/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class FeatureRenderer
{
+ AlignmentPanel ap;
AlignViewport av;
Color resBoxColour;
float transparency = 1.0f;
// A higher level for grouping features of a
// particular type
- Hashtable featureGroups = null;
+ Hashtable featureGroups = new Hashtable();
// This is actually an Integer held in the hashtable,
// Retrieved using the key feature type
String[] renderOrder;
PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+ Vector allfeatures;
+
/**
* Creates a new FeatureRenderer object.
- *
+ *
* @param av
* DOCUMENT ME!
*/
- public FeatureRenderer(AlignViewport av)
+ public FeatureRenderer(AlignmentPanel ap)
{
- this.av = av;
+ this.ap = ap;
+ this.av = ap.av;
}
+
public void transferSettings(FeatureRenderer fr)
{
- renderOrder = fr.renderOrder;
- featureGroups = fr.featureGroups;
- featureColours = fr.featureColours;
- transparency = fr.transparency;
- featureOrder = fr.featureOrder;
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
}
BufferedImage offscreenImage;
{
lastSeq = seq;
sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
- if (sequenceFeatures!=null)
+ if (sequenceFeatures!=null)
{
sfSize = sequenceFeatures.length;
}
}
-
+
if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
if (sequenceFeatures != null)
{
sfSize = sequenceFeatures.length;
- }
+ }
}
-
- if (sequenceFeatures == null)
+
+ if (sequenceFeatures == null || sfSize==0)
{
return initialCol;
}
/**
* DOCUMENT ME!
- *
+ *
* @param g
* DOCUMENT ME!
* @param seq
SequenceFeature[] sequenceFeatures;
int sfSize, sfindex, spos, epos;
- public void drawSequence(Graphics g, SequenceI seq,
+ synchronized public void drawSequence(Graphics g, SequenceI seq,
int start, int end, int y1)
{
+
if (seq.getDatasetSequence().getSequenceFeatures() == null
|| seq.getDatasetSequence().getSequenceFeatures().length == 0)
{
}
sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
}
if (lastSeq == null || seq != lastSeq
{
lastSeq = seq;
sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
- sfSize = sequenceFeatures.length;
}
if (transparency != 1 && g != null)
epos = lastSeq.findPosition(end);
}
+ sfSize = sequenceFeatures.length;
String type;
for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
{
// current feature to render
for (sfindex = 0; sfindex < sfSize; sfindex++)
{
- if (sequenceFeatures.length <= sfindex)
- {
- continue;
- }
if (!sequenceFeatures[sfindex].type.equals(type))
{
continue;
if (featureGroups != null
&& sequenceFeatures[sfindex].featureGroup != null
&&
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+ sequenceFeatures[sfindex].featureGroup.length()!=0
+ && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
&&
! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
featureGroup)).
/**
* search the alignment for all new features, give them a colour and display
* them. Then fires a PropertyChangeEvent on the changeSupport object.
- *
+ *
*/
- synchronized void findAllFeatures()
+ void findAllFeatures()
{
- findAllFeatures(true); // add all new features as visible
- if (!firing) {
- firing=true;
- changeSupport.firePropertyChange("changeSupport",null,null);
- firing=false;
+ synchronized (firing)
+ {
+ if (firing.equals(Boolean.FALSE)) {
+ firing=Boolean.TRUE;
+ findAllFeatures(true); // add all new features as visible
+ changeSupport.firePropertyChange("changeSupport",null,null);
+ firing=Boolean.FALSE;
+ }
}
}
/**
* Searches alignment for all features and updates colours
- *
+ *
* @param newMadeVisible
* if true newly added feature types will be rendered immediatly
*/
av.featuresDisplayed = new Hashtable();
}
- Vector allfeatures = new Vector();
+ allfeatures = new Vector();
Vector oldfeatures = new Vector();
- if (renderOrder!=null)
+ if (renderOrder!=null)
{
for (int i=0; i<renderOrder.length; i++) {
if (renderOrder[i]!=null)
{
if (!av.featuresDisplayed.containsKey(features[index].getType()))
{
+
+ if(featureGroups.containsKey(features[index].getType()))
+ {
+ boolean visible = ( (Boolean) featureGroups.get(
+ features[index].featureGroup)).booleanValue();
+
+ if(!visible)
+ {
+ index++;
+ continue;
+ }
+ }
+
+
if (! (features[index].begin == 0 && features[index].end == 0))
{
// If beginning and end are 0, the feature is for the whole sequence
updateRenderOrder(allfeatures);
findingFeatures = false;
}
- protected boolean firing=false;
+ protected Boolean firing=Boolean.FALSE;
/**
* replaces the current renderOrder with the unordered features in allfeatures.
* The ordering of any types in both renderOrder and allfeatures is preserved,
* the order given by getOrder or the order given in allFeatures.
* Note. this operates directly on the featureOrder hash for efficiency. TODO:
* eliminate the float storage for computing/recalling the persistent ordering
- *
+ *
* @param allFeatures
*/
private void updateRenderOrder(Vector allFeatures) {
if (initOrders)
{
setOrder(oldRender[j], (1-(1+(float)j)/(float) oldRender.length));
- }
+ }
if (allfeatures.contains(oldRender[j])) {
renderOrder[opos++] = oldRender[j]; // existing features always
// appear below new features
int i=allfeatures.size()-1;
int iSize=i;
boolean sort=false;
- String[] newf = new String[allfeatures.size()];
+ String[] newf = new String[allfeatures.size()];
float[] sortOrder = new float[allfeatures.size()];
Enumeration en = allfeatures.elements();
// sort remaining elements
while (en.hasMoreElements())
{
newf[i] = en.nextElement().toString();
- if (initOrders || !featureOrder.containsKey(newf[i]))
+ if (initOrders || !featureOrder.containsKey(newf[i]))
{
int denom = initOrders ? allfeatures.size() : featureOrder.size();
// new unordered feature - compute persistent ordering at head of
}
public Color getColour(String featureType)
{
- Color colour = (Color) featureColours.get(featureType);
- if (colour == null)
+ if (!featureColours.containsKey(featureType))
{
jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
- featureColours.put(featureType,
- colour=ucs.createColourFromName(featureType));
+ jalview.schemes.UserColourScheme();
+ Color col = ucs.createColourFromName(featureType);
+ featureColours.put(featureType, col);
+ return col;
}
- return colour;
+ else
+ return (Color) featureColours.get(featureType);
}
static String lastFeatureAdded;
static String lastFeatureGroupAdded;
static String lastDescriptionAdded;
- public boolean createNewFeatures(SequenceI[] sequences,
- SequenceFeature[] features)
- {
- return amendFeatures(sequences, features, true, null);
- }
-
int featureIndex = 0;
boolean amendFeatures(final SequenceI[] sequences,
final SequenceFeature[] features,
boolean newFeatures,
final AlignmentPanel ap)
{
+
+ featureIndex = 0;
+
JPanel bigPanel = new JPanel(new BorderLayout());
- final JComboBox name = new JComboBox();
- final JComboBox source = new JComboBox();
+ final JComboBox overlaps;
+ final JTextField name = new JTextField(25);
+ final JTextField source = new JTextField(25);
final JTextArea description = new JTextArea(3, 25);
final JSpinner start = new JSpinner();
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
+
final JPanel colour = new JPanel();
colour.setBorder(BorderFactory.createEtchedBorder());
colour.setMaximumSize(new Dimension(40, 10));
{
public void mousePressed(MouseEvent evt)
{
- colour.setBackground(
- JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground()));
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ "Select Feature Colour",
+ colour.getBackground());
+ if (col != null)
+ colour.setBackground(col);
+
}
});
- JPanel panel = new JPanel(new GridLayout(3, 2));
- panel.add(new JLabel("Sequence Feature Name: ", JLabel.RIGHT));
- panel.add(name);
- panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
- panel.add(source);
- panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
JPanel tmp = new JPanel();
+ JPanel panel = new JPanel(new GridLayout(3, 1));
+
+ ///////////////////////////////////////
+ ///MULTIPLE FEATURES AT SELECTED RESIDUE
+ if(!newFeatures && features.length>1)
+ {
+ panel = new JPanel(new GridLayout(4, 1));
+ tmp = new JPanel();
+ tmp.add(new JLabel("Select Feature: "));
+ overlaps = new JComboBox();
+ for(int i=0; i<features.length; i++)
+ {
+ overlaps.addItem(features[i].getType()
+ +"/"+features[i].getBegin()+"-"+features[i].getEnd()
+ +" ("+features[i].getFeatureGroup()+")");
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ int index = overlaps.getSelectedIndex();
+ if (index != -1)
+ {
+ featureIndex = index;
+ name.setText(features[index].getType());
+ description.setText(features[index].getDescription());
+ source.setText(features[index].getFeatureGroup());
+ start.setValue(new Integer(features[index].getBegin()));
+ end.setValue(new Integer(features[index].getEnd()));
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0],
+ features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ Color col = getColour(name.getText());
+ if (col == null)
+ {
+ col = new
+ jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+
+ colour.setBackground(col);
+ }
+ });
+
+
+ panel.add(tmp);
+ }
+ //////////
+ //////////////////////////////////////
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel("Name: ", JLabel.RIGHT));
+ tmp.add(name);
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel("Group: ", JLabel.RIGHT));
+ tmp.add(source);
+
+ tmp = new JPanel();
+ panel.add(tmp);
+ tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
tmp.add(colour);
colour.setPreferredSize(new Dimension(150, 15));
- panel.add(tmp);
- name.setEditable(true);
- source.setEditable(true);
bigPanel.add(panel, BorderLayout.NORTH);
+
panel = new JPanel();
panel.add(new JLabel("Description: ", JLabel.RIGHT));
description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
}
else
{
- lastFeatureAdded = "Jalview";
+ lastFeatureGroupAdded = "Jalview";
}
}
- Enumeration en;
- if (featureGroups != null)
+ if(newFeatures)
{
- en = featureGroups.keys();
- while (en.hasMoreElements())
- {
- source.addItem(en.nextElement().toString());
- }
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
}
-
- if (newFeatures)
+ else
{
- if (av.featuresDisplayed != null)
- {
- en = av.featuresDisplayed.keys();
- while (en.hasMoreElements())
- {
- name.addItem(en.nextElement().toString());
- }
- }
-
- name.setSelectedItem(lastFeatureAdded);
- source.setSelectedItem(lastFeatureGroupAdded);
- description.setText(
- lastDescriptionAdded == null ?
- features[0].description : lastDescriptionAdded);
-
- if (getColour(lastFeatureAdded) != null)
- {
- colour.setBackground(getColour(lastFeatureAdded));
- }
- else
- {
- colour.setBackground(new Color(60, 160, 115));
- }
-
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
}
- else if (!newFeatures)
- {
- featureIndex = 0;
- for (int f = 0; f < features.length; f++)
- {
- name.addItem(features[f].getType().toString());
- }
-
- description.setText(features[0].getDescription());
- source.setSelectedItem(features[0].getFeatureGroup());
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
- name.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent e)
- {
- int index = name.getSelectedIndex();
- if (index != -1)
- {
- featureIndex = index;
- description.setText(features[index].getDescription());
- source.setSelectedItem(features[index].getFeatureGroup());
- start.setValue(new Integer(features[index].getBegin()));
- end.setValue(new Integer(features[index].getEnd()));
- colour.setBackground(
- getColour(name.getSelectedItem().toString()));
- SearchResults highlight = new SearchResults();
- highlight.addResult(sequences[0],
- features[index].getBegin(),
- features[index].getEnd());
+ start.setValue(new Integer(features[0].getBegin()));
+ end.setValue(new Integer(features[0].getEnd()));
+ description.setText(features[0].getDescription());
+ colour.setBackground(getColour(name.getText()));
- ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
-
- }
- Color col = getColour(name.getSelectedItem().toString());
- if (col == null)
- {
- col = new
- jalview.schemes.UserColourScheme()
- .createColourFromName(name.getSelectedItem().toString());
- }
-
- colour.setBackground(col);
- }
- });
-
- }
Object[] options;
if (!newFeatures)
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
- if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
+ if (reply == JOptionPane.OK_OPTION && name.getText().length()>0)
{
// This ensures that the last sequence
// is refreshed and new features are rendered
lastSeq = null;
- lastFeatureAdded = name.getSelectedItem().toString();
- lastFeatureGroupAdded = source.getSelectedItem().toString();
+ lastFeatureAdded = name.getText().trim();
+ lastFeatureGroupAdded = source.getText().trim();
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
+
+ if(lastFeatureGroupAdded.length()<1)
+ lastFeatureGroupAdded = null;
}
if (!newFeatures)
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
sf.description = lastDescriptionAdded;
+
setColour(sf.type, colour.getBackground());
+ av.featuresDisplayed.put(sf.type,
+ new Integer(colour.getBackground().getRGB()));
+
try
{
sf.begin = ( (Integer) start.getValue()).intValue();
ffile.parseDescriptionHTML(sf, false);
}
}
- else
+ else //NEW FEATURES ADDED
{
if (reply == JOptionPane.OK_OPTION
- && name.getSelectedItem() != null
- && source.getSelectedItem() != null)
+ && lastFeatureAdded.length()>0)
{
for (int i = 0; i < sequences.length; i++)
{
features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
+ if (lastFeatureGroupAdded!=null)
+ features[i].featureGroup = lastFeatureGroupAdded;
features[i].description = lastDescriptionAdded;
sequences[i].addSequenceFeature(features[i]);
ffile.parseDescriptionHTML(features[i], false);
av.featuresDisplayed = new Hashtable();
}
- if (featureGroups == null)
+ if (lastFeatureGroupAdded != null)
{
- featureGroups = new Hashtable();
+ if (featureGroups == null)
+ featureGroups = new Hashtable();
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
}
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
-
Color col = colour.getBackground();
setColour(lastFeatureAdded, colour.getBackground());
+ av.featuresDisplayed.put(lastFeatureAdded,
+ new Integer(col.getRGB()));
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
+ findAllFeatures(false);
+
+ ap.paintAlignment(true);
- findAllFeatures();
return true;
}
}
}
- if (name.getSelectedIndex() == -1)
- {
- findAllFeatures();
- }
+ ap.paintAlignment(true);
return true;
}
setFeaturePriority(data, true);
}
/**
- *
+ *
* @param data { String(Type), Colour(Type), Boolean(Displayed) }
* @param visibleNew when true current featureDisplay list will be cleared
*/
av.featuresDisplayed = new Hashtable();
}
}
- if (data==null)
+ if (data==null)
{
return;
}
-
+
// 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
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
- *
+ *
* @param type
* Feature type string
* @param position
*/
public float setOrder(String type, float position)
{
- if (featureOrder==null)
+ if (featureOrder==null)
{
featureOrder = new Hashtable();
}
}
/**
* get the global priority (0 (top) to 1 (bottom))
- *
+ *
* @param type
* @return [0,1] or -1 for a type without a priority
*/
public float getOrder(String type) {
- if (featureOrder!=null)
+ if (featureOrder!=null)
{
if (featureOrder.containsKey(type))
{
git://source.jalview.org / jalview.git / blobdiff