/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program 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 2
* of the License, or (at your option) any later version.
- *
+ *
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
import jalview.datamodel.*;
import jalview.io.*;
-public class FeatureSettings
- extends JPanel
+public class FeatureSettings extends JPanel
{
DasSourceBrowser dassourceBrowser;
+
jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
+
JPanel settingsPane = new JPanel();
+
JPanel dasSettingsPane = new JPanel();
final FeatureRenderer fr;
+
public final AlignFrame af;
+
Object[][] originalData;
+
final JInternalFrame frame;
+
JScrollPane scrollPane = new JScrollPane();
+
JTable table;
+
JPanel groupPanel;
+
JSlider transparency = new JSlider();
JPanel transPanel = new JPanel(new FlowLayout());
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
table = new JTable();
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
- table.setDefaultRenderer(Color.class,
- new ColorRenderer());
+ table.setDefaultRenderer(Color.class, new ColorRenderer());
- table.setDefaultEditor(Color.class,
- new ColorEditor());
+ table.setDefaultEditor(Color.class, new ColorEditor());
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
public void mouseDragged(MouseEvent evt)
{
int newRow = table.rowAtPoint(evt.getPoint());
- if (newRow != selectedRow
- && selectedRow != -1
- && newRow != -1)
+ if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
{
Object[] temp = new Object[3];
temp[0] = table.getValueAt(selectedRow, 0);
dassourceBrowser = new DasSourceBrowser();
dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
- if (af.getViewport().featuresDisplayed == null || fr.renderOrder == null)
+ if (af.getViewport().featuresDisplayed == null
+ || fr.renderOrder == null)
{
fr.findAllFeatures(true); // display everything!
}
setTableData();
final PropertyChangeListener change;
- final FeatureSettings fs=this;
- fr.addPropertyChangeListener(change=new PropertyChangeListener() {
+ final FeatureSettings fs = this;
+ fr.addPropertyChangeListener(change = new PropertyChangeListener()
+ {
public void propertyChange(PropertyChangeEvent evt)
{
- if (!fs.resettingTable && !fs.handlingUpdate) {
- fs.handlingUpdate=true;
- fs.resetTable(null); // new groups may be added with new seuqence feature types only
- fs.handlingUpdate=false;
+ if (!fs.resettingTable && !fs.handlingUpdate)
+ {
+ fs.handlingUpdate = true;
+ fs.resetTable(null); // new groups may be added with new seuqence
+ // feature types only
+ fs.handlingUpdate = false;
}
}
frame = new JInternalFrame();
frame.setContentPane(this);
Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
- {
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- fr.removePropertyChangeListener(change);
- }
- ;
- });
+ frame
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent evt)
+ {
+ fr.removePropertyChangeListener(change);
+ };
+ });
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
+
/**
* true when Feature Settings are updating from feature renderer
*/
- private boolean handlingUpdate=false;
+ private boolean handlingUpdate = false;
/**
* contains a float[3] for each feature type string. created by setTableData
*/
- Hashtable typeWidth=null;
+ Hashtable typeWidth = null;
+
synchronized public void setTableData()
{
if (fr.featureGroups == null)
String group;
for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
{
- if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().
- getSequenceFeatures() == null)
+ if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+ .getSequenceFeatures() == null)
{
continue;
}
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
- getDatasetSequence().getSequenceFeatures();
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ .getDatasetSequence().getSequenceFeatures();
int index = 0;
while (index < tmpfeatures.length)
if (!allGroups.contains(group))
{
allGroups.addElement(group);
- if (group!=null)
+ if (group != null)
{
checkGroupState(group);
}
validate();
}
+
/**
- *
+ *
* @param group
* @return true if group has been seen before and is already added to set.
*/
- private boolean checkGroupState(String group) {
+ private boolean checkGroupState(String group)
+ {
boolean visible;
if (fr.featureGroups.containsKey(group))
{
- visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
- } else {
- visible=true; // new group is always made visible
- }
+ visible = ((Boolean) fr.featureGroups.get(group)).booleanValue();
+ }
+ else
+ {
+ visible = true; // new group is always made visible
+ }
- if (groupPanel == null)
- {
- groupPanel = new JPanel();
- }
+ if (groupPanel == null)
+ {
+ groupPanel = new JPanel();
+ }
- boolean alreadyAdded = false;
- for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ boolean alreadyAdded = false;
+ for (int g = 0; g < groupPanel.getComponentCount(); g++)
+ {
+ if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
{
- if ( ( (JCheckBox) groupPanel.getComponent(g))
- .getText().equals(group))
- {
- alreadyAdded = true;
- ((JCheckBox)groupPanel.getComponent(g)).setSelected(visible);
- break;
- }
+ alreadyAdded = true;
+ ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
+ break;
}
+ }
- if (alreadyAdded)
- {
+ if (alreadyAdded)
+ {
- return true;
- }
+ return true;
+ }
- fr.featureGroups.put(group, new Boolean(visible));
- final String grp = group;
- final JCheckBox check = new JCheckBox(group, visible);
- check.setFont(new Font("Serif", Font.BOLD, 12));
- check.addItemListener(new ItemListener()
+ fr.featureGroups.put(group, new Boolean(visible));
+ final String grp = group;
+ final JCheckBox check = new JCheckBox(group, visible);
+ check.setFont(new Font("Serif", Font.BOLD, 12));
+ check.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent evt)
{
- public void itemStateChanged(ItemEvent evt)
+ fr.featureGroups.put(check.getText(), new Boolean(check
+ .isSelected()));
+ af.alignPanel.seqPanel.seqCanvas.repaint();
+ if (af.alignPanel.overviewPanel != null)
{
- fr.featureGroups.put(check.getText(),
- new Boolean(check.isSelected()));
- af.alignPanel.seqPanel.seqCanvas.repaint();
- if (af.alignPanel.overviewPanel != null)
- {
- af.alignPanel.overviewPanel.updateOverviewImage();
- }
-
- resetTable(new String[] { grp } );
+ af.alignPanel.overviewPanel.updateOverviewImage();
}
- });
- groupPanel.add(check);
- return false;
+
+ resetTable(new String[]
+ { grp });
+ }
+ });
+ groupPanel.add(check);
+ return false;
}
- boolean resettingTable=false;
+
+ boolean resettingTable = false;
+
synchronized void resetTable(String[] groupChanged)
{
- if (resettingTable==true)
+ if (resettingTable == true)
{
return;
}
- resettingTable=true;
- typeWidth=new Hashtable();
- // TODO: change avWidth calculation to 'per-sequence' average and use long rather than float
- float[] avWidth=null;
+ resettingTable = true;
+ typeWidth = new Hashtable();
+ // TODO: change avWidth calculation to 'per-sequence' average and use long
+ // rather than float
+ float[] avWidth = null;
SequenceFeature[] tmpfeatures;
String group = null, type;
Vector visibleChecks = new Vector();
- //Find out which features should be visible depending on which groups
- //are selected / deselected
- //and recompute average width ordering
+ // Find out which features should be visible depending on which groups
+ // are selected / deselected
+ // and recompute average width ordering
for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
{
- tmpfeatures = af.getViewport().alignment.getSequenceAt(i).
- getDatasetSequence().getSequenceFeatures();
+ tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+ .getDatasetSequence().getSequenceFeatures();
if (tmpfeatures == null)
{
continue;
continue;
}
- if (group == null || fr.featureGroups.get(group) == null ||
- ( (Boolean) fr.featureGroups.get(group)).booleanValue())
+ if (group == null || fr.featureGroups.get(group) == null
+ || ((Boolean) fr.featureGroups.get(group)).booleanValue())
{
- if (group!=null)
+ if (group != null)
checkGroupState(group);
type = tmpfeatures[index].getType();
if (!visibleChecks.contains(type))
visibleChecks.addElement(type);
}
}
- if (!typeWidth.containsKey(tmpfeatures[index].getType())) {
- typeWidth.put(tmpfeatures[index].getType(), avWidth=new float[3]);
- } else {
+ if (!typeWidth.containsKey(tmpfeatures[index].getType()))
+ {
+ typeWidth.put(tmpfeatures[index].getType(),
+ avWidth = new float[3]);
+ }
+ else
+ {
avWidth = (float[]) typeWidth.get(tmpfeatures[index].getType());
}
avWidth[0]++;
- if (tmpfeatures[index].getBegin()>tmpfeatures[index].getEnd())
+ if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
+ {
+ avWidth[1] += 1 + tmpfeatures[index].getBegin()
+ - tmpfeatures[index].getEnd();
+ }
+ else
{
- avWidth[1]+=1+tmpfeatures[index].getBegin()-tmpfeatures[index].getEnd();
- } else {
- avWidth[1]+=1+tmpfeatures[index].getEnd()-tmpfeatures[index].getBegin();
+ avWidth[1] += 1 + tmpfeatures[index].getEnd()
+ - tmpfeatures[index].getBegin();
}
index++;
}
if (fr.renderOrder != null)
{
if (!handlingUpdate)
- fr.findAllFeatures(groupChanged!=null); // prod to update colourschemes. but don't affect display
- //First add the checks in the previous render order,
- //in case the window has been closed and reopened
+ fr.findAllFeatures(groupChanged != null); // prod to update
+ // colourschemes. but don't
+ // affect display
+ // First add the checks in the previous render order,
+ // in case the window has been closed and reopened
for (int ro = fr.renderOrder.length - 1; ro > -1; ro--)
{
type = fr.renderOrder[ro];
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getColour(type);
- data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed.containsKey(type));
+ data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
+ .containsKey(type));
dataIndex++;
visibleChecks.removeElement(type);
}
fSize = visibleChecks.size();
for (int i = 0; i < fSize; i++)
{
- //These must be extra features belonging to the group
- //which was just selected
+ // These must be extra features belonging to the group
+ // which was just selected
type = visibleChecks.elementAt(i).toString();
data[dataIndex][0] = type;
data[dataIndex][1] = fr.getColour(type);
if (data[dataIndex][1] == null)
{
- //"Colour has been updated in another view!!"
+ // "Colour has been updated in another view!!"
fr.renderOrder = null;
return;
}
if (groupPanel != null)
{
- groupPanel.setLayout(
- new GridLayout(fr.featureGroups.size() / 4 + 1, 4));
+ groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
+ 4));
groupPanel.validate();
bigPanel.add(groupPanel, BorderLayout.NORTH);
}
- updateFeatureRenderer(data, groupChanged!=null);
- resettingTable=false;
+ updateFeatureRenderer(data, groupChanged != null);
+ resettingTable = false;
}
+
/**
* reorder data based on the featureRenderers global priority list.
+ *
* @param data
*/
private void ensureOrder(Object[][] data)
{
- boolean sort=false;
+ boolean sort = false;
float[] order = new float[data.length];
- for (int i=0;i<order.length; i++)
+ for (int i = 0; i < order.length; i++)
{
order[i] = fr.getOrder(data[i][0].toString());
- if (order[i]<0)
- order[i] = fr.setOrder(data[i][0].toString(), i/order.length);
- if (i>1)
- sort = sort || order[i-1]>order[i];
+ if (order[i] < 0)
+ order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
+ if (i > 1)
+ sort = sort || order[i - 1] > order[i];
}
if (sort)
jalview.util.QuickSort.sort(order, data);
void load()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"fc"},
- new String[]
- {"Sequence Feature Colours"}, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Load Feature Colours");
chooser.setToolTipText("Load");
try
{
InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
+ file), "UTF-8");
- jalview.binding.JalviewUserColours jucs = new jalview.binding.
- JalviewUserColours();
+ jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
- for (int i = jucs.getColourCount()-1; i >=0; i--)
+ for (int i = jucs.getColourCount() - 1; i >= 0; i--)
{
String name;
- fr.setColour(name=jucs.getColour(i).getName(),
- new Color(Integer.parseInt(jucs.getColour(i).getRGB(),
- 16)));
- fr.setOrder(name,(i==0) ? 0 : i/jucs.getColourCount());
+ fr.setColour(name = jucs.getColour(i).getName(), new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+ fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
}
- if (table!=null) {
+ if (table != null)
+ {
resetTable(null);
- Object[][] data=((FeatureTableModel) table.getModel()).getData();
+ Object[][] data = ((FeatureTableModel) table.getModel())
+ .getData();
ensureOrder(data);
- updateFeatureRenderer(data,false);
+ updateFeatureRenderer(data, false);
table.repaint();
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error loading User Colour File\n" + ex);
}
void save()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"fc"},
- new String[]
- {"Sequence Feature Colours"}, "Sequence Feature Colours");
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+ .getProperty("LAST_DIRECTORY"), new String[]
+ { "fc" }, new String[]
+ { "Sequence Feature Colours" }, "Sequence Feature Colours");
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle("Save Feature Colour Scheme");
chooser.setToolTipText("Save");
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.binding.JalviewUserColours ucs = new jalview.binding.
- JalviewUserColours();
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
ucs.setSchemeName("Sequence Features");
try
{
PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ new FileOutputStream(choice), "UTF-8"));
Enumeration e = fr.featureColours.keys();
float[] sortOrder = new float[fr.featureColours.size()];
String[] sortTypes = new String[fr.featureColours.size()];
- int i=0;
+ int i = 0;
while (e.hasMoreElements())
{
sortTypes[i] = e.nextElement().toString();
- sortOrder[i] = fr.getOrder(sortTypes[i]);
+ sortOrder[i] = fr.getOrder(sortTypes[i]);
i++;
}
jalview.util.QuickSort.sort(sortOrder, sortTypes);
- sortOrder=null;
- for (i=0; i<sortTypes.length; i++) {
+ sortOrder = null;
+ for (i = 0; i < sortTypes.length; i++)
+ {
jalview.binding.Colour col = new jalview.binding.Colour();
col.setName(sortTypes[i]);
- col.setRGB(jalview.util.Format.getHexString(
- fr.getColour(col.getName())));
+ col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
+ .getName())));
ucs.addColour(col);
}
ucs.marshal(out);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
{
Boolean value = (Boolean) table.getValueAt(i, 2);
- table.setValueAt(
- new Boolean(!value.booleanValue()),
- i, 2);
+ table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
}
}
- public void orderByAvWidth() {
- if (table==null || table.getModel()==null)
+
+ public void orderByAvWidth()
+ {
+ if (table == null || table.getModel() == null)
return;
Object[][] data = ((FeatureTableModel) table.getModel()).getData();
float[] width = new float[data.length];
float[] awidth;
- float max=0;
- int num=0;
- for (int i=0;i<data.length;i++) {
- awidth = (float[]) typeWidth.get(data[i][0]);
- if (awidth[0]>0) {
- width[i] = awidth[1]/awidth[0];// *awidth[0]*awidth[2]; - better weight - but have to make per sequence, too (awidth[2])
- //if (width[i]==1) // hack to distinguish single width sequences.
- num++;
- } else {
- width[i]=0;
- }
- if (max<width[i])
- max=width[i];
+ float max = 0;
+ int num = 0;
+ for (int i = 0; i < data.length; i++)
+ {
+ awidth = (float[]) typeWidth.get(data[i][0]);
+ if (awidth[0] > 0)
+ {
+ width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
+ // weight - but have to make per
+ // sequence, too (awidth[2])
+ // if (width[i]==1) // hack to distinguish single width sequences.
+ num++;
+ }
+ else
+ {
+ width[i] = 0;
+ }
+ if (max < width[i])
+ max = width[i];
}
- boolean sort=false;
- for (int i=0;i<width.length; i++) {
- //awidth = (float[]) typeWidth.get(data[i][0]);
- if (width[i]==0)
+ boolean sort = false;
+ for (int i = 0; i < width.length; i++)
+ {
+ // awidth = (float[]) typeWidth.get(data[i][0]);
+ if (width[i] == 0)
{
width[i] = fr.getOrder(data[i][0].toString());
- if (width[i]<0)
+ if (width[i] < 0)
{
- width[i] = fr.setOrder(data[i][0].toString(), i/data.length);
+ width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
}
- } else {
- width[i] /=max; // normalize
+ }
+ else
+ {
+ width[i] /= max; // normalize
fr.setOrder(data[i][0].toString(), width[i]); // store for later
}
- if (i>0)
- sort = sort || width[i-1]>width[i];
+ if (i > 0)
+ sort = sort || width[i - 1] > width[i];
}
if (sort)
jalview.util.QuickSort.sort(width, data);
// update global priority order
- updateFeatureRenderer(data,false);
+ updateFeatureRenderer(data, false);
table.repaint();
}
+
public void close()
{
try
{
frame.setClosed(true);
+ } catch (Exception exe)
+ {
}
- catch (Exception exe)
- {}
}
{
updateFeatureRenderer(data, true);
}
+
private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
{
fr.setFeaturePriority(data, visibleNew);
}
int selectedRow = -1;
+
JTabbedPane tabbedPane = new JTabbedPane();
+
BorderLayout borderLayout1 = new BorderLayout();
+
BorderLayout borderLayout2 = new BorderLayout();
+
BorderLayout borderLayout3 = new BorderLayout();
+
JPanel bigPanel = new JPanel();
+
BorderLayout borderLayout4 = new BorderLayout();
+
JButton invert = new JButton();
+
JPanel buttonPanel = new JPanel();
+
JButton cancel = new JButton();
+
JButton ok = new JButton();
+
JButton loadColours = new JButton();
+
JButton saveColours = new JButton();
+
JPanel dasButtonPanel = new JPanel();
+
JButton fetchDAS = new JButton();
+
JButton saveDAS = new JButton();
+
JButton cancelDAS = new JButton();
+
JButton optimizeOrder = new JButton();
+
JPanel transbuttons = new JPanel(new BorderLayout());
- private void jbInit()
- throws Exception
+
+ private void jbInit() throws Exception
{
this.setLayout(borderLayout1);
settingsPane.setLayout(borderLayout2);
});
optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
optimizeOrder.setText("Optimise Order");
- optimizeOrder.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
+ optimizeOrder.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
orderByAvWidth();
}
});
{
public void stateChanged(ChangeEvent evt)
{
- fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);
+ fr.setTransparency((float) (100 - transparency.getValue()) / 100f);
af.alignPanel.paintAlignment(true);
}
});
bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
transPanel.add(transparency);
transbuttons.add(invert, java.awt.BorderLayout.NORTH);
- transbuttons.add(optimizeOrder,java.awt.BorderLayout.SOUTH);
+ transbuttons.add(optimizeOrder, java.awt.BorderLayout.SOUTH);
transPanel.add(transbuttons);
buttonPanel.add(ok);
buttonPanel.add(cancel);
Vector selectedSources = dassourceBrowser.getSelectedSources();
doDasFeatureFetch(selectedSources, true, true);
}
+
/**
* get the features from selectedSources for all or the current selection
+ *
* @param selectedSources
* @param checkDbRefs
* @param promptFetchDbRefs
*/
- private void doDasFeatureFetch(Vector selectedSources, boolean checkDbRefs, boolean promptFetchDbRefs)
+ private void doDasFeatureFetch(Vector selectedSources,
+ boolean checkDbRefs, boolean promptFetchDbRefs)
{
SequenceI[] dataset, seqs;
int iSize;
AlignViewport vp = af.getViewport();
if (vp.getSelectionGroup() != null
- && vp.getSelectionGroup().getSize() > 0)
+ && vp.getSelectionGroup().getSize() > 0)
{
iSize = vp.getSelectionGroup().getSize();
dataset = new SequenceI[iSize];
- seqs = vp.getSelectionGroup().
- getSequencesInOrder(
- vp.getAlignment());
+ seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
}
else
{
}
cancelDAS.setEnabled(true);
- dasFeatureFetcher =
- new jalview.ws.DasSequenceFeatureFetcher(
- dataset,
- this,
- selectedSources, checkDbRefs, promptFetchDbRefs);
+ dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
+ this, selectedSources, checkDbRefs, promptFetchDbRefs);
af.getViewport().setShowSequenceFeatures(true);
af.showSeqFeatures.setSelected(true);
}
+
/**
- * properly initialise DAS fetcher and then initiate a new thread to fetch features from the named sources (rather than any turned on by default)
+ * properly initialise DAS fetcher and then initiate a new thread to fetch
+ * features from the named sources (rather than any turned on by default)
+ *
* @param sources
*/
public void fetchDasFeatures(Vector sources)
{
- Thread thr = new Thread(new Runnable() {
- public void run() {
+ Thread thr = new Thread(new Runnable()
+ {
+ public void run()
+ {
// this actually initialises the das source list
dassourceBrowser.paintComponent(null); // yuk
}
});
thr.start();
- while (dassourceBrowser.loadingDasSources || dassourceBrowser.dasSources==null)
+ while (dassourceBrowser.loadingDasSources
+ || dassourceBrowser.dasSources == null)
{
- try { Thread.sleep(10); } catch (Exception e) {};
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
}
Vector resolved = new Vector();
- if (sources!=null)
+ if (sources != null)
{
- for (int i=0;i<dassourceBrowser.dasSources.length; i++)
+ for (int i = 0; i < dassourceBrowser.dasSources.length; i++)
{
if (sources.contains(dassourceBrowser.dasSources[i].getNickname()))
{
}
}
}
- if (resolved.size()==0)
+ if (resolved.size() == 0)
{
resolved = dassourceBrowser.getSelectedSources();
}
- if (resolved.size()>0)
+ if (resolved.size() > 0)
{
final Vector dassources = resolved;
- SwingUtilities.invokeLater(new Runnable() {
+ SwingUtilities.invokeLater(new Runnable()
+ {
public void run()
{
fetchDAS.setEnabled(false);
cancelDAS.setEnabled(true);
doDasFeatureFetch(dassources, true, false);
-
- }});
+
+ }
+ });
}
}
public void saveDAS_actionPerformed(ActionEvent e)
{
- dassourceBrowser.saveProperties(jalview.bin.Cache.applicationProperties);
+ dassourceBrowser
+ .saveProperties(jalview.bin.Cache.applicationProperties);
}
public void complete()
public void cancelDAS_actionPerformed(ActionEvent e)
{
- if (dasFeatureFetcher!=null)
+ if (dasFeatureFetcher != null)
{
dasFeatureFetcher.cancel();
}
fetchDAS.setEnabled(true);
cancelDAS.setEnabled(false);
}
+
public void noDasSourceActive()
{
complete();
JOptionPane.showInternalConfirmDialog(Desktop.desktop,
"No das sources were selected.\n"
- + "Please select some sources and\n"
- +" try again.",
- "No Sources Selected",
- JOptionPane.DEFAULT_OPTION,
+ + "Please select some sources and\n" + " try again.",
+ "No Sources Selected", JOptionPane.DEFAULT_OPTION,
JOptionPane.INFORMATION_MESSAGE);
}
- /////////////////////////////////////////////////////////////////////////
+ // ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
- /////////////////////////////////////////////////////////////////////////
- class FeatureTableModel
- extends AbstractTableModel
+ // ///////////////////////////////////////////////////////////////////////
+ class FeatureTableModel extends AbstractTableModel
{
FeatureTableModel(Object[][] data)
{
}
private String[] columnNames =
- {
- "Feature Type", "Colour", "Display"};
+ { "Feature Type", "Colour", "Display" };
+
private Object[][] data;
public Object[][] getData()
}
- class ColorRenderer
- extends JLabel implements TableCellRenderer
+ class ColorRenderer extends JLabel implements TableCellRenderer
{
javax.swing.border.Border unselectedBorder = null;
+
javax.swing.border.Border selectedBorder = null;
public ColorRenderer()
{
- setOpaque(true); //MUST do this for background to show up.
+ setOpaque(true); // MUST do this for background to show up.
}
- public Component getTableCellRendererComponent(
- JTable table, Object color,
- boolean isSelected, boolean hasFocus,
- int row, int column)
+ public Component getTableCellRendererComponent(JTable table,
+ Object color, boolean isSelected, boolean hasFocus, int row,
+ int column)
{
Color newColor = (Color) color;
setBackground(newColor);
if (selectedBorder == null)
{
selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getSelectionBackground());
+ table.getSelectionBackground());
}
setBorder(selectedBorder);
}
if (unselectedBorder == null)
{
unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
- table.getBackground());
+ table.getBackground());
}
setBorder(unselectedBorder);
}
setToolTipText("RGB value: " + newColor.getRed() + ", "
- + newColor.getGreen() + ", "
- + newColor.getBlue());
+ + newColor.getGreen() + ", " + newColor.getBlue());
return this;
}
}
}
-class ColorEditor
- extends AbstractCellEditor implements TableCellEditor,
- ActionListener
+class ColorEditor extends AbstractCellEditor implements TableCellEditor,
+ ActionListener
{
Color currentColor;
+
JButton button;
+
JColorChooser colorChooser;
+
JDialog dialog;
+
protected static final String EDIT = "edit";
public ColorEditor()
{
- //Set up the editor (from the table's point of view),
- //which is a button.
- //This button brings up the color chooser dialog,
- //which is the editor from the user's point of view.
+ // Set up the editor (from the table's point of view),
+ // which is a button.
+ // This button brings up the color chooser dialog,
+ // which is the editor from the user's point of view.
button = new JButton();
button.setActionCommand(EDIT);
button.addActionListener(this);
button.setBorderPainted(false);
- //Set up the dialog that the button brings up.
+ // Set up the dialog that the button brings up.
colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
- "Select new Colour",
- true, //modal
- colorChooser,
- this, //OK button handler
- null); //no CANCEL button handler
+ dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
}
/**
- * Handles events from the editor button and from
- * the dialog's OK button.
+ * Handles events from the editor button and from the dialog's OK button.
*/
public void actionPerformed(ActionEvent e)
{
if (EDIT.equals(e.getActionCommand()))
{
- //The user has clicked the cell, so
- //bring up the dialog.
+ // The user has clicked the cell, so
+ // bring up the dialog.
button.setBackground(currentColor);
colorChooser.setColor(currentColor);
dialog.setVisible(true);
- //Make the renderer reappear.
+ // Make the renderer reappear.
fireEditingStopped();
}
else
- { //User pressed dialog's "OK" button.
+ { // User pressed dialog's "OK" button.
currentColor = colorChooser.getColor();
}
}
- //Implement the one CellEditor method that AbstractCellEditor doesn't.
+ // Implement the one CellEditor method that AbstractCellEditor doesn't.
public Object getCellEditorValue()
{
return currentColor;
}
- //Implement the one method defined by TableCellEditor.
- public Component getTableCellEditorComponent(JTable table,
- Object value,
- boolean isSelected,
- int row,
- int column)
+ // Implement the one method defined by TableCellEditor.
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
{
currentColor = (Color) value;
return button;
git://source.jalview.org / jalview.git / blobdiff