-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class FeatureRenderer implements RendererI\r
-{\r
- AlignViewport av;\r
-\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup [] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while( e.hasMoreElements() )\r
- {\r
- SequenceFeature sf = (SequenceFeature)e.nextElement();\r
- if(sf.getStart()>seq.getEnd())\r
- continue;\r
-\r
- int fstart = seq.findIndex(sf.getStart())-1;\r
- int fend = seq.findIndex(sf.getEnd())-1;\r
-\r
- if( (fstart<=end && fend>=start) )\r
- {\r
- if(fstart<0) // fix for if the feature we have starts before the sequence start,\r
- fstart = 0;// but the feature end is still valid!!\r
-\r
- if(fstart==fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s))/2;\r
- int pady = height/5;\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);\r
-\r
- }\r
- else\r
- {\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
- if( jalview.util.Comparison.isGap(s) )\r
- continue;\r
-\r
- g.setColor(Color.blue);\r
- g.fillRect( (i-start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
-\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i-start),\r
- y1 + height - pady);\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer
+{
+ AlignmentPanel ap;
+ AlignViewport av;
+ Color resBoxColour;
+ float transparency = 1.0f;
+ FontMetrics fm;
+ int charOffset;
+
+ Hashtable featureColours = new Hashtable();
+
+ // A higher level for grouping features of a
+ // particular type
+ Hashtable featureGroups = new Hashtable();
+
+ // This is actually an Integer held in the hashtable,
+ // Retrieved using the key feature type
+ Object currentColour;
+
+ String[] renderOrder;
+ PropertyChangeSupport changeSupport=new PropertyChangeSupport(this);
+
+ Vector allfeatures;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public FeatureRenderer(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.av = ap.av;
+ }
+
+
+ public void transferSettings(FeatureRenderer fr)
+ {
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
+ }
+
+ BufferedImage offscreenImage;
+ boolean offscreenRender = false;
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
+ {
+ return new Color(findFeatureColour(initialCol.getRGB(),
+ seq, res));
+ }
+
+ /**
+ * This is used by the Molecule Viewer and Overview to get the accurate
+ * colourof the rendered sequence
+ */
+ public int findFeatureColour(int initialCol, SequenceI seq, int column)
+ {
+ if (!av.showSequenceFeatures)
+ {
+ return initialCol;
+ }
+
+ if (seq != lastSeq)
+ {
+ lastSeq = seq;
+ sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+ if (sequenceFeatures!=null)
+ {
+ sfSize = sequenceFeatures.length;
+ }
+ }
+
+ if (sequenceFeatures!=lastSeq.getDatasetSequence().getSequenceFeatures()) {
+ sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
+ if (sequenceFeatures != null)
+ {
+ sfSize = sequenceFeatures.length;
+ }
+ }
+
+ if (sequenceFeatures == null || sfSize==0)
+ {
+ return initialCol;
+ }
+
+
+ if (jalview.util.Comparison.isGap(lastSeq.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;
+
+ offscreenRender = true;
+
+ if (offscreenImage != null)
+ {
+ offscreenImage.setRGB(0, 0, initialCol);
+ drawSequence(offscreenImage.getGraphics(),
+ lastSeq,
+ column, column, 0);
+
+ return offscreenImage.getRGB(0, 0);
+ }
+ else
+ {
+ drawSequence(null,
+ lastSeq,
+ lastSeq.findPosition(column),
+ -1, -1);
+
+ if (currentColour == null)
+ {
+ return initialCol;
+ }
+ else
+ {
+ 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;
+ SequenceI lastSeq;
+ SequenceFeature[] sequenceFeatures;
+ int sfSize, sfindex, spos, epos;
+
+ synchronized public void drawSequence(Graphics g, SequenceI seq,
+ int start, int end, int y1)
+ {
+
+ if (seq.getDatasetSequence().getSequenceFeatures() == null
+ || seq.getDatasetSequence().getSequenceFeatures().length == 0)
+ {
+ return;
+ }
+
+ if (g != null)
+ {
+ fm = g.getFontMetrics();
+ }
+
+ if (av.featuresDisplayed == null
+ || renderOrder == null
+ || newFeatureAdded)
+ {
+ findAllFeatures();
+ if (av.featuresDisplayed.size() < 1)
+ {
+ return;
+ }
+
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+ }
+
+ if (lastSeq == null || seq != lastSeq
+ || seq.getDatasetSequence().getSequenceFeatures()!=sequenceFeatures)
+ {
+ lastSeq = seq;
+ sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
+ }
+
+ if (transparency != 1 && g != null)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(
+ AlphaComposite.getInstance(
+ AlphaComposite.SRC_OVER, transparency));
+ }
+
+ if (!offscreenRender)
+ {
+ spos = lastSeq.findPosition(start);
+ epos = lastSeq.findPosition(end);
+ }
+
+ sfSize = sequenceFeatures.length;
+ String type;
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+ {
+ type = renderOrder[renderIndex];
+
+ if (type == null || !av.featuresDisplayed.containsKey(type))
+ {
+ continue;
+ }
+
+ // 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
+ &&
+ sequenceFeatures[sfindex].featureGroup.length()!=0
+ && featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
+ &&
+ ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
+ featureGroup)).
+ booleanValue())
+ {
+ continue;
+ }
+
+ if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
+ || sequenceFeatures[sfindex].getEnd() < spos))
+ {
+ continue;
+ }
+
+ if (offscreenRender && offscreenImage == null)
+ {
+ if (sequenceFeatures[sfindex].begin <= start &&
+ sequenceFeatures[sfindex].end >= 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);
+ 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].type),
+ start, end, y1);
+ }
+
+ }
+
+ }
+
+ if (transparency != 1.0f && g != null)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(
+ AlphaComposite.getInstance(
+ AlphaComposite.SRC_OVER, 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;
+ }
+ int pady = (y1 + av.charHeight) - av.charHeight / 5;
+ 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 (offscreenRender || !av.validCharWidth)
+ {
+ continue;
+ }
+
+ g.setColor(Color.white);
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s),
+ charOffset + (av.charWidth * (i - start)),
+ pady);
+
+ }
+ }
+ }
+
+ boolean newFeatureAdded = false;
+ /**
+ * Called when alignment in associated view has new/modified features
+ * to discover and display.
+ *
+ */
+ public void featuresAdded()
+ {
+ lastSeq=null;
+ findAllFeatures();
+ }
+
+ boolean findingFeatures = false;
+ /**
+ * 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()
+ {
+ findAllFeatures(true); // add all new features as visible
+ if (!firing) {
+ firing=true;
+ changeSupport.firePropertyChange("changeSupport",null,null);
+ firing=false;
+ }
+ }
+ /**
+ * Searches alignment for all features and updates colours
+ *
+ * @param newMadeVisible
+ * if true newly added feature types will be rendered immediatly
+ */
+ synchronized void findAllFeatures(boolean newMadeVisible) {
+ newFeatureAdded = false;
+
+ if (findingFeatures)
+ {
+ newFeatureAdded = true;
+ return;
+ }
+
+ 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(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
+ // 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.containsKey(featureType))
+ {
+ 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;
+
+ 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 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)
+ {
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ "Select Feature Colour",
+ colour.getBackground());
+ if (col != null)
+ colour.setBackground(col);
+
+ }
+ });
+
+ 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());
+ av.featuresDisplayed.put(sf.type,
+ new Integer(colour.getBackground().getRGB()));
+
+ try
+ {
+ sf.begin = ( (Integer) start.getValue()).intValue();
+ sf.end = ( (Integer) end.getValue()).intValue();
+ }
+ catch (NumberFormatException ex)
+ {}
+
+ ffile.parseDescriptionHTML(sf, false);
+ }
+ }
+ else //NEW FEATURES ADDED
+ {
+ if (reply == JOptionPane.OK_OPTION
+ && lastFeatureAdded.length()>0)
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ features[i].type = lastFeatureAdded;
+ if (lastFeatureGroupAdded!=null)
+ 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 (lastFeatureGroupAdded != null)
+ {
+ if (featureGroups == null)
+ featureGroups = new Hashtable();
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
+ }
+
+ Color col = colour.getBackground();
+ setColour(lastFeatureAdded, colour.getBackground());
+ av.featuresDisplayed.put(lastFeatureAdded,
+ new Integer(col.getRGB()));
+
+ findAllFeatures(false);
+
+ ap.paintAlignment(true);
+
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ ap.paintAlignment(true);
+
+ 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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff