-
- findingFeatures = true;
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- allfeatures = new Vector();
- Vector oldfeatures = new Vector();
- if (renderOrder!=null)
- {
- for (int i=0; i<renderOrder.length; i++) {
- if (renderOrder[i]!=null)
- {
- oldfeatures.addElement(renderOrder[i]);
- }
- }
- }
- for (int i = 0; i < av.alignment.getHeight(); i++)
- {
- SequenceFeature[] features
- = av.alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures();
-
- if (features == null)
- {
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!av.featuresDisplayed.containsKey(features[index].getType()))
- {
- if (! (features[index].begin == 0 && features[index].end == 0))
- {
- // If beginning and end are 0, the feature is for the whole sequence
- // and we don't want to render the feature in the normal way
-
- if (newMadeVisible && !oldfeatures.contains(features[index].getType())) {
- // this is a new feature type on the alignment. Mark it for
- // display.
- av.featuresDisplayed.put(features[index].getType(),
- new Integer(getColour(features[index].
- getType()).getRGB()));
- setOrder(features[index].getType(),0);
- }
- }
- }
- if (!allfeatures.contains(features[index].getType()))
- {
- allfeatures.addElement(features[index].getType());
- }
- index++;
- }
- }
- updateRenderOrder(allfeatures);
- findingFeatures = false;
- }
- protected boolean firing=false;
- /**
- * replaces the current renderOrder with the unordered features in allfeatures.
- * The ordering of any types in both renderOrder and allfeatures is preserved,
- * and all new feature types are rendered on top of the existing types, in
- * 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) {
- Vector allfeatures = new Vector(allFeatures);
- String[] oldRender = renderOrder;
- renderOrder = new String[allfeatures.size()];
- boolean initOrders=(featureOrder==null);
- int opos=0;
- if (oldRender!=null && oldRender.length>0)
- {
- for (int j=0; j<oldRender.length; j++)
- {
- if (oldRender[j]!=null)
- {
- 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
- allfeatures.removeElement(oldRender[j]);
- }
- }
- }
- }
- if (allfeatures.size()==0) {
- // no new features - leave order unchanged.
- return;
- }
- int i=allfeatures.size()-1;
- int iSize=i;
- boolean sort=false;
- 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]))
- {
- int denom = initOrders ? allfeatures.size() : featureOrder.size();
- // new unordered feature - compute persistent ordering at head of
- // existing features.
- setOrder(newf[i], i/(float) denom);
- }
- // set order from newly found feature from persisted ordering.
- sortOrder[i] = 2-((Float) featureOrder.get(newf[i])).floatValue();
- if (i<iSize)
- {
- // only sort if we need to
- sort = sort || sortOrder[i]>sortOrder[i+1];
- }
- i--;
- }
- if (iSize>1 && sort)
- jalview.util.QuickSort.sort(sortOrder, newf);
- sortOrder=null;
- System.arraycopy(newf, 0, renderOrder, opos, newf.length);
- }
- public Color getColour(String featureType)
- {
- if (featureColours.get(featureType) == null)
- {
- jalview.schemes.UserColourScheme ucs = new
- jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, col);
- return col;
- }
- 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)
- {
- findAllFeatures();
-
- featureIndex = 0;
-
- JPanel bigPanel = new JPanel(new BorderLayout());
- 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));
- colour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- colour.setBackground(
- JColorChooser.showDialog(Desktop.desktop,
- "Select Feature Colour",
- colour.getBackground()));
- }
- });
-
- 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));
-
- 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));
- description.setLineWrap(true);
- panel.add(new JScrollPane(description));
-
- if (!newFeatures)
- {
- bigPanel.add(panel, BorderLayout.SOUTH);
-
- panel = new JPanel();
- panel.add(new JLabel(" Start:", JLabel.RIGHT));
- panel.add(start);
- panel.add(new JLabel(" End:", JLabel.RIGHT));
- panel.add(end);
- bigPanel.add(panel, BorderLayout.CENTER);
- }
- else
- {
- bigPanel.add(panel, BorderLayout.CENTER);
- }
-
- if (lastFeatureAdded == null)
- {
- if (features[0].type != null)
- {
- lastFeatureAdded = features[0].type;
- }
- else
- {
- lastFeatureAdded = "feature_1";
- }
- }
-
- if (lastFeatureGroupAdded == null)
- {
- if (features[0].featureGroup != null)
- {
- lastFeatureGroupAdded = features[0].featureGroup;
- }
- else
- {
- lastFeatureGroupAdded = "Jalview";
- }
- }
-
- if(newFeatures)
- {
- name.setText(lastFeatureAdded);
- source.setText(lastFeatureGroupAdded);
- }
- else
- {
- name.setText(features[0].getType());
- source.setText(features[0].getFeatureGroup());
- }
-
- start.setValue(new Integer(features[0].getBegin()));
- end.setValue(new Integer(features[0].getEnd()));
- description.setText(features[0].getDescription());
- colour.setBackground(getColour(name.getText()));
-
-
- Object[] options;
- if (!newFeatures)
- {
- options = new Object[]
- {
- "Amend", "Delete", "Cancel"};
- }
- else
- {
- options = new Object[]
- {
- "OK", "Cancel"};
- }
-
- String title = newFeatures ? "Create New Sequence Feature(s)" :
- "Amend/Delete Features for "
- + sequences[0].getName();
-
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel,
- title,
- JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE,
- null,
- options, "OK");
-
- jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
-
- 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.getText().trim();
- lastFeatureGroupAdded = source.getText().trim();
- lastDescriptionAdded = description.getText().replaceAll("\n", " ");
-
- if(lastFeatureGroupAdded.length()<1)
- lastFeatureGroupAdded = null;
- }
-
- if (!newFeatures)
- {
- SequenceFeature sf = features[featureIndex];
-
- if (reply == JOptionPane.NO_OPTION)
- {
- sequences[0].getDatasetSequence().deleteFeature(sf);
- }
- else if (reply == JOptionPane.YES_OPTION)
- {
- sf.type = lastFeatureAdded;
- sf.featureGroup = lastFeatureGroupAdded;
- sf.description = lastDescriptionAdded;
- setColour(sf.type, colour.getBackground());
- try
- {
- sf.begin = ( (Integer) start.getValue()).intValue();
- sf.end = ( (Integer) end.getValue()).intValue();
- }
- catch (NumberFormatException ex)
- {}
-
- ffile.parseDescriptionHTML(sf, false);
- }
- }
- else
- {
- if (reply == JOptionPane.OK_OPTION
- && name.getText() != null
- && source.getText() != null)
- {
- for (int i = 0; i < sequences.length; i++)
- {
- features[i].type = lastFeatureAdded;
- features[i].featureGroup = lastFeatureGroupAdded;
- features[i].description = lastDescriptionAdded;
- sequences[i].addSequenceFeature(features[i]);
- ffile.parseDescriptionHTML(features[i], false);
- }
-
- if (av.featuresDisplayed == null)
- {
- av.featuresDisplayed = new Hashtable();
- }
-
- if (featureGroups == null)
- {
- featureGroups = new Hashtable();
- }
-
-
- Color col = colour.getBackground();
- setColour(lastFeatureAdded, colour.getBackground());
-
- if(lastFeatureGroupAdded!=null)
- {
- featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
- av.featuresDisplayed.put(lastFeatureGroupAdded,
- new Integer(col.getRGB()));
- }
- findAllFeatures();
-
- return true;
- }
- else
- {
- return false;
- }
- }
-
- findAllFeatures();
-
- return true;
- }
-
- public void setColour(String featureType, Color col)
- {
- featureColours.put(featureType, col);
- }
-
- public void setTransparency(float value)
- {
- transparency = value;
- }
-
- public float getTransparency()
- {
- return transparency;
- }
- /**
- * Replace current ordering with new ordering
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- */
- public void setFeaturePriority(Object[][] data)
- {
- setFeaturePriority(data, true);
- }
- /**
- *
- * @param data { String(Type), Colour(Type), Boolean(Displayed) }
- * @param visibleNew when true current featureDisplay list will be cleared
- */
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
- {
- if (visibleNew)
- {
- if (av.featuresDisplayed != null)
- {
- av.featuresDisplayed.clear();
- }
- else
- {
- av.featuresDisplayed = new Hashtable();
- }
- }
- 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
- 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;
- }
- }
-
- }
- Hashtable featureOrder=null;
- /**
- * analogous to colour - store a normalized ordering for all feature types in
- * this rendering context.
- *
- * @param type
- * Feature type string
- * @param position
- * normalized priority - 0 means always appears on top, 1 means
- * always last.
- */
- public float setOrder(String type, float position)
- {
- if (featureOrder==null)
- {
- featureOrder = new Hashtable();
- }
- featureOrder.put(type, new Float(position));
- return position;
- }
- /**
- * 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.containsKey(type))
- {
- return ((Float)featureOrder.get(type)).floatValue();
- }
- }
- return -1;
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void addPropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.addPropertyChangeListener(listener);
- }
-
- /**
- * @param listener
- * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
- */
- public void removePropertyChangeListener(PropertyChangeListener listener)
- {
- changeSupport.removePropertyChangeListener(listener);