import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.CollectionColourScheme;
-import jalview.schemes.CollectionColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.JalviewColourScheme;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ MenuItem modifyPID = new MenuItem();
+
protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+ MenuItem modifyConservation = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
- Vector<String> links)
+ List<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
e.printStackTrace();
}
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
MenuItem item = new MenuItem(ff);
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
+ if (sg.isNucleotide())
+ {
+ conservationColour.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
+ }
+ else
+ {
+ purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
+ }
editGroupName.setLabel(MessageManager.formatMessage(
"label.name_param", new Object[] { sg.getName() }));
showText.setState(sg.getDisplayText());
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
}
}
setSelectedColour(sg.cs);
*
* @param cs
*/
- protected void setSelectedColour(CollectionColourSchemeI cs)
+ protected void setSelectedColour(ResidueShaderI cs)
{
if (cs == null || cs.getColourScheme() == null)
{
{
userDefinedColour_actionPerformed();
}
+ else if (source == modifyConservation)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
+ }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ int gSize = sg.getSize();
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceFeature> features = new ArrayList<SequenceFeature>();
for (int i = 0; i < gSize; i++)
{
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i);
- features[rsize] = new SequenceFeature(null, null, null, start,
- end, "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i));
+ features.add(new SequenceFeature(null, null, null, start, end,
+ "Jalview"));
}
}
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
+
+ if (!seqs.isEmpty())
{
- ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.setShowSequenceFeatures(true);
- ;
- ap.highlightSearchResults(null);
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ ap.av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
}
}
else
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
ap.av.getShowJVSuffix(), ap, true));
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
- if (pdbs != null&& !pdbs.isEmpty())
+ if (pdbs != null && !pdbs.isEmpty())
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, DataSourceType.URL);
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
else
{
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
noColour.setLabel(MessageManager.getString("label.none"));
noColour.addItemListener(this);
abovePIDColour.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
conservationColour.setLabel(MessageManager
- .getString("label.conservation"));
+ .getString("action.by_conservation"));
conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.addActionListener(this);
editMenu.add(copy);
copy.addActionListener(this);
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new ClustalxColourScheme(sg,
+ sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new ZappoColourScheme());
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TaylorColourScheme());
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HydrophobicColourScheme());
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new HelixColourScheme());
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new StrandColourScheme());
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new TurnColourScheme());
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new BuriedColourScheme());
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(new NucleotideColourScheme());
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
refresh();
}
public void purinePyrimidineColour_actionPerformed()
{
- getGroup().cs = new CollectionColourScheme(
+ getGroup().cs = new ResidueShader(
new PurinePyrimidineColourScheme());
refresh();
}
else
// remove PIDColouring
{
+ SliderPanel.hidePIDSlider();
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
-
+ modifyPID.setEnabled(abovePIDColour.getState());
refresh();
-
}
protected void userDefinedColour_actionPerformed()
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new PIDColourScheme());
+ sg.cs = new ResidueShader(new PIDColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
{
SequenceGroup sg = getGroup();
- sg.cs = new CollectionColourScheme(new Blosum62ColourScheme());
+ sg.cs = new ResidueShader(new Blosum62ColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
-
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
git://source.jalview.org / jalview.git / blobdiff