); + 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, width, height); + start, end, y1); } else @@ -247,7 +271,7 @@ public class FeatureRenderer seq.findIndex(sequenceFeatures[sfindex].begin) - 1, seq.findIndex(sequenceFeatures[sfindex].end) - 1, getColour(sequenceFeatures[sfindex].type), - start, end, y1, width, height); + start, end, y1); } @@ -267,7 +291,7 @@ public class FeatureRenderer 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) + int fstart, int fend, Color featureColour, int start, int end, int y1) { if (((fstart <= end) && (fend >= start))) @@ -281,7 +305,7 @@ public class FeatureRenderer { fend = end; } - + int pady = (y1 + av.charHeight) - av.charHeight / 5; for (i = fstart; i <= fend; i++) { s = seq.getSequence().charAt(i); @@ -293,13 +317,16 @@ public class FeatureRenderer g.setColor(featureColour); - g.fillRect( (i - start) * width, y1, width, height); + g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight); + + if(offscreenRender) + continue; g.setColor(Color.white); - charOffset = (width - fm.charWidth(s)) / 2; + charOffset = (av.charWidth - fm.charWidth(s)) / 2; g.drawString(String.valueOf(s), - charOffset + (width * (i - start)), - (y1 + height) - height / 5); //pady = height / 5; + charOffset + (av.charWidth * (i - start)), + pady); } } @@ -308,10 +335,11 @@ public class FeatureRenderer void findAllFeatures() { av.featuresDisplayed = new Hashtable(); + Vector allfeatures = new Vector(); for (int i = 0; i < av.alignment.getHeight(); i++) { - SequenceFeature [] features = av.alignment.getSequenceAt(i).getDatasetSequence(). - getSequenceFeatures(); + SequenceFeature [] features + = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); if (features == null) continue; @@ -323,18 +351,19 @@ public class FeatureRenderer { av.featuresDisplayed.put(features[index].getType(), new Integer( getColour(features[index].getType()).getRGB()) ); + allfeatures.addElement(features[index].getType()); } index++; } } - renderOrder = new String[av.featuresDisplayed.size()]; - Enumeration en = av.featuresDisplayed.keys(); - int i = 0; + renderOrder = new String[allfeatures.size()]; + Enumeration en = allfeatures.elements(); + int i = allfeatures.size()-1; while(en.hasMoreElements()) { renderOrder[i] = en.nextElement().toString(); - i++; + i--; } } @@ -343,15 +372,17 @@ public class FeatureRenderer return (Color)featureColours.get(featureType); } - public void addNewFeature(String name, Color col) + public void addNewFeature(String name, Color col, String group) { setColour(name, col); if(av.featuresDisplayed==null) av.featuresDisplayed = new Hashtable(); + if(group == null) + group = "NOGROUP"; - av.featuresDisplayed.put(name, "NOGROUP"); + av.featuresDisplayed.put(name, new Integer(col.getRGB())); } public void setColour(String featureType, Color col) @@ -374,21 +405,25 @@ public class FeatureRenderer // 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(); + if(av.featuresDisplayed!=null) + av.featuresDisplayed.clear(); + else + av.featuresDisplayed = new Hashtable(); renderOrder = new String[data.length]; - if(data.length>0) - for(int i=data.length-1; i>-1; 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[i] = type; - } + 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; + } }