- // 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 = new Integer(getColour(sequenceFeatures[sfindex]).getRGB());//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]), 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;
-
- }
- }
- }
- Hashtable minmax=null;
- void findAllFeatures()
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
-
- av.featuresDisplayed = new Hashtable();
- Vector allfeatures = new Vector();
- minmax = 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 (features[index].begin==0 && features[index].end==0) {
- index++;
- continue;
- }
- 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());
- }
- if (features[index].score != Float.NaN)
- {
- int nonpos= features[index].getBegin()>=1 ? 0 : 1;
- float[][] mm = (float[][]) minmax.get(features[index].getType());
- if (mm == null)
- {
- mm = new float[][] {null, null };
- minmax.put(features[index].getType(), mm);
- }
- if (mm[nonpos]==null)
- {
- mm[nonpos] = new float[] { features[index].score, features[index].score };
-
- }
- else
- {
- if (mm[nonpos][0] > features[index].score)
- {
- mm[nonpos][0] = features[index].score;
- }
- if (mm[nonpos][1] < features[index].score)
- {
- mm[nonpos][1] = features[index].score;
- }
- }
- }
-
- 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)
- {
- Object fc = featureColours.get(featureType);
- if (fc == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, col);
- return col;
- }
- else if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).getMaxColor();
- }
- // TODO: raise an implementation error here.
- return null; // Color.white;
- }
- }
- /**
- * implement graduated colouring for features with scores
- *
- * @param feature
- * @return render colour for the given feature
- */
- public Color getColour(SequenceFeature feature)
- {
- Object fc = featureColours.get(feature.type);
- if (fc == null)
- {
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(feature.type);
- featureColours.put(feature.type, col);
- return col;
- }
- else if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).findColor(feature);
- }
- // TODO: raise an implementation error here.
- return null; // Color.white;
- }
- }
-
- 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();
- }
-
- /*
- * if (visibleNew) { if (av.featuresDisplayed != null) {
- * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
- * Hashtable(); } } if (data == null) { return; }
- */
-
- 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;
- }
- }
- }
-
- /**
- * @return a simple list of feature group names or null
- */
- public String[] getGroups()
- {
- buildGroupHash();
- if (featureGroups != null)
- {
- String[] gps = new String[featureGroups.size()];
- Enumeration gn = featureGroups.keys();
- int i = 0;
- while (gn.hasMoreElements())
- {
- gps[i++] = (String) gn.nextElement();
- }
- return gps;
- }
- return null;
- }
-
- /**
- * get visible or invisible groups
- *
- * @param visible
- * true to return visible groups, false to return hidden ones.
- * @return list of groups
- */
- public String[] getGroups(boolean visible)
- {
- buildGroupHash();
- if (featureGroups != null)
- {
- Vector gp = new Vector();
-
- Enumeration gn = featureGroups.keys();
- while (gn.hasMoreElements())
- {
- String nm = (String) gn.nextElement();
- Boolean state = (Boolean) featureGroups.get(nm);
- if (state.booleanValue() == visible)
- {
- gp.addElement(nm);
- }
- }
- String[] gps = new String[gp.size()];
- gp.copyInto(gps);
-
- int i = 0;
- while (gn.hasMoreElements())
- {
- gps[i++] = (String) gn.nextElement();
- }
- return gps;
- }
- return null;
- }
-
- /**
- * set all feature groups in toset to be visible or invisible
- *
- * @param toset
- * group names
- * @param visible
- * the state of the named groups to set
- */
- public void setGroupState(String[] toset, boolean visible)
- {
- buildGroupHash();
- if (toset != null && toset.length > 0 && featureGroups != null)
- {
- boolean rdrw = false;
- for (int i = 0; i < toset.length; i++)
- {
- Object st = featureGroups.get(toset[i]);
- if (st != null)
- {
- featureGroups.put(toset[i], new Boolean(visible));
- rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
- }
- }
- if (rdrw)
- {
- if (this.av != null)
- if (this.av.featureSettings != null)
- {
- av.featureSettings.rebuildGroups();
- this.av.featureSettings.resetTable(true);
- }
- else
- {
- buildFeatureHash();
- }
- if (av != null)
- {
- av.alignmentChanged(null);
- }
- }
- }
- }
-
- /**
- * analyse alignment for groups and hash tables (used to be embedded in
- * FeatureSettings.setTableData)
- *
- * @return true if features are on the alignment
- */
- public boolean buildGroupHash()
- {
- boolean alignmentHasFeatures = false;
- if (featureGroups == null)
- {
- featureGroups = new Hashtable();
- }
- Vector allFeatures = new Vector();
- Vector allGroups = new Vector();
- SequenceFeature[] tmpfeatures;
- String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
-
- alignmentHasFeatures = true;
-
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- if (tmpfeatures[index].getFeatureGroup() != null)
- {
- group = tmpfeatures[index].featureGroup;
- if (!allGroups.contains(group))
- {
- allGroups.addElement(group);
-
- boolean visible = true;
- if (featureGroups.containsKey(group))
- {
- visible = ((Boolean) featureGroups.get(group)).booleanValue();
- }
- else
- {
- featureGroups.put(group, new Boolean(visible));
- }
- }
- }
-
- if (!allFeatures.contains(tmpfeatures[index].getType()))
- {
- allFeatures.addElement(tmpfeatures[index].getType());
- }
- index++;
- }
- }
-
- return alignmentHasFeatures;
- }
-
- /**
- * rebuild the featuresDisplayed and renderorder list based on the
- * featureGroups hash and any existing display state and force a repaint if
- * necessary
- *
- * @return true if alignment has visible features
- */
- public boolean buildFeatureHash()
- {
- boolean alignmentHasFeatures = false;
- if (featureGroups == null)
- {
- alignmentHasFeatures = buildGroupHash();
- }
- if (!alignmentHasFeatures)
- return false;
- Hashtable fdisp = av.featuresDisplayed;
- Vector allFeatures = new Vector();
- SequenceFeature[] tmpfeatures;
- String group;
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
- {
- continue;
- }
-
- alignmentHasFeatures = true;
-
- tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
- int index = 0;
- while (index < tmpfeatures.length)
- {
- boolean visible = true;
- if (tmpfeatures[index].getFeatureGroup() != null)
- {
- group = tmpfeatures[index].featureGroup;
- if (featureGroups.containsKey(group))
- {
- visible = ((Boolean) featureGroups.get(group)).booleanValue();
- }
- }
-
- if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
- {
- allFeatures.addElement(tmpfeatures[index].getType());
- }
- index++;
- }
- }
- if (allFeatures.size() > 0)
- {
- String[] neworder = new String[allFeatures.size()];
- int p = neworder.length - 1;
- for (int i = renderOrder.length - 1; i >= 0; i--)
- {
- if (allFeatures.contains(renderOrder[i]))
- {
- neworder[p--] = renderOrder[i];
- allFeatures.removeElement(renderOrder[i]);
- }
- else
- {
- av.featuresDisplayed.remove(renderOrder[i]);
- }
- }
- for (int i = allFeatures.size() - 1; i > 0; i++)
- {
- Object e = allFeatures.elementAt(i);
- if (e != null)
- {
- neworder[p--] = (String) e;
- av.featuresDisplayed.put(e, getColour((String) e));
- }
- }
- renderOrder = neworder;
- return true;
- }
-
- return alignmentHasFeatures;
- }
- /**
- *
- * @return the displayed feature type as an array of strings
- */
- protected String[] getDisplayedFeatureTypes()
- {
- String[] typ = null;
- synchronized (renderOrder)
- {
- typ = new String[renderOrder.length];
- System.arraycopy(renderOrder, 0, typ, 0, typ.length);
- for (int i = 0; i < typ.length; i++)
- {
- if (av.featuresDisplayed.get(typ[i]) == null)
- {
- typ[i] = null;
- }
- }
- }
- return typ;
- }
-}