/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
import java.awt.BorderLayout;\r
import java.awt.Font;\r
import java.awt.Color;\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
\r
public class FeatureSettings extends JPanel\r
{\r
JSlider transparency = new JSlider();\r
\r
JPanel transPanel = new JPanel(new FlowLayout());\r
- boolean alignmentHasFeatures = false;\r
\r
public FeatureSettings(AlignFrame af)\r
{\r
ex.printStackTrace();\r
}\r
\r
+ table = new JTable();\r
+ table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setDefaultRenderer(Color.class,\r
+ new ColorRenderer());\r
+\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\r
+\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
+ });\r
+\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if (newRow != selectedRow\r
+ && selectedRow != -1\r
+ && newRow != -1)\r
+ {\r
+ Object[] temp = new Object[3];\r
+ temp[0] = table.getValueAt(selectedRow, 0);\r
+ temp[1] = table.getValueAt(selectedRow, 1);\r
+ temp[2] = table.getValueAt(selectedRow, 2);\r
+\r
+ table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
+ table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
+ table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
+\r
+ table.setValueAt(temp[0], newRow, 0);\r
+ table.setValueAt(temp[1], newRow, 1);\r
+ table.setValueAt(temp[2], newRow, 2);\r
+\r
+ selectedRow = newRow;\r
+ }\r
+ }\r
+ });\r
+\r
+ scrollPane.setViewportView(table);\r
+\r
dassourceBrowser = new DasSourceBrowser();\r
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);\r
\r
if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)\r
fr.findAllFeatures();\r
\r
-\r
setTableData();\r
\r
frame = new JInternalFrame();\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
\r
- public void setTableData()\r
+ synchronized public void setTableData()\r
{\r
- alignmentHasFeatures = false;\r
-\r
if (fr.featureGroups == null)\r
fr.featureGroups = new Hashtable();\r
\r
if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
continue;\r
\r
- alignmentHasFeatures = true;\r
-\r
tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
\r
int index = 0;\r
{\r
visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
}\r
- else\r
- {\r
- fr.featureGroups.put(group, new Boolean(visible));\r
+\r
if (groupPanel == null)\r
{\r
groupPanel = new JPanel();\r
}\r
\r
+ boolean alreadyAdded = false;\r
+ for(int g=0; g<groupPanel.getComponentCount(); g++)\r
+ {\r
+ if(((JCheckBox)groupPanel.getComponent(g))\r
+ .getText().equals(group))\r
+ {\r
+ alreadyAdded = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if(alreadyAdded)\r
+ continue;\r
+\r
+ fr.featureGroups.put(group, new Boolean(visible));\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
groupPanel.add(check);\r
}\r
- }\r
-\r
}\r
\r
if (!allFeatures.contains(tmpfeatures[index].getType()))\r
}\r
}\r
\r
-\r
- if(!alignmentHasFeatures)\r
- {\r
- // try\r
- // { frame.setClosed(true); }\r
- // catch (Exception ex){}\r
-\r
- // JOptionPane.showInternalMessageDialog(\r
- /// Desktop.desktop, "No features have been added to this alignment!",\r
- //\r
- // return;\r
- }\r
-\r
resetTable(false);\r
+\r
+ validate();\r
}\r
\r
\r
System.arraycopy(data,0,originalData,0,data.length);\r
}\r
\r
- table = new JTable(new FeatureTableModel(data));\r
- scrollPane.setViewportView(table);\r
- table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
- table.setDefaultRenderer(Color.class,\r
- new ColorRenderer());\r
-\r
- table.setDefaultEditor(Color.class,\r
- new ColorEditor());\r
-\r
+ table.setModel(new FeatureTableModel(data));\r
table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
\r
- table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
-\r
- table.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- selectedRow = table.rowAtPoint(evt.getPoint());\r
- }\r
- });\r
-\r
- table.addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- int newRow = table.rowAtPoint(evt.getPoint());\r
- if(newRow!=selectedRow\r
- && selectedRow!=-1\r
- && newRow!=-1)\r
- {\r
- Object[] temp = new Object[3];\r
- temp[0] = table.getValueAt(selectedRow, 0);\r
- temp[1] = table.getValueAt(selectedRow, 1);\r
- temp[2] = table.getValueAt(selectedRow, 2);\r
-\r
- table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
- table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
- table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
-\r
- table.setValueAt(temp[0], newRow, 0);\r
- table.setValueAt(temp[1], newRow, 1);\r
- table.setValueAt(temp[2], newRow, 2);\r
-\r
- selectedRow = newRow;\r
- }\r
- }\r
- });\r
\r
if (groupPanel != null)\r
{\r
dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());\r
dasSettingsPane.setBorder(null);\r
this.add(tabbedPane, java.awt.BorderLayout.CENTER);\r
- tabbedPane.addTab("Display Settings", settingsPane );\r
+ tabbedPane.addTab("Feature Settings", settingsPane );\r
tabbedPane.addTab("DAS Settings", dasSettingsPane);\r
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);\r
transPanel.add(transparency);\r
{\r
Vector selectedSources = dassourceBrowser.getSelectedSources();\r
\r
- int uniprotCount = 0;\r
- for(int i=0; i<selectedSources.size(); i++)\r
+ SequenceI [] dataset, seqs ;\r
+ int iSize;\r
+\r
+ if(af.getViewport().getSelectionGroup()!=null\r
+ && af.getViewport().getSelectionGroup().getSize(false)>0)\r
{\r
- DasSource source = (DasSource)selectedSources.elementAt(i);\r
- DasCoordinateSystem [] coords = source.getCoordinateSystem();\r
- for(int c=0; c<coords.length; c++)\r
- {\r
- if (coords[c].getName().equalsIgnoreCase("UniProt"))\r
- {\r
- uniprotCount++;\r
- break;\r
- }\r
- }\r
+ iSize = af.getViewport().getSelectionGroup().getSize(false);\r
+ dataset = new SequenceI[iSize];\r
+ seqs = af.getViewport().getSelectionGroup().\r
+ getSequencesInOrder(\r
+ af.getViewport().getAlignment());\r
+ }\r
+ else\r
+ {\r
+ iSize = af.getViewport().getAlignment().getHeight();\r
+ seqs = af.getViewport().getAlignment().getSequencesArray();\r
}\r
\r
- System.out.println("User selection is "\r
- + (((float)uniprotCount/(float)selectedSources.size())*100)\r
- +" % Uniprot");\r
+ dataset = new SequenceI[iSize];\r
+ for (int i = 0; i < iSize; i++)\r
+ {\r
+ dataset[i] = seqs[i].getDatasetSequence();\r
+ }\r
\r
- new jalview.io.DasSequenceFeatureFetcher(af.getViewport().getAlignment(),\r
- af,\r
- selectedSources);\r
+ new jalview.io.DasSequenceFeatureFetcher(\r
+ dataset,\r
+ af,\r
+ selectedSources);\r
\r
af.getViewport().setShowSequenceFeatures(true);\r
af.showSeqFeatures.setSelected(true);\r
git://source.jalview.org / jalview.git / blobdiff