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JAL-1919 code improvement to make PDB sequence fetcher file format configurable....
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
b48070c
..
8374721
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-25,6
+25,7
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
@@
-60,6
+61,7
@@
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class AppletJmol extends EmbmenuFrame implements
import java.util.Vector;
public class AppletJmol extends EmbmenuFrame implements
@@
-129,7
+131,8
@@
public class AppletJmol extends EmbmenuFrame implements
AlignmentPanel ap;
AlignmentPanel ap;
- ArrayList _aps = new ArrayList();
+ List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+ // added to
String fileLoadingError;
String fileLoadingError;
@@
-177,10
+180,8
@@
public class AppletJmol extends EmbmenuFrame implements
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+ new String[][] { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
@@
-204,7
+205,7
@@
public class AppletJmol extends EmbmenuFrame implements
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
- MCview.PDBfile reader = null;
+ StructureFile reader = null;
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
@@
-279,10
+280,11
@@
public class AppletJmol extends EmbmenuFrame implements
dispose();
return;
}
dispose();
return;
}
- jmb.newJmolPopup(true, "Jmol", true);
+ // jmb.newJmolPopup(true, "Jmol", true);
this.addWindowListener(new WindowAdapter()
{
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
closeViewer();
public void windowClosing(WindowEvent evt)
{
closeViewer();
@@
-345,7
+347,9
@@
public class AppletJmol extends EmbmenuFrame implements
}
if (freader == null)
{
}
if (freader == null)
{
- throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
@@
-369,7
+373,7
@@
public class AppletJmol extends EmbmenuFrame implements
jmb.loadInline(string);
}
jmb.loadInline(string);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(Vector<String> chains)
{
chainMenu.removeAll();
{
chainMenu.removeAll();
@@
-379,10
+383,9
@@
public class AppletJmol extends EmbmenuFrame implements
chainMenu.add(menuItem);
CheckboxMenuItem menuItemCB;
chainMenu.add(menuItem);
CheckboxMenuItem menuItemCB;
- for (int c = 0; c < chains.size(); c++)
+ for (String ch : chains)
{
{
- menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
- true);
+ menuItemCB = new CheckboxMenuItem(ch, true);
menuItemCB.addItemListener(this);
chainMenu.add(menuItemCB);
}
menuItemCB.addItemListener(this);
chainMenu.add(menuItemCB);
}
@@
-392,9
+395,7
@@
public class AppletJmol extends EmbmenuFrame implements
void centerViewer()
{
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@
-416,6
+417,7
@@
public class AppletJmol extends EmbmenuFrame implements
this.setVisible(false);
}
this.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
@@
-536,6
+538,7
@@
public class AppletJmol extends EmbmenuFrame implements
jmb.setColourBySequence(itm == seqColour);
}
jmb.setColourBySequence(itm == seqColour);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
@@
-546,7
+549,7
@@
public class AppletJmol extends EmbmenuFrame implements
else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap);
}
else if (!allChainsSelected)
{
}
else if (!allChainsSelected)
{
@@
-554,29
+557,32
@@
public class AppletJmol extends EmbmenuFrame implements
}
}
}
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
jmb.eval(inputLine.getText());
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
jmb.eval(inputLine.getText());
- history.append("\n$ " + inputLine.getText());
+ addToHistory("$ " + inputLine.getText());
inputLine.setText("");
}
}
inputLine.setText("");
}
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
public void updateColours(Object source)
{
public void keyReleased(KeyEvent evt)
{
}
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ AlignmentPanel panel = (AlignmentPanel) source;
+ jmb.colourBySequence(panel);
}
public void updateTitleAndMenus()
}
public void updateTitleAndMenus()
@@
-587,7
+593,7
@@
public class AppletJmol extends EmbmenuFrame implements
return;
}
setChainMenuItems(jmb.chainNames);
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ jmb.colourBySequence(ap);
setTitle(jmb.getViewerTitle());
}
setTitle(jmb.getViewerTitle());
}
@@
-642,11
+648,13
@@
public class AppletJmol extends EmbmenuFrame implements
{
Dimension currentSize = new Dimension();
{
Dimension currentSize = new Dimension();
+ @Override
public void update(Graphics g)
{
paint(g);
}
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
currentSize = this.getSize();
public void paint(Graphics g)
{
currentSize = this.getSize();
@@
-695,11
+703,25
@@
public class AppletJmol extends EmbmenuFrame implements
{
for (int i = 0; i < _aps.size(); i++)
{
{
for (int i = 0; i < _aps.size(); i++)
{
- if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+ if (_aps.get(i).av.getAlignment() == alignment)
{
{
- return ((AlignmentPanel) _aps.get(i));
+ return (_aps.get(i));
}
}
return ap;
}
}
}
return ap;
}
+
+ /**
+ * Append the given text to the history object
+ *
+ * @param text
+ */
+ public void addToHistory(String text)
+ {
+ // actually currently never initialised
+ if (history != null)
+ {
+ history.append("\n" + text);
+ }
+ }
}
}