src/jalview/appletgui/FeatureSettings.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.appletgui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 import java.awt.*;\r
  23 import java.util.*;\r
  24 import java.awt.event.*;\r
  25 \r
  26 \r
  27 public class FeatureSettings extends Panel implements ItemListener,\r
  28     MouseListener, MouseMotionListener\r
  29 {\r
  30   final FeatureRenderer fr;\r
  31   final AlignmentPanel ap;\r
  32   final AlignViewport av;\r
  33   final Frame frame;\r
  34   Panel groupPanel;\r
  35   Panel featurePanel = new Panel();\r
  36   ScrollPane scrollPane;\r
  37 \r
  38   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
  39   {\r
  40     this.ap = ap;\r
  41     this.av = av;\r
  42     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
  43 \r
  44     setTableData();\r
  45 \r
  46     this.setLayout(new BorderLayout());\r
  47     scrollPane = new ScrollPane();\r
  48     scrollPane.add(featurePanel);\r
  49     add(scrollPane, BorderLayout.CENTER);\r
  50     if(groupPanel!=null)\r
  51     {\r
  52       groupPanel.setLayout(\r
  53           new GridLayout(groupPanel.getComponentCount() / 4, 4));\r
  54       groupPanel.validate();\r
  55 \r
  56       add(groupPanel, BorderLayout.NORTH);\r
  57     }\r
  58     frame = new Frame();\r
  59     frame.add(this);\r
  60     int height = featurePanel.getComponentCount()*50 ;\r
  61     if (height>400)\r
  62       height = 400;\r
  63 \r
  64     jalview.bin.JalviewLite.addFrame(frame, "Feature Settings", 250,\r
  65                                      height);\r
  66   }\r
  67 \r
  68   void setTableData()\r
  69   {\r
  70     if(fr.featureGroups==null)\r
  71       fr.featureGroups = new Hashtable();\r
  72     else\r
  73       fr.featureGroups.clear();\r
  74 \r
  75     Vector allFeatures = new Vector();\r
  76     SequenceFeature[] tmpfeatures;\r
  77 \r
  78     for (int i = 0; i < av.alignment.getHeight(); i++)\r
  79     {\r
  80       if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
  81         continue;\r
  82 \r
  83       tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
  84       int index = 0;\r
  85       while (index < tmpfeatures.length)\r
  86       {\r
  87         if(tmpfeatures[index].getFeatureGroup()!=null\r
  88            && tmpfeatures[index].getFeatureGroup().length()>0\r
  89            && !fr.featureGroups.containsKey(tmpfeatures[index].getFeatureGroup()))\r
  90         {\r
  91           fr.featureGroups.put(tmpfeatures[index].getFeatureGroup(), new Boolean(true));\r
  92           if(groupPanel==null)\r
  93           {\r
  94             groupPanel = new Panel();\r
  95           }\r
  96 \r
  97           Checkbox check = new Checkbox(tmpfeatures[index].getFeatureGroup(), true);\r
  98           check.setFont(new Font("Serif", Font.BOLD, 12));\r
  99           check.addItemListener(this);\r
 100           groupPanel.add(check);\r
 101         }\r
 102 \r
 103         if (!allFeatures.contains(tmpfeatures[index].getType()))\r
 104         {\r
 105             allFeatures.addElement(tmpfeatures[index].getType());\r
 106         }\r
 107 \r
 108 \r
 109         index ++;\r
 110       }\r
 111     }\r
 112 \r
 113     resetTable();\r
 114     featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));\r
 115     featurePanel.validate();\r
 116   }\r
 117 \r
 118   void resetTable()\r
 119   {\r
 120     featurePanel.removeAll();\r
 121     Enumeration groups = fr.featureGroups.keys();\r
 122     SequenceFeature [] tmpfeatures;\r
 123     String group, type;\r
 124     Vector checksAdded = new Vector();\r
 125 \r
 126     while(groups.hasMoreElements())\r
 127     {\r
 128      group = groups.nextElement().toString();\r
 129      if ( !( (Boolean) fr.featureGroups.get(group)).booleanValue())\r
 130        continue;\r
 131 \r
 132      for (int i = 0; i < av.alignment.getHeight(); i++)\r
 133        {\r
 134          if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
 135            continue;\r
 136 \r
 137          tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
 138          int index = 0;\r
 139          while (index < tmpfeatures.length)\r
 140          {\r
 141            if (tmpfeatures[index].getFeatureGroup() != null &&\r
 142                tmpfeatures[index].getFeatureGroup().equals(group))\r
 143            {\r
 144              type = tmpfeatures[index].getType();\r
 145              if(!checksAdded.contains(type))\r
 146              {\r
 147                checksAdded.addElement(type);\r
 148                Checkbox check = new Checkbox(type, true);\r
 149                check.addMouseListener(this);\r
 150                check.addMouseMotionListener(this);\r
 151                check.setBackground(fr.getColour(type));\r
 152                check.addItemListener(this);\r
 153                featurePanel.add(check);\r
 154              }\r
 155            }\r
 156            index++;\r
 157          }\r
 158      }\r
 159    }\r
 160    featurePanel.validate();\r
 161    if(scrollPane!=null)\r
 162      scrollPane.validate();\r
 163   }\r
 164 \r
 165   public void itemStateChanged(ItemEvent evt)\r
 166   {\r
 167     if (evt != null)\r
 168     {\r
 169       //Is the source a top level featureGroup?\r
 170       Checkbox source = (Checkbox) evt.getSource();\r
 171       if (fr.featureGroups.containsKey(source.getLabel()))\r
 172       {\r
 173         fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));\r
 174         ap.seqPanel.seqCanvas.repaint();\r
 175         if (ap.overviewPanel != null)\r
 176           ap.overviewPanel.updateOverviewImage();\r
 177 \r
 178         resetTable();\r
 179         return;\r
 180       }\r
 181     }\r
 182 \r
 183       Component[] comps = featurePanel.getComponents();\r
 184       int cSize = comps.length;\r
 185 \r
 186       Object[][] tmp = new Object[cSize][3];\r
 187       int tmpSize = 0;\r
 188       for (int i = 0; i < cSize; i++)\r
 189       {\r
 190         Checkbox check = (Checkbox) comps[i];\r
 191         if(!check.getState())\r
 192           continue;\r
 193 \r
 194         tmp[tmpSize][0] = check.getLabel();\r
 195         tmp[tmpSize][1] = fr.getColour(check.getLabel());\r
 196         tmp[tmpSize][2] = new Boolean(check.getState());\r
 197         tmpSize++;\r
 198       }\r
 199 \r
 200       Object[][]data = new Object[tmpSize][3];\r
 201       System.arraycopy(tmp, 0, data,0, tmpSize);\r
 202 \r
 203       fr.setFeaturePriority(data);\r
 204       ap.seqPanel.seqCanvas.repaint();\r
 205       if (ap.overviewPanel != null)\r
 206         ap.overviewPanel.updateOverviewImage();\r
 207   }\r
 208 \r
 209   Checkbox selectedCheck;\r
 210   boolean dragging = false;\r
 211 \r
 212   public void mousePressed(MouseEvent evt)\r
 213   {\r
 214     selectedCheck = (Checkbox)evt.getSource();\r
 215   }\r
 216 \r
 217   public void mouseDragged(MouseEvent evt)\r
 218   {\r
 219       dragging = true;\r
 220   }\r
 221 \r
 222   public void mouseReleased(MouseEvent evt)\r
 223   {\r
 224     Component comp = null;\r
 225     Checkbox  target = null;\r
 226 \r
 227     int height = evt.getY()+evt.getComponent().getLocation().y;\r
 228 \r
 229 \r
 230     if(height > this.getSize().height)\r
 231      {\r
 232        comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);\r
 233      }\r
 234      else if(height < 0)\r
 235      {\r
 236        comp = featurePanel.getComponent(0);\r
 237      }\r
 238      else\r
 239      {\r
 240        comp = featurePanel.getComponentAt(evt.getX(),\r
 241                                   evt.getY() +\r
 242                                   evt.getComponent().getLocation().y);\r
 243      }\r
 244 \r
 245     if(comp!=null && comp instanceof Checkbox)\r
 246       target = (Checkbox)comp;\r
 247 \r
 248     if (selectedCheck != null && target != null && selectedCheck != target)\r
 249     {\r
 250       int targetIndex = -1;\r
 251       for(int i=0; i<featurePanel.getComponentCount(); i++)\r
 252       {\r
 253           if(target==featurePanel.getComponent(i))\r
 254           { targetIndex = i; break; }\r
 255       }\r
 256 \r
 257 \r
 258       featurePanel.remove(selectedCheck);\r
 259       featurePanel.add(selectedCheck, targetIndex);\r
 260       featurePanel.validate();\r
 261       itemStateChanged(null);\r
 262     }\r
 263   }\r
 264 \r
 265 \r
 266   public void mouseEntered(MouseEvent evt){}\r
 267   public void mouseExited(MouseEvent evt){}\r
 268   public void mouseClicked(MouseEvent evt){}\r
 269   public void mouseMoved(MouseEvent evt){}\r
 270 }\r