final FeatureRenderer fr;\r
final AlignmentPanel ap;\r
final AlignViewport av;\r
- Hashtable allFeatures;\r
Object [][] originalData;\r
final JInternalFrame frame;\r
JScrollPane scrollPane = new JScrollPane();\r
JTable table;\r
JPanel groupPanel;\r
\r
+ boolean alignmentHasFeatures = false;\r
+\r
public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
{\r
this.ap = ap;\r
if(groupPanel!=null)\r
{\r
groupPanel.setLayout(\r
- new GridLayout(groupPanel.getComponentCount()/3, 4));\r
+ new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
+\r
groupPanel.validate();\r
bigPanel.add(groupPanel, BorderLayout.NORTH);\r
}\r
\r
void setTableData()\r
{\r
+ alignmentHasFeatures = false;\r
+\r
if (fr.featureGroups == null)\r
fr.featureGroups = new Hashtable();\r
- else\r
- fr.featureGroups.clear();\r
\r
- allFeatures = new Hashtable();\r
- SequenceFeature[] features;\r
+ Vector allFeatures = new Vector();\r
+ Vector allGroups = new Vector();\r
+ SequenceFeature[] tmpfeatures;\r
+ String group;\r
\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
- getSequenceFeatures();\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ continue;\r
\r
- if (features == null)\r
- continue;\r
+ alignmentHasFeatures = true;\r
\r
- int index = 0;\r
- while (index < features.length)\r
- {\r
- if(features[index].getFeatureGroup()!=null\r
- && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ if(tmpfeatures[index].getFeatureGroup()!=null)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
+ if(!allGroups.contains(group))\r
+ {\r
+ allGroups.addElement(group);\r
+\r
+ boolean visible = true;\r
+ if (fr.featureGroups.containsKey(group))\r
+ {\r
+ visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
+ }\r
+\r
+ fr.featureGroups.put(group, new Boolean(visible));\r
+\r
+ if (groupPanel == null)\r
+ {\r
+ groupPanel = new JPanel();\r
+ }\r
+\r
+ final JCheckBox check = new JCheckBox(group, visible);\r
+ check.setFont(new Font("Serif", Font.BOLD, 12));\r
+ check.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ fr.featureGroups.put(check.getText(),\r
+ new Boolean(check.isSelected()));\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ if (ap.overviewPanel != null)\r
+ ap.overviewPanel.updateOverviewImage();\r
+\r
+ resetTable(true);\r
+ }\r
+ });\r
+ groupPanel.add(check);\r
+\r
+ }\r
+\r
+ }\r
+\r
+ if (!allFeatures.contains(tmpfeatures[index].getType()))\r
{\r
- fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));\r
- if(groupPanel==null)\r
- groupPanel = new JPanel();\r
-\r
- final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);\r
- check.setFont(new Font("Serif", Font.BOLD, 12));\r
- check.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (fr.featureGroups.containsKey(check.getText()))\r
- {\r
- fr.featureGroups.put(check.getText(),\r
- new Boolean(check.isSelected()));\r
- ap.seqPanel.seqCanvas.repaint();\r
- if (ap.overviewPanel != null)\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- resetTable();\r
- }\r
- });\r
- groupPanel.add(check);\r
+ allFeatures.addElement(tmpfeatures[index].getType());\r
}\r
- if (!allFeatures.contains(features[index].getType()))\r
- {\r
- if(features[index].featureGroup!=null)\r
- allFeatures.put(features[index].getType(), features[index].featureGroup);\r
- else\r
- allFeatures.put(features[index].getType(), "NOGROUP");\r
- }\r
- index++;\r
+ index ++;\r
}\r
}\r
- if(allFeatures.size()<1)\r
+\r
+\r
+ if(!alignmentHasFeatures)\r
{\r
try\r
{ frame.setClosed(true); }\r
return;\r
}\r
\r
- resetTable();\r
+ resetTable(false);\r
}\r
\r
- void resetTable()\r
+ void resetTable(boolean groupsChanged)\r
{\r
- int fSize = allFeatures.size();\r
+ SequenceFeature [] tmpfeatures;\r
+ String group=null, type;\r
+ Vector visibleChecks = new Vector();\r
\r
- String type;\r
- boolean originalExists = false;\r
- if (originalData != null)\r
- originalExists = true;\r
- else\r
- originalData = new Object[fSize][3];\r
+ //Find out which features should be visible depending on which groups\r
+ //are selected / deselected\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
+ continue;\r
\r
- Object[][] tmp = new Object[fSize][3];\r
- int tmpIndex = 0;\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
\r
- Enumeration en = allFeatures.keys();\r
- int i=0;\r
- while(en.hasMoreElements())\r
- {\r
- type = en.nextElement().toString();\r
- Color col = fr.getColour(type);\r
+ if (group==null || fr.featureGroups.get(group)==null ||\r
+ ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
+ {\r
+ type = tmpfeatures[index].getType();\r
+ if(!visibleChecks.contains(type) )\r
+ {\r
+ visibleChecks.addElement(type);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+\r
+ int fSize = visibleChecks.size();\r
+ Object [][] data = new Object[fSize][3];\r
+ int dataIndex = 0;\r
\r
- //This will ignore any features which are in groups not shown\r
- Object visibleGroup = fr.featureGroups.get(allFeatures.get(type));\r
- if(visibleGroup == null\r
- || ((Boolean)(visibleGroup)).booleanValue())\r
+ if(fr.renderOrder!=null)\r
+ {\r
+ //First add the checks in the previous render order,\r
+ //in case the window has been closed and reopened\r
+ for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
{\r
- tmp[tmpIndex][0] = type;\r
- tmp[tmpIndex][1] = col;\r
- if (av.featuresDisplayed != null)\r
- tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
- else\r
- tmp[tmpIndex][2] = new Boolean(true);\r
-\r
- tmpIndex++;\r
- }\r
+ type = fr.renderOrder[ro];\r
\r
+ if(!visibleChecks.contains(type))\r
+ continue;\r
\r
- if (!originalExists)\r
- {\r
- originalData[i][0] = type;\r
- originalData[i][1] = col;\r
- if (av.featuresDisplayed != null)\r
- originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));\r
- else\r
- originalData[i][2] = new Boolean(true);\r
+ data[dataIndex][0] = type;\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
+ dataIndex++;\r
+ visibleChecks.removeElement(type);\r
}\r
- i++;\r
}\r
\r
- Object [][]data = new Object[tmpIndex][3];\r
- System.arraycopy(tmp, 0, data,0, tmpIndex);\r
+ fSize = visibleChecks.size();\r
+ for(int i=0; i<fSize; i++)\r
+ {\r
+ //These must be extra features belonging to the group\r
+ //which was just selected\r
+ type = visibleChecks.elementAt(i).toString();\r
+ data[dataIndex][0] = type;\r
+ data[dataIndex][1] = fr.getColour(type);\r
+ data[dataIndex][2] = new Boolean(true);\r
+ dataIndex++;\r
+ }\r
+\r
+ if(originalData==null)\r
+ {\r
+ originalData = new Object[data.length][3];\r
+ System.arraycopy(data,0,originalData,0,data.length);\r
+ }\r
\r
table = new JTable(new FeatureTableModel(data));\r
scrollPane.setViewportView(table);\r
return data;\r
}\r
\r
+ public void setData(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
+\r
public int getColumnCount() {\r
return columnNames.length;\r
}\r
git://source.jalview.org / jalview.git / blobdiff