-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.image.*;\r
-import javax.swing.JComboBox;\r
-import javax.swing.JPanel;\r
-import javax.swing.JLabel;\r
-import javax.swing.JOptionPane;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class FeatureRenderer\r
-{\r
- AlignViewport av;\r
- Color resBoxColour;\r
- float transparency = 1.0f;\r
- FontMetrics fm;\r
- int charOffset;\r
-\r
- Hashtable featureColours = new Hashtable();\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
- /**\r
- * Creates a new FeatureRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void transferSettings(FeatureRenderer fr)\r
- {\r
- renderOrder = fr.renderOrder;\r
- featureGroups = fr.featureGroups;\r
- featureColours = fr.featureColours;\r
- transparency = fr.transparency;\r
- }\r
-\r
- BufferedImage offscreenImage;\r
- boolean offscreenRender = false;\r
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)\r
- {\r
- return new Color( findFeatureColour (initialCol.getRGB(),\r
- seq, res ));\r
- }\r
-\r
- /**\r
- * This is used by the Molecule Viewer and Overview to\r
- * get the accurate colourof the rendered sequence\r
- */\r
- public int findFeatureColour(int initialCol, SequenceI seq, int column)\r
- {\r
- if(!av.showSequenceFeatures)\r
- return initialCol;\r
-\r
- if(seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();\r
- if(sequenceFeatures==null)\r
- return initialCol;\r
-\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))\r
- return Color.white.getRGB();\r
-\r
-\r
- //Only bother making an offscreen image if transparency is applied\r
- if(transparency!=1.0f && offscreenImage==null)\r
- {\r
- offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);\r
- }\r
-\r
- currentColour = null;\r
-\r
- offscreenRender = true;\r
-\r
- if(offscreenImage!=null)\r
- {\r
- offscreenImage.setRGB(0,0,initialCol);\r
- drawSequence(offscreenImage.getGraphics(),\r
- lastSeq,\r
- column,column,0);\r
-\r
- return offscreenImage.getRGB(0,0);\r
- }\r
- else\r
- {\r
- drawSequence(null,\r
- lastSeq,\r
- lastSeq.findPosition(column),\r
- -1, -1);\r
-\r
- if (currentColour == null)\r
- return initialCol;\r
- else\r
- return ((Integer)currentColour).intValue();\r
- }\r
-\r
-\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
- SequenceI lastSeq;\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)\r
- {\r
- if ( seq.getDatasetSequence().getSequenceFeatures() == null\r
- || seq.getDatasetSequence().getSequenceFeatures().length==0)\r
- return;\r
-\r
- if(g!=null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- if (av.featuresDisplayed == null\r
- || renderOrder==null\r
- || newFeatureAdded)\r
- {\r
- findAllFeatures();\r
- if(av.featuresDisplayed.size()<1)\r
- return;\r
-\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
- if(lastSeq==null || seq!=lastSeq)\r
- {\r
- lastSeq = seq;\r
- sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();\r
- sfSize = sequenceFeatures.length;\r
- }\r
-\r
-\r
- if (transparency != 1 && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, transparency));\r
- }\r
-\r
- if(!offscreenRender)\r
- {\r
- spos = lastSeq.findPosition(start);\r
- epos = lastSeq.findPosition(end);\r
- }\r
-\r
-\r
- String type;\r
- for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)\r
- {\r
- type = renderOrder[renderIndex];\r
-\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.length<=sfindex)\r
- {\r
- continue;\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 (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos\r
- || sequenceFeatures[sfindex].getEnd() < spos))\r
- continue;\r
-\r
- if (offscreenRender && offscreenImage==null)\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
- 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);\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);\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);\r
-\r
-\r
- }\r
-\r
- }\r
-\r
- if(transparency!=1.0f && g!=null)\r
- {\r
- Graphics2D g2 = (Graphics2D) g;\r
- g2.setComposite(\r
- AlphaComposite.getInstance(\r
- AlphaComposite.SRC_OVER, 1.0f));\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)\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
- int pady = (y1 + av.charHeight) - av.charHeight / 5;\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) * av.charWidth, y1, av.charWidth,av.charHeight);\r
-\r
- if(offscreenRender || !av.validCharWidth)\r
- continue;\r
-\r
- g.setColor(Color.white);\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- g.drawString(String.valueOf(s),\r
- charOffset + (av.charWidth * (i - start)),\r
- pady);\r
-\r
- }\r
- }\r
- }\r
-\r
-\r
- boolean newFeatureAdded = false;\r
-\r
- public void featuresAdded()\r
- {\r
- findAllFeatures();\r
- }\r
-\r
- boolean findingFeatures = false;\r
- synchronized void findAllFeatures()\r
- {\r
- newFeatureAdded = false;\r
-\r
- if(findingFeatures)\r
- {\r
- newFeatureAdded = true;\r
- return;\r
- }\r
-\r
- findingFeatures = true;\r
- jalview.schemes.UserColourScheme ucs = new\r
- jalview.schemes.UserColourScheme();\r
-\r
- if(av.featuresDisplayed==null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- av.featuresDisplayed.clear();\r
-\r
- Vector allfeatures = new Vector();\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceFeature [] features\r
- = av.alignment.getSequenceAt(i).getDatasetSequence().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
- if(!(features[index].begin == 0 && features[index].end ==0))\r
- {\r
- // If beginning and end are 0, the feature is for the whole sequence\r
- // and we don't want to render the feature in the normal way\r
-\r
- if (getColour(features[index].getType()) == null)\r
- {\r
- featureColours.put(features[index].getType(),\r
- ucs.createColourFromName(features[index].\r
- getType()));\r
- }\r
-\r
- av.featuresDisplayed.put(features[index].getType(),\r
- new Integer(getColour(features[index].\r
- getType()).getRGB()));\r
- allfeatures.addElement(features[index].getType());\r
- }\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
- findingFeatures = false;\r
- }\r
-\r
- public Color getColour(String featureType)\r
- {\r
- Color colour = (Color)featureColours.get(featureType);\r
- return colour;\r
- }\r
-\r
-\r
- static String lastFeatureAdded = "feature_1";\r
- static String lastSourceAdded = "Jalview";\r
-\r
- public boolean createNewFeatures(SequenceI[] sequences,\r
- SequenceFeature [] features)\r
- {\r
-\r
- JComboBox name = new JComboBox();\r
- JComboBox source = new JComboBox();\r
-\r
- JPanel panel = new JPanel(new GridLayout(2, 2));\r
- panel.add(new JLabel("New Sequence Feature Name"));\r
- panel.add(name);\r
- panel.add(new JLabel("Source:"));\r
- panel.add(source);\r
- // name.setPreferredSize(new Dimension(300, 20));\r
- name.setEditable(true);\r
- source.setEditable(true);\r
-\r
- Enumeration en;\r
- if (av.featuresDisplayed != null)\r
- {\r
- en = av.featuresDisplayed.keys();\r
- while (en.hasMoreElements())\r
- {\r
- name.addItem(en.nextElement().toString());\r
- }\r
- }\r
-\r
- if (featureGroups != null)\r
- {\r
- en = featureGroups.keys();\r
- while (en.hasMoreElements())\r
- {\r
- source.addItem(en.nextElement().toString());\r
- }\r
- }\r
-\r
- name.setSelectedItem(lastFeatureAdded);\r
- source.setSelectedItem(lastSourceAdded);\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- panel, "Create New Sequence Feature(s)",\r
- JOptionPane.OK_CANCEL_OPTION);\r
-\r
-\r
- if(reply==JOptionPane.OK_OPTION\r
- && name.getSelectedItem()!=null\r
- && source.getSelectedItem()!=null)\r
- {\r
- lastFeatureAdded = name.getSelectedItem().toString();\r
- lastSourceAdded = source.getSelectedItem().toString();\r
- for(int i=0; i<sequences.length; i++)\r
- {\r
- features[i].type = lastFeatureAdded;\r
- features[i].featureGroup = lastSourceAdded;\r
- sequences[i].addSequenceFeature(features[i]);\r
- }\r
-\r
- if (av.featuresDisplayed == null)\r
- av.featuresDisplayed = new Hashtable();\r
-\r
- if(featureGroups==null)\r
- featureGroups = new Hashtable();\r
-\r
- featureGroups.put(lastSourceAdded, new Boolean(true));\r
-\r
- Color col = getColour(lastFeatureAdded);\r
- if(col==null)\r
- {\r
- col = new Color(60, 160, 115);\r
- setColour(lastFeatureAdded, col);\r
- }\r
-\r
- av.featuresDisplayed.put(lastSourceAdded, new Integer(col.getRGB()));\r
- findAllFeatures();\r
- return true;\r
- }\r
- else\r
- return false;\r
-\r
- }\r
-\r
- public void setColour(String featureType, Color col)\r
- {\r
- featureColours.put(featureType, col);\r
- }\r
-\r
- public void setTransparency(float value)\r
- {\r
- transparency = value;\r
- }\r
-\r
- public float getTransparency()\r
- {\r
- return transparency;\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
- else\r
- av.featuresDisplayed = new Hashtable();\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
-\r
-\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+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.*;
+import jalview.schemes.GraduatedColor;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class FeatureRenderer implements jalview.api.FeatureRenderer
+{
+ AlignmentPanel ap;
+
+ AlignViewport av;
+
+ Color resBoxColour;
+
+ /**
+ * global transparency for feature
+ */
+ 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 class FeatureRendererSettings implements Cloneable
+ {
+ String[] renderOrder;
+
+ Hashtable featureGroups;
+
+ Hashtable featureColours;
+
+ float transparency;
+
+ Hashtable featureOrder;
+
+ public FeatureRendererSettings(String[] renderOrder,
+ Hashtable featureGroups, Hashtable featureColours,
+ float transparency, Hashtable featureOrder)
+ {
+ super();
+ this.renderOrder = renderOrder;
+ this.featureGroups = featureGroups;
+ this.featureColours = featureColours;
+ this.transparency = transparency;
+ this.featureOrder = featureOrder;
+ }
+
+ /**
+ * create an independent instance of the feature renderer settings
+ *
+ * @param fr
+ */
+ public FeatureRendererSettings(FeatureRenderer fr)
+ {
+ renderOrder = null;
+ featureGroups = new Hashtable();
+ featureColours = new Hashtable();
+ featureOrder = new Hashtable();
+ if (fr.renderOrder != null)
+ {
+ this.renderOrder = new String[fr.renderOrder.length];
+ System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
+ renderOrder.length);
+ }
+ if (fr.featureGroups != null)
+ {
+ this.featureGroups = new Hashtable(fr.featureGroups);
+ }
+ if (fr.featureColours != null)
+ {
+ this.featureColours = new Hashtable(fr.featureColours);
+ }
+ Enumeration en = fr.featureColours.keys();
+ while (en.hasMoreElements())
+ {
+ Object next = en.nextElement();
+ Object val = featureColours.get(next);
+ if (val instanceof GraduatedColor)
+ {
+ featureColours
+ .put(next, new GraduatedColor((GraduatedColor) val));
+ }
+ }
+ this.transparency = fr.transparency;
+ if (fr.featureOrder != null)
+ {
+ this.featureOrder = new Hashtable(fr.featureOrder);
+ }
+ }
+ }
+
+ public FeatureRendererSettings getSettings()
+ {
+ return new FeatureRendererSettings(this);
+ }
+
+ public void transferSettings(FeatureRendererSettings fr)
+ {
+ this.renderOrder = fr.renderOrder;
+ this.featureGroups = fr.featureGroups;
+ this.featureColours = fr.featureColours;
+ this.transparency = fr.transparency;
+ this.featureOrder = fr.featureOrder;
+ }
+
+ public void transferSettings(FeatureRenderer fr)
+ {
+ FeatureRendererSettings frs = new FeatureRendererSettings(fr);
+ this.renderOrder = frs.renderOrder;
+ this.featureGroups = frs.featureGroups;
+ this.featureColours = frs.featureColours;
+ this.transparency = frs.transparency;
+ this.featureOrder = frs.featureOrder;
+ if (av != null && av!=fr.av)
+ {
+ // copy over the displayed feature settings
+ if (fr.av != null)
+ {
+ if (fr.av.featuresDisplayed != null)
+ {
+ // update display settings
+ if (av.featuresDisplayed == null)
+ {
+ av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
+ }
+ else
+ {
+ av.featuresDisplayed.clear();
+ Enumeration en = fr.av.featuresDisplayed.keys();
+ while (en.hasMoreElements())
+ {
+ av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
+ }
+
+ }
+ }
+ }
+ }
+ }
+
+ 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 synchronized 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;
+ // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
+ 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;
+
+ /**
+ * show scores as heights
+ */
+ protected boolean varyHeight = false;
+
+ 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)
+ {
+ // this is passed out to the overview and other sequence renderers
+ // (e.g. molecule viewer) to get displayed colour for rendered
+ // sequence
+ currentColour = new Integer(
+ getColour(sequenceFeatures[sfindex]).getRGB());
+ // used to be retreived from av.featuresDisplayed
+ // 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,
+ getColour(sequenceFeatures[sfindex])
+ // 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,
+ getColour(sequenceFeatures[sfindex])
+ // new Color(((Integer) av.featuresDisplayed
+ // .get(sequenceFeatures[sfindex].type)).intValue())
+ , start, end, y1);
+
+ }
+ else if (showFeature(sequenceFeatures[sfindex]))
+ {
+ if (av.showSeqFeaturesHeight
+ && sequenceFeatures[sfindex].score != Float.NaN)
+ {
+ renderScoreFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1,
+ normaliseScore(sequenceFeatures[sfindex]));
+ }
+ else
+ {
+ renderFeature(g, seq,
+ seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
+ seq.findIndex(sequenceFeatures[sfindex].end) - 1,
+ getColour(sequenceFeatures[sfindex]), start, end, y1);
+ }
+ }
+
+ }
+
+ }
+
+ if (transparency != 1.0f && g != null)
+ {
+ Graphics2D g2 = (Graphics2D) g;
+ g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ 1.0f));
+ }
+ }
+
+ Hashtable minmax = new Hashtable();
+
+ /**
+ * normalise a score against the max/min bounds for the feature type.
+ *
+ * @param sequenceFeature
+ * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
+ * (0-255) value.
+ */
+ private final byte[] normaliseScore(SequenceFeature sequenceFeature)
+ {
+ float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+ final byte[] r = new byte[]
+ { 0, (byte) 255 };
+ if (mm != null)
+ {
+ if (r[0] != 0 || mm[0] < 0.0)
+ {
+ r[0] = 1;
+ r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+ }
+ else
+ {
+ r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
+ }
+ }
+ return r;
+ }
+
+ 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);
+
+ }
+ }
+ }
+
+ void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
+ Color featureColour, int start, int end, int y1, byte[] bs)
+ {
+
+ 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;
+ int ystrt = 0, yend = av.charHeight;
+ if (bs[0] != 0)
+ {
+ // signed - zero is always middle of residue line.
+ if (bs[1] < 128)
+ {
+ yend = av.charHeight * (128 - bs[1]) / 512;
+ ystrt = av.charHeight - yend / 2;
+ }
+ else
+ {
+ ystrt = av.charHeight / 2;
+ yend = av.charHeight * (bs[1] - 128) / 512;
+ }
+ }
+ else
+ {
+ yend = av.charHeight * bs[1] / 255;
+ ystrt = av.charHeight - yend;
+
+ }
+ for (i = fstart; i <= fend; i++)
+ {
+ s = seq.getCharAt(i);
+
+ if (jalview.util.Comparison.isGap(s))
+ {
+ continue;
+ }
+
+ g.setColor(featureColour);
+ int x = (i - start) * av.charWidth;
+ g.drawRect(x, y1, av.charWidth, av.charHeight);
+ g.fillRect(x, y1 + ystrt, av.charWidth, yend);
+
+ if (offscreenRender || !av.validCharWidth)
+ {
+ continue;
+ }
+
+ g.setColor(Color.black);
+ 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.
+ *
+ */
+ void findAllFeatures()
+ {
+ 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
+ */
+ 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]);
+ }
+ }
+ }
+ if (minmax == null)
+ {
+ minmax = new Hashtable();
+ }
+ 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());
+ }
+ 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++;
+ }
+ }
+ updateRenderOrder(allfeatures);
+ findingFeatures = 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, 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
+ * New Cability: updates min/max for colourscheme range if its dynamic
+ *
+ * @param allFeatures
+ */
+ private void updateRenderOrder(Vector allFeatures)
+ {
+ Vector allfeatures = new Vector(allFeatures);
+ String[] oldRender = renderOrder;
+ renderOrder = new String[allfeatures.size()];
+ Object mmrange, fc = null;
+ 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 (minmax != null)
+ {
+ mmrange = minmax.get(oldRender[j]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(oldRender[j]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(
+ ((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ 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 (minmax != null)
+ {
+ // update from new features minmax if necessary
+ mmrange = minmax.get(newf[i]);
+ if (mmrange != null)
+ {
+ fc = featureColours.get(newf[i]);
+ if (fc != null && fc instanceof GraduatedColor
+ && ((GraduatedColor) fc).isAutoScale())
+ {
+ ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
+ ((float[][]) mmrange)[0][1]);
+ }
+ }
+ }
+ 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);
+ }
+
+ /**
+ * get a feature style object for the given type string. Creates a
+ * java.awt.Color for a featureType with no existing colourscheme. TODO:
+ * replace return type with object implementing standard abstract colour/style
+ * interface
+ *
+ * @param featureType
+ * @return java.awt.Color or GraduatedColor
+ */
+ public Object getFeatureStyle(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, fc = col);
+ }
+ return fc;
+ }
+
+ /**
+ * return a nominal colour for this feature
+ *
+ * @param featureType
+ * @return standard color, or maximum colour for graduated colourscheme
+ */
+ public Color getColour(String featureType)
+ {
+ Object fc = getFeatureStyle(featureType);
+
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).getMaxColor();
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + featureType);
+ }
+
+ /**
+ * calculate the render colour for a specific feature using current feature
+ * settings.
+ *
+ * @param feature
+ * @return render colour for the given feature
+ */
+ public Color getColour(SequenceFeature feature)
+ {
+ Object fc = getFeatureStyle(feature.getType());
+ if (fc instanceof Color)
+ {
+ return (Color) fc;
+ }
+ else
+ {
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).findColor(feature);
+ }
+ }
+ throw new Error("Implementation Error: Unrecognised render object "
+ + fc.getClass() + " for features of type " + feature.getType());
+ }
+
+ private boolean showFeature(SequenceFeature sequenceFeature)
+ {
+ Object fc = getFeatureStyle(sequenceFeature.type);
+ if (fc instanceof GraduatedColor)
+ {
+ return ((GraduatedColor) fc).isColored(sequenceFeature);
+ }
+ else
+ {
+ return true;
+ }
+ }
+
+ // // /////////////
+ // // Feature Editing Dialog
+ // // Will be refactored in next release.
+
+ static String lastFeatureAdded;
+
+ static String lastFeatureGroupAdded;
+
+ static String lastDescriptionAdded;
+
+ Object oldcol, fcol;
+
+ int featureIndex = 0;
+
+ boolean amendFeatures(final SequenceI[] sequences,
+ final SequenceFeature[] features, boolean newFeatures,
+ final AlignmentPanel ap)
+ {
+
+ featureIndex = 0;
+
+ final 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 FeatureRenderer me = this;
+ final JLabel colour = new JLabel();
+ colour.setOpaque(true);
+ // colour.setBorder(BorderFactory.createEtchedBorder());
+ colour.setMaximumSize(new Dimension(30, 16));
+ colour.addMouseListener(new MouseAdapter()
+ {
+ FeatureColourChooser fcc = null;
+
+ public void mousePressed(MouseEvent evt)
+ {
+ if (fcol instanceof Color)
+ {
+ Color col = JColorChooser.showDialog(Desktop.desktop,
+ "Select Feature Colour", ((Color) fcol));
+ if (col != null)
+ {
+ fcol = col;
+ updateColourButton(bigPanel, colour, col);
+ }
+ }
+ else
+ {
+
+ if (fcc == null)
+ {
+ final String type = features[featureIndex].getType();
+ fcc = new FeatureColourChooser(me, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+
+ fcc.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ fcol = fcc.getLastColour();
+ fcc = null;
+ setColour(type, fcol);
+ updateColourButton(bigPanel, colour, fcol);
+ }
+ });
+
+ }
+ }
+ }
+ });
+ 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);
+
+ }
+ Object col = getFeatureStyle(name.getText());
+ if (col == null)
+ {
+ col = new jalview.schemes.UserColourScheme()
+ .createColourFromName(name.getText());
+ }
+ oldcol = fcol = col;
+ updateColourButton(bigPanel, colour, 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));
+ colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
+ colour.setForeground(Color.black);
+ colour.setHorizontalAlignment(SwingConstants.CENTER);
+ colour.setVerticalAlignment(SwingConstants.CENTER);
+ colour.setHorizontalTextPosition(SwingConstants.CENTER);
+ colour.setVerticalTextPosition(SwingConstants.CENTER);
+ bigPanel.add(panel, BorderLayout.NORTH);
+
+ panel = new JPanel();
+ panel.add(new JLabel("Description: ", JLabel.RIGHT));
+ description.setFont(JvSwingUtils.getTextAreaFont());
+ 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());
+ updateColourButton(bigPanel, colour,
+ (oldcol = fcol = getFeatureStyle(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", " ");
+ // TODO: determine if the null feature group is valid
+ 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, fcol);
+ av.featuresDisplayed.put(sf.type, getColour(sf.type));
+
+ 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));
+ }
+ setColour(lastFeatureAdded, fcol);
+ av.featuresDisplayed.put(lastFeatureAdded,
+ getColour(lastFeatureAdded));
+
+ findAllFeatures(false);
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ ap.paintAlignment(true);
+
+ return true;
+ }
+
+ /**
+ * update the amend feature button dependent on the given style
+ *
+ * @param bigPanel
+ * @param col
+ * @param col2
+ */
+ protected void updateColourButton(JPanel bigPanel, JLabel colour,
+ Object col2)
+ {
+ colour.removeAll();
+ colour.setIcon(null);
+ colour.setToolTipText(null);
+ colour.setText("");
+
+ if (col2 instanceof Color)
+ {
+ colour.setBackground((Color) col2);
+ }
+ else
+ {
+ colour.setBackground(bigPanel.getBackground());
+ colour.setForeground(Color.black);
+ FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
+ // colour.setForeground(colour.getBackground());
+ }
+ }
+
+ public void setColour(String featureType, Object col)
+ {
+ // overwrite
+ // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
+ // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
+ // Object c = featureColours.get(featureType);
+ // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
+ // !((GraduatedColor)c).getMaxColor().equals(_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, data[i][1]); // todo : typesafety - feature color
+ // interface object
+ 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