-\r
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.appletgui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
-\r
-\r
- // A higher level for grouping features of a\r
- // particular type\r
- Hashtable featureGroups = null;\r
-\r
- // This is actually an Integer held in the hashtable,\r
- // Retrieved using the key feature type\r
- Object currentColour;\r
-\r
- String [] renderOrder;\r
-\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- initColours();\r
- }\r
-\r
-\r
- public void transferSettings(FeatureRenderer fr)\r
- {\r
- renderOrder = fr.renderOrder;\r
- featureGroups = fr.featureGroups;\r
- featureColours = fr.featureColours;\r
- }\r
-\r
-\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
- {\r
- overview = true;\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- lastSequence = seq;\r
- sequenceFeatures = lastSequence.getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
-\r
- if(jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))\r
- return Color.white;\r
-\r
- currentColour = null;\r
-\r
- drawSequence(null, lastSequence, lastSequence.findPosition(i), -1,-1, -1, -1);\r
-\r
- if(currentColour==null)\r
- return initialCol;\r
-\r
- return new Color( ((Integer)currentColour).intValue() );\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer to get the accurate colour\r
- * of the rendered sequence\r
- */\r
- boolean overview = false;\r
-\r
- int white = Color.white.getRGB();\r
- public int findFeatureColour(int initialCol, int seqIndex, int column)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seqIndex!=lastSequenceIndex)\r
- {\r
- lastSequence = av.alignment.getSequenceAt(seqIndex);\r
- lastSequenceIndex = seqIndex;\r
- sequenceFeatures = lastSequence.getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))\r
- return Color.white.getRGB();\r
-\r
- currentColour = null;\r
-\r
- drawSequence(null, lastSequence, lastSequence.findPosition(column), -1,-1, -1, -1);\r
-\r
- if(currentColour==null)\r
- return initialCol;\r
-\r
- return ((Integer)currentColour).intValue();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- // String type;\r
- // SequenceFeature sf;\r
- int lastSequenceIndex=-1;\r
- SequenceI lastSequence;\r
- SequenceFeature [] sequenceFeatures;\r
- int sfSize, sfindex, spos, epos;\r
-\r
- public void drawSequence(Graphics g, SequenceI seq,\r
- int start, int end, int y1, int width, int height)\r
- {\r
- if ( seq.getSequenceFeatures() == null\r
- || seq.getSequenceFeatures().length==0)\r
- return;\r
-\r
-\r
- if (av.featuresDisplayed == null || renderOrder==null)\r
- {\r
- findAllFeatures();\r
- if(av.featuresDisplayed.size()<1)\r
- return;\r
-\r
- sequenceFeatures = seq.getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
- if(lastSequence==null || seq!=lastSequence)\r
- {\r
- lastSequence = seq;\r
- sequenceFeatures = seq.getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
- if(!overview)\r
- {\r
- spos = lastSequence.findPosition(start);\r
- epos = lastSequence.findPosition(end);\r
- if(g!=null)\r
- fm = g.getFontMetrics();\r
- }\r
- String type;\r
- for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
- if(!av.featuresDisplayed.containsKey(type))\r
- continue;\r
-\r
- // loop through all features in sequence to find\r
- // current feature to render\r
- for (sfindex = 0; sfindex < sfSize; sfindex++)\r
- {\r
- if (!sequenceFeatures[sfindex].type.equals(type))\r
- continue;\r
-\r
- if (featureGroups != null\r
- && sequenceFeatures[sfindex].featureGroup != null\r
- &&\r
- featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
- &&\r
- ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).\r
- booleanValue())\r
- {\r
- continue;\r
- }\r
-\r
- if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
-\r
- if (overview)\r
- {\r
- if (sequenceFeatures[sfindex].begin <= start &&\r
- sequenceFeatures[sfindex].end >= start)\r
- {\r
- currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].\r
- type);\r
- }\r
-\r
- }\r
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))\r
- {\r
-\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- new Color( ( (Integer) av.featuresDisplayed.get(\r
- sequenceFeatures[sfindex].type)).intValue()),\r
- start, end, y1, width, height);\r
-\r
- }\r
- else\r
- renderFeature(g, seq,\r
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,\r
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,\r
- getColour(sequenceFeatures[sfindex].type),\r
- start, end, y1, width, height);\r
-\r
- }\r
- }\r
- }\r
-\r
-\r
- char s;\r
- int i;\r
- void renderFeature(Graphics g, SequenceI seq,\r
- int fstart, int fend, Color featureColour, int start, int end, int y1, int width, int height)\r
- {\r
-\r
- if (((fstart <= end) && (fend >= start)))\r
- {\r
- if (fstart < start)\r
- { // fix for if the feature we have starts before the sequence start,\r
- fstart = start; // but the feature end is still valid!!\r
- }\r
-\r
- if (fend >= end)\r
- {\r
- fend = end;\r
- }\r
-\r
- for (i = fstart; i <= fend; i++)\r
- {\r
- s = seq.getSequence().charAt(i);\r
-\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- g.setColor(featureColour);\r
-\r
- g.fillRect( (i - start) * width, y1, width, height);\r
-\r
- if(!av.validCharWidth)\r
- continue;\r
-\r
- g.setColor(Color.white);\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + (width * (i - start)),\r
- (y1 + height) - height / 5); //pady = height / 5;\r
-\r
- }\r
- }\r
- }\r
-\r
- void findAllFeatures()\r
- {\r
- av.featuresDisplayed = new Hashtable();\r
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
-\r
- if (features == null)\r
- continue;\r
-\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if (!av.featuresDisplayed.containsKey(features[index].getType()))\r
- {\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer( getColour(features[index].getType()).getRGB()) );\r
- allfeatures.addElement(features[index].getType());\r
- }\r
- index++;\r
- }\r
- }\r
-\r
- renderOrder = new String[allfeatures.size()];\r
- Enumeration en = allfeatures.elements();\r
- int i = allfeatures.size()-1;\r
- while(en.hasMoreElements())\r
- {\r
- renderOrder[i] = en.nextElement().toString();\r
- i--;\r
- }\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- return (Color)featureColours.get(featureType);\r
- }\r
-\r
- public void addNewFeature(String name, Color col)\r
- {\r
-\r
- setColour(name, col);\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
-\r
- av.featuresDisplayed.put(name, "NOGROUP");\r
- }\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\r
- }\r
-\r
- public void setFeaturePriority(Object [][] data)\r
- {\r
- // The feature table will display high priority\r
- // features at the top, but theses are the ones\r
- // we need to render last, so invert the data\r
- if(av.featuresDisplayed!=null)\r
- av.featuresDisplayed.clear();\r
-\r
- renderOrder = new String[data.length];\r
-\r
- if (data.length > 0)\r
- for (int i = 0; i < data.length; i++)\r
- {\r
- String type = data[i][0].toString();\r
- setColour(type, (Color) data[i][1]);\r
- if ( ( (Boolean) data[i][2]).booleanValue())\r
- {\r
- av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));\r
- }\r
-\r
- renderOrder[data.length - i - 1] = type;\r
- }\r
- }\r
-\r
- Hashtable featureColours = new Hashtable();\r
- void initColours()\r
- {\r
- featureColours.put("active site", new Color(255, 75, 0));\r
- featureColours.put("binding site", new Color(245, 85, 0));\r
- featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
- featureColours.put("chain", new Color(225, 105, 0));\r
- featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
- featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
- featureColours.put("cross-link", new Color(195, 135, 0));\r
- featureColours.put("disulfide bond", new Color(185, 145, 0));\r
- featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
- featureColours.put("domain", new Color(165, 165, 0));\r
- featureColours.put("glycosylation site", new Color(155, 175, 0));\r
- featureColours.put("helix", new Color(145, 185, 0));\r
- featureColours.put("initiator methionine", new Color(135, 195, 5));\r
- featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
- featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
- featureColours.put("modified residue", new Color(105, 225, 35));\r
- featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
- featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
- featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
- featureColours.put("nucleotide phosphate-binding region",\r
- new Color(65, 245, 75));\r
- featureColours.put("peptide", new Color(55, 235, 85));\r
- featureColours.put("propeptide", new Color(45, 225, 95));\r
- featureColours.put("region of interest", new Color(35, 215, 105));\r
- featureColours.put("repeat", new Color(25, 205, 115));\r
- featureColours.put("selenocysteine", new Color(15, 195, 125));\r
- featureColours.put("sequence conflict", new Color(5, 185, 135));\r
- featureColours.put("sequence variant", new Color(0, 175, 145));\r
- featureColours.put("short sequence motif", new Color(0, 165, 155));\r
- featureColours.put("signal peptide", new Color(0, 155, 165));\r
- featureColours.put("site", new Color(0, 145, 175));\r
- featureColours.put("splice variant", new Color(0, 135, 185));\r
- featureColours.put("strand", new Color(0, 125, 195));\r
- featureColours.put("topological domain", new Color(0, 115, 205));\r
- featureColours.put("transit peptide", new Color(0, 105, 215));\r
- featureColours.put("transmembrane region", new Color(0, 95, 225));\r
- featureColours.put("turn", new Color(0, 85, 235));\r
- featureColours.put("unsure residue", new Color(0, 75, 245));\r
- featureColours.put("zinc finger region", new Color(0, 65, 255));\r
- }\r
-\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer extends
+ jalview.renderer.seqfeatures.FeatureRenderer
+{
+
+ // Holds web links for feature groups and feature types
+ // in the form label|link
+ Hashtable featureLinks = null;
+
+ /**
+ * Creates a new FeatureRenderer object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ */
+ public FeatureRenderer(AlignmentViewport av)
+ {
+ super();
+ this.av = av;
+
+ setTransparencyAvailable(!System.getProperty("java.version")
+ .startsWith("1.1"));
+ }
+
+ static String lastFeatureAdded;
+
+ static String lastFeatureGroupAdded;
+
+ static String lastDescriptionAdded;
+
+ int featureIndex = 0;
+
+ boolean deleteFeature = false;
+
+ FeatureColourPanel colourPanel;
+
+ class FeatureColourPanel extends Panel
+ {
+ String label = "";
+
+ private Color maxCol;
+
+ private boolean isColourByLabel, isGcol;
+
+ /**
+ * render a feature style in the amend feature dialog box
+ */
+ public void updateColor(Object newcol)
+ {
+
+ Color bg, col = null;
+ GraduatedColor gcol = null;
+ String vlabel = "";
+ if (newcol instanceof Color)
+ {
+ isGcol = false;
+ col = (Color) newcol;
+ gcol = null;
+ }
+ else if (newcol instanceof GraduatedColor)
+ {
+ isGcol = true;
+ gcol = (GraduatedColor) newcol;
+ col = null;
+ }
+ else
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_colour_for_mycheckbox"));
+ }
+ if (col != null)
+ {
+ setBackground(bg = col);
+ }
+ else
+ {
+ if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ vlabel += " "
+ + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
+ : "(<)");
+ }
+ if (isColourByLabel = gcol.isColourByLabel())
+ {
+ setBackground(bg = Color.white);
+ vlabel += " (by Label)";
+ }
+ else
+ {
+ setBackground(bg = gcol.getMinColor());
+ maxCol = gcol.getMaxColor();
+ }
+ }
+ label = vlabel;
+ setBackground(bg);
+ repaint();
+ }
+
+ FeatureColourPanel()
+ {
+ super(null);
+ }
+
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ if (isGcol)
+ {
+ if (isColourByLabel)
+ {
+ g.setColor(Color.white);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+ g.setColor(Color.black);
+ Font f = new Font("Verdana", Font.PLAIN, 10);
+ g.setFont(f);
+ g.drawString(MessageManager.getString("label.label"), 0, 0);
+ }
+ else
+ {
+ g.setColor(maxCol);
+ g.fillRect(d.width / 2, 0, d.width / 2, d.height);
+
+ }
+ }
+ }
+
+ }
+
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+ Panel bigPanel = new Panel(new BorderLayout());
+ final TextField name = new TextField(16);
+ final TextField source = new TextField(16);
+ final TextArea description = new TextArea(3, 35);
+ final TextField start = new TextField(8);
+ final TextField end = new TextField(8);
+ final Choice overlaps;
+ Button deleteButton = new Button("Delete");
+ deleteFeature = false;
+
+ colourPanel = new FeatureColourPanel();
+ colourPanel.setSize(110, 15);
+ final FeatureRenderer fr = this;
+
+ Panel panel = new Panel(new GridLayout(3, 1));
+
+ featureIndex = 0; // feature to be amended.
+ Panel tmp;
+
+ // /////////////////////////////////////
+ // /MULTIPLE FEATURES AT SELECTED RESIDUE
+ if (!newFeatures && features.length > 1)
+ {
+ panel = new Panel(new GridLayout(4, 1));
+ tmp = new Panel();
+ tmp.add(new Label("Select Feature: "));
+ overlaps = new Choice();
+ for (int i = 0; i < features.length; i++)
+ {
+ String item = features[i].getType() + "/" + features[i].getBegin()
+ + "-" + features[i].getEnd();
+
+ if (features[i].getFeatureGroup() != null)
+ {
+ item += " (" + features[i].getFeatureGroup() + ")";
+ }
+
+ overlaps.addItem(item);
+ }
+
+ tmp.add(overlaps);
+
+ overlaps.addItemListener(new java.awt.event.ItemListener()
+ {
+ public void itemStateChanged(java.awt.event.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.setText(features[index].getBegin() + "");
+ end.setText(features[index].getEnd() + "");
+
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequences[0], features[index].getBegin(),
+ features[index].getEnd());
+
+ ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
+
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+
+ colourPanel.updateColor(col);
+ }
+ });
+
+ panel.add(tmp);
+ }
+ // ////////
+ // ////////////////////////////////////
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Name: ", Label.RIGHT));
+ tmp.add(name);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Group: ", Label.RIGHT));
+ tmp.add(source);
+
+ tmp = new Panel();
+ panel.add(tmp);
+ tmp.add(new Label("Colour: ", Label.RIGHT));
+ tmp.add(colourPanel);
+
+ bigPanel.add(panel, BorderLayout.NORTH);
+
+ panel = new Panel();
+ panel.add(new Label("Description: ", Label.RIGHT));
+ panel.add(new ScrollPane().add(description));
+
+ if (!newFeatures)
+ {
+ bigPanel.add(panel, BorderLayout.SOUTH);
+
+ panel = new Panel();
+ panel.add(new Label(" Start:", Label.RIGHT));
+ panel.add(start);
+ panel.add(new Label(" End:", Label.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
+ {
+ lastFeatureAdded = "Jalview";
+ }
+ }
+
+ String title = newFeatures ? MessageManager
+ .getString("label.create_new_sequence_features")
+ : MessageManager.formatMessage("label.amend_delete_features",
+ new String[]
+ { sequences[0].getName() });
+
+ final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
+ 240);
+
+ dialog.setMainPanel(bigPanel);
+
+ if (newFeatures)
+ {
+ name.setText(lastFeatureAdded);
+ source.setText(lastFeatureGroupAdded);
+ }
+ else
+ {
+ dialog.ok.setLabel(MessageManager.getString("label.amend"));
+ dialog.buttonPanel.add(deleteButton, 1);
+ deleteButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ deleteFeature = true;
+ dialog.setVisible(false);
+ }
+ });
+ name.setText(features[0].getType());
+ source.setText(features[0].getFeatureGroup());
+ }
+
+ start.setText(features[0].getBegin() + "");
+ end.setText(features[0].getEnd() + "");
+ description.setText(features[0].getDescription());
+ Color col = getColour(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ Object fcol = getFeatureStyle(name.getText());
+ // simply display the feature color in a box
+ colourPanel.updateColor(fcol);
+ dialog.setResizable(true);
+ // TODO: render the graduated color in the box.
+ colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
+ {
+ public void mousePressed(java.awt.event.MouseEvent evt)
+ {
+ if (!colourPanel.isGcol)
+ {
+ new UserDefinedColours(fr, ap.alignFrame);
+ }
+ else
+ {
+ FeatureColourChooser fcc = new FeatureColourChooser(
+ ap.alignFrame, name.getText());
+ dialog.transferFocus();
+ }
+ }
+ });
+ dialog.setVisible(true);
+
+ jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+
+ if (dialog.accept)
+ {
+ // 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().replace('\n', ' ');
+ }
+
+ if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
+ {
+ lastFeatureGroupAdded = null;
+ }
+
+ if (!newFeatures)
+ {
+
+ SequenceFeature sf = features[featureIndex];
+ if (dialog.accept)
+ {
+ sf.type = lastFeatureAdded;
+ sf.featureGroup = lastFeatureGroupAdded;
+ sf.description = lastDescriptionAdded;
+ if (!colourPanel.isGcol)
+ {
+ // update colour - otherwise its already done.
+ setColour(sf.type, colourPanel.getBackground());
+ }
+ try
+ {
+ sf.begin = Integer.parseInt(start.getText());
+ sf.end = Integer.parseInt(end.getText());
+ } catch (NumberFormatException ex)
+ {
+ }
+
+ ffile.parseDescriptionHTML(sf, false);
+ setVisible(lastFeatureAdded); // if user edited name then make sure new
+ // type is visible
+ }
+ if (deleteFeature)
+ {
+ sequences[0].deleteFeature(sf);
+ }
+
+ }
+ else
+ {
+ if (dialog.accept && name.getText().length() > 0)
+ {
+ 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);
+ }
+
+ Color newColour = colourPanel.getBackground();
+ // setColour(lastFeatureAdded, fcol);
+
+ if (lastFeatureGroupAdded != null)
+ {
+ setGroupVisibility(lastFeatureGroupAdded, true);
+ }
+ setColour(lastFeatureAdded, newColour); // was fcol
+ setVisible(lastFeatureAdded);
+ findAllFeatures(false); // different to original applet behaviour ?
+ // findAllFeatures();
+ }
+ else
+ {
+ // no update to the alignment
+ return false;
+ }
+ }
+ // refresh the alignment and the feature settings dialog
+ if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
+ {
+ ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
+ }
+ // findAllFeatures();
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+}